sbuild (Debian sbuild) 0.85.0 (04 January 2023) on debian-ci-siliconvalley +==============================================================================+ | lambda-align 1.0.3-8 (armhf) Sun, 01 Feb 2026 22:44:03 +0000 | +==============================================================================+ Package: lambda-align Version: 1.0.3-8 Source Version: 1.0.3-8 Distribution: unstable Machine Architecture: amd64 Host Architecture: armhf Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-e4e71451-9bfc-4e88-8573-68261047703e' with '<>' I: NOTICE: Log filtering will replace 'build/lambda-align-LhSSVL/resolver-yJX4RC' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://localhost:3142/debian unstable InRelease Get:2 http://localhost:3142/debian unstable/main armhf Packages [9617 kB] Fetched 9617 kB in 1s (10.2 MB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'lambda-align' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/lambda-align.git Please use: git clone https://salsa.debian.org/med-team/lambda-align.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 334 kB of source archives. Get:1 http://localhost:3142/debian unstable/main lambda-align 1.0.3-8 (dsc) [2122 B] Get:2 http://localhost:3142/debian unstable/main lambda-align 1.0.3-8 (tar) [323 kB] Get:3 http://localhost:3142/debian unstable/main lambda-align 1.0.3-8 (diff) [8648 B] Fetched 334 kB in 1s (372 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/lambda-align-LhSSVL/lambda-align-1.0.3' with '<>' I: NOTICE: Log filtering will replace 'build/lambda-align-LhSSVL' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libseqan2-dev, cmake, zlib1g-dev, libbz2-dev, openssl, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf Filtered Build-Depends: debhelper-compat (= 13), libseqan2-dev, cmake, zlib1g-dev, libbz2-dev, openssl, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf dpkg-deb: warning: root directory /<>/sbuild-build-depends-main-dummy has unusual owner or group 1000:119 dpkg-deb: hint: you might need to pass --root-owner-group, see for further details dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [769 B] Get:5 copy:/<>/apt_archive ./ Packages [812 B] Fetched 2190 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Execute external solver... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabihf bsdextrautils cmake cmake-data cpp-15-arm-linux-gnueabihf cpp-arm-linux-gnueabihf crossbuild-essential-armhf debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file g++-15-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-15-arm-linux-gnueabihf gcc-15-arm-linux-gnueabihf-base gcc-15-base:armhf gcc-15-cross-base gcc-arm-linux-gnueabihf gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13t64 libasan8:armhf libasan8-armhf-cross libatomic1:armhf libatomic1-armhf-cross libbrotli1 libbz2-1.0:armhf libbz2-dev:armhf libc-gconv-modules-extra:armhf libc6:armhf libc6-armhf-cross libc6-dev:armhf libc6-dev-armhf-cross libcom-err2 libcurl4t64 libdebhelper-perl libelf1t64 libexpat1 libfakeroot libffi8 libfile-stripnondeterminism-perl libgcc-15-dev:armhf libgcc-15-dev-armhf-cross libgcc-s1:armhf libgcc-s1-armhf-cross libgnutls30t64 libgomp1:armhf libgomp1-armhf-cross libgssapi-krb5-2 libidn2-0 libjsoncpp26 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap2 libmagic-mgc libmagic1t64 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-ossl0 libp11-kit0 libpipeline1 libproc2-0 libpsl5t64 librhash1 librtmp1 libsasl2-2 libsasl2-modules-db libseqan2-dev libssh2-1t64 libstdc++-15-dev:armhf libstdc++-15-dev-armhf-cross libstdc++6:armhf libstdc++6-armhf-cross libtasn1-6 libtool libubsan1:armhf libubsan1-armhf-cross libuchardet0 libunistring5 libuv1t64 libxml2-16 linux-libc-dev-armhf-cross m4 man-db openssl po-debconf procps sensible-utils zlib1g:armhf zlib1g-dev:armhf Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc cmake-doc cmake-format elpa-cmake-mode ninja-build gcc-15-locales cpp-15-doc cpp-doc dh-make gcc-15-doc manpages-dev flex bison gdb-arm-linux-gnueabihf gcc-doc gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff lrzip glibc-doc:armhf libc-l10n:armhf locales:armhf libnss-nis:armhf libnss-nisplus:armhf manpages-dev:armhf gnutls-bin krb5-doc krb5-user libstdc++-15-doc:armhf libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser ca-certificates libmail-box-perl Recommended packages: curl | wget | lynx bzip2-doc:armhf libidn2-0:armhf ca-certificates libarchive-cpio-perl krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl psmisc linux-sysctl-defaults The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabihf bsdextrautils cmake cmake-data cpp-15-arm-linux-gnueabihf cpp-arm-linux-gnueabihf crossbuild-essential-armhf debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file g++-15-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-15-arm-linux-gnueabihf gcc-15-arm-linux-gnueabihf-base gcc-15-base:armhf gcc-15-cross-base gcc-arm-linux-gnueabihf gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13t64 libasan8:armhf libasan8-armhf-cross libatomic1:armhf libatomic1-armhf-cross libbrotli1 libbz2-1.0:armhf libbz2-dev:armhf libc-gconv-modules-extra:armhf libc6:armhf libc6-armhf-cross libc6-dev:armhf libc6-dev-armhf-cross libcom-err2 libcurl4t64 libdebhelper-perl libelf1t64 libexpat1 libfakeroot libffi8 libfile-stripnondeterminism-perl libgcc-15-dev:armhf libgcc-15-dev-armhf-cross libgcc-s1:armhf libgcc-s1-armhf-cross libgnutls30t64 libgomp1:armhf libgomp1-armhf-cross libgssapi-krb5-2 libidn2-0 libjsoncpp26 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap2 libmagic-mgc libmagic1t64 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-ossl0 libp11-kit0 libpipeline1 libproc2-0 libpsl5t64 librhash1 librtmp1 libsasl2-2 libsasl2-modules-db libseqan2-dev libssh2-1t64 libstdc++-15-dev:armhf libstdc++-15-dev-armhf-cross libstdc++6:armhf libstdc++6-armhf-cross libtasn1-6 libtool libubsan1:armhf libubsan1-armhf-cross libuchardet0 libunistring5 libuv1t64 libxml2-16 linux-libc-dev-armhf-cross m4 man-db openssl po-debconf procps sbuild-build-depends-main-dummy:armhf sensible-utils zlib1g:armhf zlib1g-dev:armhf 0 upgraded, 104 newly installed, 0 to remove and 0 not upgraded. Need to get 108 MB of archives. After this operation, 417 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [944 B] Get:2 http://localhost:3142/debian unstable/main amd64 libexpat1 amd64 2.7.4-1 [116 kB] Get:3 http://localhost:3142/debian unstable/main amd64 libncursesw6 amd64 6.6+20251231-1 [137 kB] Get:4 http://localhost:3142/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9+b1 [66.1 kB] Get:5 http://localhost:3142/debian unstable/main amd64 procps amd64 2:4.0.4-9+b1 [883 kB] Get:6 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:7 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5+b1 [338 kB] Get:8 http://localhost:3142/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5+b1 [110 kB] Get:9 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.46-5+b1 [43.8 kB] Get:10 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.23.2-1 [245 kB] Get:11 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b1 [68.8 kB] Get:12 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.23.0-10 [1194 kB] Get:13 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.41.3-3 [99.1 kB] Get:14 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.8-2 [42.1 kB] Get:15 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:16 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.20-2 [325 kB] Get:17 http://localhost:3142/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:18 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:19 http://localhost:3142/debian unstable/main amd64 automake all 1:1.18.1-3 [878 kB] Get:20 http://localhost:3142/debian unstable/main amd64 autopoint all 0.23.2-1 [772 kB] Get:21 http://localhost:3142/debian unstable/main amd64 binutils-arm-linux-gnueabihf amd64 2.45.90.20260201-1 [1557 kB] Get:22 http://localhost:3142/debian unstable/main amd64 cmake-data all 4.2.3-1 [2556 kB] Get:23 http://localhost:3142/debian unstable/main amd64 libxml2-16 amd64 2.15.1+dfsg-2+b1 [641 kB] Get:24 http://localhost:3142/debian unstable/main amd64 libarchive13t64 amd64 3.8.5-1 [362 kB] Get:25 http://localhost:3142/debian unstable/main amd64 libnghttp3-9 amd64 1.12.0-1 [68.4 kB] Get:26 http://localhost:3142/debian unstable/main amd64 libngtcp2-16 amd64 1.16.0-1 [136 kB] Get:27 http://localhost:3142/debian unstable/main amd64 libbrotli1 amd64 1.2.0-1 [308 kB] Get:28 http://localhost:3142/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-2 [33.1 kB] Get:29 http://localhost:3142/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b8 [25.1 kB] Get:30 http://localhost:3142/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-2 [81.1 kB] Get:31 http://localhost:3142/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b1 [9784 B] Get:32 http://localhost:3142/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-2 [337 kB] Get:33 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http://localhost:3142/debian unstable/main amd64 libp11-kit0 amd64 0.25.10-1+b1 [444 kB] Get:44 http://localhost:3142/debian unstable/main amd64 libtasn1-6 amd64 4.21.0-2 [50.4 kB] Get:45 http://localhost:3142/debian unstable/main amd64 libgnutls30t64 amd64 3.8.11-3 [1509 kB] Get:46 http://localhost:3142/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3+b1 [60.7 kB] Get:47 http://localhost:3142/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1+b1 [245 kB] Get:48 http://localhost:3142/debian unstable/main amd64 libcurl4t64 amd64 8.18.0-2 [412 kB] Get:49 http://localhost:3142/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-5 [82.6 kB] Get:50 http://localhost:3142/debian unstable/main amd64 librhash1 amd64 1.4.6-1.1 [135 kB] Get:51 http://localhost:3142/debian unstable/main amd64 libuv1t64 amd64 1.51.0-2+b1 [156 kB] Get:52 http://localhost:3142/debian unstable/main amd64 cmake amd64 4.2.3-1 [13.0 MB] Get:53 http://localhost:3142/debian unstable/main amd64 gcc-15-arm-linux-gnueabihf-base amd64 15.2.0-7cross1 [53.5 kB] Get:54 http://localhost:3142/debian unstable/main amd64 cpp-15-arm-linux-gnueabihf amd64 15.2.0-7cross1 [11.2 MB] Get:55 http://localhost:3142/debian unstable/main amd64 cpp-arm-linux-gnueabihf amd64 4:15.2.0-5 [5336 B] Get:56 http://localhost:3142/debian unstable/main amd64 gcc-15-cross-base all 15.2.0-7cross1 [48.9 kB] Get:57 http://localhost:3142/debian unstable/main amd64 libc6-armhf-cross all 2.42-10cross1 [1258 kB] Get:58 http://localhost:3142/debian unstable/main amd64 libgcc-s1-armhf-cross all 15.2.0-7cross1 [36.9 kB] Get:59 http://localhost:3142/debian unstable/main amd64 libgomp1-armhf-cross all 15.2.0-7cross1 [112 kB] Get:60 http://localhost:3142/debian unstable/main amd64 libatomic1-armhf-cross all 15.2.0-7cross1 [6888 B] Get:61 http://localhost:3142/debian unstable/main amd64 libasan8-armhf-cross all 15.2.0-7cross1 [2623 kB] Get:62 http://localhost:3142/debian unstable/main amd64 libstdc++6-armhf-cross all 15.2.0-7cross1 [575 kB] Get:63 http://localhost:3142/debian unstable/main amd64 libubsan1-armhf-cross all 15.2.0-7cross1 [1074 kB] Get:64 http://localhost:3142/debian unstable/main amd64 libgcc-15-dev-armhf-cross all 15.2.0-7cross1 [762 kB] Get:65 http://localhost:3142/debian unstable/main amd64 gcc-15-arm-linux-gnueabihf amd64 15.2.0-7cross1 [21.2 MB] Get:66 http://localhost:3142/debian unstable/main amd64 gcc-arm-linux-gnueabihf amd64 4:15.2.0-5 [1456 B] Get:67 http://localhost:3142/debian unstable/main amd64 linux-libc-dev-armhf-cross all 6.18.5-1cross1 [2351 kB] Get:68 http://localhost:3142/debian unstable/main amd64 libc6-dev-armhf-cross all 2.42-10cross1 [1346 kB] Get:69 http://localhost:3142/debian unstable/main amd64 libstdc++-15-dev-armhf-cross all 15.2.0-7cross1 [2410 kB] Get:70 http://localhost:3142/debian unstable/main amd64 g++-15-arm-linux-gnueabihf amd64 15.2.0-7cross1 [12.2 MB] Get:71 http://localhost:3142/debian unstable/main amd64 g++-arm-linux-gnueabihf amd64 4:15.2.0-5 [1208 B] Get:72 http://localhost:3142/debian unstable/main amd64 crossbuild-essential-armhf all 12.12 [3548 B] Get:73 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.29 [92.6 kB] Get:74 http://localhost:3142/debian unstable/main amd64 libtool all 2.5.4-9 [540 kB] Get:75 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get:76 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:77 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get:78 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get:79 http://localhost:3142/debian unstable/main amd64 libelf1t64 amd64 0.194-1 [185 kB] Get:80 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get:81 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.23.2-1 [1687 kB] Get:82 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:83 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Get:84 http://localhost:3142/debian unstable/main amd64 debhelper all 13.29 [943 kB] Get:85 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.37.2-1 [29.9 kB] Get:86 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.37.2-1 [76.2 kB] Get:87 http://localhost:3142/debian unstable/main armhf gcc-15-base armhf 15.2.0-12 [54.1 kB] Get:88 http://localhost:3142/debian unstable/main armhf libgcc-s1 armhf 15.2.0-12 [36.8 kB] Get:89 http://localhost:3142/debian unstable/main armhf libc-gconv-modules-extra armhf 2.42-11 [1161 kB] Get:90 http://localhost:3142/debian unstable/main armhf libc6 armhf 2.42-11 [1489 kB] Get:91 http://localhost:3142/debian unstable/main armhf libasan8 armhf 15.2.0-12 [2633 kB] Get:92 http://localhost:3142/debian unstable/main armhf libatomic1 armhf 15.2.0-12 [7136 B] Get:93 http://localhost:3142/debian unstable/main armhf libbz2-1.0 armhf 1.0.8-6+b1 [35.3 kB] Get:94 http://localhost:3142/debian unstable/main armhf libc6-dev armhf 2.42-11 [1351 kB] Get:95 http://localhost:3142/debian unstable/main armhf libbz2-dev armhf 1.0.8-6+b1 [28.9 kB] Get:96 http://localhost:3142/debian unstable/main armhf libgomp1 armhf 15.2.0-12 [115 kB] Get:97 http://localhost:3142/debian unstable/main armhf libstdc++6 armhf 15.2.0-12 [623 kB] Get:98 http://localhost:3142/debian unstable/main armhf libubsan1 armhf 15.2.0-12 [1075 kB] Get:99 http://localhost:3142/debian unstable/main armhf libgcc-15-dev armhf 15.2.0-12 [768 kB] Get:100 http://localhost:3142/debian unstable/main amd64 libseqan2-dev all 2.5.2-1 [1224 kB] Get:101 http://localhost:3142/debian unstable/main armhf libstdc++-15-dev armhf 15.2.0-12 [2445 kB] Get:102 http://localhost:3142/debian unstable/main amd64 openssl amd64 3.5.5-1 [1500 kB] Get:103 http://localhost:3142/debian unstable/main armhf zlib1g armhf 1:1.3.dfsg+really1.3.1-2 [75.5 kB] Get:104 http://localhost:3142/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-2 [905 kB] Preconfiguring packages ... Fetched 108 MB in 1s (192 MB/s) Selecting previously unselected package libexpat1:amd64. (Reading database ... 12976 files and directories currently installed.) Preparing to unpack .../000-libexpat1_2.7.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.4-1) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../001-libncursesw6_6.6+20251231-1_amd64.deb ... Unpacking libncursesw6:amd64 (6.6+20251231-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-9+b1_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-9+b1) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.4-9+b1_amd64.deb ... Unpacking procps (2:4.0.4-9+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. 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Setting up linux-libc-dev-armhf-cross (6.18.5-1cross1) ... Setting up autopoint (0.23.2-1) ... Setting up libncursesw6:amd64 (6.6+20251231-1) ... Setting up libk5crypto3:amd64 (1.22.1-2) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-10) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.12.0-1) ... Setting up libffi8:amd64 (3.5.2-3+b1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2+b1) ... Setting up procps (2:4.0.4-9+b1) ... Setting up libtasn1-6:amd64 (4.21.0-2) ... Setting up libngtcp2-16:amd64 (1.16.0-1) ... Setting up cmake-data (4.2.3-1) ... Setting up librhash1:amd64 (1.4.6-1.1) ... Setting up libkrb5-3:amd64 (1.22.1-2) ... Setting up libssh2-1t64:amd64 (1.11.1-1+b1) ... Setting up gcc-15-cross-base (15.2.0-7cross1) ... Setting up gcc-15-base:armhf (15.2.0-12) ... Setting up openssl (3.5.5-1) ... Setting up binutils-arm-linux-gnueabihf (2.45.90.20260201-1) ... Setting up cpp-15-arm-linux-gnueabihf (15.2.0-7cross1) ... Setting up libarchive13t64:amd64 (3.8.5-1) ... Setting up libldap2:amd64 (2.6.10+dfsg-1+b1) ... Setting up cpp-arm-linux-gnueabihf (4:15.2.0-5) ... Setting up automake (1:1.18.1-3) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libgomp1-armhf-cross (15.2.0-7cross1) ... Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.2-1) ... Setting up libtool (2.5.4-9) ... Setting up libgcc-s1-armhf-cross (15.2.0-7cross1) ... Setting up libc6-dev-armhf-cross (2.42-10cross1) ... Setting up libidn2-0:amd64 (2.3.8-4+b1) ... Setting up libatomic1-armhf-cross (15.2.0-7cross1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libstdc++6-armhf-cross (15.2.0-7cross1) ... Setting up libp11-kit0:amd64 (0.25.10-1+b1) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-2) ... Setting up libubsan1-armhf-cross (15.2.0-7cross1) ... Setting up libngtcp2-crypto-ossl0:amd64 (1.16.0-1) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-10) ... Setting up libgnutls30t64:amd64 (3.8.11-3) ... Setting up libasan8-armhf-cross (15.2.0-7cross1) ... Setting up po-debconf (1.0.22) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b2) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3+b1) ... Setting up libgcc-15-dev-armhf-cross (15.2.0-7cross1) ... Setting up gcc-15-arm-linux-gnueabihf (15.2.0-7cross1) ... Setting up libcurl4t64:amd64 (8.18.0-2) ... Setting up debhelper (13.29) ... Setting up libstdc++-15-dev-armhf-cross (15.2.0-7cross1) ... Setting up cmake (4.2.3-1) ... Setting up gcc-arm-linux-gnueabihf (4:15.2.0-5) ... Setting up g++-15-arm-linux-gnueabihf (15.2.0-7cross1) ... Setting up g++-arm-linux-gnueabihf (4:15.2.0-5) ... Setting up crossbuild-essential-armhf (12.12) ... Setting up libgcc-s1:armhf (15.2.0-12) ... Setting up libc6:armhf (2.42-11) ... Setting up libasan8:armhf (15.2.0-12) ... Setting up libc6-dev:armhf (2.42-11) ... Setting up libbz2-1.0:armhf (1.0.8-6+b1) ... Setting up libstdc++6:armhf (15.2.0-12) ... Setting up libbz2-dev:armhf (1.0.8-6+b1) ... Setting up zlib1g:armhf (1:1.3.dfsg+really1.3.1-2) ... Setting up libgomp1:armhf (15.2.0-12) ... Setting up libatomic1:armhf (15.2.0-12) ... Setting up libubsan1:armhf (15.2.0-12) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-2) ... Setting up libgcc-15-dev:armhf (15.2.0-12) ... Setting up libstdc++-15-dev:armhf (15.2.0-12) ... Setting up sbuild-build-depends-main-dummy:armhf (0.invalid.0) ... Processing triggers for libc-bin (2.42-11) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-32-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.129-1 (2025-03-06) amd64 (x86_64) Toolchain package versions: binutils_2.45.90.20260201-1 dpkg-dev_1.23.5 g++-15_15.2.0-12 gcc-15_15.2.0-12 libc6-dev_2.42-11 libstdc++-15-dev_15.2.0-12 libstdc++-15-dev-armhf-cross_15.2.0-7cross1 libstdc++6_15.2.0-12 libstdc++6-armhf-cross_15.2.0-7cross1 linux-libc-dev_6.18.5-1 Package versions: apt_3.1.15 apt-utils_3.1.15 autoconf_2.72-3.1 automake_1:1.18.1-3 autopoint_0.23.2-1 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.8 bash_5.3-1 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zlib1g_1:1.3.dfsg+really1.3.1-2 zlib1g-dev_1:1.3.dfsg+really1.3.1-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: lambda-align Binary: lambda-align Architecture: any Version: 1.0.3-8 Maintainer: Debian Med Packaging Team Uploaders: Sascha Steinbiss , Homepage: https://seqan.github.io/lambda Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/lambda-align Vcs-Git: https://salsa.debian.org/med-team/lambda-align.git Testsuite: autopkgtest Testsuite-Triggers: cmake, coreutils, diffutils, gzip, openssl Build-Depends: debhelper-compat (= 13), libseqan2-dev, cmake, zlib1g-dev, libbz2-dev, openssl Package-List: lambda-align deb science optional arch=any Checksums-Sha1: abf40a7204b2c249152a7e4275c6adb3628fe8cf 322730 lambda-align_1.0.3.orig.tar.gz eb1568d0f92821f82f873041a5b0410747d77805 8648 lambda-align_1.0.3-8.debian.tar.xz Checksums-Sha256: 324f90dbc095c56792a77a002e64a98465a4853f74a141a1182e7a6f540545a2 322730 lambda-align_1.0.3.orig.tar.gz 19c895a9b1e31fa9bf0dd5d851f23450b80e39da78d879c853873e00889a2d81 8648 lambda-align_1.0.3-8.debian.tar.xz Files: b18d7c968b8c52851c8037dfc8066bce 322730 lambda-align_1.0.3.orig.tar.gz 26e4b06ea7f6b38b474e6e34c9c3135b 8648 lambda-align_1.0.3-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmj3Pt8RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGc0A//cd6AkDOHbSn/99/wTFcDnPaLt4ZKrtCu m/i13NjZ8+R/a05JDZQn0EEOmsei+Xo6rOHTijNtyn97qqyesfF00qAenru9MNGm ANXbmP/dHkFaKDfpaBGJ183MCSZ3+vnFhwyIFP29PgCJ0P7EDR8zECTWVsb8qxvT Lj17KJuT5YKTlhpLuroYuQjn/IC2cu2N5HUhGTpUU5oPh0ycEKfbVZuJEgxgZCDo MKoN4DNUOHmRS44G64THZ5PFx7VFTE/t6Yxutq5t4wHGWpZqszprvpplYvAmQM6m 8TFBQajHJSj2fTtiYzSMhlp9Kfh5DsZ7pGMTN4vXXGi0ANuX5HTg6eiKVzcGaPJM 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info: unpacking lambda-align_1.0.3-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying set-seqan-cmake-dir.patch dpkg-source: info: applying force-link-rt-pthread.patch dpkg-source: info: applying 0004-make-test-not-depend-on-CXX.