sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | rna-star 2.7.4a+dfsg-1 (arm64) Tue, 09 Jun 2020 22:09:53 +0000 | +==============================================================================+ Package: rna-star Version: 2.7.4a+dfsg-1 Source Version: 2.7.4a+dfsg-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: arm64 Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-12f7141f-0b84-471a-b16c-5a5db9e69359' with '<>' I: NOTICE: Log filtering will replace 'build/rna-star-GJFNcb/resolver-FBtzSn' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [146 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2020-06-09-0800.34.pdiff [7601 B] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2020-06-09-1402.27.pdiff [5755 B] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2020-06-09-2002.47.pdiff [7250 B] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2020-06-09-2002.47.pdiff [7250 B] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-06-09-0800.34.pdiff [7252 B] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-06-09-1402.27.pdiff [9831 B] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-06-09-2002.47.pdiff [9491 B] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-06-09-2002.47.pdiff [9491 B] Get:10 http://debian.oregonstate.edu/debian unstable/main arm64 Packages [8077 kB] Fetched 8327 kB in 7s (1116 kB/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: 'rna-star' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/rna-star.git Please use: git clone https://salsa.debian.org/med-team/rna-star.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 791 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main rna-star 2.7.4a+dfsg-1 (dsc) [2177 B] Get:2 http://debian.oregonstate.edu/debian unstable/main rna-star 2.7.4a+dfsg-1 (tar) [414 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main rna-star 2.7.4a+dfsg-1 (diff) [375 kB] Fetched 791 kB in 0s (41.6 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/rna-star-GJFNcb/rna-star-2.7.4a+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/rna-star-GJFNcb' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libhts-dev, vim-common, xxd, zlib1g-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 Filtered Build-Depends: debhelper-compat (= 13), libhts-dev, vim-common, xxd, zlib1g-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 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 [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [425 B] Get:5 copy:/<>/apt_archive ./ Packages [517 B] Fetched 1899 B in 0s (72.0 kB/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... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu bsdmainutils build-essential cpp-9-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-9 g++-9-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-10-base:arm64 gcc-10-cross-base gcc-9-aarch64-linux-gnu gcc-9-aarch64-linux-gnu-base gcc-9-base:arm64 gcc-9-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:arm64 libasan5-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libbrotli1:arm64 libbsd0 libbz2-1.0:arm64 libc6:arm64 libc6-arm64-cross libc6-dev libc6-dev:arm64 libc6-dev-arm64-cross libcom-err2:arm64 libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:arm64 libcrypt1:arm64 libcurl3-gnutls:arm64 libdb5.3:arm64 libdebhelper-perl libdebian-dpkgcross-perl libdeflate0:arm64 libdpkg-perl libelf1 libffi7:arm64 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:arm64 libgcc-9-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libgcrypt20:arm64 libglib2.0-0 libgmp10:arm64 libgnutls30:arm64 libgomp1:arm64 libgomp1-arm64-cross libgpg-error0:arm64 libgssapi-krb5-2:arm64 libhogweed5:arm64 libhts-dev:arm64 libhts3:arm64 libicu67 libidn2-0:arm64 libio-string-perl libitm1:arm64 libitm1-arm64-cross libk5crypto3:arm64 libkeyutils1:arm64 libkrb5-3:arm64 libkrb5support0:arm64 libldap-2.4-2:arm64 libldap-common liblocale-gettext-perl liblsan0:arm64 liblsan0-arm64-cross liblzma-dev:arm64 liblzma5:arm64 libmagic-mgc libmagic1 libnettle7:arm64 libnghttp2-14:arm64 libp11-kit0:arm64 libperl5.30 libpipeline1 libpsl5:arm64 librtmp1:arm64 libsasl2-2:arm64 libsasl2-modules-db:arm64 libsigsegv2 libssh2-1:arm64 libssl1.1:arm64 libstdc++-9-dev libstdc++-9-dev:arm64 libstdc++-9-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libsub-override-perl libtasn1-6:arm64 libtool libtsan0:arm64 libtsan0-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libunistring2:arm64 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:arm64 linux-libc-dev-arm64-cross m4 man-db perl perl-modules-5.30 po-debconf sensible-utils ucf vim-common xxd zlib1g:arm64 zlib1g-dev:arm64 Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican | wordlist whois vacation gcc-9-locales cpp-doc dh-make binutils-multiarch debian-keyring g++-multilib g++-9-multilib gcc-9-doc manpages-dev flex bison gdb-aarch64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:arm64 libc-l10n:arm64 locales:arm64 glibc-doc manpages-dev:arm64 gnupg | gnupg2 git bzr rng-tools:arm64 gnutls-bin:arm64 krb5-doc:arm64 krb5-user:arm64 liblzma-doc:arm64 libstdc++-9-doc libstdc++-9-doc:arm64 libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl libtap-harness-archive-perl libmail-box-perl Recommended packages: gnupg | gnupg2 libalgorithm-merge-perl curl | wget | lynx ca-certificates:arm64 libfile-fcntllock-perl libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libgpg-error-l10n:arm64 krb5-locales:arm64 publicsuffix:arm64 libsasl2-modules:arm64 libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl netbase libmail-sendmail-perl vim | vim-gtk3 | vim-athena | vim-nox | vim-tiny The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu bsdmainutils build-essential cpp-9-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-9 g++-9-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-10-base:arm64 gcc-10-cross-base gcc-9-aarch64-linux-gnu gcc-9-aarch64-linux-gnu-base gcc-9-base:arm64 gcc-9-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:arm64 libasan5-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libbrotli1:arm64 libbsd0 libbz2-1.0:arm64 libc6:arm64 libc6-arm64-cross libc6-dev libc6-dev:arm64 libc6-dev-arm64-cross libcom-err2:arm64 libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:arm64 libcrypt1:arm64 libcurl3-gnutls:arm64 libdb5.3:arm64 libdebhelper-perl libdebian-dpkgcross-perl libdeflate0:arm64 libdpkg-perl libelf1 libffi7:arm64 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:arm64 libgcc-9-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libgcrypt20:arm64 libglib2.0-0 libgmp10:arm64 libgnutls30:arm64 libgomp1:arm64 libgomp1-arm64-cross libgpg-error0:arm64 libgssapi-krb5-2:arm64 libhogweed5:arm64 libhts-dev:arm64 libhts3:arm64 libicu67 libidn2-0:arm64 libio-string-perl libitm1:arm64 libitm1-arm64-cross libk5crypto3:arm64 libkeyutils1:arm64 libkrb5-3:arm64 libkrb5support0:arm64 libldap-2.4-2:arm64 libldap-common liblocale-gettext-perl liblsan0:arm64 liblsan0-arm64-cross liblzma-dev:arm64 liblzma5:arm64 libmagic-mgc libmagic1 libnettle7:arm64 libnghttp2-14:arm64 libp11-kit0:arm64 libperl5.30 libpipeline1 libpsl5:arm64 librtmp1:arm64 libsasl2-2:arm64 libsasl2-modules-db:arm64 libsigsegv2 libssh2-1:arm64 libssl1.1:arm64 libstdc++-9-dev libstdc++-9-dev:arm64 libstdc++-9-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libsub-override-perl libtasn1-6:arm64 libtool libtsan0:arm64 libtsan0-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libunistring2:arm64 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:arm64 linux-libc-dev-arm64-cross m4 man-db perl perl-modules-5.30 po-debconf sbuild-build-depends-main-dummy:arm64 sensible-utils ucf vim-common xxd zlib1g:arm64 zlib1g-dev:arm64 0 upgraded, 144 newly installed, 0 to remove and 0 not upgraded. Need to get 103 MB of archives. After this operation, 414 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [940 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-5 [920 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.2-1 [1315 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 perl-modules-5.30 all 5.30.3-4 [2806 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 