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.armhf DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=crossqa OLDPWD=/home/crossqa PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SBUILD_CONFIG=/tmp/tmp.altXyVXC77/sbuild.conf SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=crossqa SCHROOT_SESSION_ID=sid-amd64-sbuild-e4e71451-9bfc-4e88-8573-68261047703e SCHROOT_UID=1000 SCHROOT_USER=crossqa SHELL=/bin/sh USER=crossqa XDG_SESSION_CLASS=user dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aarmhf -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package lambda-align dpkg-buildpackage: info: source version 1.0.3-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type arm-linux-gnueabihf does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --builddirectory=build debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -f *.1 dh_auto_clean -- make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--builddirectory=build dh_clean -O--builddirectory=build debian/rules binary-arch dh binary-arch --builddirectory=build dh_update_autotools_config -a -O--builddirectory=build dh_autoreconf -a -O--builddirectory=build debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- -DLAMBDA_NATIVE_BUILD=OFF -DLAMBDA_MMAPPED_DB=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_POLICY_VERSION_MINIMUM=3.5 cd build && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/arm-linux-gnueabihf-pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_SYSTEM_NAME=Linux -DCMAKE_SYSTEM_PROCESSOR=armv7l -DCMAKE_C_COMPILER=arm-linux-gnueabihf-gcc -DCMAKE_CXX_COMPILER=arm-linux-gnueabihf-g\+\+ -DPKG_CONFIG_EXECUTABLE=/usr/bin/arm-linux-gnueabihf-pkg-config -DPKGCONFIG_EXECUTABLE=/usr/bin/arm-linux-gnueabihf-pkg-config -DQMAKE_EXECUTABLE=/usr/bin/arm-linux-gnueabihf-qmake -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -DBUILD_TESTING:BOOL=OFF -DLAMBDA_NATIVE_BUILD=OFF -DLAMBDA_MMAPPED_DB=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_POLICY_VERSION_MINIMUM=3.5 .. CMake Deprecation Warning at CMakeLists.txt:5 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. Compiler Detection -- The CXX compiler identification is GNU 15.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/arm-linux-gnueabihf-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done Dependency detection -- These dependencies where found: OPENMP TRUE -fopenmp ZLIB TRUE 1.3.1 BZIP2 TRUE 1.0.8 SEQAN TRUE 2.5.2 -- The requirements where met. Build configuration -- LAMBDA version is: 1.0.2 -- The following options are selected for the build: LAMBDA_FASTBUILD OFF LAMBDA_LINGAPS_OPT OFF LAMBDA_MMAPPED_DB ON LAMBDA_NATIVE_BUILD OFF LAMBDA_STATIC_BUILD OFF -- Run 'cmake -LH' to get a comment on each option. -- Remove CMakeCache.txt and re-run cmake with -DOPTIONNAME=ON|OFF to change an option. Setting up unit tests CMake Deprecation Warning at tests/CMakeLists.txt:5 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring done (0.8s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_C_COMPILER CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED PKGCONFIG_EXECUTABLE PKG_CONFIG_EXECUTABLE QMAKE_EXECUTABLE -- Build files have been written to: /<>/build make[1]: Leaving directory '/<>' dh_auto_build -a -O--builddirectory=build cd build && make -j1 INSTALL="install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/<>/build' /usr/bin/cmake -S/<> -B/<>/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/build/CMakeFiles /<>/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/build' make -f src/CMakeFiles/lambda.dir/build.make src/CMakeFiles/lambda.dir/depend make[3]: Entering directory '/<>/build' cd /<>/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src /<>/build /<>/build/src /<>/build/src/CMakeFiles/lambda.dir/DependInfo.cmake "--color=" lambda make[3]: Leaving directory '/<>/build' make -f src/CMakeFiles/lambda.dir/build.make src/CMakeFiles/lambda.dir/build make[3]: Entering directory '/<>/build' [ 25%] Building CXX object src/CMakeFiles/lambda.dir/lambda.cpp.o cd /<>/build/src && /usr/bin/arm-linux-gnueabihf-g++ -DCMAKE_BUILD_TYPE=\"Release\" -DLAMBDA_MMAPPED_DB=1 -DSEQAN_APP_VERSION=\"1.0.2\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP="1 -DSEQAN_GLOBAL_EXCEPTION_HANDLER" -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"\" -DSEQAN_VERSION_STRING=\"2.5.2\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-vla -flto=16 -O3 -DNDEBUG -s -fopenmp -MD -MT src/CMakeFiles/lambda.dir/lambda.cpp.o -MF CMakeFiles/lambda.dir/lambda.cpp.o.d -o CMakeFiles/lambda.dir/lambda.cpp.o -c /<>/src/lambda.cpp In file included from /<>/src/lambda.cpp:32: /<>/src/options.hpp:323:21: warning: macro ‘__DATE__’ might prevent reproducible builds [-Wdate-time] 323 | setDate(parser, __DATE__); | ^~~~~~~~ In file included from /<>/src/lambda.cpp:31: /<>/src/output.hpp:28:17: error: ‘seqan’ is not a namespace-name 28 | using namespace seqan; | ^~~~~ /<>/src/output.hpp: In function ‘void blastMatchOneCigar(TCigar&, const TBlastMatch&, const TLocalHolder&)’: /<>/src/output.hpp:112:29: error: expected nested-name-specifier before ‘Value’ [-Wtemplate-body] 112 | using TCElem = typename Value::Type; | ^~~~~ /<>/src/output.hpp:128:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 128 | appendValue(cigar, TCElem('H', leftFrameClip + leftClip)); | ^~~~~~ /<>/src/output.hpp:128:32: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated) /<>/src/output.hpp:132:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 132 | appendValue(cigar, TCElem('H', leftFrameClip)); | ^~~~~~ /<>/src/output.hpp:134:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 134 | appendValue(cigar, TCElem('S', leftClip)); | ^~~~~~ /<>/src/output.hpp:147:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 147 | appendValue(cigar, TCElem('D', count * transFac)); | ^~~~~~ /<>/src/output.hpp:157:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 157 | appendValue(cigar, TCElem('I', count * transFac)); | ^~~~~~ /<>/src/output.hpp:167:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 167 | appendValue(cigar, TCElem('M', count * transFac)); | ^~~~~~ /<>/src/output.hpp:173:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 173 | appendValue(cigar, TCElem('H', rightFrameClip + rightClip)); | ^~~~~~ /<>/src/output.hpp:177:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 177 | appendValue(cigar, TCElem('S', rightClip)); | ^~~~~~ /<>/src/output.hpp:179:32: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 179 | appendValue(cigar, TCElem('H', rightFrameClip)); | ^~~~~~ /<>/src/output.hpp: In function ‘void blastMatchTwoCigar(TCigar&, TCigar&, const TBlastMatch&, const TLocalHolder&)’: /<>/src/output.hpp:194:29: error: expected nested-name-specifier before ‘Value’ [-Wtemplate-body] 194 | using TCElem = typename Value::Type; | ^~~~~ /<>/src/output.hpp:208:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 208 | appendValue(dnaCigar, TCElem('H', leftFrameClip + 3 * leftClip)); | ^~~~~~ /<>/src/output.hpp:210:36: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 210 | appendValue(protCigar, TCElem('H', leftClip)); | ^~~~~~ /<>/src/output.hpp:215:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 215 | appendValue(dnaCigar, TCElem('H', leftFrameClip)); | ^~~~~~ /<>/src/output.hpp:219:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 219 | appendValue(dnaCigar, TCElem('S', 3 * leftClip)); | ^~~~~~ /<>/src/output.hpp:220:36: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 220 | appendValue(protCigar, TCElem('S', leftClip)); | ^~~~~~ /<>/src/output.hpp:235:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 235 | appendValue(dnaCigar, TCElem('D', count * 3)); | ^~~~~~ /<>/src/output.hpp:236:36: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 236 | appendValue(protCigar, TCElem('D', count)); | ^~~~~~ /<>/src/output.hpp:248:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 248 | appendValue(dnaCigar, TCElem('I', count * 3)); | ^~~~~~ /<>/src/output.hpp:249:36: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 249 | appendValue(protCigar, TCElem('I', count)); | ^~~~~~ /<>/src/output.hpp:261:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 261 | appendValue(dnaCigar, TCElem('M', count * 3)); | ^~~~~~ /<>/src/output.hpp:262:36: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 262 | appendValue(protCigar, TCElem('M', count)); | ^~~~~~ /<>/src/output.hpp:269:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 269 | appendValue(dnaCigar, TCElem('H', rightFrameClip + 3 * rightClip)); | ^~~~~~ /<>/src/output.hpp:271:36: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 271 | appendValue(protCigar, TCElem('H', rightClip)); | ^~~~~~ /<>/src/output.hpp:277:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 277 | appendValue(dnaCigar, TCElem('S', 3 * rightClip)); | ^~~~~~ /<>/src/output.hpp:278:36: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 278 | appendValue(protCigar, TCElem('S', rightClip)); | ^~~~~~ /<>/src/output.hpp:282:35: error: there are no arguments to ‘TCElem’ that depend on a template parameter, so a declaration of ‘TCElem’ must be available [-Wtemplate-body] 282 | appendValue(dnaCigar, TCElem('H', rightFrameClip)); | ^~~~~~ /<>/src/output.hpp: In function ‘void myWriteHeader(TGH&, const TLambdaOptions&)’: /<>/src/output.hpp:316:35: error: ‘seqan’ has not been declared [-Wtemplate-body] 316 | auto & context = seqan::context(globalHolder.outfileBam); | ^~~~~ /<>/src/output.hpp:317:35: error: there are no arguments to ‘contigLengths’ that depend on a template parameter, so a declaration of ‘contigLengths’ must be available [-Wtemplate-body] 317 | auto & subjSeqLengths = contigLengths(context); | ^~~~~~~~~~~~~ /<>/src/output.hpp:318:35: error: there are no arguments to ‘contigNames’ that depend on a template parameter, so a declaration of ‘contigNames’ must be available [-Wtemplate-body] 318 | auto & subjIds = contigNames(context); | ^~~~~~~~~~~ /<>/src/output.hpp:342:74: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-Wtemplate-body] 342 | std::find(begin(globalHolder.subjIds[i], Standard()), | ^~~~~~~~ /<>/src/output.hpp:343:72: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-Wtemplate-body] 343 | end(globalHolder.subjIds[i], Standard()), | ^~~~~~~~ /<>/src/output.hpp:345:66: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-Wtemplate-body] 345 | - begin(globalHolder.subjIds[i], Standard())); | ^~~~~~~~ /<>/src/output.hpp:347:17: error: ‘BamHeaderRecord’ does not name a type [-Wtemplate-body] 347 | typedef BamHeaderRecord::TTag TTag; | ^~~~~~~~~~~~~~~ /<>/src/output.hpp:350:9: error: ‘BamHeader’ was not declared in this scope; did you mean ‘seqan2::BamHeader’? [-Wtemplate-body] 350 | BamHeader header; | ^~~~~~~~~ | seqan2::BamHeader In file included from /usr/include/seqan/bam_io.h:60, from /usr/include/seqan/seq_io/bam_sam.h:39, from /usr/include/seqan/seq_io.h:55, from /<>/src/lambda.cpp:27: /usr/include/seqan/bam_io/bam_header_record.h:192:33: note: ‘seqan2::BamHeader’ declared here 192 | typedef String BamHeader; | ^~~~~~~~~ /<>/src/output.hpp:352:9: error: ‘BamHeaderRecord’ was not declared in this scope; did you mean ‘seqan2::BamHeaderRecord’? [-Wtemplate-body] 352 | BamHeaderRecord firstRecord; | ^~~~~~~~~~~~~~~ | seqan2::BamHeaderRecord /usr/include/seqan/bam_io/bam_header_record.h:163:7: note: ‘seqan2::BamHeaderRecord’ declared here 163 | class BamHeaderRecord | ^~~~~~~~~~~~~~~ /<>/src/output.hpp:353:9: error: ‘firstRecord’ was not declared in this scope [-Wtemplate-body] 353 | firstRecord.type = BAM_HEADER_FIRST; | ^~~~~~~~~~~ /<>/src/output.hpp:353:28: error: ‘BAM_HEADER_FIRST’ was not declared in this scope; did you mean ‘seqan2::BAM_HEADER_FIRST’? [-Wtemplate-body] 353 | firstRecord.type = BAM_HEADER_FIRST; | ^~~~~~~~~~~~~~~~ | seqan2::BAM_HEADER_FIRST /usr/include/seqan/bam_io/bam_header_record.h:76:5: note: ‘seqan2::BAM_HEADER_FIRST’ declared here 76 | BAM_HEADER_FIRST = 0, | ^~~~~~~~~~~~~~~~ /<>/src/output.hpp:354:39: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-Wtemplate-body] 354 | appendValue(firstRecord.tags, TTag("VN", "1.4")); | ^~~~ /<>/src/output.hpp:356:39: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-Wtemplate-body] 356 | appendValue(firstRecord.tags, TTag("GO", "query")); | ^~~~ /<>/src/output.hpp:357:21: error: ‘header’ was not declared in this scope [-Wtemplate-body] 357 | appendValue(header, firstRecord); | ^~~~~~ /<>/src/output.hpp:357:9: error: there are no arguments to ‘appendValue’ that depend on a template parameter, so a declaration of ‘appendValue’ must be available [-Wtemplate-body] 357 | appendValue(header, firstRecord); | ^~~~~~~~~~~ /<>/src/output.hpp:362:28: error: expected ‘;’ before ‘pgRecord’ [-Wtemplate-body] 362 | BamHeaderRecord pgRecord; | ^~~~~~~~~ | ; /<>/src/output.hpp:363:13: error: ‘pgRecord’ was not declared in this scope [-Wtemplate-body] 363 | pgRecord.type = BAM_HEADER_PROGRAM; | ^~~~~~~~ /<>/src/output.hpp:363:29: error: ‘BAM_HEADER_PROGRAM’ was not declared in this scope; did you mean ‘seqan2::BAM_HEADER_PROGRAM’? [-Wtemplate-body] 363 | pgRecord.type = BAM_HEADER_PROGRAM; | ^~~~~~~~~~~~~~~~~~ | seqan2::BAM_HEADER_PROGRAM /usr/include/seqan/bam_io/bam_header_record.h:79:5: note: ‘seqan2::BAM_HEADER_PROGRAM’ declared here 79 | BAM_HEADER_PROGRAM = 3, | ^~~~~~~~~~~~~~~~~~ /<>/src/output.hpp:364:40: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-Wtemplate-body] 364 | appendValue(pgRecord.tags, TTag("ID", "lambda")); | ^~~~ /<>/src/output.hpp:365:40: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-Wtemplate-body] 365 | appendValue(pgRecord.tags, TTag("PN", "lambda")); | ^~~~ /<>/src/output.hpp:366:40: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-Wtemplate-body] 366 | appendValue(pgRecord.tags, TTag("VN", SEQAN_APP_VERSION)); | ^~~~ /<>/src/output.hpp:368:13: error: there are no arguments to ‘appendValue’ that depend on a template parameter, so a declaration of ‘appendValue’ must be available [-Wtemplate-body] 368 | appendValue(header, pgRecord); | ^~~~~~~~~~~ /<>/src/output.hpp:372:24: error: expected ‘;’ before ‘hpRecord0’ [-Wtemplate-body] 372 | BamHeaderRecord hpRecord0; | ^~~~~~~~~~ | ; /<>/src/output.hpp:373:9: error: ‘hpRecord0’ was not declared in this scope [-Wtemplate-body] 373 | hpRecord0.type = BAM_HEADER_COMMENT; | ^~~~~~~~~ /<>/src/output.hpp:373:26: error: ‘BAM_HEADER_COMMENT’ was not declared in this scope; did you mean ‘seqan2::BAM_HEADER_COMMENT’? [-Wtemplate-body] 373 | hpRecord0.type = BAM_HEADER_COMMENT; | ^~~~~~~~~~~~~~~~~~ | seqan2::BAM_HEADER_COMMENT /usr/include/seqan/bam_io/bam_header_record.h:80:5: note: ‘seqan2::BAM_HEADER_COMMENT’ declared here 80 | BAM_HEADER_COMMENT = 4 | ^~~~~~~~~~~~~~~~~~ /<>/src/output.hpp:374:37: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-Wtemplate-body] 374 | appendValue(hpRecord0.tags, TTag("CO", "Lambda is a high performance BLAST compatible local aligner, " | ^~~~ /<>/src/output.hpp:376:9: error: there are no arguments to ‘appendValue’ that depend on a template parameter, so a declaration of ‘appendValue’ must be available [-Wtemplate-body] 376 | appendValue(header, hpRecord0); | ^~~~~~~~~~~ /<>/src/output.hpp:377:24: error: expected ‘;’ before ‘hpRecord1’ [-Wtemplate-body] 377 | BamHeaderRecord hpRecord1; | ^~~~~~~~~~ | ; /<>/src/output.hpp:378:9: error: ‘hpRecord1’ was not declared in this scope [-Wtemplate-body] 378 | hpRecord1.type = BAM_HEADER_COMMENT; | ^~~~~~~~~ /<>/src/output.hpp:379:37: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-Wtemplate-body] 379 | appendValue(hpRecord1.tags, TTag("CO", "SAM/BAM dialect documentation is available here: " | ^~~~ /<>/src/output.hpp:381:9: error: there are no arguments to ‘appendValue’ that depend on a template parameter, so a declaration of ‘appendValue’ must be available [-Wtemplate-body] 381 | appendValue(header, hpRecord1); | ^~~~~~~~~~~ /<>/src/output.hpp:382:24: error: expected ‘;’ before ‘hpRecord2’ [-Wtemplate-body] 382 | BamHeaderRecord hpRecord2; | ^~~~~~~~~~ | ; /<>/src/output.hpp:383:9: error: ‘hpRecord2’ was not declared in this scope [-Wtemplate-body] 383 | hpRecord2.type = BAM_HEADER_COMMENT; | ^~~~~~~~~ /<>/src/output.hpp:384:37: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-Wtemplate-body] 384 | appendValue(hpRecord2.tags, TTag("CO", "If you use any results found by Lambda, please cite " | ^~~~ /<>/src/output.hpp:386:9: error: there are no arguments to ‘appendValue’ that depend on a template parameter, so a declaration of ‘appendValue’ must be available [-Wtemplate-body] 386 | appendValue(header, hpRecord2); | ^~~~~~~~~~~ /<>/src/output.hpp:389:24: error: expected ‘;’ before ‘tagRecord’ [-Wtemplate-body] 389 | BamHeaderRecord tagRecord; | ^~~~~~~~~~ | ; /<>/src/output.hpp:390:9: error: ‘tagRecord’ was not declared in this scope [-Wtemplate-body] 390 | tagRecord.type = BAM_HEADER_COMMENT; | ^~~~~~~~~ /<>/src/output.hpp:392:34: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-Wtemplate-body] 392 | for (unsigned i = 0; i < length(SamBamExtraTags<>::keyDescPairs); ++i) | ^~~~~~ /<>/src/output.hpp:402:37: error: there are no arguments to ‘TTag’ that depend on a template parameter, so a declaration of ‘TTag’ must be available [-Wtemplate-body] 402 | appendValue(tagRecord.tags, TTag("CO", columnHeaders)); | ^~~~ /<>/src/output.hpp:403:9: error: there are no arguments to ‘appendValue’ that depend on a template parameter, so a declaration of ‘appendValue’ must be available [-Wtemplate-body] 403 | appendValue(header, tagRecord); | ^~~~~~~~~~~ /<>/src/output.hpp:409:38: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-Wtemplate-body] 409 | for (unsigned i = 0; i < length(header); ++i) | ^~~~~~ /<>/src/output.hpp:410:64: error: ‘seqan’ has not been declared [-Wtemplate-body] 410 | write(globalHolder.outfileBam.iter, header[i], seqan::context(globalHolder.outfileBam), Sam()); | ^~~~~ /<>/src/output.hpp:410:105: error: there are no arguments to ‘Sam’ that depend on a template parameter, so a declaration of ‘Sam’ must be available [-Wtemplate-body] 410 | write(globalHolder.outfileBam.iter, header[i], seqan::context(globalHolder.outfileBam), Sam()); | ^~~ /<>/src/output.hpp: In function ‘void myWriteRecord(TLH&, const TRecord&)’: /<>/src/output.hpp:438:21: error: ‘BamAlignmentRecord’ was not declared in this scope; did you mean ‘seqan2::BamAlignmentRecord’? [-Wtemplate-body] 438 | std::vector bamRecords; | ^~~~~~~~~~~~~~~~~~ | seqan2::BamAlignmentRecord In file included from /usr/include/seqan/bam_io.h:59: /usr/include/seqan/bam_io/bam_alignment_record.h:241:7: note: ‘seqan2::BamAlignmentRecord’ declared here 241 | class BamAlignmentRecord : public BamAlignmentRecordCore | ^~~~~~~~~~~~~~~~~~ /<>/src/output.hpp:438:39: error: template argument 1 is invalid [-Wtemplate-body] 438 | std::vector bamRecords; | ^ /<>/src/output.hpp:438:39: error: template argument 2 is invalid [-Wtemplate-body] /<>/src/output.hpp:439:20: error: request for member ‘resize’ in ‘bamRecords’, which is of non-class type ‘int’ [-Wtemplate-body] 439 | bamRecords.resize(record.matches.size()); | ^~~~~~ /<>/src/output.hpp:441:9: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’? [-Wtemplate-body] 441 | String> protCigar; | ^~~~~~ | seqan2::String In file included from /usr/include/seqan/sequence.h:105, from /<>/src/lambda.cpp:25: /usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here 290 | class String; | ^~~~~~ /<>/src/output.hpp:441:16: error: ‘CigarElement’ was not declared in this scope; did you mean ‘seqan2::CigarElement’? [-Wtemplate-body] 441 | String> protCigar; | ^~~~~~~~~~~~ | seqan2::CigarElement In file included from /usr/include/seqan/bam_io.h:58: /usr/include/seqan/bam_io/cigar.h:93:8: note: ‘seqan2::CigarElement’ declared here 93 | struct CigarElement | ^~~~~~~~~~~~ /<>/src/output.hpp:441:29: error: expected primary-expression before ‘>>’ token [-Wtemplate-body] 441 | String> protCigar; | ^~ /<>/src/output.hpp:441:32: error: ‘protCigar’ was not declared in this scope [-Wtemplate-body] 441 | String> protCigar; | ^~~~~~~~~ /<>/src/output.hpp:444:42: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-Wtemplate-body] 444 | auto mIt = begin(record.matches, Standard()); | ^~~~~~~~ /<>/src/output.hpp:445:28: error: there are no arguments to ‘begin’ that depend on a template parameter, so a declaration of ‘begin’ must be available [-Wtemplate-body] 445 | for (auto & bamR : bamRecords) | ^~~~~~~~~~ /<>/src/output.hpp:445:28: error: there are no arguments to ‘end’ that depend on a template parameter, so a declaration of ‘end’ must be available [-Wtemplate-body] /<>/src/output.hpp:458:31: error: ‘BAM_FLAG_SECONDARY’ was not declared in this scope; did you mean ‘seqan2::BAM_FLAG_SECONDARY’? [-Wtemplate-body] 458 | bamR.flag = BAM_FLAG_SECONDARY; // all are secondary for now | ^~~~~~~~~~~~~~~~~~ | seqan2::BAM_FLAG_SECONDARY /usr/include/seqan/bam_io/bam_alignment_record.h:107:5: note: ‘seqan2::BAM_FLAG_SECONDARY’ declared here 107 | BAM_FLAG_SECONDARY = 0x0100, | ^~~~~~~~~~~~~~~~~~ /<>/src/output.hpp:460:32: error: ‘BAM_FLAG_RC’ was not declared in this scope; did you mean ‘seqan2::BAM_FLAG_RC’? [-Wtemplate-body] 460 | bamR.flag |= BAM_FLAG_RC; | ^~~~~~~~~~~ | seqan2::BAM_FLAG_RC /usr/include/seqan/bam_io/bam_alignment_record.h:103:5: note: ‘seqan2::BAM_FLAG_RC’ declared here 103 | BAM_FLAG_RC = 0x0010, | ^~~~~~~~~~~ /<>/src/output.hpp:463:64: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-Wtemplate-body] 463 | std::find(begin(mIt->qId, Standard()), | ^~~~~~~~ /<>/src/output.hpp:464:62: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-Wtemplate-body] 464 | end(mIt->qId, Standard()), | ^~~~~~~~ /<>/src/output.hpp:466:56: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-Wtemplate-body] 466 | - begin(mIt->qId, Standard())); | ^~~~~~~~ /<>/src/output.hpp:473:17: error: there are no arguments to ‘clear’ that depend on a template parameter, so a declaration of ‘clear’ must be available [-Wtemplate-body] 473 | clear(protCigar); | ^~~~~ /<>/src/output.hpp:475:44: error: ‘BlastProgram’ has not been declared [-Wtemplate-body] 475 | if ((lH.gH.blastProgram == BlastProgram::BLASTP) || (lH.gH.blastProgram == BlastProgram::TBLASTN)) | ^~~~~~~~~~~~ /<>/src/output.hpp:475:92: error: ‘BlastProgram’ has not been declared [-Wtemplate-body] 475 | if ((lH.gH.blastProgram == BlastProgram::BLASTP) || (lH.gH.blastProgram == BlastProgram::TBLASTN)) | ^~~~~~~~~~~~ /<>/src/output.hpp:484:44: error: ‘BlastProgram’ has not been declared [-Wtemplate-body] 484 | if ((lH.gH.blastProgram != BlastProgram::BLASTP) && (lH.gH.blastProgram != BlastProgram::TBLASTN)) | ^~~~~~~~~~~~ /<>/src/output.hpp:484:92: error: ‘BlastProgram’ has not been declared [-Wtemplate-body] 484 | if ((lH.gH.blastProgram != BlastProgram::BLASTP) && (lH.gH.blastProgram != BlastProgram::TBLASTN)) | ^~~~~~~~~~~~ /<>/src/output.hpp:489:77: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-Wtemplate-body] 489 | if ((lH.options.samBamSeq > 1) || (mIt == begin(record.matches, Standard()))) | ^~~~~~~~ /<>/src/output.hpp:501:39: error: ‘BlastProgram’ has not been declared [-Wtemplate-body] 501 | if (lH.gH.blastProgram == BlastProgram::BLASTN) | ^~~~~~~~~~~~ /<>/src/output.hpp:574:44: error: ‘BlastProgram’ has not been declared [-Wtemplate-body] 574 | if ((lH.gH.blastProgram == BlastProgram::BLASTN) || (!writeSeq)) | ^~~~~~~~~~~~ /<>/src/output.hpp:593:21: error: there are no arguments to ‘empty’ that depend on a template parameter, so a declaration of ‘empty’ must be available [-Wtemplate-body] 593 | if (empty(protCigar)) | ^~~~~ /<>/src/output.hpp:599:21: error: there are no arguments to ‘clear’ that depend on a template parameter, so a declaration of ‘clear’ must be available [-Wtemplate-body] 599 | clear(protCigarString); | ^~~~~ /<>/src/output.hpp:600:46: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-Wtemplate-body] 600 | for (unsigned i = 0; i < length(protCigar); ++i) | ^~~~~~ /<>/src/output.hpp:602:25: error: there are no arguments to ‘appendNumber’ that depend on a template parameter, so a declaration of ‘appendNumber’ must be available [-Wtemplate-body] 602 | appendNumber(protCigarString, protCigar[i].count); | ^~~~~~~~~~~~ /<>/src/output.hpp:603:25: error: there are no arguments to ‘appendValue’ that depend on a template parameter, so a declaration of ‘appendValue’ must be available [-Wtemplate-body] 603 | appendValue(protCigarString, protCigar[i].operation); | ^~~~~~~~~~~ /<>/src/output.hpp:624:20: error: request for member ‘front’ in ‘bamRecords’, which is of non-class type ‘int’ [-Wtemplate-body] 624 | bamRecords.front().flag -= BAM_FLAG_SECONDARY; // remove BAM_FLAG_SECONDARY for first | ^~~~~ /<>/src/output.hpp:624:36: error: ‘BAM_FLAG_SECONDARY’ was not declared in this scope; did you mean ‘seqan2::BAM_FLAG_SECONDARY’? [-Wtemplate-body] 624 | bamRecords.front().flag -= BAM_FLAG_SECONDARY; // remove BAM_FLAG_SECONDARY for first | ^~~~~~~~~~~~~~~~~~ | seqan2::BAM_FLAG_SECONDARY /usr/include/seqan/bam_io/bam_alignment_record.h:107:5: note: ‘seqan2::BAM_FLAG_SECONDARY’ declared here 107 | BAM_FLAG_SECONDARY = 0x0100, | ^~~~~~~~~~~~~~~~~~ /<>/src/output.hpp:628:29: error: there are no arguments to ‘begin’ that depend on a template parameter, so a declaration of ‘begin’ must be available [-Wtemplate-body] 628 | for (auto & r : bamRecords) | ^~~~~~~~~~ /<>/src/output.hpp:628:29: error: there are no arguments to ‘end’ that depend on a template parameter, so a declaration of ‘end’ must be available [-Wtemplate-body] /<>/src/options.hpp: At global scope: /<>/src/options.hpp:61:25: error: ‘Dna5’ was not declared in this scope; did you mean ‘seqan2::Dna5’? 