libperl5.30 amd64 5.30.3-4 [4019 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 perl amd64 5.30.3-4 [290 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main arm64 gcc-10-base arm64 10.1.0-3 [197 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main arm64 gcc-9-base arm64 9.3.0-13 [197 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 xxd amd64 2:8.2.0716-3 [157 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 vim-common all 2:8.2.0716-3 [192 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.38-5 [262 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.38-5 [120 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.38-5 [67.9 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0042 [73.9 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11.1 [341 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.2-1 [775 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-aarch64-linux-gnu amd64 2.34-8 [2790 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.16-1 [104 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.30-8 [2631 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev amd64 9.3.0-13 [1701 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9 amd64 9.3.0-13 [10.7 MB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:9.2.1-3.1 [1644 B] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libdpkg-perl all 1.19.7 [1414 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-dev all 1.19.7 [1773 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.8 [7640 B] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-aarch64-linux-gnu-base amd64 9.3.0-13cross1 [197 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-aarch64-linux-gnu amd64 9.3.0-13cross1 [6548 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-aarch64-linux-gnu amd64 4:9.2.1-3.1 [16.7 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.3.0-13cross1 [193 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-cross-base all 10.1.0-3cross1 [194 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-arm64-cross all 2.30-2cross1 [1246 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-arm64-cross all 10.1.0-3cross1 [34.7 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-arm64-cross all 10.1.0-3cross1 [89.0 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libitm1-arm64-cross all 10.1.0-3cross1 [23.3 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-arm64-cross all 10.1.0-3cross1 [9252 B] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-arm64-cross all 9.3.0-13cross1 [347 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 liblsan0-arm64-cross all 10.1.0-3cross1 [125 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libtsan0-arm64-cross all 10.1.0-3cross1 [285 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-arm64-cross all 10.1.0-3cross1 [411 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-arm64-cross all 10.1.0-3cross1 [122 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-arm64-cross all 9.3.0-13cross1 [891 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-aarch64-linux-gnu amd64 9.3.0-13cross1 [6934 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-aarch64-linux-gnu amd64 4:9.2.1-3.1 [1460 B] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-arm64-cross all 5.4.19-1cross1 [1153 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-arm64-cross all 2.30-2cross1 [2265 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-arm64-cross all 9.3.0-13cross1 [1640 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-aarch64-linux-gnu amd64 9.3.0-13cross1 [7134 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 g++-aarch64-linux-gnu amd64 4:9.2.1-3.1 [1180 B] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libicu67 amd64 67.1-2 [8610 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.10+dfsg-5+b1 [710 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-2 [343 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-arm64 all 12.8 [6644 B] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-14 [513 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 