61 | struct SizeTypePosMeta_ | ^~~~ | seqan2::Dna5 In file included from /usr/include/seqan/basic/basic_alphabet.h:93, from /usr/include/seqan/basic/basic_container.h:47, from /usr/include/seqan/basic.h:71, from /<>/src/lambda.cpp:24: /usr/include/seqan/basic/alphabet_residue.h:134:42: note: ‘seqan2::Dna5’ declared here 134 | typedef SimpleType Dna5; | ^~~~ /<>/src/options.hpp:61:29: error: template argument 1 is invalid 61 | struct SizeTypePosMeta_ | ^ /<>/src/options.hpp:76:8: error: ‘SAValue’ is not a class template 76 | struct SAValue, TSpec2>, TSpec3> > | ^~~~~~~ /<>/src/options.hpp:76:16: error: ‘StringSet’ was not declared in this scope; did you mean ‘seqan2::StringSet’? 76 | struct SAValue, TSpec2>, TSpec3> > | ^~~~~~~~~ | seqan2::StringSet In file included from /usr/include/seqan/sequence.h:133: /usr/include/seqan/sequence/sequence_concatenator.h:50:7: note: ‘seqan2::StringSet’ declared here 50 | class StringSet; | ^~~~~~~~~ /<>/src/options.hpp:76:26: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’? 76 | struct SAValue, TSpec2>, TSpec3> > | ^~~~~~ | seqan2::String /usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here 290 | class String; | ^~~~~~ /<>/src/options.hpp:76:33: error: ‘ReducedAminoAcid’ was not declared in this scope; did you mean ‘seqan2::ReducedAminoAcid’? 76 | struct SAValue, TSpec2>, TSpec3> > | ^~~~~~~~~~~~~~~~ | seqan2::ReducedAminoAcid In file included from /usr/include/seqan/reduced_aminoacid.h:43, from /<>/src/lambda.cpp:28: /usr/include/seqan/reduced_aminoacid/reduced_aminoacid_base.h:79:7: note: ‘seqan2::ReducedAminoAcid’ declared here 79 | using ReducedAminoAcid = SimpleType >; | ^~~~~~~~~~~~~~~~ /<>/src/options.hpp:76:15: error: expected ‘;’ before ‘,’ token 76 | struct SAValue, TSpec2>, TSpec3> > | ^ ~ | ; /<>/src/options.hpp:82:8: error: ‘SAValue’ is not a class template 82 | struct SAValue, TFunctor>, TSpec3> > | ^~~~~~~ /<>/src/options.hpp:82:16: error: ‘StringSet’ was not declared in this scope; did you mean ‘seqan2::StringSet’? 82 | struct SAValue, TFunctor>, TSpec3> > | ^~~~~~~~~ | seqan2::StringSet /usr/include/seqan/sequence/sequence_concatenator.h:50:7: note: ‘seqan2::StringSet’ declared here 50 | class StringSet; | ^~~~~~~~~ /<>/src/options.hpp:82:26: error: ‘ModifiedString’ was not declared in this scope; did you mean ‘seqan2::ModifiedString’? 82 | struct SAValue, TFunctor>, TSpec3> > | ^~~~~~~~~~~~~~ | seqan2::ModifiedString In file included from /usr/include/seqan/modifier.h:61, from /usr/include/seqan/file.h:59, from /usr/include/seqan/stream.h:62, from /usr/include/seqan/arg_parse.h:46, from /<>/src/lambda.cpp:26: /usr/include/seqan/modifier/modifier_iterator.h:46:49: note: ‘seqan2::ModifiedString’ declared here 46 | template class ModifiedString; | ^~~~~~~~~~~~~~ /<>/src/options.hpp:82:41: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’? 82 | struct SAValue, TFunctor>, TSpec3> > | ^~~~~~ | seqan2::String /usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here 290 | class String; | ^~~~~~ /<>/src/options.hpp:82:15: error: expected ‘;’ before ‘,’ token 82 | struct SAValue, TFunctor>, TSpec3> > | ^ ~ | ; /<>/src/options.hpp:88:8: error: ‘SAValue’ is not a class template 88 | struct SAValue, TSpec3> > | ^~~~~~~ /<>/src/options.hpp:88:16: error: ‘StringSet’ was not declared in this scope; did you mean ‘seqan2::StringSet’? 88 | struct SAValue, TSpec3> > | ^~~~~~~~~ | seqan2::StringSet /usr/include/seqan/sequence/sequence_concatenator.h:50:7: note: ‘seqan2::StringSet’ declared here 50 | class StringSet; | ^~~~~~~~~ /<>/src/options.hpp:88:26: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’? 88 | struct SAValue, TSpec3> > | ^~~~~~ | seqan2::String /usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here 290 | class String; | ^~~~~~ /<>/src/options.hpp:88:15: error: expected ‘;’ before ‘,’ token 88 | struct SAValue, TSpec3> > | ^ ~ | ; /<>/src/options.hpp:94:8: error: ‘DefaultIndexStringSpec’ is not a class template 94 | struct DefaultIndexStringSpec> | ^~~~~~~~~~~~~~~~~~~~~~ /<>/src/options.hpp:94:31: error: ‘StringSet’ was not declared in this scope; did you mean ‘seqan2::StringSet’? 94 | struct DefaultIndexStringSpec> | ^~~~~~~~~ | seqan2::StringSet /usr/include/seqan/sequence/sequence_concatenator.h:50:7: note: ‘seqan2::StringSet’ declared here 50 | class StringSet; | ^~~~~~~~~ /<>/src/options.hpp:94:55: error: expected unqualified-id before ‘>’ token 94 | struct DefaultIndexStringSpec> | ^~ /<>/src/options.hpp:105:8: error: ‘FormattedFileContext’ is not a class template 105 | struct FormattedFileContext, TStorageSpec> | ^~~~~~~~~~~~~~~~~~~~ /<>/src/options.hpp:105:29: error: ‘FormattedFile’ was not declared in this scope; did you mean ‘seqan2::FormattedFile’? 105 | struct FormattedFileContext, TStorageSpec> | ^~~~~~~~~~~~~ | seqan2::FormattedFile In file included from /usr/include/seqan/stream.h:111: /usr/include/seqan/stream/formatted_file.h:213:8: note: ‘seqan2::FormattedFile’ declared here 213 | struct FormattedFile | ^~~~~~~~~~~~~ /<>/src/options.hpp:105:43: error: ‘Bam’ was not declared in this scope; did you mean ‘seqan2::Bam’? 105 | struct FormattedFileContext, TStorageSpec> | ^~~ | seqan2::Bam In file included from /usr/include/seqan/bam_io.h:70: /usr/include/seqan/bam_io/read_bam.h:55:19: note: ‘seqan2::Bam’ declared here 55 | typedef Tag Bam; | ^~~ /<>/src/options.hpp:105:60: error: ‘BlastTabular’ was not declared in this scope; did you mean ‘seqan2::BlastTabular’? 105 | struct FormattedFileContext, TStorageSpec> | ^~~~~~~~~~~~ | seqan2::BlastTabular In file included from /usr/include/seqan/blast.h:62, from /<>/src/output.hpp:25: /usr/include/seqan/blast/blast_tabular.h:86:28: note: ‘seqan2::BlastTabular’ declared here 86 | typedef Tag BlastTabular; | ^~~~~~~~~~~~ /<>/src/options.hpp:105:28: error: expected ‘;’ before ‘,’ token 105 | struct FormattedFileContext, TStorageSpec> | ^ ~ | ; /<>/src/options.hpp:121:23: error: ‘MMap’ does not name a type 121 | using TAlloc = MMap<>; | ^~~~ /<>/src/options.hpp:125:23: error: ‘WaveletTree’ does not name a type 125 | using Bwt = WaveletTree >; | ^~~~~~~~~~~ /<>/src/options.hpp:126:23: error: ‘Levels’ does not name a type 126 | using Sentinels = Levels >; | ^~~~~~ /<>/src/options.hpp:132:18: error: ‘FMIndex’ does not name a type 132 | using TFMIndex = FMIndex; | ^~~~~~~ /<>/src/options.hpp:136:22: error: ‘StringSet’ does not name a type 136 | using TCDStringSet = StringSet > >; | ^~~~~~~~~ /<>/src/options.hpp:138:11: error: ‘BlastProgram’ has not been declared 138 | template | ^~~~~~~~~~~~ /<>/src/options.hpp:140:45: error: ‘p’ was not declared in this scope 140 | (p == BlastProgram::BLASTN) || | ^ /<>/src/options.hpp:140:50: error: ‘BlastProgram’ was not declared in this scope; did you mean ‘seqan2::BlastProgram’? 140 | (p == BlastProgram::BLASTN) || | ^~~~~~~~~~~~ | seqan2::BlastProgram In file included from /usr/include/seqan/blast.h:59: /usr/include/seqan/blast/blast_base.h:84:12: note: ‘seqan2::BlastProgram’ declared here 84 | enum class BlastProgram : uint8_t | ^~~~~~~~~~~~ /<>/src/options.hpp:140:64: error: wrong number of template arguments (1, should be 3) 140 | (p == BlastProgram::BLASTN) || | ^~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/15/bits/move.h:37, from /usr/arm-linux-gnueabihf/include/c++/15/bits/exception_ptr.h:41, from /usr/arm-linux-gnueabihf/include/c++/15/exception:168, from /usr/arm-linux-gnueabihf/include/c++/15/ios:43, from /usr/arm-linux-gnueabihf/include/c++/15/bits/ostream.h:43, from /usr/arm-linux-gnueabihf/include/c++/15/ostream:42, from /usr/arm-linux-gnueabihf/include/c++/15/iostream:43, from /<>/src/lambda.cpp:22: /usr/arm-linux-gnueabihf/include/c++/15/type_traits:2460:12: note: provided for ‘template struct std::conditional’ 2460 | struct conditional | ^~~~~~~~~~~ /<>/src/options.hpp:140:70: error: expected identifier before ‘)’ token 140 | (p == BlastProgram::BLASTN) || | ^ /<>/src/options.hpp:146:11: error: ‘BlastProgram’ has not been declared 146 | template | ^~~~~~~~~~~~ /<>/src/options.hpp:148:45: error: ‘p’ was not declared in this scope 148 | (p == BlastProgram::BLASTN) || | ^ /<>/src/options.hpp:148:50: error: ‘BlastProgram’ was not declared in this scope; did you mean ‘seqan2::BlastProgram’? 148 | (p == BlastProgram::BLASTN) || | ^~~~~~~~~~~~ | seqan2::BlastProgram /usr/include/seqan/blast/blast_base.h:84:12: note: ‘seqan2::BlastProgram’ declared here 84 | enum class BlastProgram : uint8_t | ^~~~~~~~~~~~ /<>/src/options.hpp:148:64: error: wrong number of template arguments (1, should be 3) 148 | (p == BlastProgram::BLASTN) || | ^~~~~~ /usr/arm-linux-gnueabihf/include/c++/15/type_traits:2460:12: note: provided for ‘template struct std::conditional’ 2460 | struct conditional | ^~~~~~~~~~~ /<>/src/options.hpp:148:70: error: expected identifier before ‘)’ token 148 | (p == BlastProgram::BLASTN) || | ^ /<>/src/options.hpp:154:11: error: ‘BlastProgram’ has not been declared 154 | template | ^~~~~~~~~~~~ /<>/src/options.hpp:155:46: error: ‘p’ was not declared in this scope 155 | using TransAlph = typename std::conditional<(p == BlastProgram::BLASTN), | ^ /<>/src/options.hpp:155:51: error: ‘BlastProgram’ was not declared in this scope; did you mean ‘seqan2::BlastProgram’? 155 | using TransAlph = typename std::conditional<(p == BlastProgram::BLASTN), | ^~~~~~~~~~~~ | seqan2::BlastProgram /usr/include/seqan/blast/blast_base.h:84:12: note: ‘seqan2::BlastProgram’ declared here 84 | enum class BlastProgram : uint8_t | ^~~~~~~~~~~~ /<>/src/options.hpp:155:65: error: wrong number of template arguments (1, should be 3) 155 | using TransAlph = typename std::conditional<(p == BlastProgram::BLASTN), | ^~~~~~ /usr/arm-linux-gnueabihf/include/c++/15/type_traits:2460:12: note: provided for ‘template struct std::conditional’ 2460 | struct conditional | ^~~~~~~~~~~ /<>/src/options.hpp:155:71: error: expected identifier before ‘)’ token 155 | using TransAlph = typename std::conditional<(p == BlastProgram::BLASTN), | ^ /<>/src/options.hpp:160:11: error: ‘BlastProgram’ has not been declared 160 | template | ^~~~~~~~~~~~ /<>/src/options.hpp:161:44: error: ‘p’ was not declared in this scope 161 | using RedAlph = typename std::conditional<(p == BlastProgram::BLASTN), | ^ /<>/src/options.hpp:161:49: error: ‘BlastProgram’ was not declared in this scope; did you mean ‘seqan2::BlastProgram’? 161 | using RedAlph = typename std::conditional<(p == BlastProgram::BLASTN), | ^~~~~~~~~~~~ | seqan2::BlastProgram /usr/include/seqan/blast/blast_base.h:84:12: note: ‘seqan2::BlastProgram’ declared here 84 | enum class BlastProgram : uint8_t | ^~~~~~~~~~~~ /<>/src/options.hpp:161:63: error: wrong number of template arguments (1, should be 3) 161 | using RedAlph = typename std::conditional<(p == BlastProgram::BLASTN), | ^~~~~~ /usr/arm-linux-gnueabihf/include/c++/15/type_traits:2460:12: note: provided for ‘template struct std::conditional’ 2460 | struct conditional | ^~~~~~~~~~~ /<>/src/options.hpp:161:69: error: expected identifier before ‘)’ token 161 | using RedAlph = typename std::conditional<(p == BlastProgram::BLASTN), | ^ /<>/src/options.hpp:216:5: error: ‘GeneticCodeSpec’ does not name a type 216 | GeneticCodeSpec geneticCode = CANONICAL; | ^~~~~~~~~~~~~~~ /<>/src/options.hpp:218:5: error: ‘BlastProgram’ does not name a type 218 | BlastProgram blastProgram = BlastProgram::BLASTX; | ^~~~~~~~~~~~ /<>/src/options.hpp: In constructor ‘SharedOptions::SharedOptions()’: /<>/src/options.hpp:227:18: error: ‘isTerminal’ was not declared in this scope; did you mean ‘seqan2::isTerminal’? 227 | isTerm = isTerminal(); | ^~~~~~~~~~ | seqan2::isTerminal In file included from /usr/include/seqan/arg_parse/tool_doc.h:40, from /usr/include/seqan/arg_parse.h:65: /usr/include/seqan/misc/terminal.h:98:13: note: ‘seqan2::isTerminal’ declared here 98 | inline bool isTerminal() | ^~~~~~~~~~ /<>/src/options.hpp:231:13: error: ‘getTerminalSize’ was not declared in this scope; did you mean ‘seqan2::getTerminalSize’? 231 | getTerminalSize(terminalCols, _rows); | ^~~~~~~~~~~~~~~ | seqan2::getTerminalSize /usr/include/seqan/misc/terminal.h:196:13: note: ‘seqan2::getTerminalSize’ declared here 196 | inline bool getTerminalSize(unsigned & cols, unsigned & rows) | ^~~~~~~~~~~~~~~ /<>/src/options.hpp: At global scope: /<>/src/options.hpp:245:17: error: ‘BlastMatchField’ was not declared in this scope; did you mean ‘seqan2::BlastMatchField’? 245 | std::vector::Enum> columns; | ^~~~~~~~~~~~~~~ | seqan2::BlastMatchField /usr/include/seqan/blast/blast_tabular.h:295:8: note: ‘seqan2::BlastMatchField’ declared here 295 | struct BlastMatchField | ^~~~~~~~~~~~~~~ /<>/src/options.hpp:245:33: error: template argument 1 is invalid 245 | std::vector::Enum> columns; | ^ /<>/src/options.hpp:245:33: error: template argument 2 is invalid /<>/src/options.hpp:245:36: error: expected ‘;’ at end of member declaration 245 | std::vector::Enum> columns; | ^~~~ | ; /<>/src/options.hpp:245:40: error: expected unqualified-id before ‘>’ token 245 | std::vector::Enum> columns; | ^ /<>/src/options.hpp:317:1: error: variable or field ‘sharedSetup’ declared void 317 | sharedSetup(ArgumentParser & parser) | ^~~~~~~~~~~ /<>/src/options.hpp:317:13: error: ‘ArgumentParser’ was not declared in this scope; did you mean ‘seqan2::ArgumentParser’? 317 | sharedSetup(ArgumentParser & parser) | ^~~~~~~~~~~~~~ | seqan2::ArgumentParser In file included from /usr/include/seqan/arg_parse.h:71: /usr/include/seqan/arg_parse/argument_parser.h:152:7: note: ‘seqan2::ArgumentParser’ declared here 152 | class ArgumentParser | ^~~~~~~~~~~~~~ /<>/src/options.hpp:317:30: error: ‘parser’ was not declared in this scope; did you mean ‘pause’? 317 | sharedSetup(ArgumentParser & parser) | ^~~~~~ | pause /<>/src/options.hpp:394:1: error: ‘ArgumentParser’ does not name a type 394 | ArgumentParser::ParseResult | ^~~~~~~~~~~~~~ /<>/src/options.hpp:397:1: error: ‘ArgumentParser’ does not name a type 397 | ArgumentParser::ParseResult | ^~~~~~~~~~~~~~ /<>/src/options.hpp:1030:1: error: ‘ArgumentParser’ does not name a type 1030 | ArgumentParser::ParseResult | ^~~~~~~~~~~~~~ /<>/src/options.hpp:1211:1: error: ‘ArgumentParser’ does not name a type 1211 | ArgumentParser::ParseResult | ^~~~~~~~~~~~~~ /<>/src/options.hpp:1280:11: error: ‘AminoAcid’ was not declared in this scope; did you mean ‘seqan2::AminoAcid’? 1280 | _alphName(AminoAcid const & /**/) | ^~~~~~~~~ | seqan2::AminoAcid /usr/include/seqan/basic/alphabet_residue.h:550:47: note: ‘seqan2::AminoAcid’ declared here 550 | typedef SimpleType AminoAcid; | ^~~~~~~~~ /<>/src/options.hpp:1286:1: error: redefinition of ‘constexpr const char* const _alphName’ 1286 | _alphName(ReducedAminoAcid const & /**/) | ^~~~~~~~~ /<>/src/options.hpp:1280:1: note: ‘constexpr const char* const _alphName’ previously defined here 1280 | _alphName(AminoAcid const & /**/) | ^~~~~~~~~ /<>/src/options.hpp:1286:11: error: ‘ReducedAminoAcid’ was not declared in this scope; did you mean ‘seqan2::ReducedAminoAcid’? 1286 | _alphName(ReducedAminoAcid const & /**/) | ^~~~~~~~~~~~~~~~ | seqan2::ReducedAminoAcid /usr/include/seqan/reduced_aminoacid/reduced_aminoacid_base.h:79:7: note: ‘seqan2::ReducedAminoAcid’ declared here 79 | using ReducedAminoAcid = SimpleType >; | ^~~~~~~~~~~~~~~~ /<>/src/options.hpp:1286:28: error: ‘Murphy10’ was not declared in this scope; did you mean ‘seqan2::Murphy10’? 1286 | _alphName(ReducedAminoAcid const & /**/) | ^~~~~~~~ | seqan2::Murphy10 In file included from /usr/include/seqan/reduced_aminoacid.h:57: /usr/include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_base.h:85:24: note: ‘seqan2::Murphy10’ declared here 85 | typedef Tag Murphy10; | ^~~~~~~~ /<>/src/options.hpp:1286:38: error: expected primary-expression before ‘const’ 1286 | _alphName(ReducedAminoAcid const & /**/) | ^~~~~ /<>/src/options.hpp:1310:1: error: redefinition of ‘constexpr const char* const _alphName’ 1310 | _alphName(Dna const & /**/) | ^~~~~~~~~ /<>/src/options.hpp:1280:1: note: ‘constexpr const char* const _alphName’ previously defined here 1280 | _alphName(AminoAcid const & /**/) | ^~~~~~~~~ /<>/src/options.hpp:1310:11: error: ‘Dna’ was not declared in this scope; did you mean ‘seqan2::Dna’? 1310 | _alphName(Dna const & /**/) | ^~~ | seqan2::Dna /usr/include/seqan/basic/alphabet_residue.h:94:41: note: ‘seqan2::Dna’ declared here 94 | typedef SimpleType Dna; | ^~~ /<>/src/options.hpp:1316:1: error: redefinition of ‘constexpr const char* const _alphName’ 1316 | _alphName(Dna5 const & /**/) | ^~~~~~~~~ /<>/src/options.hpp:1280:1: note: ‘constexpr const char* const _alphName’ previously defined here 1280 | _alphName(AminoAcid const & /**/) | ^~~~~~~~~ /<>/src/options.hpp:1316:11: error: ‘Dna5’ was not declared in this scope; did you mean ‘seqan2::Dna5’? 1316 | _alphName(Dna5 const & /**/) | ^~~~ | seqan2::Dna5 /usr/include/seqan/basic/alphabet_residue.h:134:42: note: ‘seqan2::Dna5’ declared here 134 | typedef SimpleType Dna5; | ^~~~ /<>/src/options.hpp: In function ‘void printOptions(const LambdaOptions&)’: /<>/src/options.hpp:1362:41: error: ‘BlastProgram’ has not been declared [-Wtemplate-body] 1362 | << ((TGH::blastProgram != BlastProgram::BLASTN) && | ^~~~~~~~~~~~ /<>/src/options.hpp:1363:41: error: ‘BlastProgram’ has not been declared [-Wtemplate-body] 1363 | (TGH::blastProgram != BlastProgram::BLASTP) | ^~~~~~~~~~~~ /<>/src/options.hpp:1364:43: error: ‘const struct LambdaOptions’ has no member named ‘geneticCode’ [-Wtemplate-body] 1364 | ? std::to_string(options.geneticCode) | ^~~~~~~~~~~ /<>/src/options.hpp:1368:62: error: ‘OrigQryAlph’ was not declared in this scope [-Wtemplate-body] 1368 | << " original alphabet (query):" << _alphName(OrigQryAlph()) | ^~~~~~~~~~~ /<>/src/options.hpp:1368:93: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 1368 | << " original alphabet (query):" << _alphName(OrigQryAlph()) | ^ /<>/src/options.hpp:1370:62: error: ‘OrigSubjAlph’ was not declared in this scope [-Wtemplate-body] 1370 | << " original alphabet (subj): " << _alphName(OrigSubjAlph()) | ^~~~~~~~~~~~ /<>/src/options.hpp:1370:94: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 1370 | << " original alphabet (subj): " << _alphName(OrigSubjAlph()) | ^ /<>/src/options.hpp:1372:62: error: ‘TransAlph’ was not declared in this scope [-Wtemplate-body] 1372 | << " translated alphabet: " << _alphName(TransAlph()) | ^~~~~~~~~ /<>/src/options.hpp:1372:91: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 1372 | << " translated alphabet: " << _alphName(TransAlph()) | ^ In file included from /<>/src/lambda.cpp:33: /<>/src/holders.hpp: In function ‘void printStats(const StatsHolder&, const LambdaOptions&)’: /<>/src/holders.hpp:141:24: error: ‘_numberOfDigits’ was not declared in this scope; did you mean ‘seqan2::_numberOfDigits’? 141 | auto const w = _numberOfDigits(rem); // number of digits | ^~~~~~~~~~~~~~~ | seqan2::_numberOfDigits In file included from /usr/include/seqan/blast.h:67: /usr/include/seqan/blast/blast_report_out.h:192:1: note: ‘seqan2::_numberOfDigits’ declared here 192 | _numberOfDigits(T const number) | ^~~~~~~~~~~~~~~ /<>/src/holders.hpp:182:24: error: ‘_numberOfDigits’ was not declared in this scope; did you mean ‘seqan2::_numberOfDigits’? 182 | auto const w = _numberOfDigits(stats.hitsFinal); | ^~~~~~~~~~~~~~~ | seqan2::_numberOfDigits /usr/include/seqan/blast/blast_report_out.h:192:1: note: ‘seqan2::_numberOfDigits’ declared here 192 | _numberOfDigits(T const number) | ^~~~~~~~~~~~~~~ /<>/src/holders.hpp: At global scope: /<>/src/holders.hpp:215:11: error: ‘BlastProgram’ has not been declared 215 | BlastProgram p, | ^~~~~~~~~~~~ /<>/src/holders.hpp:216:11: error: ‘BlastTabularSpec’ has not been declared 216 | BlastTabularSpec h> | ^~~~~~~~~~~~~~~~ /<>/src/holders.hpp:220:28: error: ‘RedAlph’ does not name a type; did you mean ‘TRedAlph_’? [-Wtemplate-body] 220 | using TRedAlph = RedAlph; // ensures == Dna5 for BlastN | ^~~~~~~ | TRedAlph_ /<>/src/holders.hpp:221:34: error: ‘TRedAlph’ was not declared in this scope; did you mean ‘TRedAlph_’? [-Wtemplate-body] 221 | using TMatch = Match; | ^~~~~~~~ | TRedAlph_ /<>/src/holders.hpp:221:42: error: template argument 1 is invalid [-Wtemplate-body] 221 | using TMatch = Match; | ^ /<>/src/holders.hpp:223:22: error: ‘BlastProgram’ does not name a type [-Wtemplate-body] 223 | static constexpr BlastProgram blastProgram = p; | ^~~~~~~~~~~~ /<>/src/holders.hpp:224:77: error: ‘TFMIndex’ was not declared in this scope [-Wtemplate-body] 224 | static constexpr bool indexIsFM = std::is_same>::value; | ^~~~~~~~ /<>/src/holders.hpp:224:85: error: template argument 2 is invalid [-Wtemplate-body] 224 | static constexpr bool indexIsFM = std::is_same>::value; | ^ /<>/src/holders.hpp:224:90: error: ‘::value’ has not been declared; did you mean ‘seqan2::value’? [-Wtemplate-body] 224 | static constexpr bool indexIsFM = std::is_same>::value; | ^~~~~ | seqan2::value In file included from /usr/include/seqan/seeds.h:77, from /usr/include/seqan/align_extend.h:42, from /<>/src/holders.hpp:25: /usr/include/seqan/seeds/basic_iter_indirect.h:173:1: note: ‘seqan2::value’ declared here 173 | value(Iter > const & iter) | ^~~~~ /<>/src/holders.hpp:225:65: error: ‘TransAlph’ was not declared in this scope [-Wtemplate-body] 225 | static constexpr bool alphReduction = !std::is_same, TRedAlph>::value; | ^~~~~~~~~ /<>/src/holders.hpp:225:75: error: ‘p’ was not declared in this scope [-Wtemplate-body] 225 | static constexpr bool alphReduction = !std::is_same, TRedAlph>::value; | ^ /<>/src/holders.hpp:225:76: error: wrong number of template arguments (1, should be 2) [-Wtemplate-body] 225 | static constexpr bool alphReduction = !std::is_same, TRedAlph>::value; | ^ /usr/arm-linux-gnueabihf/include/c++/15/type_traits:799:12: note: provided for ‘template struct std::is_same’ 799 | struct is_same; | ^~~~~~~ /<>/src/holders.hpp:225:79: error: ‘constexpr’ static data member ‘TRedAlph’ must have an initializer [-Wtemplate-body] 225 | static constexpr bool alphReduction = !std::is_same, TRedAlph>::value; | ^~~~~~~~ /<>/src/holders.hpp:225:79: error: expected ‘;’ at end of member declaration [-Wtemplate-body] 225 | static constexpr bool alphReduction = !std::is_same, TRedAlph>::value; | ^~~~~~~~ | ; /<>/src/holders.hpp:225:87: error: expected unqualified-id before ‘>’ token [-Wtemplate-body] 225 | static constexpr bool alphReduction = !std::is_same, TRedAlph>::value; | ^ /<>/src/holders.hpp:228:27: error: ‘Alloc’ does not name a type; did you mean ‘alloca’? [-Wtemplate-body] 228 | using TStringTag = Alloc<>; | ^~~~~ | alloca /<>/src/holders.hpp:230:30: error: ‘MMap’ does not name a type [-Wtemplate-body] 230 | using TDirectStringTag = MMap<>; | ^~~~ /<>/src/holders.hpp:234:22: error: ‘TStringTag’ does not name a type [-Wtemplate-body] 234 | using TQryTag = TStringTag; | ^~~~~~~~~~ /<>/src/holders.hpp:235:22: error: ‘TDirectStringTag’ does not name a type [-Wtemplate-body] 235 | using TSubjTag = TDirectStringTag; // even if subjects were translated they are now loaded from disk | ^~~~~~~~~~~~~~~~ /<>/src/holders.hpp:238:29: error: ‘StringSet’ does not name a type [-Wtemplate-body] 238 | using TUntransQrySeqs = StringSet, TQryTag>, Owner>>; | ^~~~~~~~~ /<>/src/holders.hpp:242:28: error: ‘StringSet’ does not name a type [-Wtemplate-body] 242 | using TTransSeqs = StringSet, TSpec>, Owner>>; | ^~~~~~~~~ /<>/src/holders.hpp:243:28: error: ‘TTransSeqs’ does not name a type [-Wtemplate-body] 243 | using TTransQrySeqs = TTransSeqs; | ^~~~~~~~~~ /<>/src/holders.hpp:244:28: error: ‘TTransSeqs’ does not name a type [-Wtemplate-body] 244 | using TTransSubjSeqs = TTransSeqs; | ^~~~~~~~~~ /<>/src/holders.hpp:247:29: error: ‘TTransSubjSeqs’ was not declared in this scope [-Wtemplate-body] 247 | TTransSubjSeqs, // real type | ^~~~~~~~~~~~~~ /<>/src/holders.hpp:248:29: error: ‘TTransSubjSeqs’ was not declared in this scope [-Wtemplate-body] 248 | TTransSubjSeqs &>::type; // will be initialized in constructor | ^~~~~~~~~~~~~~ /<>/src/holders.hpp:248:45: error: template argument 2 is invalid [-Wtemplate-body] 248 | TTransSubjSeqs &>::type; // will be initialized in constructor | ^ /<>/src/holders.hpp:248:45: error: template argument 3 is invalid [-Wtemplate-body] /<>/src/holders.hpp:248:46: error: expected identifier before ‘::’ token [-Wtemplate-body] 248 | TTransSubjSeqs &>::type; // will be initialized in constructor | ^~ /<>/src/holders.hpp:252:31: error: ‘ModifiedString’ does not name a type [-Wtemplate-body] 252 | using TRedAlphModString = ModifiedString, TSpec>, | ^~~~~~~~~~~~~~ /<>/src/holders.hpp:257:29: error: ‘StringSet’ was not declared in this scope; did you mean ‘seqan2::StringSet’? [-Wtemplate-body] 257 | StringSet, Owner>>, // modview | ^~~~~~~~~ | seqan2::StringSet /usr/include/seqan/sequence/sequence_concatenator.h:50:7: note: ‘seqan2::StringSet’ declared here 50 | class StringSet; | ^~~~~~~~~ /<>/src/holders.hpp:257:39: error: ‘TRedAlphModString’ was not declared in this scope [-Wtemplate-body] 257 | StringSet, Owner>>, // modview | ^~~~~~~~~~~~~~~~~ /<>/src/holders.hpp:257:57: error: ‘TQryTag’ was not declared in this scope [-Wtemplate-body] 257 | StringSet, Owner>>, // modview | ^~~~~~~ /<>/src/holders.hpp:257:64: error: wrong number of template arguments (2, should be 3) [-Wtemplate-body] 257 | StringSet, Owner>>, // modview | ^ /usr/arm-linux-gnueabihf/include/c++/15/type_traits:2460:12: note: provided for ‘template struct std::conditional’ 2460 | struct conditional | ^~~~~~~~~~~ /<>/src/holders.hpp:257:65: error: expected identifier before ‘,’ token [-Wtemplate-body] 257 | StringSet, Owner>>, // modview | ^ /<>/src/holders.hpp:261:29: error: ‘StringSet’ was not declared in this scope; did you mean ‘seqan2::StringSet’? [-Wtemplate-body] 261 | StringSet, Owner>>, // modview | ^~~~~~~~~ | seqan2::StringSet /usr/include/seqan/sequence/sequence_concatenator.h:50:7: note: ‘seqan2::StringSet’ declared here 50 | class StringSet; | ^~~~~~~~~ /<>/src/holders.hpp:261:39: error: ‘TRedAlphModString’ was not declared in this scope [-Wtemplate-body] 261 | StringSet, Owner>>, // modview | ^~~~~~~~~~~~~~~~~ /<>/src/holders.hpp:261:57: error: ‘TSubjTag’ was not declared in this scope [-Wtemplate-body] 261 | StringSet, Owner>>, // modview | ^~~~~~~~ /<>/src/holders.hpp:261:65: error: wrong number of template arguments (2, should be 3) [-Wtemplate-body] 261 | StringSet, Owner>>, // modview | ^ /usr/arm-linux-gnueabihf/include/c++/15/type_traits:2460:12: note: provided for ‘template struct std::conditional’ 2460 | struct conditional | ^~~~~~~~~~~ /<>/src/holders.hpp:261:66: error: expected identifier before ‘,’ token [-Wtemplate-body] 261 | StringSet, Owner>>, // modview | ^ /<>/src/holders.hpp:266:27: error: ‘StringSet’ does not name a type [-Wtemplate-body] 266 | using TIds = StringSet, Owner>>; | ^~~~~~~~~ /<>/src/holders.hpp:267:27: error: ‘TIds’ does not name a type [-Wtemplate-body] 267 | using TQryIds = TIds; | ^~~~ /<>/src/holders.hpp:268:27: error: ‘TIds’ does not name a type [-Wtemplate-body] 268 | using TSubjIds = TIds; | ^~~~ /<>/src/holders.hpp:272:27: error: ‘Index’ does not name a type [-Wtemplate-body] 272 | using TDbIndex = Index::type, TIndexSpec>; | ^~~~~ /<>/src/holders.hpp:275:69: error: ‘Dna5’ was not declared in this scope; did you mean ‘seqan2::Dna5’? [-Wtemplate-body] 275 | using TScoreScheme = std::conditional_t::value, | ^~~~ | seqan2::Dna5 /usr/include/seqan/basic/alphabet_residue.h:134:42: note: ‘seqan2::Dna5’ declared here 134 | typedef SimpleType Dna5; | ^~~~ /<>/src/holders.hpp:275:73: error: type/value mismatch at argument 1 in template parameter list for ‘template struct std::is_same’ [-Wtemplate-body] 275 | using TScoreScheme = std::conditional_t::value, | ^ /<>/src/holders.hpp:275:73: note: expected a type, got ‘GlobalDataHolder, >::TRedAlph’ /<>/src/holders.hpp:275:73: error: template argument 2 is invalid [-Wtemplate-body] /<>/src/holders.hpp:276:46: error: ‘Score’ was not declared in this scope; did you mean ‘seqan2::Score’? [-Wtemplate-body] 276 | Score, | ^~~~~ | seqan2::Score In file included from /usr/include/seqan/score.h:45, from /usr/include/seqan/graph_align.h:45, from /usr/include/seqan/align.h:59, from /usr/include/seqan/bam_io.h:50: /usr/include/seqan/score/score_base.h:68:7: note: ‘seqan2::Score’ declared here 68 | class Score; | ^~~~~ /<>/src/holders.hpp:276:63: error: wrong number of template arguments (2, should be 3) [-Wtemplate-body] 276 | Score, | ^ /usr/arm-linux-gnueabihf/include/c++/15/type_traits:2841:11: note: provided for ‘template using std::conditional_t = typename std::conditional::type’ 2841 | using conditional_t = typename conditional<_Cond, _Iftrue, _Iffalse>::type; | ^~~~~~~~~~~~~ /<>/src/holders.hpp:279:27: error: ‘BlastIOContext’ does not name a type [-Wtemplate-body] 279 | using TIOContext = BlastIOContext; | ^~~~~~~~~~~~~~ /<>/src/holders.hpp:280:27: error: ‘FormattedFile’ does not name a type [-Wtemplate-body] 280 | using TFile = FormattedFile; | ^~~~~~~~~~~~~ /<>/src/holders.hpp:281:27: error: ‘FormattedFile’ does not name a type [-Wtemplate-body] 281 | using TBamFile = FormattedFile; | ^~~~~~~~~~~~~ /<>/src/holders.hpp:284:36: error: expected nested-name-specifier before ‘StringSetLimits’ [-Wtemplate-body] 284 | using TPositions = typename StringSetLimits::Type; | ^~~~~~~~~~~~~~~ /<>/src/holders.hpp:285:27: error: ‘StringSet’ does not name a type [-Wtemplate-body] 285 | using TMasking = StringSet, Owner>>; | ^~~~~~~~~ /<>/src/holders.hpp:288:5: error: ‘TDbIndex’ does not name a type [-Wtemplate-body] 288 | TDbIndex dbIndex; | ^~~~~~~~ /<>/src/holders.hpp:290:5: error: ‘TUntransQrySeqs’ does not name a type [-Wtemplate-body] 290 | TUntransQrySeqs untranslatedQrySeqs; // used iff outformat is sam or bam | ^~~~~~~~~~~~~~~ /<>/src/holders.hpp:292:5: error: ‘TTransQrySeqs’ does not name a type [-Wtemplate-body] 292 | TTransQrySeqs qrySeqs; | ^~~~~~~~~~~~~ /<>/src/holders.hpp:293:5: error: ‘TTransSubjReal’ does not name a type [-Wtemplate-body] 293 | TTransSubjReal subjSeqs; | ^~~~~~~~~~~~~~ /<>/src/holders.hpp:295:5: error: ‘TRedQrySeqs’ does not name a type [-Wtemplate-body] 295 | TRedQrySeqs redQrySeqs; | ^~~~~~~~~~~ /<>/src/holders.hpp:296:5: error: ‘TRedSubjSeqs’ does not name a type [-Wtemplate-body] 296 | TRedSubjSeqs redSubjSeqs; | ^~~~~~~~~~~~ /<>/src/holders.hpp:298:5: error: ‘TQryIds’ does not name a type [-Wtemplate-body] 298 | TQryIds qryIds; | ^~~~~~~ /<>/src/holders.hpp:299:5: error: ‘TSubjIds’ does not name a type [-Wtemplate-body] 299 | TSubjIds subjIds; | ^~~~~~~~ /<>/src/holders.hpp:301:5: error: ‘TFile’ does not name a type; did you mean ‘gzFile’? [-Wtemplate-body] 301 | TFile outfile; | ^~~~~ | gzFile /<>/src/holders.hpp:302:5: error: ‘TBamFile’ does not name a type [-Wtemplate-body] 302 | TBamFile outfileBam; | ^~~~~~~~ /<>/src/holders.hpp:304:5: error: ‘TPositions’ does not name a type [-Wtemplate-body] 304 | TPositions untransQrySeqLengths; // used iff qIsTranslated(p) | ^~~~~~~~~~ /<>/src/holders.hpp:305:5: error: ‘TPositions’ does not name a type [-Wtemplate-body] 305 | TPositions untransSubjSeqLengths; // used iff sIsTranslated(p) | ^~~~~~~~~~ /<>/src/holders.hpp:307:5: error: ‘TMasking’ does not name a type [-Wtemplate-body] 307 | TMasking segIntStarts; | ^~~~~~~~ /<>/src/holders.hpp:308:5: error: ‘TMasking’ does not name a type [-Wtemplate-body] 308 | TMasking segIntEnds; | ^~~~~~~~ /<>/src/holders.hpp:357:36: error: expected nested-name-specifier before ‘Value’ [-Wtemplate-body] 357 | using TRedQrySeq = typename Value::type>::Type; | ^~~~~ /<>/src/holders.hpp:358:27: error: ‘StringSet’ does not name a type [-Wtemplate-body] 358 | using TSeeds = StringSet::Type>; | ^~~~~~~~~ /<>/src/holders.hpp:359:27: error: ‘Index’ does not name a type [-Wtemplate-body] 359 | using TSeedIndex = Index>; | ^~~~~ /<>/src/holders.hpp:366:22: error: ‘BlastProgram’ does not name a type [-Wtemplate-body] 366 | static constexpr BlastProgram blastProgram = TGlobalHolder::blastProgram; | ^~~~~~~~~~~~ /<>/src/holders.hpp:376:5: error: ‘TSeeds’ does not name a type [-Wtemplate-body] 376 | TSeeds seeds; | ^~~~~~ /<>/src/holders.hpp:377:5: error: ‘TSeedIndex’ does not name a type [-Wtemplate-body] 377 | TSeedIndex seedIndex; | ^~~~~~~~~~ /<>/src/holders.hpp:384:24: error: ‘Gaps’ does not name a type [-Wtemplate-body] 384 | using TAlignRow0 = Gaps::Type>::Type, | ^~~~ /<>/src/holders.hpp:386:24: error: ‘Gaps’ does not name a type [-Wtemplate-body] 386 | using TAlignRow1 = Gaps::Type>::Type, | ^~~~ /<>/src/holders.hpp:392:25: error: ‘DPCell_’ does not name a type [-Wtemplate-body] 392 | using TDPCell = DPCell_; | ^~~~~~~ /<>/src/holders.hpp:393:34: error: expected nested-name-specifier before ‘TraceBitMap_’ [-Wtemplate-body] 393 | using TTraceValue = typename TraceBitMap_::Type; | ^~~~~~~~~~~~ /<>/src/holders.hpp:394:25: error: ‘String’ does not name a type [-Wtemplate-body] 394 | using TScoreHost = String >; | ^~~~~~ /<>/src/holders.hpp:395:25: error: ‘String’ does not name a type [-Wtemplate-body] 395 | using TTraceHost = String >; | ^~~~~~ /<>/src/holders.hpp:396:25: error: ‘DPContext’ does not name a type [-Wtemplate-body] 396 | using TDPContext = DPContext; | ^~~~~~~~~ /<>/src/holders.hpp:398:28: error: ‘AliExtContext_’ does not name a type [-Wtemplate-body] 398 | using TAliExtContext = AliExtContext_; | ^~~~~~~~~~~~~~ /<>/src/holders.hpp:400:5: error: ‘TAliExtContext’ does not name a type [-Wtemplate-body] 400 | TAliExtContext alignContext; | ^~~~~~~~~~~~~~ /<>/src/holders.hpp: In member function ‘void LocalDataHolder::init(uint64_t)’: /<>/src/holders.hpp:431:58: error: ‘blastProgram’ was not declared in this scope [-Wtemplate-body] 431 | indexBeginQry -= (indexBeginQry % qNumFrames(blastProgram)); | ^~~~~~~~~~~~ /<>/src/holders.hpp:431:47: error: there are no arguments to ‘qNumFrames’ that depend on a template parameter, so a declaration of ‘qNumFrames’ must be available [-Wtemplate-body] 431 | indexBeginQry -= (indexBeginQry % qNumFrames(blastProgram)); | ^~~~~~~~~~ /<>/src/holders.hpp:432:43: error: there are no arguments to ‘qNumFrames’ that depend on a template parameter, so a declaration of ‘qNumFrames’ must be available [-Wtemplate-body] 432 | indexEndQry -= (indexEndQry % qNumFrames(blastProgram)); | ^~~~~~~~~~ /<>/src/holders.hpp:435:40: error: ‘blastProgram’ was not declared in this scope [-Wtemplate-body] 435 | indexBeginQry = qNumFrames(blastProgram) * i; | ^~~~~~~~~~~~ /<>/src/holders.hpp:435:29: error: there are no arguments to ‘qNumFrames’ that depend on a template parameter, so a declaration of ‘qNumFrames’ must be available [-Wtemplate-body] 435 | indexBeginQry = qNumFrames(blastProgram) * i; | ^~~~~~~~~~ /<>/src/holders.hpp:436:27: error: there are no arguments to ‘qNumFrames’ that depend on a template parameter, so a declaration of ‘qNumFrames’ must be available [-Wtemplate-body] 436 | indexEndQry = qNumFrames(blastProgram) * (i+1); | ^~~~~~~~~~ /<>/src/holders.hpp:439:15: error: ‘seeds’ was not declared in this scope [-Wtemplate-body] 439 | clear(seeds); | ^~~~~ /<>/src/holders.hpp:439:9: error: there are no arguments to ‘clear’ that depend on a template parameter, so a declaration of ‘clear’ must be available [-Wtemplate-body] 439 | clear(seeds); | ^~~~~ /<>/src/holders.hpp:440:15: error: ‘seedIndex’ was not declared in this scope [-Wtemplate-body] 440 | clear(seedIndex); | ^~~~~~~~~ /<>/src/holders.hpp:440:9: error: there are no arguments to ‘clear’ that depend on a template parameter, so a declaration of ‘clear’ must be available [-Wtemplate-body] 440 | clear(seedIndex); | ^~~~~ In file included from /<>/src/lambda.hpp:43, from /<>/src/lambda.cpp:34: /<>/src/misc.hpp: At global scope: /<>/src/misc.hpp:80:18: error: ‘Iter’ does not name a type 80 | const Iter, | ^~~~ /<>/src/misc.hpp:80:22: error: expected ‘,’ or ‘...’ before ‘<’ token 80 | const Iter, | ^ /<>/src/misc.hpp: In function ‘std::basic_ostream& operator<<(std::basic_ostream&, int)’: /<>/src/misc.hpp:84:13: error: ‘it’ was not declared in this scope; did you mean ‘int’? [-Wtemplate-body] 84 | out << *it; | ^~ | int /<>/src/misc.hpp: At global scope: /<>/src/misc.hpp:145:17: error: ‘Gaps’ was not declared in this scope; did you mean ‘seqan2::Gaps’? 145 | localAlignment2(Gaps & row0, | ^~~~ | seqan2::Gaps In file included from /usr/include/seqan/align.h:82: /usr/include/seqan/align/gaps_base.h:144:7: note: ‘seqan2::Gaps’ declared here 144 | class Gaps; | ^~~~ /<>/src/misc.hpp:145:30: error: expected primary-expression before ‘,’ token 145 | localAlignment2(Gaps & row0, | ^ /<>/src/misc.hpp:145:42: error: expected primary-expression before ‘>’ token 145 | localAlignment2(Gaps & row0, | ^ /<>/src/misc.hpp:145:46: error: ‘row0’ was not declared in this scope 145 | localAlignment2(Gaps & row0, | ^~~~ /<>/src/misc.hpp:146:17: error: ‘Gaps’ was not declared in this scope; did you mean ‘seqan2::Gaps’? 146 | Gaps & row1, | ^~~~ | seqan2::Gaps /usr/include/seqan/align/gaps_base.h:144:7: note: ‘seqan2::Gaps’ declared here 144 | class Gaps; | ^~~~ /<>/src/misc.hpp:146:30: error: expected primary-expression before ‘,’ token 146 | Gaps & row1, | ^ /<>/src/misc.hpp:146:42: error: expected primary-expression before ‘>’ token 146 | Gaps & row1, | ^ /<>/src/misc.hpp:146:46: error: ‘row1’ was not declared in this scope 146 | Gaps & row1, | ^~~~ /<>/src/misc.hpp:147:17: error: ‘Score’ was not declared in this scope; did you mean ‘seqan2::Score’? 147 | Score const & scoringScheme, | ^~~~~ | seqan2::Score /usr/include/seqan/score/score_base.h:68:7: note: ‘seqan2::Score’ declared here 68 | class Score; | ^~~~~ /<>/src/misc.hpp:147:34: error: expected primary-expression before ‘,’ token 147 | Score const & scoringScheme, | ^ /<>/src/misc.hpp:147:46: error: expected primary-expression before ‘>’ token 147 | Score const & scoringScheme, | ^ /<>/src/misc.hpp:147:48: error: expected primary-expression before ‘const’ 147 | Score const & scoringScheme, | ^~~~~ /<>/src/misc.hpp:148:17: error: expected primary-expression before ‘int’ 148 | int const lowerDiag, | ^~~ /<>/src/misc.hpp:149:17: error: expected primary-expression before ‘int’ 149 | int const upperDiag, | ^~~ /<>/src/misc.hpp:150:31: error: expected primary-expression before ‘&’ token 150 | TAlignContext & alignContext) | ^ /<>/src/misc.hpp:150:33: error: ‘alignContext’ was not declared in this scope; did you mean ‘TAlignContext’? 150 | TAlignContext & alignContext) | ^~~~~~~~~~~~ | TAlignContext /<>/src/misc.hpp:150:46: error: expected ‘;’ before ‘{’ token 150 | TAlignContext & alignContext) | ^ | ; 151 | { | ~ /<>/src/misc.hpp:187:1: error: variable or field ‘readRecords’ declared void 187 | readRecords(TCDStringSet>> & meta, | ^~~~~~~~~~~ /<>/src/misc.hpp:187:13: error: ‘TCDStringSet’ was not declared in this scope; did you mean ‘TSeqStringSet’? 187 | readRecords(TCDStringSet>> & meta, | ^~~~~~~~~~~~ | TSeqStringSet /<>/src/misc.hpp:187:26: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’? 187 | readRecords(TCDStringSet>> & meta, | ^~~~~~ | seqan2::String /usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here 290 | class String; | ^~~~~~ /<>/src/misc.hpp:187:33: error: expected primary-expression before ‘char’ 187 | readRecords(TCDStringSet>> & meta, | ^~~~ /<>/src/misc.hpp:187:39: error: ‘Alloc’ was not declared in this scope; did you mean ‘seqan2::Alloc’? 187 | readRecords(TCDStringSet>> & meta, | ^~~~~ | seqan2::Alloc /usr/include/seqan/sequence/string_base.h:59:8: note: ‘seqan2::Alloc’ declared here 59 | struct Alloc {}; | ^~~~~ /<>/src/misc.hpp:187:54: error: expected primary-expression before ‘>>’ token 187 | readRecords(TCDStringSet>> & meta, | ^~ /<>/src/misc.hpp:187:56: error: expected primary-expression before ‘>’ token 187 | readRecords(TCDStringSet>> & meta, | ^ /<>/src/misc.hpp:187:60: error: ‘meta’ was not declared in this scope 187 | readRecords(TCDStringSet>> & meta, | ^~~~ /<>/src/misc.hpp:188:27: error: expected primary-expression before ‘&’ token 188 | TSeqStringSet & seq, | ^ /<>/src/misc.hpp:188:29: error: ‘seq’ was not declared in this scope; did you mean ‘__pstl::execution::v1::seq’? 188 | TSeqStringSet & seq, | ^~~ | __pstl::execution::v1::seq In file included from /usr/arm-linux-gnueabihf/include/c++/15/pstl/glue_algorithm_defs.h:16, from /usr/arm-linux-gnueabihf/include/c++/15/algorithm:89, from /usr/include/seqan/basic/debug_test_system.h:156, from /usr/include/seqan/basic/basic_debug.h:52, from /usr/include/seqan/basic.h:49: /usr/arm-linux-gnueabihf/include/c++/15/pstl/execution_defs.h:42:46: note: ‘__pstl::execution::v1::seq’ declared here 42 | _GLIBCXX17_INLINE constexpr sequenced_policy seq{}; | ^~~ /<>/src/misc.hpp:189:13: error: ‘FormattedFile’ was not declared in this scope; did you mean ‘seqan2::FormattedFile’? 189 | FormattedFile & file, | ^~~~~~~~~~~~~ | seqan2::FormattedFile /usr/include/seqan/stream/formatted_file.h:213:8: note: ‘seqan2::FormattedFile’ declared here 213 | struct FormattedFile | ^~~~~~~~~~~~~ /<>/src/misc.hpp:189:27: error: ‘Fastq’ was not declared in this scope; did you mean ‘seqan2::Fastq’? 