13.1 [187 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.8.1-1 [25.2 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.8.1-1 [14.9 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-5 [151 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.64.3-1 [1341 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 13.1 [1012 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main arm64 libgcc-s1 arm64 10.1.0-3 [34.7 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main arm64 libcrypt1 arm64 1:4.4.16-1 [90.4 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main arm64 libc6 arm64 2.30-8 [2468 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main arm64 libasan5 arm64 9.3.0-13 [354 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main arm64 libatomic1 arm64 10.1.0-3 [9456 B] Get:97 http://debian.oregonstate.edu/debian unstable/main arm64 libbrotli1 arm64 1.0.7-6.1 [265 kB] Get:98 http://debian.oregonstate.edu/debian unstable/main arm64 libbz2-1.0 arm64 1.0.8-3 [46.4 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main arm64 linux-libc-dev arm64 5.6.14-1 [1094 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main arm64 libcrypt-dev arm64 1:4.4.16-1 [111 kB] Get:101 http://debian.oregonstate.edu/debian unstable/main arm64 libc6-dev arm64 2.30-8 [2281 kB] Get:102 http://debian.oregonstate.edu/debian unstable/main arm64 libcom-err2 arm64 1.45.6-1 [71.6 kB] Get:103 http://debian.oregonstate.edu/debian unstable/main arm64 libgmp10 arm64 2:6.2.0+dfsg-4 [230 kB] Get:104 http://debian.oregonstate.edu/debian unstable/main arm64 libnettle7 arm64 3.5.1+really3.5.1-2 [233 kB] Get:105 http://debian.oregonstate.edu/debian unstable/main arm64 libhogweed5 arm64 3.5.1+really3.5.1-2 [135 kB] Get:106 http://debian.oregonstate.edu/debian unstable/main arm64 libunistring2 arm64 0.9.10-4 [372 kB] Get:107 http://debian.oregonstate.edu/debian unstable/main arm64 libidn2-0 arm64 2.3.0-1 [84.8 kB] Get:108 http://debian.oregonstate.edu/debian unstable/main arm64 libffi7 arm64 3.3-4 [20.5 kB] Get:109 http://debian.oregonstate.edu/debian unstable/main arm64 libp11-kit0 arm64 0.23.20-1 [315 kB] Get:110 http://debian.oregonstate.edu/debian unstable/main arm64 libtasn1-6 arm64 4.16.0-2 [53.5 kB] Get:111 http://debian.oregonstate.edu/debian unstable/main arm64 libgnutls30 arm64 3.6.14-1 [1171 kB] Get:112 http://debian.oregonstate.edu/debian unstable/main arm64 libkrb5support0 arm64 1.17-10 [64.1 kB] Get:113 http://debian.oregonstate.edu/debian unstable/main arm64 libk5crypto3 arm64 1.17-10 [116 kB] Get:114 http://debian.oregonstate.edu/debian unstable/main arm64 libkeyutils1 arm64 1.6.1-2 [15.4 kB] Get:115 http://debian.oregonstate.edu/debian unstable/main arm64 libssl1.1 arm64 1.1.1g-1 [1379 kB] Get:116 http://debian.oregonstate.edu/debian unstable/main arm64 libkrb5-3 arm64 1.17-10 [349 kB] Get:117 http://debian.oregonstate.edu/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.17-10 [149 kB] Get:118 http://debian.oregonstate.edu/debian unstable/main arm64 libdb5.3 arm64 5.3.28+dfsg1-0.6 [622 kB] Get:119 http://debian.oregonstate.edu/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2 [69.2 kB] Get:120 http://debian.oregonstate.edu/debian unstable/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2 [105 kB] Get:121 http://debian.oregonstate.edu/debian unstable/main amd64 libldap-common all 2.4.50+dfsg-1 [92.9 kB] Get:122 http://debian.oregonstate.edu/debian unstable/main arm64 libldap-2.4-2 arm64 2.4.50+dfsg-1 [218 kB] Get:123 http://debian.oregonstate.edu/debian unstable/main arm64 libnghttp2-14 arm64 1.41.0-2 [68.8 kB] Get:124 http://debian.oregonstate.edu/debian unstable/main arm64 libpsl5 arm64 0.21.0-1.1 [55.1 kB] Get:125 http://debian.oregonstate.edu/debian unstable/main arm64 zlib1g arm64 1:1.2.11.dfsg-2 [87.9 kB] Get:126 http://debian.oregonstate.edu/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b1 [59.4 kB] Get:127 http://debian.oregonstate.edu/debian unstable/main arm64 libgpg-error0 arm64 1.38-1 [74.6 kB] Get:128 http://debian.oregonstate.edu/debian unstable/main arm64 libgcrypt20 arm64 1.8.5-5 [487 kB] Get:129 http://debian.oregonstate.edu/debian unstable/main arm64 libssh2-1 arm64 1.8.0-2.1 [135 kB] Get:130 http://debian.oregonstate.edu/debian unstable/main arm64 libcurl3-gnutls arm64 7.68.0-1 [299 kB] Get:131 http://debian.oregonstate.edu/debian unstable/main arm64 libdeflate0 arm64 1.6-1 [51.5 kB] Get:132 http://debian.oregonstate.edu/debian unstable/main arm64 libgomp1 arm64 10.1.0-3 [91.0 kB] Get:133 http://debian.oregonstate.edu/debian unstable/main arm64 libitm1 arm64 10.1.0-3 [23.8 kB] Get:134 http://debian.oregonstate.edu/debian unstable/main arm64 liblsan0 arm64 10.1.0-3 [126 kB] Get:135 http://debian.oregonstate.edu/debian unstable/main arm64 libtsan0 arm64 10.1.0-3 [293 kB] Get:136 http://debian.oregonstate.edu/debian unstable/main arm64 libstdc++6 arm64 10.1.0-3 [450 kB] Get:137 http://debian.oregonstate.edu/debian unstable/main arm64 libubsan1 arm64 10.1.0-3 [123 kB] Get:138 http://debian.oregonstate.edu/debian unstable/main arm64 libgcc-9-dev arm64 9.3.0-13 [887 kB] Get:139 http://debian.oregonstate.edu/debian unstable/main arm64 liblzma5 arm64 5.2.4-1+b1 [149 kB] Get:140 http://debian.oregonstate.edu/debian unstable/main arm64 libhts3 arm64 1.10.2-3 [337 kB] Get:141 http://debian.oregonstate.edu/debian unstable/main arm64 liblzma-dev arm64 5.2.4-1+b1 [209 kB] Get:142 http://debian.oregonstate.edu/debian unstable/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Get:143 http://debian.oregonstate.edu/debian unstable/main arm64 libhts-dev arm64 1.10.2-3 [4848 kB] Get:144 http://debian.oregonstate.edu/debian unstable/main arm64 libstdc++-9-dev arm64 9.3.0-13 [1659 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 103 MB in 2s (63.0 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 10322 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../002-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../003-groff-base_1.22.4-5_amd64.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../004-libpipeline1_1.5.2-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.2-2) ... Selecting previously unselected package man-db. Preparing to unpack .../005-man-db_2.9.2-1_amd64.deb ... Unpacking man-db (2.9.2-1) ... 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Selecting previously unselected package sensible-utils. Preparing to unpack .../012-sensible-utils_0.0.12+nmu1_all.deb ... Unpacking sensible-utils (0.0.12+nmu1) ... Selecting previously unselected package xxd. Preparing to unpack .../013-xxd_2%3a8.2.0716-3_amd64.deb ... Unpacking xxd (2:8.2.0716-3) ... Selecting previously unselected package vim-common. Preparing to unpack .../014-vim-common_2%3a8.2.0716-3_all.deb ... Unpacking vim-common (2:8.2.0716-3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../015-libmagic-mgc_1%3a5.38-5_amd64.deb ... Unpacking libmagic-mgc (1:5.38-5) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../016-libmagic1_1%3a5.38-5_amd64.deb ... Unpacking libmagic1:amd64 (1:5.38-5) ... Selecting previously unselected package file. Preparing to unpack .../017-file_1%3a5.38-5_amd64.deb ... Unpacking file (1:5.38-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../018-gettext-base_0.19.8.1-10_amd64.deb ... Unpacking gettext-base (0.19.8.1-10) ... Selecting previously unselected package ucf. Preparing to unpack .../019-ucf_3.0042_all.deb ... Moving old data out of the way Unpacking ucf (3.0042) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../020-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../021-m4_1.4.18-4_amd64.deb ... Unpacking m4 (1.4.18-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../022-autoconf_2.69-11.1_all.deb ... Unpacking autoconf (2.69-11.