189 | FormattedFile & file, | ^~~~~ | seqan2::Fastq In file included from /usr/include/seqan/seq_io.h:52: /usr/include/seqan/seq_io/fasta_fastq.h:59:24: note: ‘seqan2::Fastq’ declared here 59 | typedef Tag Fastq; | ^~~~~ /<>/src/misc.hpp:189:34: error: ‘Input’ was not declared in this scope; did you mean ‘seqan2::Input’? 189 | FormattedFile & file, | ^~~~~ | seqan2::Input In file included from /usr/include/seqan/file.h:71: /usr/include/seqan/file/file_interface.h:165:21: note: ‘seqan2::Input’ declared here 165 | typedef Tag Input; | ^~~~~ /<>/src/misc.hpp:189:46: error: expected primary-expression before ‘>’ token 189 | FormattedFile & file, | ^ /<>/src/misc.hpp:189:50: error: ‘file’ was not declared in this scope 189 | FormattedFile & file, | ^~~~ /<>/src/misc.hpp:190:19: error: expected primary-expression before ‘maxRecords’ 190 | TSize maxRecords) | ^~~~~~~~~~ /<>/src/misc.hpp:231:15: error: ‘TCDStringSet’ was not declared in this scope 231 | myReadRecords(TCDStringSet> & ids, | ^~~~~~~~~~~~ /<>/src/misc.hpp:231:28: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’? 231 | myReadRecords(TCDStringSet> & ids, | ^~~~~~ | seqan2::String /usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here 290 | class String; | ^~~~~~ /<>/src/misc.hpp:231:35: error: expected primary-expression before ‘char’ 231 | myReadRecords(TCDStringSet> & ids, | ^~~~ /<>/src/misc.hpp:231:47: error: expected primary-expression before ‘>>’ token 231 | myReadRecords(TCDStringSet> & ids, | ^~ /<>/src/misc.hpp:231:52: error: ‘ids’ was not declared in this scope 231 | myReadRecords(TCDStringSet> & ids, | ^~~ /<>/src/misc.hpp:232:15: error: ‘TCDStringSet’ was not declared in this scope 232 | TCDStringSet> & seqs, | ^~~~~~~~~~~~ /<>/src/misc.hpp:232:28: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’? 232 | TCDStringSet> & seqs, | ^~~~~~ | seqan2::String /usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here 290 | class String; | ^~~~~~ /<>/src/misc.hpp:232:35: error: ‘Dna5’ was not declared in this scope; did you mean ‘seqan2::Dna5’? 232 | TCDStringSet> & seqs, | ^~~~ | seqan2::Dna5 /usr/include/seqan/basic/alphabet_residue.h:134:42: note: ‘seqan2::Dna5’ declared here 134 | typedef SimpleType Dna5; | ^~~~ /<>/src/misc.hpp:232:47: error: expected primary-expression before ‘>>’ token 232 | TCDStringSet> & seqs, | ^~ /<>/src/misc.hpp:232:52: error: ‘seqs’ was not declared in this scope 232 | TCDStringSet> & seqs, | ^~~~ /<>/src/misc.hpp:233:51: error: expected primary-expression before ‘&’ token 233 | TFile & file) | ^ /<>/src/misc.hpp:233:53: error: ‘file’ was not declared in this scope 233 | TFile & file) | ^~~~ /<>/src/misc.hpp:233:57: error: expression list treated as compound expression in initializer [-fpermissive] 233 | TFile & file) | ^ /<>/src/misc.hpp:233:58: error: expected ‘;’ before ‘{’ token 233 | TFile & file) | ^ | ; 234 | { | ~ /<>/src/misc.hpp:258:1: error: redefinition of ‘template int myReadRecords’ 258 | myReadRecords(TCDStringSet> & ids, | ^~~~~~~~~~~~~ /<>/src/misc.hpp:231:1: note: ‘template int myReadRecords’ previously declared here 231 | myReadRecords(TCDStringSet> & ids, | ^~~~~~~~~~~~~ /<>/src/misc.hpp:258:15: error: ‘TCDStringSet’ was not declared in this scope 258 | myReadRecords(TCDStringSet> & ids, | ^~~~~~~~~~~~ /<>/src/misc.hpp:258:28: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’? 258 | myReadRecords(TCDStringSet> & ids, | ^~~~~~ | seqan2::String /usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here 290 | class String; | ^~~~~~ /<>/src/misc.hpp:258:35: error: expected primary-expression before ‘char’ 258 | myReadRecords(TCDStringSet> & ids, | ^~~~ /<>/src/misc.hpp:258:47: error: expected primary-expression before ‘>>’ token 258 | myReadRecords(TCDStringSet> & ids, | ^~ /<>/src/misc.hpp:258:58: error: ‘ids’ was not declared in this scope 258 | myReadRecords(TCDStringSet> & ids, | ^~~ /<>/src/misc.hpp:259:15: error: ‘TCDStringSet’ was not declared in this scope 259 | TCDStringSet> & seqs, | ^~~~~~~~~~~~ /<>/src/misc.hpp:259:28: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’? 259 | TCDStringSet> & seqs, | ^~~~~~ | seqan2::String /usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here 290 | class String; | ^~~~~~ /<>/src/misc.hpp:259:35: error: ‘AminoAcid’ was not declared in this scope; did you mean ‘seqan2::AminoAcid’? 259 | TCDStringSet> & seqs, | ^~~~~~~~~ | seqan2::AminoAcid /usr/include/seqan/basic/alphabet_residue.h:550:47: note: ‘seqan2::AminoAcid’ declared here 550 | typedef SimpleType AminoAcid; | ^~~~~~~~~ /<>/src/misc.hpp:259:52: error: expected primary-expression before ‘>>’ token 259 | TCDStringSet> & seqs, | ^~ /<>/src/misc.hpp:259:58: error: ‘seqs’ was not declared in this scope 259 | TCDStringSet> & seqs, | ^~~~ /<>/src/misc.hpp:260:57: error: expected primary-expression before ‘&’ token 260 | TFile & file) | ^ /<>/src/misc.hpp:260:59: error: ‘file’ was not declared in this scope 260 | TFile & file) | ^~~~ /<>/src/lambda.hpp:54:11: error: ‘BlastProgram’ has not been declared 54 | BlastProgram p, | ^~~~~~~~~~~~ /<>/src/lambda.hpp:55:11: error: ‘BlastTabularSpec’ has not been declared 55 | BlastTabularSpec h> | ^~~~~~~~~~~~~~~~ /<>/src/lambda.hpp:79:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 79 | public ::std::binary_function < TSav, TSav, bool > | ^~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/15/string:51, from /usr/arm-linux-gnueabihf/include/c++/15/bits/locale_classes.h:42, from /usr/arm-linux-gnueabihf/include/c++/15/bits/ios_base.h:43, from /usr/arm-linux-gnueabihf/include/c++/15/ios:46: /usr/arm-linux-gnueabihf/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /<>/src/lambda.hpp:101:11: error: ‘BlastTabularSpec’ has not been declared 101 | template >/src/lambda.hpp:102:11: error: ‘BlastProgram’ has not been declared 102 | BlastProgram p, | ^~~~~~~~~~~~ /<>/src/lambda.hpp:107:71: error: ‘p’ was not declared in this scope 107 | prepareScoringMore(GlobalDataHolder & globalHolder, | ^ /<>/src/lambda.hpp:107:74: error: ‘h’ was not declared in this scope 107 | prepareScoringMore(GlobalDataHolder & globalHolder, | ^ /<>/src/lambda.hpp:107:75: error: template argument 4 is invalid 107 | prepareScoringMore(GlobalDataHolder & globalHolder, | ^ /<>/src/lambda.hpp:107:75: error: template argument 5 is invalid /<>/src/lambda.hpp: In function ‘void prepareScoringMore(int&, const LambdaOptions&, const std::true_type&)’: /<>/src/lambda.hpp:111:40: error: request for member ‘outfile’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 111 | setScoreMatch(context(globalHolder.outfile).scoringScheme, options.match); | ^~~~~~~ /<>/src/lambda.hpp:111:19: error: there are no arguments to ‘context’ that depend on a template parameter, so a declaration of ‘context’ must be available [-Wtemplate-body] 111 | setScoreMatch(context(globalHolder.outfile).scoringScheme, options.match); | ^~~~~~~ /<>/src/lambda.hpp:112:43: error: request for member ‘outfile’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 112 | setScoreMismatch(context(globalHolder.outfile).scoringScheme, options.misMatch); | ^~~~~~~ /<>/src/lambda.hpp:112:22: error: there are no arguments to ‘context’ that depend on a template parameter, so a declaration of ‘context’ must be available [-Wtemplate-body] 112 | setScoreMismatch(context(globalHolder.outfile).scoringScheme, options.misMatch); | ^~~~~~~ /<>/src/lambda.hpp: At global scope: /<>/src/lambda.hpp:115:11: error: ‘BlastTabularSpec’ has not been declared 115 | template >/src/lambda.hpp:116:11: error: ‘BlastProgram’ has not been declared 116 | BlastProgram p, | ^~~~~~~~~~~~ /<>/src/lambda.hpp:121:71: error: ‘p’ was not declared in this scope 121 | prepareScoringMore(GlobalDataHolder & globalHolder, | ^ /<>/src/lambda.hpp:121:74: error: ‘h’ was not declared in this scope 121 | prepareScoringMore(GlobalDataHolder & globalHolder, | ^ /<>/src/lambda.hpp:121:75: error: template argument 4 is invalid 121 | prepareScoringMore(GlobalDataHolder & globalHolder, | ^ /<>/src/lambda.hpp:121:75: error: template argument 5 is invalid /<>/src/lambda.hpp: In function ‘void prepareScoringMore(int&, const LambdaOptions&, const std::false_type&)’: /<>/src/lambda.hpp:130:53: error: request for member ‘outfile’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 130 | setScoreMatrixById(context(globalHolder.outfile).scoringScheme._internalScheme, | ^~~~~~~ /<>/src/lambda.hpp:130:32: error: there are no arguments to ‘context’ that depend on a template parameter, so a declaration of ‘context’ must be available [-Wtemplate-body] 130 | setScoreMatrixById(context(globalHolder.outfile).scoringScheme._internalScheme, | ^~~~~~~ /<>/src/lambda.hpp:131:32: error: ‘AminoAcidScoreMatrixID’ has not been declared [-Wtemplate-body] 131 | AminoAcidScoreMatrixID::BLOSUM45); | ^~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.hpp:134:53: error: request for member ‘outfile’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 134 | setScoreMatrixById(context(globalHolder.outfile).scoringScheme._internalScheme, | ^~~~~~~ /<>/src/lambda.hpp:134:32: error: there are no arguments to ‘context’ that depend on a template parameter, so a declaration of ‘context’ must be available [-Wtemplate-body] 134 | setScoreMatrixById(context(globalHolder.outfile).scoringScheme._internalScheme, | ^~~~~~~ /<>/src/lambda.hpp:135:32: error: ‘AminoAcidScoreMatrixID’ has not been declared [-Wtemplate-body] 135 | AminoAcidScoreMatrixID::BLOSUM62); | ^~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.hpp:138:53: error: request for member ‘outfile’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 138 | setScoreMatrixById(context(globalHolder.outfile).scoringScheme._internalScheme, | ^~~~~~~ /<>/src/lambda.hpp:138:32: error: there are no arguments to ‘context’ that depend on a template parameter, so a declaration of ‘context’ must be available [-Wtemplate-body] 138 | setScoreMatrixById(context(globalHolder.outfile).scoringScheme._internalScheme, | ^~~~~~~ /<>/src/lambda.hpp:139:32: error: ‘AminoAcidScoreMatrixID’ has not been declared [-Wtemplate-body] 139 | AminoAcidScoreMatrixID::BLOSUM80); | ^~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.hpp: At global scope: /<>/src/lambda.hpp:146:11: error: ‘BlastTabularSpec’ has not been declared 146 | template >/src/lambda.hpp:147:11: error: ‘BlastProgram’ has not been declared 147 | BlastProgram p, | ^~~~~~~~~~~~ /<>/src/lambda.hpp:152:67: error: ‘p’ was not declared in this scope 152 | prepareScoring(GlobalDataHolder & globalHolder, | ^ /<>/src/lambda.hpp:152:70: error: ‘h’ was not declared in this scope 152 | prepareScoring(GlobalDataHolder & globalHolder, | ^ /<>/src/lambda.hpp:152:71: error: template argument 4 is invalid 152 | prepareScoring(GlobalDataHolder & globalHolder, | ^ /<>/src/lambda.hpp:152:71: error: template argument 5 is invalid /<>/src/lambda.hpp: In function ‘int prepareScoring(int&, const LambdaOptions&)’: /<>/src/lambda.hpp:155:78: error: ‘p’ was not declared in this scope [-Wtemplate-body] 155 | using TGlobalHolder = GlobalDataHolder; | ^ /<>/src/lambda.hpp:155:81: error: ‘h’ was not declared in this scope [-Wtemplate-body] 155 | using TGlobalHolder = GlobalDataHolder; | ^ /<>/src/lambda.hpp:155:82: error: template argument 4 is invalid [-Wtemplate-body] 155 | using TGlobalHolder = GlobalDataHolder; | ^ /<>/src/lambda.hpp:155:82: error: template argument 5 is invalid [-Wtemplate-body] /<>/src/lambda.hpp:158:92: error: wrong number of template arguments (1, should be 2) [-Wtemplate-body] 158 | std::is_same>()); | ^~ /usr/arm-linux-gnueabihf/include/c++/15/type_traits:799:12: note: provided for ‘template struct std::is_same’ 799 | struct is_same; | ^~~~~~~ /<>/src/lambda.hpp:160:47: error: request for member ‘outfile’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 160 | setScoreGapOpenBlast(context(globalHolder.outfile).scoringScheme, options.gapOpen); | ^~~~~~~ /<>/src/lambda.hpp:160:26: error: there are no arguments to ‘context’ that depend on a template parameter, so a declaration of ‘context’ must be available [-Wtemplate-body] 160 | setScoreGapOpenBlast(context(globalHolder.outfile).scoringScheme, options.gapOpen); | ^~~~~~~ /<>/src/lambda.hpp:161:44: error: request for member ‘outfile’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 161 | setScoreGapExtend(context(globalHolder.outfile).scoringScheme, options.gapExtend); | ^~~~~~~ /<>/src/lambda.hpp:161:23: error: there are no arguments to ‘context’ that depend on a template parameter, so a declaration of ‘context’ must be available [-Wtemplate-body] 161 | setScoreGapExtend(context(globalHolder.outfile).scoringScheme, options.gapExtend); | ^~~~~~~ /<>/src/lambda.hpp:163:39: error: request for member ‘outfile’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 163 | if (!isValid(context(globalHolder.outfile).scoringScheme)) | ^~~~~~~ /<>/src/lambda.hpp:163:18: error: there are no arguments to ‘context’ that depend on a template parameter, so a declaration of ‘context’ must be available [-Wtemplate-body] 163 | if (!isValid(context(globalHolder.outfile).scoringScheme)) | ^~~~~~~ /<>/src/lambda.hpp: At global scope: /<>/src/lambda.hpp:176:11: error: ‘BlastTabularSpec’ has not been declared 176 | template >/src/lambda.hpp:177:11: error: ‘BlastProgram’ has not been declared 177 | BlastProgram p, | ^~~~~~~~~~~~ /<>/src/lambda.hpp:182:65: error: ‘p’ was not declared in this scope 182 | loadSubjects(GlobalDataHolder & globalHolder, | ^ /<>/src/lambda.hpp:182:68: error: ‘h’ was not declared in this scope 182 | loadSubjects(GlobalDataHolder & globalHolder, | ^ /<>/src/lambda.hpp:182:69: error: template argument 4 is invalid 182 | loadSubjects(GlobalDataHolder & globalHolder, | ^ /<>/src/lambda.hpp:182:69: error: template argument 5 is invalid /<>/src/lambda.hpp: In function ‘int loadSubjects(int&, const LambdaOptions&)’: /<>/src/lambda.hpp:185:68: error: ‘p’ was not declared in this scope [-Wtemplate-body] 185 | using TGH = GlobalDataHolder; | ^ /<>/src/lambda.hpp:185:71: error: ‘h’ was not declared in this scope [-Wtemplate-body] 185 | using TGH = GlobalDataHolder; | ^ /<>/src/lambda.hpp:185:72: error: template argument 4 is invalid [-Wtemplate-body] 185 | using TGH = GlobalDataHolder; | ^ /<>/src/lambda.hpp:185:72: error: template argument 5 is invalid [-Wtemplate-body] /<>/src/lambda.hpp:190:5: error: ‘CharString’ was not declared in this scope; did you mean ‘seqan2::CharString’? [-Wtemplate-body] 190 | CharString _dbSeqs; | ^~~~~~~~~~ | seqan2::CharString In file included from /usr/include/seqan/sequence.h:112: /usr/include/seqan/sequence/sequence_shortcuts.h:55:36: note: ‘seqan2::CharString’ declared here 55 | typedef String > CharString; | ^~~~~~~~~~ /<>/src/lambda.hpp:192:9: error: ‘TGH’ has not been declared [-Wtemplate-body] 192 | if (TGH::indexIsFM || TGH::alphReduction) // otherwise sequences are loaded as part of index | ^~~ /<>/src/lambda.hpp:192:27: error: ‘TGH’ has not been declared [-Wtemplate-body] 192 | if (TGH::indexIsFM || TGH::alphReduction) // otherwise sequences are loaded as part of index | ^~~ /<>/src/lambda.hpp:194:17: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 194 | start = sysTime(); | ^~~~~~~ /<>/src/lambda.hpp:198:9: error: ‘_dbSeqs’ was not declared in this scope [-Wtemplate-body] 198 | _dbSeqs = options.dbFile; | ^~~~~~~ /<>/src/lambda.hpp:199:9: error: there are no arguments to ‘append’ that depend on a template parameter, so a declaration of ‘append’ must be available [-Wtemplate-body] 199 | append(_dbSeqs, "."); | ^~~~~~ /<>/src/lambda.hpp:200:35: error: ‘TransAlph’ was not declared in this scope [-Wtemplate-body] 200 | append(_dbSeqs, _alphName(TransAlph

())); | ^~~~~~~~~ /<>/src/lambda.hpp:200:48: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 200 | append(_dbSeqs, _alphName(TransAlph

())); | ^ /<>/src/lambda.hpp:200:49: error: ‘_alphName’ cannot be used as a function [-Wtemplate-body] 200 | append(_dbSeqs, _alphName(TransAlph

())); | ^ /<>/src/lambda.hpp:200:9: error: there are no arguments to ‘append’ that depend on a template parameter, so a declaration of ‘append’ must be available [-Wtemplate-body] 200 | append(_dbSeqs, _alphName(TransAlph

())); | ^~~~~~ /<>/src/lambda.hpp:202:33: error: request for member ‘subjSeqs’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 202 | ret = open(globalHolder.subjSeqs, toCString(_dbSeqs), OPEN_RDONLY); | ^~~~~~~~ /<>/src/lambda.hpp:202:43: error: there are no arguments to ‘toCString’ that depend on a template parameter, so a declaration of ‘toCString’ must be available [-Wtemplate-body] 202 | ret = open(globalHolder.subjSeqs, toCString(_dbSeqs), OPEN_RDONLY); | ^~~~~~~~~ /<>/src/lambda.hpp:202:63: error: ‘OPEN_RDONLY’ was not declared in this scope; did you mean ‘seqan2::OPEN_RDONLY’? [-Wtemplate-body] 202 | ret = open(globalHolder.subjSeqs, toCString(_dbSeqs), OPEN_RDONLY); | ^~~~~~~~~~~ | seqan2::OPEN_RDONLY /usr/include/seqan/file/file_interface.h:149:5: note: ‘seqan2::OPEN_RDONLY’ declared here 149 | OPEN_RDONLY = 1, | ^~~~~~~~~~~ /<>/src/lambda.hpp:210:33: error: request for member ‘subjSeqs’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 210 | if (length(globalHolder.subjSeqs) == 0) | ^~~~~~~~ /<>/src/lambda.hpp:210:13: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-Wtemplate-body] 210 | if (length(globalHolder.subjSeqs) == 0) | ^~~~~~ /<>/src/lambda.hpp:216:13: error: ‘TGH’ has not been declared [-Wtemplate-body] 216 | if (TGH::alphReduction) | ^~~ /<>/src/lambda.hpp:217:26: error: request for member ‘redSubjSeqs’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 217 | globalHolder.redSubjSeqs.limits = globalHolder.subjSeqs.limits; | ^~~~~~~~~~~ /<>/src/lambda.hpp:217:60: error: request for member ‘subjSeqs’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 217 | globalHolder.redSubjSeqs.limits = globalHolder.subjSeqs.limits; | ^~~~~~~~ /<>/src/lambda.hpp:219:18: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 219 | finish = sysTime() - start; | ^~~~~~~ /<>/src/lambda.hpp:222:37: error: request for member ‘subjSeqs’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 222 | length(globalHolder.subjSeqs), "\n\n"); | ^~~~~~~~ /<>/src/lambda.hpp:222:17: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-Wtemplate-body] 222 | length(globalHolder.subjSeqs), "\n\n"); | ^~~~~~ /<>/src/lambda.hpp:225:13: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 225 | start = sysTime(); | ^~~~~~~ /<>/src/lambda.hpp:229:5: error: ‘_dbSeqs’ was not declared in this scope [-Wtemplate-body] 229 | _dbSeqs = options.dbFile; | ^~~~~~~ /<>/src/lambda.hpp:230:5: error: there are no arguments to ‘append’ that depend on a template parameter, so a declaration of ‘append’ must be available [-Wtemplate-body] 230 | append(_dbSeqs, ".ids"); | ^~~~~~ /<>/src/lambda.hpp:231:29: error: request for member ‘subjIds’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 231 | ret = open(globalHolder.subjIds, toCString(_dbSeqs), OPEN_RDONLY); | ^~~~~~~ /<>/src/lambda.hpp:231:38: error: there are no arguments to ‘toCString’ that depend on a template parameter, so a declaration of ‘toCString’ must be available [-Wtemplate-body] 231 | ret = open(globalHolder.subjIds, toCString(_dbSeqs), OPEN_RDONLY); | ^~~~~~~~~ /<>/src/lambda.hpp:231:58: error: ‘OPEN_RDONLY’ was not declared in this scope; did you mean ‘seqan2::OPEN_RDONLY’? [-Wtemplate-body] 231 | ret = open(globalHolder.subjIds, toCString(_dbSeqs), OPEN_RDONLY); | ^~~~~~~~~~~ | seqan2::OPEN_RDONLY /usr/include/seqan/file/file_interface.h:149:5: note: ‘seqan2::OPEN_RDONLY’ declared here 149 | OPEN_RDONLY = 1, | ^~~~~~~~~~~ /<>/src/lambda.hpp:238:14: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 238 | finish = sysTime() - start; | ^~~~~~~ /<>/src/lambda.hpp:242:26: error: request for member ‘outfile’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 242 | context(globalHolder.outfile).dbName = options.dbFile; | ^~~~~~~ /<>/src/lambda.hpp:242:5: error: there are no arguments to ‘context’ that depend on a template parameter, so a declaration of ‘context’ must be available [-Wtemplate-body] 242 | context(globalHolder.outfile).dbName = options.dbFile; | ^~~~~~~ /<>/src/lambda.hpp:246:9: error: there are no arguments to ‘sIsTranslated’ that depend on a template parameter, so a declaration of ‘sIsTranslated’ must be available [-Wtemplate-body] 246 | if (sIsTranslated(p)) | ^~~~~~~~~~~~~ /<>/src/lambda.hpp:248:17: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 248 | start = sysTime(); | ^~~~~~~ /<>/src/lambda.hpp:253:9: error: there are no arguments to ‘append’ that depend on a template parameter, so a declaration of ‘append’ must be available [-Wtemplate-body] 253 | append(_dbSeqs, ".untranslengths"); | ^~~~~~ /<>/src/lambda.hpp:254:33: error: request for member ‘untransSubjSeqLengths’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 254 | ret = open(globalHolder.untransSubjSeqLengths, toCString(_dbSeqs), OPEN_RDONLY); | ^~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.hpp:254:56: error: there are no arguments to ‘toCString’ that depend on a template parameter, so a declaration of ‘toCString’ must be available [-Wtemplate-body] 254 | ret = open(globalHolder.untransSubjSeqLengths, toCString(_dbSeqs), OPEN_RDONLY); | ^~~~~~~~~ /<>/src/lambda.hpp:262:18: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 262 | finish = sysTime() - start; | ^~~~~~~ /<>/src/lambda.hpp: In function ‘int loadDbIndexFromDisk(TGlobalHolder&, const LambdaOptions&)’: /<>/src/lambda.hpp:281:20: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 281 | double start = sysTime(); | ^~~~~~~ /<>/src/lambda.hpp:282:24: error: there are no arguments to ‘toCString’ that depend on a template parameter, so a declaration of ‘toCString’ must be available [-Wtemplate-body] 282 | std::string path = toCString(options.dbFile); | ^~~~~~~~~ /<>/src/lambda.hpp:290:39: error: ‘BlastProgram’ has not been declared [-Wtemplate-body] 290 | if ((globalHolder.blastProgram != BlastProgram::BLASTN) && // BLASTN indexes are compatible | ^~~~~~~~~~~~ /<>/src/lambda.hpp:291:54: error: there are no arguments to ‘toCString’ that depend on a template parameter, so a declaration of ‘toCString’ must be available [-Wtemplate-body] 291 | ((TGlobalHolder::alphReduction && fileExists(toCString(path + ".txt.concat"))) || | ^~~~~~~~~ /<>/src/lambda.hpp:292:83: error: there are no arguments to ‘toCString’ that depend on a template parameter, so a declaration of ‘toCString’ must be available [-Wtemplate-body] 292 | (!TGlobalHolder::alphReduction && TGlobalHolder::indexIsFM && !fileExists(toCString(path + ".lf.drv.wtc.24"))))) | ^~~~~~~~~ /<>/src/lambda.hpp:301:56: error: ‘OPEN_RDONLY’ was not declared in this scope; did you mean ‘seqan2::OPEN_RDONLY’? [-Wtemplate-body] 301 | int ret = open(globalHolder.dbIndex, path.c_str(), OPEN_RDONLY); | ^~~~~~~~~~~ | seqan2::OPEN_RDONLY /usr/include/seqan/file/file_interface.h:149:5: note: ‘seqan2::OPEN_RDONLY’ declared here 149 | OPEN_RDONLY = 1, | ^~~~~~~~~~~ /<>/src/lambda.hpp:315:21: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 315 | double finish = sysTime() - start; | ^~~~~~~ /<>/src/lambda.hpp: At global scope: /<>/src/lambda.hpp:339:11: error: ‘BlastTabularSpec’ has not been declared 339 | template >/src/lambda.hpp:340:11: error: ‘BlastProgram’ has not been declared 340 | BlastProgram p, | ^~~~~~~~~~~~ /<>/src/lambda.hpp:345:69: error: ‘p’ was not declared in this scope 345 | loadSegintervals(GlobalDataHolder & globalHolder, | ^ /<>/src/lambda.hpp:345:72: error: ‘h’ was not declared in this scope 345 | loadSegintervals(GlobalDataHolder & globalHolder, | ^ /<>/src/lambda.hpp:345:73: error: template argument 4 is invalid 345 | loadSegintervals(GlobalDataHolder & globalHolder, | ^ /<>/src/lambda.hpp:345:73: error: template argument 5 is invalid /<>/src/lambda.hpp: In function ‘int loadSegintervals(int&, const LambdaOptions&)’: /<>/src/lambda.hpp:349:20: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 349 | double start = sysTime(); | ^~~~~~~ /<>/src/lambda.hpp:353:5: error: ‘CharString’ was not declared in this scope; did you mean ‘seqan2::CharString’? [-Wtemplate-body] 353 | CharString segFileS = options.dbFile; | ^~~~~~~~~~ | seqan2::CharString /usr/include/seqan/sequence/sequence_shortcuts.h:55:36: note: ‘seqan2::CharString’ declared here 55 | typedef String > CharString; | ^~~~~~~~~~ /<>/src/lambda.hpp:354:12: error: ‘segFileS’ was not declared in this scope [-Wtemplate-body] 354 | append(segFileS, ".binseg_s.concat"); | ^~~~~~~~ /<>/src/lambda.hpp:354:5: error: there are no arguments to ‘append’ that depend on a template parameter, so a declaration of ‘append’ must be available [-Wtemplate-body] 354 | append(segFileS, ".binseg_s.concat"); | ^~~~~~ /<>/src/lambda.hpp:355:15: error: expected ‘;’ before ‘segFileE’ [-Wtemplate-body] 355 | CharString segFileE = options.dbFile; | ^~~~~~~~~ | ; /<>/src/lambda.hpp:356:12: error: ‘segFileE’ was not declared in this scope [-Wtemplate-body] 356 | append(segFileE, ".binseg_e.concat"); | ^~~~~~~~ /<>/src/lambda.hpp:356:5: error: there are no arguments to ‘append’ that depend on a template parameter, so a declaration of ‘append’ must be available [-Wtemplate-body] 356 | append(segFileE, ".binseg_e.concat"); | ^~~~~~ /<>/src/lambda.hpp:360:15: error: there are no arguments to ‘toCString’ that depend on a template parameter, so a declaration of ‘toCString’ must be available [-Wtemplate-body] 360 | if ((stat(toCString(segFileS), &buffer) == 0) && | ^~~~~~~~~ /<>/src/lambda.hpp:361:15: error: there are no arguments to ‘toCString’ that depend on a template parameter, so a declaration of ‘toCString’ must be available [-Wtemplate-body] 361 | (stat(toCString(segFileE), &buffer) == 0)) | ^~~~~~~~~ /<>/src/lambda.hpp:364:26: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-Wtemplate-body] 364 | resize(segFileS, length(segFileS) - 7); | ^~~~~~ /<>/src/lambda.hpp:365:26: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-Wtemplate-body] 365 | resize(segFileE, length(segFileE) - 7); | ^~~~~~ /<>/src/lambda.hpp:367:35: error: request for member ‘segIntStarts’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 367 | fail = !open(globalHolder.segIntStarts, toCString(segFileS), OPEN_RDONLY); | ^~~~~~~~~~~~ /<>/src/lambda.hpp:367:49: error: there are no arguments to ‘toCString’ that depend on a template parameter, so a declaration of ‘toCString’ must be available [-Wtemplate-body] 367 | fail = !open(globalHolder.segIntStarts, toCString(segFileS), OPEN_RDONLY); | ^~~~~~~~~ /<>/src/lambda.hpp:367:70: error: ‘OPEN_RDONLY’ was not declared in this scope; did you mean ‘seqan2::OPEN_RDONLY’? [-Wtemplate-body] 367 | fail = !open(globalHolder.segIntStarts, toCString(segFileS), OPEN_RDONLY); | ^~~~~~~~~~~ | seqan2::OPEN_RDONLY /usr/include/seqan/file/file_interface.h:149:5: note: ‘seqan2::OPEN_RDONLY’ declared here 149 | OPEN_RDONLY = 1, | ^~~~~~~~~~~ /<>/src/lambda.hpp:369:39: error: request for member ‘segIntEnds’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 369 | fail = !open(globalHolder.segIntEnds, toCString(segFileE), OPEN_RDONLY); | ^~~~~~~~~~ /<>/src/lambda.hpp:369:51: error: there are no arguments to ‘toCString’ that depend on a template parameter, so a declaration of ‘toCString’ must be available [-Wtemplate-body] 369 | fail = !open(globalHolder.segIntEnds, toCString(segFileE), OPEN_RDONLY); | ^~~~~~~~~ /<>/src/lambda.hpp:382:21: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 382 | double finish = sysTime() - start; | ^~~~~~~ /<>/src/lambda.hpp: At global scope: /<>/src/lambda.hpp:398:1: error: variable or field ‘loadQueryImplTrans’ declared void 398 | loadQueryImplTrans(TCDStringSet> & target, | ^~~~~~~~~~~~~~~~~~ /<>/src/lambda.hpp:398:20: error: ‘TCDStringSet’ was not declared in this scope 398 | loadQueryImplTrans(TCDStringSet> & target, | ^~~~~~~~~~~~ /<>/src/lambda.hpp:398:33: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’? 398 | loadQueryImplTrans(TCDStringSet> & target, | ^~~~~~ | seqan2::String /usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here 290 | class String; | ^~~~~~ /<>/src/lambda.hpp:398:51: error: expected primary-expression before ‘,’ token 398 | loadQueryImplTrans(TCDStringSet> & target, | ^ /<>/src/lambda.hpp:398:59: error: expected primary-expression before ‘>>’ token 398 | loadQueryImplTrans(TCDStringSet> & target, | ^~ /<>/src/lambda.hpp:398:64: error: ‘target’ was not declared in this scope; did you mean ‘seqan2::target’? 398 | loadQueryImplTrans(TCDStringSet> & target, | ^~~~~~ | seqan2::target In file included from /usr/include/seqan/graph_types.h:48, from /usr/include/seqan/graph_align.h:47: /usr/include/seqan/graph_types/graph_edgestump.h:552:1: note: ‘seqan2::target’ declared here 552 | target(EdgeStump const* es) | ^~~~~~ /<>/src/lambda.hpp:399:20: error: ‘TCDStringSet’ was not declared in this scope 399 | TCDStringSet> & source, | ^~~~~~~~~~~~ /<>/src/lambda.hpp:399:33: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’? 399 | TCDStringSet> & source, | ^~~~~~ | seqan2::String /usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here 290 | class String; | ^~~~~~ /<>/src/lambda.hpp:399:51: error: expected primary-expression before ‘,’ token 399 | TCDStringSet> & source, | ^ /<>/src/lambda.hpp:399:59: error: expected primary-expression before ‘>>’ token 399 | TCDStringSet> & source, | ^~ /<>/src/lambda.hpp:399:64: error: ‘source’ was not declared in this scope; did you mean ‘seqan2::source’? 399 | TCDStringSet> & source, | ^~~~~~ | seqan2::source In file included from /usr/include/seqan/pipe.h:56, from /usr/include/seqan/index.h:42, from /<>/src/options.hpp:33: /usr/include/seqan/pipe/pipe_base.h:362:5: note: ‘seqan2::source’ declared here 362 | source(Pipe &me) { | ^~~~~~ /<>/src/lambda.hpp:400:63: error: expected primary-expression before ‘&’ token 400 | TUntransLengths & untransQrySeqLengths, | ^ /<>/src/lambda.hpp:400:65: error: ‘untransQrySeqLengths’ was not declared in this scope 400 | TUntransLengths & untransQrySeqLengths, | ^~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.hpp:401:57: error: expected primary-expression before ‘const’ 401 | LambdaOptions const & options) | ^~~~~ /<>/src/lambda.hpp:432:1: error: variable or field ‘loadQueryImplTrans’ declared void 432 | loadQueryImplTrans(TCDStringSet, TSpec1>> & target, | ^~~~~~~~~~~~~~~~~~ /<>/src/lambda.hpp:432:20: error: ‘TCDStringSet’ was not declared in this scope 432 | loadQueryImplTrans(TCDStringSet, TSpec1>> & target, | ^~~~~~~~~~~~ /<>/src/lambda.hpp:432:33: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’? 432 | loadQueryImplTrans(TCDStringSet, TSpec1>> & target, | ^~~~~~ | seqan2::String /usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here 290 | class String; | ^~~~~~ /<>/src/lambda.hpp:432:40: error: ‘TransAlph’ was not declared in this scope 432 | loadQueryImplTrans(TCDStringSet, TSpec1>> & target, | ^~~~~~~~~ /<>/src/lambda.hpp:432:50: error: ‘BlastProgram’ has not been declared 432 | loadQueryImplTrans(TCDStringSet, TSpec1>> & target, | ^~~~~~~~~~~~ /<>/src/lambda.hpp:432:71: error: expected primary-expression before ‘,’ token 432 | loadQueryImplTrans(TCDStringSet, TSpec1>> & target, | ^ /<>/src/lambda.hpp:432:79: error: expected primary-expression before ‘>>’ token 432 | loadQueryImplTrans(TCDStringSet, TSpec1>> & target, | ^~ /<>/src/lambda.hpp:432:84: error: ‘target’ was not declared in this scope; did you mean ‘seqan2::target’? 432 | loadQueryImplTrans(TCDStringSet, TSpec1>> & target, | ^~~~~~ | seqan2::target /usr/include/seqan/graph_types/graph_edgestump.h:552:1: note: ‘seqan2::target’ declared here 552 | target(EdgeStump const* es) | ^~~~~~ /<>/src/lambda.hpp:433:20: error: ‘TCDStringSet’ was not declared in this scope 433 | TCDStringSet, TSpec2>> & source, | ^~~~~~~~~~~~ /<>/src/lambda.hpp:433:33: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’? 433 | TCDStringSet, TSpec2>> & source, | ^~~~~~ | seqan2::String /usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here 290 | class String; | ^~~~~~ /<>/src/lambda.hpp:433:40: error: ‘TransAlph’ was not declared in this scope 433 | TCDStringSet, TSpec2>> & source, | ^~~~~~~~~ /<>/src/lambda.hpp:433:50: error: ‘BlastProgram’ has not been declared 433 | TCDStringSet, TSpec2>> & source, | ^~~~~~~~~~~~ /<>/src/lambda.hpp:433:71: error: expected primary-expression before ‘,’ token 433 | TCDStringSet, TSpec2>> & source, | ^ /<>/src/lambda.hpp:433:79: error: expected primary-expression before ‘>>’ token 433 | TCDStringSet, TSpec2>> & source, | ^~ /<>/src/lambda.hpp:433:84: error: ‘source’ was not declared in this scope; did you mean ‘seqan2::source’? 433 | TCDStringSet, TSpec2>> & source, | ^~~~~~ | seqan2::source /usr/include/seqan/pipe/pipe_base.h:362:5: note: ‘seqan2::source’ declared here 362 | source(Pipe &me) { | ^~~~~~ /<>/src/lambda.hpp:434:83: error: expected primary-expression before ‘&’ token 434 | TUntransLengths & /**/, | ^ /<>/src/lambda.hpp:434:89: error: expected primary-expression before ‘,’ token 434 | TUntransLengths & /**/, | ^ /<>/src/lambda.hpp:435:77: error: expected primary-expression before ‘const’ 435 | LambdaOptions const & options) | ^~~~~ /<>/src/lambda.hpp:476:1: error: variable or field ‘loadQueryImplTrans’ declared void 476 | loadQueryImplTrans(TCDStringSet, TSpec1>> & target, | ^~~~~~~~~~~~~~~~~~ /<>/src/lambda.hpp:476:20: error: ‘TCDStringSet’ was not declared in this scope 476 | loadQueryImplTrans(TCDStringSet, TSpec1>> & target, | ^~~~~~~~~~~~ /<>/src/lambda.hpp:476:33: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’? 476 | loadQueryImplTrans(TCDStringSet, TSpec1>> & target, | ^~~~~~ | seqan2::String /usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here 290 | class String; | ^~~~~~ /<>/src/lambda.hpp:476:40: error: ‘TransAlph’ was not declared in this scope 476 | loadQueryImplTrans(TCDStringSet, TSpec1>> & target, | ^~~~~~~~~ /<>/src/lambda.hpp:476:50: error: ‘BlastProgram’ has not been declared 476 | loadQueryImplTrans(TCDStringSet, TSpec1>> & target, | ^~~~~~~~~~~~ /<>/src/lambda.hpp:476:71: error: expected primary-expression before ‘,’ token 476 | loadQueryImplTrans(TCDStringSet, TSpec1>> & target, | ^ /<>/src/lambda.hpp:476:79: error: expected primary-expression before ‘>>’ token 476 | loadQueryImplTrans(TCDStringSet, TSpec1>> & target, | ^~ /<>/src/lambda.hpp:476:84: error: ‘target’ was not declared in this scope; did you mean ‘seqan2::target’? 476 | loadQueryImplTrans(TCDStringSet, TSpec1>> & target, | ^~~~~~ | seqan2::target /usr/include/seqan/graph_types/graph_edgestump.h:552:1: note: ‘seqan2::target’ declared here 552 | target(EdgeStump const* es) | ^~~~~~ /<>/src/lambda.hpp:477:20: error: ‘TCDStringSet’ was not declared in this scope 477 | TCDStringSet, TSpec2>> & source, | ^~~~~~~~~~~~ /<>/src/lambda.hpp:477:33: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’? 477 | TCDStringSet, TSpec2>> & source, | ^~~~~~ | seqan2::String /usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here 290 | class String; | ^~~~~~ /<>/src/lambda.hpp:477:40: error: ‘TransAlph’ was not declared in this scope 477 | TCDStringSet, TSpec2>> & source, | ^~~~~~~~~ /<>/src/lambda.hpp:477:50: error: ‘BlastProgram’ has not been declared 477 | TCDStringSet, TSpec2>> & source, | ^~~~~~~~~~~~ /<>/src/lambda.hpp:477:71: error: expected primary-expression before ‘,’ token 477 | TCDStringSet, TSpec2>> & source, | ^ /<>/src/lambda.hpp:477:79: error: expected primary-expression before ‘>>’ token 477 | TCDStringSet, TSpec2>> & source, | ^~ /<>/src/lambda.hpp:477:84: error: ‘source’ was not declared in this scope; did you mean ‘seqan2::source’? 477 | TCDStringSet, TSpec2>> & source, | ^~~~~~ | seqan2::source /usr/include/seqan/pipe/pipe_base.h:362:5: note: ‘seqan2::source’ declared here 362 | source(Pipe &me) { | ^~~~~~ /<>/src/lambda.hpp:478:46: error: expected primary-expression before ‘&’ token 478 | TUntransLengths & /**/, | ^ /<>/src/lambda.hpp:478:52: error: expected primary-expression before ‘,’ token 478 | TUntransLengths & /**/, | ^ /<>/src/lambda.hpp:479:40: error: expected primary-expression before ‘const’ 479 | LambdaOptions const & /**/) | ^~~~~ /<>/src/lambda.hpp:485:11: error: ‘BlastTabularSpec’ has not been declared 485 | template >/src/lambda.hpp:486:11: error: ‘BlastProgram’ has not been declared 486 | BlastProgram p, | ^~~~~~~~~~~~ /<>/src/lambda.hpp:491:62: error: ‘p’ was not declared in this scope 491 | loadQuery(GlobalDataHolder & globalHolder, | ^ /<>/src/lambda.hpp:491:65: error: ‘h’ was not declared in this scope 491 | loadQuery(GlobalDataHolder & globalHolder, | ^ /<>/src/lambda.hpp:491:66: error: template argument 4 is invalid 491 | loadQuery(GlobalDataHolder & globalHolder, | ^ /<>/src/lambda.hpp:491:66: error: template argument 5 is invalid /<>/src/lambda.hpp: In function ‘int loadQuery(int&, const LambdaOptions&)’: /<>/src/lambda.hpp:494:68: error: ‘p’ was not declared in this scope [-Wtemplate-body] 494 | using TGH = GlobalDataHolder; | ^ /<>/src/lambda.hpp:494:71: error: ‘h’ was not declared in this scope [-Wtemplate-body] 494 | using TGH = GlobalDataHolder; | ^ /<>/src/lambda.hpp:494:72: error: template argument 4 is invalid [-Wtemplate-body] 494 | using TGH = GlobalDataHolder; | ^ /<>/src/lambda.hpp:494:72: error: template argument 5 is invalid [-Wtemplate-body] /<>/src/lambda.hpp:495:20: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 495 | double start = sysTime(); | ^~~~~~~ /<>/src/lambda.hpp:500:5: error: ‘TCDStringSet’ was not declared in this scope [-Wtemplate-body] 500 | TCDStringSet, typename TGH::TQryTag>> origSeqs; | ^~~~~~~~~~~~ /<>/src/lambda.hpp:500:18: error: ‘String’ was not declared in this scope; did you mean ‘seqan2::String’? [-Wtemplate-body] 500 | TCDStringSet, typename TGH::TQryTag>> origSeqs; | ^~~~~~ | seqan2::String /usr/include/seqan/sequence/string_base.h:290:7: note: ‘seqan2::String’ declared here 290 | class String; | ^~~~~~ /<>/src/lambda.hpp:500:25: error: ‘OrigQryAlph’ was not declared in this scope [-Wtemplate-body] 500 | TCDStringSet, typename TGH::TQryTag>> origSeqs; | ^~~~~~~~~~~ /<>/src/lambda.hpp:500:39: error: expected primary-expression before ‘,’ token [-Wtemplate-body] 500 | TCDStringSet, typename TGH::TQryTag>> origSeqs; | ^ /<>/src/lambda.hpp:500:50: error: ‘TGH’ has not been declared [-Wtemplate-body] 500 | TCDStringSet, typename TGH::TQryTag>> origSeqs; | ^~~ /<>/src/lambda.hpp:500:62: error: expected ‘(’ before ‘>>’ token [-Wtemplate-body] 500 | TCDStringSet, typename TGH::TQryTag>> origSeqs; | ^~ | ( /<>/src/lambda.hpp:500:65: error: ‘origSeqs’ was not declared in this scope [-Wtemplate-body] 500 | TCDStringSet, typename TGH::TQryTag>> origSeqs; | ^~~~~~~~ /<>/src/lambda.hpp:505:9: error: ‘SeqFileIn’ was not declared in this scope; did you mean ‘seqan2::SeqFileIn’? [-Wtemplate-body] 505 | SeqFileIn infile(toCString(options.queryFile)); | ^~~~~~~~~ | seqan2::SeqFileIn In file included from /usr/include/seqan/seq_io.h:61: /usr/include/seqan/seq_io/sequence_file.h:59:41: note: ‘seqan2::SeqFileIn’ declared here 59 | typedef FormattedFile SeqFileIn; | ^~~~~~~~~ /<>/src/lambda.hpp:506:32: error: missing template arguments before ‘(’ token [-Wtemplate-body] 506 | int ret = myReadRecords(globalHolder.qryIds, origSeqs, infile); | ^ /<>/src/lambda.hpp:506:46: error: request for member ‘qryIds’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 506 | int ret = myReadRecords(globalHolder.qryIds, origSeqs, infile); | ^~~~~~ /<>/src/lambda.hpp:506:64: error: ‘infile’ was not declared in this scope; did you mean ‘inline’? [-Wtemplate-body] 506 | int ret = myReadRecords(globalHolder.qryIds, origSeqs, infile); | ^~~~~~ | inline /<>/src/lambda.hpp:510:11: error: ‘IOError’ does not name a type [-Wtemplate-body] 510 | catch(IOError const & e) | ^~~~~~~ /<>/src/lambda.hpp:510:18: error: expected ‘)’ before ‘const’ [-Wtemplate-body] 510 | catch(IOError const & e) | ~ ^~~~~~ | ) /<>/src/lambda.hpp:510:19: error: expected ‘{’ before ‘const’ [-Wtemplate-body] 510 | catch(IOError const & e) | ^~~~~ /<>/src/lambda.hpp:510:28: error: expected initializer before ‘)’ token [-Wtemplate-body] 510 | catch(IOError const & e) | ^ /<>/src/lambda.hpp:518:37: error: request for member ‘qrySeqs’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 518 | loadQueryImplTrans(globalHolder.qrySeqs, | ^~~~~~~ /<>/src/lambda.hpp:520:37: error: request for member ‘untransQrySeqLengths’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 520 | globalHolder.untransQrySeqLengths, | ^~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.hpp:518:5: error: there are no arguments to ‘loadQueryImplTrans’ that depend on a template parameter, so a declaration of ‘loadQueryImplTrans’ must be available [-Wtemplate-body] 518 | loadQueryImplTrans(globalHolder.qrySeqs, | ^~~~~~~~~~~~~~~~~~ /<>/src/lambda.hpp:524:36: error: request for member ‘blastProgram’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 524 | if (qIsTranslated(globalHolder.blastProgram) && (options.outFileFormat > 0) && | ^~~~~~~~~~~~ /<>/src/lambda.hpp:524:9: error: there are no arguments to ‘qIsTranslated’ that depend on a template parameter, so a declaration of ‘qIsTranslated’ must be available [-Wtemplate-body] 524 | if (qIsTranslated(globalHolder.blastProgram) && (options.outFileFormat > 0) && | ^~~~~~~~~~~~~ /<>/src/lambda.hpp:526:42: error: request for member ‘untranslatedQrySeqs’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 526 | std::swap(origSeqs, globalHolder.untranslatedQrySeqs); | ^~~~~~~~~~~~~~~~~~~ /<>/src/lambda.hpp:528:9: error: ‘TGH’ has not been declared [-Wtemplate-body] 528 | if (TGH::alphReduction) | ^~~ /<>/src/lambda.hpp:529:22: error: request for member ‘redQrySeqs’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 529 | globalHolder.redQrySeqs.limits = globalHolder.qrySeqs.limits; | ^~~~~~~~~~ /<>/src/lambda.hpp:529:55: error: request for member ‘qrySeqs’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 529 | globalHolder.redQrySeqs.limits = globalHolder.qrySeqs.limits; | ^~~~~~~ /<>/src/lambda.hpp:531:21: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 531 | double finish = sysTime() - start; | ^~~~~~~ /<>/src/lambda.hpp:535:40: error: request for member ‘qrySeqs’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 535 | for (auto const & s : globalHolder.qrySeqs) | ^~~~~~~ /<>/src/lambda.hpp:536:13: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-Wtemplate-body] 536 | if (length(s) > maxLen) | ^~~~~~ /<>/src/lambda.hpp:537:22: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-Wtemplate-body] 537 | maxLen = length(s); | ^~~~~~ /<>/src/lambda.hpp:541:33: error: request for member ‘qrySeqs’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 541 | length(globalHolder.qrySeqs), "\nLongest query sequence: ", | ^~~~~~~ /<>/src/lambda.hpp:541:13: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-Wtemplate-body] 541 | length(globalHolder.qrySeqs), "\nLongest query sequence: ", | ^~~~~~ /<>/src/lambda.hpp:544:29: error: request for member ‘qrySeqs’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 544 | if (length(globalHolder.qrySeqs) == 0) | ^~~~~~~ /<>/src/lambda.hpp:544:9: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-Wtemplate-body] 544 | if (length(globalHolder.qrySeqs) == 0) | ^~~~~~ /<>/src/lambda.hpp:550:29: error: request for member ‘qrySeqs’ in ‘globalHolder’, which is of non-class type ‘int’ [-Wtemplate-body] 550 | if (length(globalHolder.qrySeqs) >= std::numeric_limits::max()) | ^~~~~~~ /<>/src/lambda.hpp:550:9: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-Wtemplate-body] 550 | if (length(globalHolder.qrySeqs) >= std::numeric_limits::max()) | ^~~~~~ /<>/src/lambda.hpp:550:87: error: template argument 1 is invalid [-Wtemplate-body] 550 | if (length(globalHolder.qrySeqs) >= std::numeric_limits::max()) | ^ /<>/src/lambda.hpp:553:68: error: template argument 1 is invalid [-Wtemplate-body] 553 | << std::numeric_limits::max() | ^ /<>/src/lambda.hpp:558:65: error: template argument 1 is invalid [-Wtemplate-body] 558 | if (maxLen >= std::numeric_limits::max()) | ^ /<>/src/lambda.hpp:561:96: error: template argument 1 is invalid [-Wtemplate-body] 561 | << "The maximum length is " << std::numeric_limits::max() | ^ /<>/src/lambda.hpp: In function ‘int generateSeeds(TLocalHolder&)’: /<>/src/lambda.hpp:590:20: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 590 | double start = sysTime(); | ^~~~~~~ /<>/src/lambda.hpp:602:25: error: there are no arguments to ‘Generous’ that depend on a template parameter, so a declaration of ‘Generous’ must be available [-Wtemplate-body] 602 | Generous()); | ^~~~~~~~ /<>/src/lambda.hpp:603:42: error: there are no arguments to ‘Generous’ that depend on a template parameter, so a declaration of ‘Generous’ must be available [-Wtemplate-body] 603 | appendValue(lH.seedRefs, i, Generous()); | ^~~~~~~~ /<>/src/lambda.hpp:604:42: error: there are no arguments to ‘Generous’ that depend on a template parameter, so a declaration of ‘Generous’ must be available [-Wtemplate-body] 604 | appendValue(lH.seedRanks, j, Generous()); | ^~~~~~~~ /<>/src/lambda.hpp:609:21: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 609 | double finish = sysTime() - start; | ^~~~~~~ /<>/src/lambda.hpp: In function ‘int generateTrieOverSeeds(TLocalHolder&)’: /<>/src/lambda.hpp:638:20: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 638 | double start = sysTime(); | ^~~~~~~ /<>/src/lambda.hpp:640:22: error: expected nested-name-specifier before ‘Fibre’ [-Wtemplate-body] 640 | typedef typename Fibre::Type TSa; | ^~~~~ /<>/src/lambda.hpp:640:27: error: expected initializer before ‘<’ token [-Wtemplate-body] 640 | typedef typename Fibre::Type TSa; | ^ /<>/src/lambda.hpp:643:5: error: ‘TSa’ was not declared in this scope [-Wtemplate-body] 643 | TSa & sa = indexSA(lH.seedIndex); | ^~~ /<>/src/lambda.hpp:643:11: error: ‘sa’ was not declared in this scope [-Wtemplate-body] 643 | TSa & sa = indexSA(lH.seedIndex); | ^~ /<>/src/lambda.hpp:647:23: error: there are no arguments to ‘value’ that depend on a template parameter, so a declaration of ‘value’ must be available [-Wtemplate-body] 647 | assignValueI1(value(sa,u), u); | ^~~~~ /<>/src/lambda.hpp:648:23: error: there are no arguments to ‘value’ that depend on a template parameter, so a declaration of ‘value’ must be available [-Wtemplate-body] 648 | assignValueI2(value(sa,u), 0); | ^~~~~ /<>/src/lambda.hpp:650:72: error: wrong number of template arguments (1, should be 2) [-Wtemplate-body] 650 | Comp::Type, typename TLocalHolder::TSeeds const> comp(lH.seeds); | ^ /<>/src/lambda.hpp:78:8: note: provided for ‘template struct Comp’ 78 | struct Comp : | ^~~~ /<>/src/lambda.hpp:651:25: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-Wtemplate-body] 651 | std::sort(begin(sa, Standard()), end(sa, Standard()), comp); | ^~~~~~~~ /<>/src/lambda.hpp:651:46: error: there are no arguments to ‘Standard’ that depend on a template parameter, so a declaration of ‘Standard’ must be available [-Wtemplate-body] 651 | std::sort(begin(sa, Standard()), end(sa, Standard()), comp); | ^~~~~~~~ /<>/src/lambda.hpp:652:14: error: expected nested-name-specifier before ‘Iterator’ [-Wtemplate-body] 652 | typename Iterator >::Type it(lH.seedIndex); // instantiate | ^~~~~~~~ /<>/src/lambda.hpp:652:14: error: expected ‘(’ before ‘Iterator’ [-Wtemplate-body] 652 | typename Iterator >::Type it(lH.seedIndex); // instantiate | ^~~~~~~~ | ( /<>/src/lambda.hpp:653:21: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 653 | double finish = sysTime() - start; | ^~~~~~~ /<>/src/lambda.hpp:659:24: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-Wtemplate-body] 659 | length(sa), " fibres in SeedIndex. ");; | ^~~~~~ /<>/src/lambda.hpp: In function ‘void __searchDoubleIndex(TLocalHolder&)’: /<>/src/lambda.hpp:811:20: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 811 | double start = sysTime(); | ^~~~~~~ /<>/src/lambda.hpp:813:26: error: ‘Finder_’ does not name a type [-Wtemplate-body] 813 | using LambdaFinder = Finder_>/src/lambda.hpp:819:5: error: ‘LambdaFinder’ was not declared in this scope [-Wtemplate-body] 819 | LambdaFinder finder; | ^~~~~~~~~~~~ /<>/src/lambda.hpp:821:28: error: ‘LambdaFinder’ is not a type [-Wtemplate-body] 821 | auto delegate = [&lH] (LambdaFinder const & finder) | ^~~~~~~~~~~~ /<>/src/lambda.hpp: In lambda function: /<>/src/lambda.hpp:823:51: error: request for member ‘patternStack’ in ‘finder’, which is of non-class type ‘const int’ [-Wtemplate-body] 823 | auto qryOccs = getOccurrences(back(finder.patternStack)); | ^~~~~~~~~~~~ /<>/src/lambda.hpp:823:39: error: there are no arguments to ‘back’ that depend on a template parameter, so a declaration of ‘back’ must be available [-Wtemplate-body] 823 | auto qryOccs = getOccurrences(back(finder.patternStack)); | ^~~~ /<>/src/lambda.hpp:824:52: error: request for member ‘textStack’ in ‘finder’, which is of non-class type ‘const int’ [-Wtemplate-body] 824 | auto subjOccs = getOccurrences(back(finder.textStack)); | ^~~~~~~~~ /<>/src/lambda.hpp:824:40: error: there are no arguments to ‘back’ that depend on a template parameter, so a declaration of ‘back’ must be available [-Wtemplate-body] 824 | auto subjOccs = getOccurrences(back(finder.textStack)); | ^~~~ /<>/src/lambda.hpp: In function ‘void __searchDoubleIndex(TLocalHolder&)’: /<>/src/lambda.hpp:833:11: error: ‘finder’ was not declared in this scope; did you mean ‘rindex’? [-Wtemplate-body] 833 | _find(finder, lH.gH.dbIndex, lH.seedIndex, lH.options.maxSeedDist, delegate); | ^~~~~~ | rindex /<>/src/lambda.hpp:835:21: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 835 | double finish = sysTime() - start; | ^~~~~~~ /<>/src/lambda.hpp: In function ‘void __searchSingleIndex(TLocalHolder&)’: /<>/src/lambda.hpp:847:22: error: expected nested-name-specifier before ‘Iterator’ [-Wtemplate-body] 847 | typedef typename Iterator::Type TSeedsIt; | ^~~~~~~~ /<>/src/lambda.hpp:847:30: error: expected initializer before ‘<’ token [-Wtemplate-body] 847 | typedef typename Iterator::Type TSeedsIt; | ^ /<>/src/lambda.hpp:848:22: error: expected nested-name-specifier before ‘Iterator’ [-Wtemplate-body] 848 | typedef typename Iterator>::Type TIndexIt; | ^~~~~~~~ /<>/src/lambda.hpp:848:30: error: expected initializer before ‘<’ token [-Wtemplate-body] 848 | typedef typename Iterator>::Type TIndexIt; | ^ /<>/src/lambda.hpp:857:28: error: ‘TIndexIt’ has not been declared [-Wtemplate-body] 857 | auto delegate = [&lH] (TIndexIt & indexIt, | ^~~~~~~~ /<>/src/lambda.hpp:858:28: error: ‘TSeedsIt’ has not been declared [-Wtemplate-body] 858 | TSeedsIt const & seedsIt, | ^~~~~~~~ /<>/src/lambda.hpp: In lambda function: /<>/src/lambda.hpp:861:23: error: there are no arguments to ‘position’ that depend on a template parameter, so a declaration of ‘position’ must be available [-Wtemplate-body] 861 | auto qryOcc = position(seedsIt); | ^~~~~~~~ /<>/src/lambda.hpp:862:25: error: there are no arguments to ‘getOccurrences’ that depend on a template parameter, so a declaration of ‘getOccurrences’ must be available [-Wtemplate-body] 862 | auto subjOccs = getOccurrences(indexIt); | ^~~~~~~~~~~~~~ /<>/src/lambda.hpp: In function ‘void __searchSingleIndex(TLocalHolder&)’: /<>/src/lambda.hpp:871:10: error: ‘Backtracking’ was not declared in this scope; did you mean ‘seqan2::Backtracking’? [-Wtemplate-body] 871 | Backtracking()); | ^~~~~~~~~~~~ | seqan2::Backtracking In file included from /usr/include/seqan/index.h:224: /usr/include/seqan/index/find_backtracking.h:49:8: note: ‘seqan2::Backtracking’ declared here 49 | struct Backtracking; | ^~~~~~~~~~~~ /<>/src/lambda.hpp:871:31: error: expected primary-expression before ‘>’ token [-Wtemplate-body] 871 | Backtracking()); | ^ /<>/src/lambda.hpp:871:33: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 871 | Backtracking()); | ^ /<>/src/lambda.hpp: In function ‘void search(TLocalHolder&)’: /<>/src/lambda.hpp:889:18: error: ‘Backtracking’ was not declared in this scope; did you mean ‘seqan2::Backtracking’? [-Wtemplate-body] 889 | __search>(lH); | ^~~~~~~~~~~~ | seqan2::Backtracking /usr/include/seqan/index/find_backtracking.h:49:8: note: ‘seqan2::Backtracking’ declared here 49 | struct Backtracking; | ^~~~~~~~~~~~ /<>/src/lambda.hpp:889:31: error: ‘Exact’ was not declared in this scope; did you mean ‘seqan2::Exact’? [-Wtemplate-body] 889 | __search>(lH); | ^~~~~ | seqan2::Exact In file included from /usr/include/seqan/sequence.h:94: /usr/include/seqan/sequence/sequence_interface.h:120:24: note: ‘seqan2::Exact’ declared here 120 | typedef Tag Exact; | ^~~~~ /<>/src/lambda.hpp:891:18: error: ‘Backtracking’ was not declared in this scope; did you mean ‘seqan2::Backtracking’? [-Wtemplate-body] 891 | __search>(lH); | ^~~~~~~~~~~~ | seqan2::Backtracking /usr/include/seqan/index/find_backtracking.h:49:8: note: ‘seqan2::Backtracking’ declared here 49 | struct Backtracking; | ^~~~~~~~~~~~ /<>/src/lambda.hpp:891:31: error: ‘HammingDistance’ was not declared in this scope; did you mean ‘seqan2::HammingDistance’? [-Wtemplate-body] 891 | __search>(lH); | ^~~~~~~~~~~~~~~ | seqan2::HammingDistance In file included from /usr/include/seqan/basic/basic_fundamental.h:66, from /usr/include/seqan/basic.h:58: /usr/include/seqan/basic/fundamental_tags.h:361:37: note: ‘seqan2::HammingDistance’ declared here 361 | typedef Tag HammingDistance; | ^~~~~~~~~~~~~~~ /<>/src/lambda.hpp: In function ‘void sortMatches(TLocalHolder&)’: /<>/src/lambda.hpp:916:20: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 916 | double start = sysTime(); | ^~~~~~~ /<>/src/lambda.hpp:934:21: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 934 | double finish = sysTime() - start; | ^~~~~~~ /<>/src/lambda.hpp: In function ‘int computeBlastMatch(TBlastMatch&, const typename TLocalHolder::TMatch&, TLocalHolder&)’: /<>/src/lambda.hpp:1177:9: error: ‘Tuple’ was not declared in this scope; did you mean ‘seqan2::Tuple’? [-Wtemplate-body] 1177 | Tuple positions = | ^~~~~ | seqan2::Tuple In file included from /usr/include/seqan/basic/basic_aggregate.h:59, from /usr/include/seqan/basic.h:98: /usr/include/seqan/basic/tuple_base.h:88:8: note: ‘seqan2::Tuple’ declared here 88 | struct Tuple | ^~~~~ /<>/src/lambda.hpp:1177:15: error: expected primary-expression before ‘decltype’ [-Wtemplate-body] 1177 | Tuple positions = | ^~~~~~~~~~~~~~~~~~~ /<>/src/lambda.hpp:1189:44: error: ‘positions’ was not declared in this scope [-Wtemplate-body] 1189 | positions, | ^~~~~~~~~ /<>/src/lambda.hpp:1190:44: error: ‘EXTEND_BOTH’ was not declared in this scope; did you mean ‘seqan2::EXTEND_BOTH’? [-Wtemplate-body] 1190 | EXTEND_BOTH, | ^~~~~~~~~~~ | seqan2::EXTEND_BOTH In file included from /usr/include/seqan/seeds.h:71: /usr/include/seqan/seeds/seeds_extension.h:128:5: note: ‘seqan2::EXTEND_BOTH’ declared here 128 | EXTEND_BOTH = 3 | ^~~~~~~~~~~ /<>/src/lambda.hpp:1195:44: error: there are no arguments to ‘True’ that depend on a template parameter, so a declaration of ‘True’ must be available [-Wtemplate-body] 1195 | True(), | ^~~~ /<>/src/lambda.hpp:1196:44: error: there are no arguments to ‘True’ that depend on a template parameter, so a declaration of ‘True’ must be available [-Wtemplate-body] 1196 | True(), | ^~~~ /<>/src/lambda.hpp:1205:44: error: ‘positions’ was not declared in this scope [-Wtemplate-body] 1205 | positions, | ^~~~~~~~~ /<>/src/lambda.hpp:1206:44: error: ‘EXTEND_BOTH’ was not declared in this scope; did you mean ‘seqan2::EXTEND_BOTH’? [-Wtemplate-body] 1206 | EXTEND_BOTH, | ^~~~~~~~~~~ | seqan2::EXTEND_BOTH /usr/include/seqan/seeds/seeds_extension.h:128:5: note: ‘seqan2::EXTEND_BOTH’ declared here 128 | EXTEND_BOTH = 3 | ^~~~~~~~~~~ /<>/src/lambda.hpp:1211:44: error: there are no arguments to ‘True’ that depend on a template parameter, so a declaration of ‘True’ must be available [-Wtemplate-body] 1211 | True(), | ^~~~ /<>/src/lambda.hpp:1212:44: error: there are no arguments to ‘False’ that depend on a template parameter, so a declaration of ‘False’ must be available [-Wtemplate-body] 1212 | False(), | ^~~~~ /<>/src/lambda.hpp:1224:44: error: ‘positions’ was not declared in this scope [-Wtemplate-body] 1224 | positions, | ^~~~~~~~~ /<>/src/lambda.hpp:1225:44: error: ‘EXTEND_BOTH’ was not declared in this scope; did you mean ‘seqan2::EXTEND_BOTH’? [-Wtemplate-body] 1225 | EXTEND_BOTH, | ^~~~~~~~~~~ | seqan2::EXTEND_BOTH /usr/include/seqan/seeds/seeds_extension.h:128:5: note: ‘seqan2::EXTEND_BOTH’ declared here 128 | EXTEND_BOTH = 3 | ^~~~~~~~~~~ /<>/src/lambda.hpp:1230:44: error: there are no arguments to ‘False’ that depend on a template parameter, so a declaration of ‘False’ must be available [-Wtemplate-body] 1230 | False(), | ^~~~~ /<>/src/lambda.hpp:1231:44: error: there are no arguments to ‘True’ that depend on a template parameter, so a declaration of ‘True’ must be available [-Wtemplate-body] 1231 | True(), | ^~~~ /<>/src/lambda.hpp:1240:44: error: ‘positions’ was not declared in this scope [-Wtemplate-body] 1240 | positions, | ^~~~~~~~~ /<>/src/lambda.hpp:1241:44: error: ‘EXTEND_BOTH’ was not declared in this scope; did you mean ‘seqan2::EXTEND_BOTH’? [-Wtemplate-body] 1241 | EXTEND_BOTH, | ^~~~~~~~~~~ | seqan2::EXTEND_BOTH /usr/include/seqan/seeds/seeds_extension.h:128:5: note: ‘seqan2::EXTEND_BOTH’ declared here 128 | EXTEND_BOTH = 3 | ^~~~~~~~~~~ /<>/src/lambda.hpp:1246:44: error: there are no arguments to ‘False’ that depend on a template parameter, so a declaration of ‘False’ must be available [-Wtemplate-body] 1246 | False(), | ^~~~~ /<>/src/lambda.hpp:1247:44: error: there are no arguments to ‘False’ that depend on a template parameter, so a declaration of ‘False’ must be available [-Wtemplate-body] 1247 | False(), | ^~~~~ /<>/src/lambda.hpp: In function ‘int iterateMatches(TLocalHolder&)’: /<>/src/lambda.hpp:1332:27: error: ‘BlastMatch’ does not name a type [-Wtemplate-body] 1332 | using TBlastMatch = BlastMatch< | ^~~~~~~~~~ /<>/src/lambda.hpp:1339:27: error: ‘BlastRecord’ does not name a type [-Wtemplate-body] 1339 | using TBlastRecord = BlastRecord; | ^~~~~~~~~~~ /<>/src/lambda.hpp:1345:20: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 1345 | double start = sysTime(); | ^~~~~~~ /<>/src/lambda.hpp:1372:9: error: ‘TBlastRecord’ was not declared in this scope [-Wtemplate-body] 1372 | TBlastRecord record(lH.gH.qryIds[trueQryId]); | ^~~~~~~~~~~~ /<>/src/lambda.hpp:1374:9: error: ‘record’ was not declared in this scope [-Wtemplate-body] 1374 | record.qLength = (qIsTranslated(lH.gH.blastProgram) | ^~~~~~ /<>/src/lambda.hpp:1454:29: error: there are no arguments to ‘back’ that depend on a template parameter, so a declaration of ‘back’ must be available [-Wtemplate-body] 1454 | auto & bm = back(record.matches); | ^~~~ /<>/src/lambda.hpp:1611:13: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-Wtemplate-body] 1611 | if (length(record.matches) > 0) | ^~~~~~ /<>/src/lambda.hpp:1637:25: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 1637 | double finish = sysTime() - start; | ^~~~~~~ /<>/src/lambda.cpp: At global scope: /<>/src/lambda.cpp:57:11: error: ‘BlastTabularSpec’ has not been declared 57 | BlastTabularSpec h> | ^~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:61:10: error: ‘BlastTabularSpecSelector’ has not been declared 61 | BlastTabularSpecSelector const &); | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:61:34: error: expected ‘,’ or ‘...’ before ‘<’ token 61 | BlastTabularSpecSelector const &); | ^ /<>/src/lambda.cpp:64:11: error: ‘BlastTabularSpec’ has not been declared 64 | BlastTabularSpec h, | ^~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:65:11: error: ‘BlastProgram’ has not been declared 65 | BlastProgram p> | ^~~~~~~~~~~~ /<>/src/lambda.cpp:69:10: error: ‘BlastTabularSpecSelector’ has not been declared 69 | BlastTabularSpecSelector const &, | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:69:34: error: expected ‘,’ or ‘...’ before ‘<’ token 69 | BlastTabularSpecSelector const &, | ^ /<>/src/lambda.cpp:74:11: error: ‘BlastTabularSpec’ has not been declared 74 | BlastTabularSpec h, | ^~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:75:11: error: ‘BlastProgram’ has not been declared 75 | BlastProgram p> | ^~~~~~~~~~~~ /<>/src/lambda.cpp:79:10: error: ‘BlastTabularSpecSelector’ has not been declared 79 | BlastTabularSpecSelector const &, | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:79:34: error: expected ‘,’ or ‘...’ before ‘<’ token 79 | BlastTabularSpecSelector const &, | ^ /<>/src/lambda.cpp:86:11: error: ‘BlastTabularSpec’ has not been declared 86 | BlastTabularSpec h, | ^~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:87:11: error: ‘BlastProgram’ has not been declared 87 | BlastProgram p> | ^~~~~~~~~~~~ /<>/src/lambda.cpp:91:10: error: ‘BlastTabularSpecSelector’ has not been declared 91 | BlastTabularSpecSelector const &, | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:91:34: error: expected ‘,’ or ‘...’ before ‘<’ token 91 | BlastTabularSpecSelector const &, | ^ /<>/src/lambda.cpp:100:11: error: ‘BlastProgram’ has not been declared 100 | BlastProgram p, | ^~~~~~~~~~~~ /<>/src/lambda.cpp:101:11: error: ‘BlastTabularSpec’ has not been declared 101 | BlastTabularSpec h> | ^~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:105:10: error: ‘BlastTabularSpecSelector’ has not been declared 105 | BlastTabularSpecSelector const &, | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:105:34: error: expected ‘,’ or ‘...’ before ‘<’ token 105 | BlastTabularSpecSelector const &, | ^ /<>/src/lambda.cpp: In function ‘int main(int, const char**)’: /<>/src/lambda.cpp:119:12: error: ‘ArgumentParser’ is not a member of ‘seqan’; did you mean ‘seqan2::ArgumentParser’? 119 | seqan::ArgumentParser parser; | ^~~~~~~~~~~~~~ /usr/include/seqan/arg_parse/argument_parser.h:152:7: note: ‘seqan2::ArgumentParser’ declared here 152 | class ArgumentParser | ^~~~~~~~~~~~~~ /<>/src/lambda.cpp:121:12: error: ‘seqan::ArgumentParser’ has not been declared 121 | seqan::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv); | ^~~~~~~~~~~~~~ /<>/src/lambda.cpp:126:9: error: ‘res’ was not declared in this scope 126 | if (res != seqan::ArgumentParser::PARSE_OK) | ^~~ /<>/src/lambda.cpp:126:23: error: ‘seqan::ArgumentParser’ has not been declared 126 | if (res != seqan::ArgumentParser::PARSE_OK) | ^~~~~~~~~~~~~~ /<>/src/lambda.cpp:127:30: error: ‘seqan::ArgumentParser’ has not been declared 127 | return res == seqan::ArgumentParser::PARSE_ERROR; | ^~~~~~~~~~~~~~ /<>/src/lambda.cpp: In function ‘int argConv0(const LambdaOptions&)’: /<>/src/lambda.cpp:138:5: error: ‘CharString’ was not declared in this scope; did you mean ‘seqan2::CharString’? 138 | CharString output = options.output; | ^~~~~~~~~~ | seqan2::CharString /usr/include/seqan/sequence/sequence_shortcuts.h:55:36: note: ‘seqan2::CharString’ declared here 55 | typedef String > CharString; | ^~~~~~~~~~ /<>/src/lambda.cpp:139:18: error: ‘output’ was not declared in this scope 139 | if (endsWith(output, ".gz")) | ^~~~~~ /<>/src/lambda.cpp:139:9: error: ‘endsWith’ was not declared in this scope; did you mean ‘seqan2::endsWith’? 139 | if (endsWith(output, ".gz")) | ^~~~~~~~ | seqan2::endsWith In file included from /usr/include/seqan/sequence.h:99: /usr/include/seqan/sequence/segment_utils.h:90:13: note: ‘seqan2::endsWith’ declared here 90 | inline bool endsWith(TLhs const & lhs, TRhs const & rhs) | ^~~~~~~~ /<>/src/lambda.cpp:140:33: error: ‘length’ was not declared in this scope; did you mean ‘seqan2::length’? 140 | output = prefix(output, length(output) - 3); | ^~~~~~ | seqan2::length In file included from /usr/include/seqan/seeds.h:79: /usr/include/seqan/seeds/seeds_seed_set_unordered.h:177:1: note: ‘seqan2::length’ declared here 177 | length(SeedSet const & seedSet) | ^~~~~~ /<>/src/lambda.cpp:140:18: error: ‘prefix’ was not declared in this scope; did you mean ‘seqan2::prefix’? 140 | output = prefix(output, length(output) - 3); | ^~~~~~ | seqan2::prefix In file included from /usr/include/seqan/index/index_pizzachili.h:39, from /usr/include/seqan/index.h:194: /usr/include/seqan/index/index_pizzachili_string.h:719:1: note: ‘seqan2::prefix’ declared here 719 | prefix( | ^~~~~~ /<>/src/lambda.cpp:142:33: error: ‘length’ was not declared in this scope; did you mean ‘seqan2::length’? 142 | output = prefix(output, length(output) - 4); | ^~~~~~ | seqan2::length /usr/include/seqan/seeds/seeds_seed_set_unordered.h:177:1: note: ‘seqan2::length’ declared here 177 | length(SeedSet const & seedSet) | ^~~~~~ /<>/src/lambda.cpp:142:18: error: ‘prefix’ was not declared in this scope; did you mean ‘seqan2::prefix’? 142 | output = prefix(output, length(output) - 4); | ^~~~~~ | seqan2::prefix /usr/include/seqan/index/index_pizzachili_string.h:719:1: note: ‘seqan2::prefix’ declared here 719 | prefix( | ^~~~~~ /<>/src/lambda.cpp:144:18: error: ‘output’ was not declared in this scope 144 | if (endsWith(output, ".m0")) | ^~~~~~ /<>/src/lambda.cpp:144:9: error: ‘endsWith’ was not declared in this scope; did you mean ‘seqan2::endsWith’? 144 | if (endsWith(output, ".m0")) | ^~~~~~~~ | seqan2::endsWith /usr/include/seqan/sequence/segment_utils.h:90:13: note: ‘seqan2::endsWith’ declared here 90 | inline bool endsWith(TLhs const & lhs, TRhs const & rhs) | ^~~~~~~~ /<>/src/lambda.cpp:145:34: error: ‘BlastReport’ was not declared in this scope; did you mean ‘seqan2::BlastReport’? 145 | return argConv1(options, BlastReport(), BlastTabularSpecSelector()); | ^~~~~~~~~~~ | seqan2::BlastReport /usr/include/seqan/blast/blast_report_out.h:78:27: note: ‘seqan2::BlastReport’ declared here 78 | typedef Tag BlastReport; | ^~~~~~~~~~~ /<>/src/lambda.cpp:145:49: error: ‘BlastTabularSpecSelector’ was not declared in this scope; did you mean ‘seqan2::BlastTabularSpecSelector’? 145 | return argConv1(options, BlastReport(), BlastTabularSpecSelector()); | ^~~~~~~~~~~~~~~~~~~~~~~~ | seqan2::BlastTabularSpecSelector /usr/include/seqan/blast/blast_tabular.h:156:8: note: ‘seqan2::BlastTabularSpecSelector’ declared here 156 | struct BlastTabularSpecSelector | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:145:74: error: ‘BlastTabularSpec’ has not been declared 145 | return argConv1(options, BlastReport(), BlastTabularSpecSelector()); | ^~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:145:105: error: expected primary-expression before ‘)’ token 145 | return argConv1(options, BlastReport(), BlastTabularSpecSelector()); | ^ /<>/src/lambda.cpp:147:34: error: ‘BlastTabular’ was not declared in this scope; did you mean ‘seqan2::BlastTabular’? 