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../023-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../024-automake_1%3a1.16.2-1_all.deb ... Unpacking automake (1:1.16.2-1) ... Selecting previously unselected package autopoint. Preparing to unpack .../025-autopoint_0.19.8.1-10_all.deb ... Unpacking autopoint (0.19.8.1-10) ... Selecting previously unselected package binutils-aarch64-linux-gnu. Preparing to unpack .../026-binutils-aarch64-linux-gnu_2.34-8_amd64.deb ... Unpacking binutils-aarch64-linux-gnu (2.34-8) ... Selecting previously unselected package libcrypt-dev:amd64. Preparing to unpack .../027-libcrypt-dev_1%3a4.4.16-1_amd64.deb ... Unpacking libcrypt-dev:amd64 (1:4.4.16-1) ... Selecting previously unselected package libc6-dev:amd64. Preparing to unpack .../028-libc6-dev_2.30-8_amd64.deb ... Unpacking libc6-dev:amd64 (2.30-8) ... Selecting previously unselected package libstdc++-9-dev:amd64. Preparing to unpack .../029-libstdc++-9-dev_9.3.0-13_amd64.deb ... Unpacking libstdc++-9-dev:amd64 (9.3.0-13) ... Selecting previously unselected package g++-9. Preparing to unpack .../030-g++-9_9.3.0-13_amd64.deb ... Unpacking g++-9 (9.3.0-13) ... Selecting previously unselected package g++. Preparing to unpack .../031-g++_4%3a9.2.1-3.1_amd64.deb ... Unpacking g++ (4:9.2.1-3.1) ... Selecting previously unselected package libdpkg-perl. Preparing to unpack .../032-libdpkg-perl_1.19.7_all.deb ... Unpacking libdpkg-perl (1.19.7) ... Selecting previously unselected package dpkg-dev. Preparing to unpack .../033-dpkg-dev_1.19.7_all.deb ... Unpacking dpkg-dev (1.19.7) ... Selecting previously unselected package build-essential. Preparing to unpack .../034-build-essential_12.8_amd64.deb ... Unpacking build-essential (12.8) ... Selecting previously unselected package gcc-9-aarch64-linux-gnu-base:amd64. Preparing to unpack .../035-gcc-9-aarch64-linux-gnu-base_9.3.0-13cross1_amd64.deb ... Unpacking gcc-9-aarch64-linux-gnu-base:amd64 (9.3.0-13cross1) ... Selecting previously unselected package cpp-9-aarch64-linux-gnu. Preparing to unpack .../036-cpp-9-aarch64-linux-gnu_9.3.0-13cross1_amd64.deb ... Unpacking cpp-9-aarch64-linux-gnu (9.3.0-13cross1) ... Selecting previously unselected package cpp-aarch64-linux-gnu. Preparing to unpack .../037-cpp-aarch64-linux-gnu_4%3a9.2.1-3.1_amd64.deb ... Unpacking cpp-aarch64-linux-gnu (4:9.2.1-3.1) ... Selecting previously unselected package cross-config. Preparing to unpack .../038-cross-config_2.6.15-3_all.deb ... Unpacking cross-config (2.6.15-3) ... Selecting previously unselected package gcc-9-cross-base. Preparing to unpack .../039-gcc-9-cross-base_9.3.0-13cross1_all.deb ... Unpacking gcc-9-cross-base (9.3.0-13cross1) ... Selecting previously unselected package gcc-10-cross-base. Preparing to unpack .../040-gcc-10-cross-base_10.1.0-3cross1_all.deb ... Unpacking gcc-10-cross-base (10.1.0-3cross1) ... Selecting previously unselected package libc6-arm64-cross. Preparing to unpack .../041-libc6-arm64-cross_2.30-2cross1_all.deb ... Unpacking libc6-arm64-cross (2.30-2cross1) ... Selecting previously unselected package libgcc-s1-arm64-cross. 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Preparing to unpack .../047-liblsan0-arm64-cross_10.1.0-3cross1_all.deb ... Unpacking liblsan0-arm64-cross (10.1.0-3cross1) ... Selecting previously unselected package libtsan0-arm64-cross. Preparing to unpack .../048-libtsan0-arm64-cross_10.1.0-3cross1_all.deb ... Unpacking libtsan0-arm64-cross (10.1.0-3cross1) ... Selecting previously unselected package libstdc++6-arm64-cross. Preparing to unpack .../049-libstdc++6-arm64-cross_10.1.0-3cross1_all.deb ... Unpacking libstdc++6-arm64-cross (10.1.0-3cross1) ... Selecting previously unselected package libubsan1-arm64-cross. Preparing to unpack .../050-libubsan1-arm64-cross_10.1.0-3cross1_all.deb ... Unpacking libubsan1-arm64-cross (10.1.0-3cross1) ... Selecting previously unselected package libgcc-9-dev-arm64-cross. Preparing to unpack .../051-libgcc-9-dev-arm64-cross_9.3.0-13cross1_all.deb ... Unpacking libgcc-9-dev-arm64-cross (9.3.0-13cross1) ... Selecting previously unselected package gcc-9-aarch64-linux-gnu. Preparing to unpack .../052-gcc-9-aarch64-linux-gnu_9.3.0-13cross1_amd64.deb ... Unpacking gcc-9-aarch64-linux-gnu (9.3.0-13cross1) ... Selecting previously unselected package gcc-aarch64-linux-gnu. Preparing to unpack .../053-gcc-aarch64-linux-gnu_4%3a9.2.1-3.1_amd64.deb ... Unpacking gcc-aarch64-linux-gnu (4:9.2.1-3.1) ... Selecting previously unselected package linux-libc-dev-arm64-cross. Preparing to unpack .../054-linux-libc-dev-arm64-cross_5.4.19-1cross1_all.deb ... Unpacking linux-libc-dev-arm64-cross (5.4.19-1cross1) ... Selecting previously unselected package libc6-dev-arm64-cross. Preparing to unpack .../055-libc6-dev-arm64-cross_2.30-2cross1_all.deb ... Unpacking libc6-dev-arm64-cross (2.30-2cross1) ... Selecting previously unselected package libstdc++-9-dev-arm64-cross. Preparing to unpack .../056-libstdc++-9-dev-arm64-cross_9.3.0-13cross1_all.deb ... Unpacking libstdc++-9-dev-arm64-cross (9.3.0-13cross1) ... Selecting previously unselected package g++-9-aarch64-linux-gnu. Preparing to unpack .../057-g++-9-aarch64-linux-gnu_9.3.0-13cross1_amd64.deb ... Unpacking g++-9-aarch64-linux-gnu (9.3.0-13cross1) ... Selecting previously unselected package g++-aarch64-linux-gnu. Preparing to unpack .../058-g++-aarch64-linux-gnu_4%3a9.2.1-3.1_amd64.deb ... Unpacking g++-aarch64-linux-gnu (4:9.2.1-3.1) ... Selecting previously unselected package libconfig-inifiles-perl. Preparing to unpack .../059-libconfig-inifiles-perl_3.000003-1_all.deb ... Unpacking libconfig-inifiles-perl (3.000003-1) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../060-libio-string-perl_1.08-3_all.deb ... Unpacking libio-string-perl (1.08-3) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../061-libicu67_67.1-2_amd64.deb ... Unpacking libicu67:amd64 (67.1-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../062-libxml2_2.9.10+dfsg-5+b1_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-5+b1) ... Selecting previously unselected package libxml-namespacesupport-perl. Preparing to unpack .../063-libxml-namespacesupport-perl_1.12-1_all.deb ... Unpacking libxml-namespacesupport-perl (1.12-1) ... Selecting previously unselected package libxml-sax-base-perl. Preparing to unpack .../064-libxml-sax-base-perl_1.09-1_all.deb ... Unpacking libxml-sax-base-perl (1.09-1) ... Selecting previously unselected package libxml-sax-perl. Preparing to unpack .../065-libxml-sax-perl_1.02+dfsg-1_all.deb ... Unpacking libxml-sax-perl (1.02+dfsg-1) ... Selecting previously unselected package libxml-libxml-perl. Preparing to unpack .../066-libxml-libxml-perl_2.0134+dfsg-2_amd64.deb ... Unpacking libxml-libxml-perl (2.0134+dfsg-2) ... Selecting previously unselected package libxml-simple-perl. Preparing to unpack .../067-libxml-simple-perl_2.25-1_all.deb ... Unpacking libxml-simple-perl (2.25-1) ... Selecting previously unselected package libyaml-perl. Preparing to unpack .../068-libyaml-perl_1.30-1_all.deb ... Unpacking libyaml-perl (1.30-1) ... Selecting previously unselected package libconfig-auto-perl. Preparing to unpack .../069-libconfig-auto-perl_0.44-1_all.deb ... Unpacking libconfig-auto-perl (0.44-1) ... Selecting previously unselected package libfile-which-perl. Preparing to unpack .../070-libfile-which-perl_1.23-1_all.deb ... Unpacking libfile-which-perl (1.23-1) ... Selecting previously unselected package libfile-homedir-perl. Preparing to unpack .../071-libfile-homedir-perl_1.004-1_all.deb ... Unpacking libfile-homedir-perl (1.004-1) ... Selecting previously unselected package libdebian-dpkgcross-perl. Preparing to unpack .../072-libdebian-dpkgcross-perl_2.6.15-3_all.deb ... Unpacking libdebian-dpkgcross-perl (2.6.15-3) ... Selecting previously unselected package dpkg-cross. Preparing to unpack .../073-dpkg-cross_2.6.15-3_all.deb ... Unpacking dpkg-cross (2.6.15-3) ... Selecting previously unselected package crossbuild-essential-arm64. Preparing to unpack .../074-crossbuild-essential-arm64_12.8_all.deb ... Unpacking crossbuild-essential-arm64 (12.8) ... Selecting previously unselected package libtool. Preparing to unpack .../075-libtool_2.4.6-14_all.deb ... Unpacking libtool (2.4.6-14) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../076-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../077-libdebhelper-perl_13.1_all.deb ... Unpacking libdebhelper-perl (13.1) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../078-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../079-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... 