147 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector()); | ^~~~~~~~~~~~ | seqan2::BlastTabular /usr/include/seqan/blast/blast_tabular.h:86:28: note: ‘seqan2::BlastTabular’ declared here 86 | typedef Tag BlastTabular; | ^~~~~~~~~~~~ /<>/src/lambda.cpp:147:50: error: ‘BlastTabularSpecSelector’ was not declared in this scope; did you mean ‘seqan2::BlastTabularSpecSelector’? 147 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector()); | ^~~~~~~~~~~~~~~~~~~~~~~~ | seqan2::BlastTabularSpecSelector /usr/include/seqan/blast/blast_tabular.h:156:8: note: ‘seqan2::BlastTabularSpecSelector’ declared here 156 | struct BlastTabularSpecSelector | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:147:75: error: ‘BlastTabularSpec’ has not been declared 147 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector()); | ^~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:147:106: error: expected primary-expression before ‘)’ token 147 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector()); | ^ /<>/src/lambda.cpp:149:34: error: ‘BlastTabular’ was not declared in this scope; did you mean ‘seqan2::BlastTabular’? 149 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector()); | ^~~~~~~~~~~~ | seqan2::BlastTabular /usr/include/seqan/blast/blast_tabular.h:86:28: note: ‘seqan2::BlastTabular’ declared here 86 | typedef Tag BlastTabular; | ^~~~~~~~~~~~ /<>/src/lambda.cpp:149:50: error: ‘BlastTabularSpecSelector’ was not declared in this scope; did you mean ‘seqan2::BlastTabularSpecSelector’? 149 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector()); | ^~~~~~~~~~~~~~~~~~~~~~~~ | seqan2::BlastTabularSpecSelector /usr/include/seqan/blast/blast_tabular.h:156:8: note: ‘seqan2::BlastTabularSpecSelector’ declared here 156 | struct BlastTabularSpecSelector | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:149:75: error: ‘BlastTabularSpec’ has not been declared 149 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector()); | ^~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:149:103: error: expected primary-expression before ‘)’ token 149 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector()); | ^ /<>/src/lambda.cpp:151:34: error: ‘BlastTabular’ was not declared in this scope; did you mean ‘seqan2::BlastTabular’? 151 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector()); | ^~~~~~~~~~~~ | seqan2::BlastTabular /usr/include/seqan/blast/blast_tabular.h:86:28: note: ‘seqan2::BlastTabular’ declared here 86 | typedef Tag BlastTabular; | ^~~~~~~~~~~~ /<>/src/lambda.cpp:151:50: error: ‘BlastTabularSpecSelector’ was not declared in this scope; did you mean ‘seqan2::BlastTabularSpecSelector’? 151 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector()); | ^~~~~~~~~~~~~~~~~~~~~~~~ | seqan2::BlastTabularSpecSelector /usr/include/seqan/blast/blast_tabular.h:156:8: note: ‘seqan2::BlastTabularSpecSelector’ declared here 156 | struct BlastTabularSpecSelector | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:151:75: error: ‘BlastTabularSpec’ has not been declared 151 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector()); | ^~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:151:103: error: expected primary-expression before ‘)’ token 151 | return argConv1(options, BlastTabular(), BlastTabularSpecSelector()); | ^ /<>/src/lambda.cpp: At global scope: /<>/src/lambda.cpp:158:11: error: ‘BlastTabularSpec’ has not been declared 158 | BlastTabularSpec h> | ^~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:162:10: error: ‘BlastTabularSpecSelector’ has not been declared 162 | BlastTabularSpecSelector const &) | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:162:34: error: expected ‘,’ or ‘...’ before ‘<’ token 162 | BlastTabularSpecSelector const &) | ^ /<>/src/lambda.cpp: In function ‘int argConv1(const LambdaOptions&, const TOutFormat&, int)’: /<>/src/lambda.cpp:164:20: error: ‘const struct LambdaOptions’ has no member named ‘blastProgram’ [-Wtemplate-body] 164 | switch(options.blastProgram) | ^~~~~~~~~~~~ /<>/src/lambda.cpp:167:14: error: ‘BlastProgram’ has not been declared [-Wtemplate-body] 167 | case BlastProgram::BLASTN: | ^~~~~~~~~~~~ /<>/src/lambda.cpp:170:29: error: ‘BlastTabularSpecSelector’ was not declared in this scope; did you mean ‘seqan2::BlastTabularSpecSelector’? [-Wtemplate-body] 170 | BlastTabularSpecSelector(), | ^~~~~~~~~~~~~~~~~~~~~~~~ | seqan2::BlastTabularSpecSelector /usr/include/seqan/blast/blast_tabular.h:156:8: note: ‘seqan2::BlastTabularSpecSelector’ declared here 156 | struct BlastTabularSpecSelector | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:170:54: error: ‘h’ was not declared in this scope [-Wtemplate-body] 170 | BlastTabularSpecSelector(), | ^ /<>/src/lambda.cpp:170:57: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 170 | BlastTabularSpecSelector(), | ^ /<>/src/lambda.cpp:171:29: error: ‘BlastProgramSelector’ was not declared in this scope; did you mean ‘seqan2::BlastProgramSelector’? [-Wtemplate-body] 171 | BlastProgramSelector(), | ^~~~~~~~~~~~~~~~~~~~ | seqan2::BlastProgramSelector /usr/include/seqan/blast/blast_base.h:133:8: note: ‘seqan2::BlastProgramSelector’ declared here 133 | struct BlastProgramSelector | ^~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:171:50: error: ‘BlastProgram’ has not been declared [-Wtemplate-body] 171 | BlastProgramSelector(), | ^~~~~~~~~~~~ /<>/src/lambda.cpp:171:72: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 171 | BlastProgramSelector(), | ^ /<>/src/lambda.cpp:172:29: error: there are no arguments to ‘Dna5’ that depend on a template parameter, so a declaration of ‘Dna5’ must be available [-Wtemplate-body] 172 | Dna5()); | ^~~~ /<>/src/lambda.cpp:174:14: error: ‘BlastProgram’ has not been declared [-Wtemplate-body] 174 | case BlastProgram::BLASTP: | ^~~~~~~~~~~~ /<>/src/lambda.cpp:177:57: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 177 | BlastTabularSpecSelector(), | ^ /<>/src/lambda.cpp:178:50: error: ‘BlastProgram’ has not been declared [-Wtemplate-body] 178 | BlastProgramSelector()); | ^~~~~~~~~~~~ /<>/src/lambda.cpp:178:72: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 178 | BlastProgramSelector()); | ^ /<>/src/lambda.cpp:179:14: error: ‘BlastProgram’ has not been declared [-Wtemplate-body] 179 | case BlastProgram::BLASTX: | ^~~~~~~~~~~~ /<>/src/lambda.cpp:182:57: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 182 | BlastTabularSpecSelector(), | ^ /<>/src/lambda.cpp:183:50: error: ‘BlastProgram’ has not been declared [-Wtemplate-body] 183 | BlastProgramSelector()); | ^~~~~~~~~~~~ /<>/src/lambda.cpp:183:72: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 183 | BlastProgramSelector()); | ^ /<>/src/lambda.cpp:185:14: error: ‘BlastProgram’ has not been declared [-Wtemplate-body] 185 | case BlastProgram::TBLASTN: | ^~~~~~~~~~~~ /<>/src/lambda.cpp:188:57: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 188 | BlastTabularSpecSelector(), | ^ /<>/src/lambda.cpp:189:50: error: ‘BlastProgram’ has not been declared [-Wtemplate-body] 189 | BlastProgramSelector()); | ^~~~~~~~~~~~ /<>/src/lambda.cpp:189:73: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 189 | BlastProgramSelector()); | ^ /<>/src/lambda.cpp:190:14: error: ‘BlastProgram’ has not been declared [-Wtemplate-body] 190 | case BlastProgram::TBLASTX: | ^~~~~~~~~~~~ /<>/src/lambda.cpp:193:57: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 193 | BlastTabularSpecSelector(), | ^ /<>/src/lambda.cpp:194:50: error: ‘BlastProgram’ has not been declared [-Wtemplate-body] 194 | BlastProgramSelector()); | ^~~~~~~~~~~~ /<>/src/lambda.cpp:194:73: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 194 | BlastProgramSelector()); | ^ /<>/src/lambda.cpp: At global scope: /<>/src/lambda.cpp:206:11: error: ‘BlastTabularSpec’ has not been declared 206 | BlastTabularSpec h, | ^~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:207:11: error: ‘BlastProgram’ has not been declared 207 | BlastProgram p> | ^~~~~~~~~~~~ /<>/src/lambda.cpp:211:10: error: ‘BlastTabularSpecSelector’ has not been declared 211 | BlastTabularSpecSelector const &, | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:211:34: error: expected ‘,’ or ‘...’ before ‘<’ token 211 | BlastTabularSpecSelector const &, | ^ /<>/src/lambda.cpp: In function ‘int argConv2(const LambdaOptions&, const TOutFormat&, int)’: /<>/src/lambda.cpp:214:16: error: ‘BlastTabularSpecSelector’ does not name a type [-Wtemplate-body] 214 | using Th = BlastTabularSpecSelector; | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:215:16: error: ‘BlastProgramSelector’ does not name a type [-Wtemplate-body] 215 | using Tp = BlastProgramSelector

; | ^~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:219:52: error: there are no arguments to ‘Th’ that depend on a template parameter, so a declaration of ‘Th’ must be available [-Wtemplate-body] 219 | return argConv3(options, TOutFormat(), Th(), Tp(), AminoAcid()); | ^~ /<>/src/lambda.cpp:219:58: error: there are no arguments to ‘Tp’ that depend on a template parameter, so a declaration of ‘Tp’ must be available [-Wtemplate-body] 219 | return argConv3(options, TOutFormat(), Th(), Tp(), AminoAcid()); | ^~ /<>/src/lambda.cpp:219:64: error: there are no arguments to ‘AminoAcid’ that depend on a template parameter, so a declaration of ‘AminoAcid’ must be available [-Wtemplate-body] 219 | return argConv3(options, TOutFormat(), Th(), Tp(), AminoAcid()); | ^~~~~~~~~ /<>/src/lambda.cpp:221:52: error: there are no arguments to ‘Th’ that depend on a template parameter, so a declaration of ‘Th’ must be available [-Wtemplate-body] 221 | return argConv3(options, TOutFormat(), Th(), Tp(), ReducedAminoAcid()); | ^~ /<>/src/lambda.cpp:221:58: error: there are no arguments to ‘Tp’ that depend on a template parameter, so a declaration of ‘Tp’ must be available [-Wtemplate-body] 221 | return argConv3(options, TOutFormat(), Th(), Tp(), ReducedAminoAcid()); | ^~ /<>/src/lambda.cpp:221:64: error: ‘ReducedAminoAcid’ was not declared in this scope; did you mean ‘seqan2::ReducedAminoAcid’? [-Wtemplate-body] 221 | return argConv3(options, TOutFormat(), Th(), Tp(), ReducedAminoAcid()); | ^~~~~~~~~~~~~~~~ | seqan2::ReducedAminoAcid /usr/include/seqan/reduced_aminoacid/reduced_aminoacid_base.h:79:7: note: ‘seqan2::ReducedAminoAcid’ declared here 79 | using ReducedAminoAcid = SimpleType >; | ^~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:221:81: error: ‘Murphy10’ was not declared in this scope; did you mean ‘seqan2::Murphy10’? [-Wtemplate-body] 221 | return argConv3(options, TOutFormat(), Th(), Tp(), ReducedAminoAcid()); | ^~~~~~~~ | seqan2::Murphy10 /usr/include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_base.h:85:24: note: ‘seqan2::Murphy10’ declared here 85 | typedef Tag Murphy10; | ^~~~~~~~ /<>/src/lambda.cpp:221:91: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 221 | return argConv3(options, TOutFormat(), Th(), Tp(), ReducedAminoAcid()); | ^ /<>/src/lambda.cpp: At global scope: /<>/src/lambda.cpp:242:11: error: ‘BlastTabularSpec’ has not been declared 242 | BlastTabularSpec h, | ^~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:243:11: error: ‘BlastProgram’ has not been declared 243 | BlastProgram p> | ^~~~~~~~~~~~ /<>/src/lambda.cpp:247:10: error: ‘BlastTabularSpecSelector’ has not been declared 247 | BlastTabularSpecSelector const &, | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:247:34: error: expected ‘,’ or ‘...’ before ‘<’ token 247 | BlastTabularSpecSelector const &, | ^ /<>/src/lambda.cpp: In function ‘int argConv3(const LambdaOptions&, const TOutFormat&, int)’: /<>/src/lambda.cpp:268:25: error: ‘BlastTabularSpecSelector’ was not declared in this scope; did you mean ‘seqan2::BlastTabularSpecSelector’? [-Wtemplate-body] 268 | BlastTabularSpecSelector(), | ^~~~~~~~~~~~~~~~~~~~~~~~ | seqan2::BlastTabularSpecSelector /usr/include/seqan/blast/blast_tabular.h:156:8: note: ‘seqan2::BlastTabularSpecSelector’ declared here 156 | struct BlastTabularSpecSelector | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:268:50: error: ‘h’ was not declared in this scope [-Wtemplate-body] 268 | BlastTabularSpecSelector(), | ^ /<>/src/lambda.cpp:268:53: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 268 | BlastTabularSpecSelector(), | ^ /<>/src/lambda.cpp:269:25: error: ‘BlastProgramSelector’ was not declared in this scope; did you mean ‘seqan2::BlastProgramSelector’? [-Wtemplate-body] 269 | BlastProgramSelector

(), | ^~~~~~~~~~~~~~~~~~~~ | seqan2::BlastProgramSelector /usr/include/seqan/blast/blast_base.h:133:8: note: ‘seqan2::BlastProgramSelector’ declared here 133 | struct BlastProgramSelector | ^~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:269:46: error: ‘p’ was not declared in this scope [-Wtemplate-body] 269 | BlastProgramSelector

(), | ^ /<>/src/lambda.cpp:269:49: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 269 | BlastProgramSelector

(), | ^ /<>/src/lambda.cpp:271:25: error: there are no arguments to ‘AffineGaps’ that depend on a template parameter, so a declaration of ‘AffineGaps’ must be available [-Wtemplate-body] 271 | AffineGaps()); | ^~~~~~~~~~ /<>/src/lambda.cpp: At global scope: /<>/src/lambda.cpp:277:11: error: ‘BlastTabularSpec’ has not been declared 277 | BlastTabularSpec h, | ^~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:278:11: error: ‘BlastProgram’ has not been declared 278 | BlastProgram p> | ^~~~~~~~~~~~ /<>/src/lambda.cpp:282:10: error: ‘BlastTabularSpecSelector’ has not been declared 282 | BlastTabularSpecSelector const &, | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:282:34: error: expected ‘,’ or ‘...’ before ‘<’ token 282 | BlastTabularSpecSelector const &, | ^ /<>/src/lambda.cpp: In function ‘int argConv4(const LambdaOptions&, const TOutFormat&, int)’: /<>/src/lambda.cpp:316:25: error: ‘IndexSa’ was not declared in this scope; did you mean ‘seqan2::IndexSa’? [-Wtemplate-body] 316 | return realMain>(options, | ^~~~~~~ | seqan2::IndexSa In file included from /usr/include/seqan/index.h:142: /usr/include/seqan/index/index_sa_stree.h:58:8: note: ‘seqan2::IndexSa’ declared here 58 | struct IndexSa {}; | ^~~~~~~ /<>/src/lambda.cpp:316:16: error: parse error in template argument list [-Wtemplate-body] 316 | return realMain>(options, | ^~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:318:36: error: ‘BlastTabularSpecSelector’ was not declared in this scope; did you mean ‘seqan2::BlastTabularSpecSelector’? [-Wtemplate-body] 318 | BlastTabularSpecSelector(), | ^~~~~~~~~~~~~~~~~~~~~~~~ | seqan2::BlastTabularSpecSelector /usr/include/seqan/blast/blast_tabular.h:156:8: note: ‘seqan2::BlastTabularSpecSelector’ declared here 156 | struct BlastTabularSpecSelector | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:318:61: error: ‘h’ was not declared in this scope [-Wtemplate-body] 318 | BlastTabularSpecSelector(), | ^ /<>/src/lambda.cpp:318:64: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 318 | BlastTabularSpecSelector(), | ^ /<>/src/lambda.cpp:319:36: error: ‘BlastProgramSelector’ was not declared in this scope; did you mean ‘seqan2::BlastProgramSelector’? [-Wtemplate-body] 319 | BlastProgramSelector

(), | ^~~~~~~~~~~~~~~~~~~~ | seqan2::BlastProgramSelector /usr/include/seqan/blast/blast_base.h:133:8: note: ‘seqan2::BlastProgramSelector’ declared here 133 | struct BlastProgramSelector | ^~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:319:57: error: ‘p’ was not declared in this scope [-Wtemplate-body] 319 | BlastProgramSelector

(), | ^ /<>/src/lambda.cpp:319:60: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 319 | BlastProgramSelector

(), | ^ /<>/src/lambda.cpp:323:25: error: ‘TFMIndex’ was not declared in this scope [-Wtemplate-body] 323 | return realMain>(options, | ^~~~~~~~ /<>/src/lambda.cpp:323:16: error: parse error in template argument list [-Wtemplate-body] 323 | return realMain>(options, | ^~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:325:36: error: ‘BlastTabularSpecSelector’ was not declared in this scope; did you mean ‘seqan2::BlastTabularSpecSelector’? [-Wtemplate-body] 325 | BlastTabularSpecSelector(), | ^~~~~~~~~~~~~~~~~~~~~~~~ | seqan2::BlastTabularSpecSelector /usr/include/seqan/blast/blast_tabular.h:156:8: note: ‘seqan2::BlastTabularSpecSelector’ declared here 156 | struct BlastTabularSpecSelector | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:325:61: error: ‘h’ was not declared in this scope [-Wtemplate-body] 325 | BlastTabularSpecSelector(), | ^ /<>/src/lambda.cpp:325:64: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 325 | BlastTabularSpecSelector(), | ^ /<>/src/lambda.cpp:326:36: error: ‘BlastProgramSelector’ was not declared in this scope; did you mean ‘seqan2::BlastProgramSelector’? [-Wtemplate-body] 326 | BlastProgramSelector

(), | ^~~~~~~~~~~~~~~~~~~~ | seqan2::BlastProgramSelector /usr/include/seqan/blast/blast_base.h:133:8: note: ‘seqan2::BlastProgramSelector’ declared here 133 | struct BlastProgramSelector | ^~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:326:57: error: ‘p’ was not declared in this scope [-Wtemplate-body] 326 | BlastProgramSelector

(), | ^ /<>/src/lambda.cpp:326:60: error: expected primary-expression before ‘)’ token [-Wtemplate-body] 326 | BlastProgramSelector

(), | ^ /<>/src/lambda.cpp: At global scope: /<>/src/lambda.cpp:341:11: error: ‘BlastProgram’ has not been declared 341 | BlastProgram p, | ^~~~~~~~~~~~ /<>/src/lambda.cpp:342:11: error: ‘BlastTabularSpec’ has not been declared 342 | BlastTabularSpec h> | ^~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:346:10: error: ‘BlastTabularSpecSelector’ has not been declared 346 | BlastTabularSpecSelector const &, | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/lambda.cpp:346:34: error: expected ‘,’ or ‘...’ before ‘<’ token 346 | BlastTabularSpecSelector const &, | ^ /<>/src/lambda.cpp: In function ‘int realMain(const LambdaOptions&, const TOutFormat&, int)’: /<>/src/lambda.cpp:351:78: error: ‘p’ was not declared in this scope [-Wtemplate-body] 351 | using TGlobalHolder = GlobalDataHolder; | ^ /<>/src/lambda.cpp:351:81: error: ‘h’ was not declared in this scope [-Wtemplate-body] 351 | using TGlobalHolder = GlobalDataHolder; | ^ /<>/src/lambda.cpp:351:82: error: template argument 4 is invalid [-Wtemplate-body] 351 | using TGlobalHolder = GlobalDataHolder; | ^ /<>/src/lambda.cpp:351:82: error: template argument 5 is invalid [-Wtemplate-body] /<>/src/lambda.cpp:352:42: error: ‘TGlobalHolder’ was not declared in this scope; did you mean ‘GlobalDataHolder’? [-Wtemplate-body] 352 | using TLocalHolder = LocalDataHolder; | ^~~~~~~~~~~~~ | GlobalDataHolder /<>/src/lambda.cpp:352:72: error: template argument 1 is invalid [-Wtemplate-body] 352 | using TLocalHolder = LocalDataHolder; | ^ /<>/src/lambda.cpp:359:22: error: ‘TLocalHolder’ was not declared in this scope; did you mean ‘totalorder’? [-Wtemplate-body] 359 | printOptions(options); | ^~~~~~~~~~~~ | totalorder /<>/src/lambda.cpp:361:18: error: expected ‘;’ before ‘globalHolder’ [-Wtemplate-body] 361 | TGlobalHolder globalHolder; | ^~~~~~~~~~~~~ | ; /<>/src/lambda.cpp:364:30: error: ‘globalHolder’ was not declared in this scope; did you mean ‘GlobalDataHolder’? [-Wtemplate-body] 364 | int ret = prepareScoring(globalHolder, options); | ^~~~~~~~~~~~ | GlobalDataHolder /<>/src/lambda.cpp:421:20: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 421 | double start = sysTime(); | ^~~~~~~ /<>/src/lambda.cpp:428:27: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-Wtemplate-body] 428 | : length(globalHolder.qryIds)); | ^~~~~~ /<>/src/lambda.cpp:434:9: error: ‘TLocalHolder’ was not declared in this scope; did you mean ‘totalorder’? [-Wtemplate-body] 434 | TLocalHolder localHolder(options, globalHolder); | ^~~~~~~~~~~~ | totalorder /<>/src/lambda.cpp:441:13: error: ‘localHolder’ was not declared in this scope [-Wtemplate-body] 441 | localHolder.init(t); | ^~~~~~~~~~~ /<>/src/lambda.cpp:481:35: error: ‘localHolder’ was not declared in this scope [-Wtemplate-body] 481 | globalHolder.stats += localHolder.stats; | ^~~~~~~~~~~ /<>/src/lambda.cpp:492:42: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body] 492 | myPrint(options, 2, "Runtime: ", sysTime() - start, "s.\n\n"); | ^~~~~~~ make[3]: *** [src/CMakeFiles/lambda.dir/build.make:82: src/CMakeFiles/lambda.dir/lambda.cpp.o] Error 1 make[3]: Leaving directory '/<>/build' make[2]: *** [CMakeFiles/Makefile2:135: src/CMakeFiles/lambda.dir/all] Error 2 make[2]: Leaving directory '/<>/build' make[1]: *** [Makefile:159: all] Error 2 make[1]: Leaving directory '/<>/build' dh_auto_build: error: cd build && make -j1 INSTALL="install --strip-program=true" VERBOSE=1 returned exit code 2 make: *** [debian/rules:8: binary-arch] Error 25 dpkg-buildpackage: error: debian/rules binary-arch subprocess failed with exit status 2 -------------------------------------------------------------------------------- Build finished at 2026-02-01T22:44:30Z +------------------------------------------------------------------------------+ | Finished Timed Build Commands | +------------------------------------------------------------------------------+ rm -Rf /<>/ ----------------------------------------------------- I: Finished running 'rm -Rf /<>/'. Finished processing commands. -------------------------------------------------------------------------------- Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: n/a Build-Time: 8 Distribution: unstable Fail-Stage: build Foreign Architectures: armhf Host Architecture: armhf Install-Time: 10 Job: lambda-align_1.0.3-8 Machine Architecture: amd64 Package: lambda-align Package-Time: 27 Source-Version: 1.0.3-8 Space: n/a Status: attempted Version: 1.0.3-8 -------------------------------------------------------------------------------- Finished at 2026-02-01T22:44:30Z Build needed 00:00:27, no disk space