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Setting up libpipeline1:amd64 (1.5.2-2) ... Setting up perl-modules-5.30 (5.30.3-4) ... Setting up libicu67:amd64 (67.1-2) ... Setting up libmagic-mgc (1:5.38-5) ... Setting up libglib2.0-0:amd64 (2.64.3-1) ... No schema files found: doing nothing. Setting up gcc-9-aarch64-linux-gnu-base:amd64 (9.3.0-13cross1) ... Setting up libmagic1:amd64 (1:5.38-5) ... Setting up linux-libc-dev:arm64 (5.6.14-1) ... Setting up gettext-base (0.19.8.1-10) ... Setting up binutils-aarch64-linux-gnu (2.34-8) ... Setting up cpp-9-aarch64-linux-gnu (9.3.0-13cross1) ... Setting up file (1:5.38-5) ... Setting up libldap-common (2.4.50+dfsg-1) ... Setting up xxd (2:8.2.0716-3) ... Setting up gcc-10-base:arm64 (10.1.0-3) ... Setting up cpp-aarch64-linux-gnu (4:9.2.1-3.1) ... Setting up autotools-dev (20180224.1) ... Setting up cross-config (2.6.15-3) ... Setting up vim-common (2:8.2.0716-3) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up libc6-arm64-cross (2.30-2cross1) ... Setting up autopoint (0.19.8.1-10) ... Setting up gcc-9-cross-base (9.3.0-13cross1) ... Setting up gcc-10-cross-base (10.1.0-3cross1) ... Setting up linux-libc-dev-arm64-cross (5.4.19-1cross1) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up libcrypt-dev:amd64 (1:4.4.16-1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libperl5.30:amd64 (5.30.3-4) ... Setting up libc6-dev:amd64 (2.30-8) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.10+dfsg-5+b1) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up gcc-9-base:arm64 (9.3.0-13) ... Setting up libgcc-s1-arm64-cross (10.1.0-3cross1) ... Setting up libatomic1-arm64-cross (10.1.0-3cross1) ... Setting up liblsan0-arm64-cross (10.1.0-3cross1) ... Setting up libgomp1-arm64-cross (10.1.0-3cross1) ... Setting up libstdc++-9-dev:amd64 (9.3.0-13) ... Setting up libtool (2.4.6-14) ... Setting up libtsan0-arm64-cross (10.1.0-3cross1) ... Setting up m4 (1.4.18-4) ... Setting up libc6-dev-arm64-cross (2.30-2cross1) ... Setting up libasan5-arm64-cross (9.3.0-13cross1) ... Setting up libstdc++6-arm64-cross (10.1.0-3cross1) ... Setting up perl (5.30.3-4) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:amd64 (0.6.13-1) ... Setting up libitm1-arm64-cross (10.1.0-3cross1) ... Setting up ucf (3.0042) ... Setting up g++-9 (9.3.0-13) ... Setting up libdpkg-perl (1.19.7) ... Setting up autoconf (2.69-11.1) ... Setting up g++ (4:9.2.1-3.1) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up libsub-override-perl (0.09-2) ... Setting up automake (1:1.16.2-1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-which-perl (1.23-1) ... Setting up gettext (0.19.8.1-10) ... Setting up libubsan1-arm64-cross (10.1.0-3cross1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.1) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up libgcc-9-dev-arm64-cross (9.3.0-13cross1) ... Setting up man-db (2.9.2-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libyaml-perl (1.30-1) ... Setting up dpkg-dev (1.19.7) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up gcc-9-aarch64-linux-gnu (9.3.0-13cross1) ... Setting up build-essential (12.8) ... Setting up libstdc++-9-dev-arm64-cross (9.3.0-13cross1) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libfile-stripnondeterminism-perl (1.8.1-1) ... Setting up gcc-aarch64-linux-gnu (4:9.2.1-3.1) ... Setting up po-debconf (1.0.21) ... Setting up libxml-sax-perl (1.02+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up g++-9-aarch64-linux-gnu (9.3.0-13cross1) ... Setting up libxml-libxml-perl (2.0134+dfsg-2) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up dh-strip-nondeterminism (1.8.1-1) ... Setting up g++-aarch64-linux-gnu (4:9.2.1-3.1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3) ... Setting up dpkg-cross (2.6.15-3) ... Setting up crossbuild-essential-arm64 (12.8) ... Setting up libcrypt1:arm64 (1:4.4.16-1) ... Setting up libgcc-s1:arm64 (10.1.0-3) ... Setting up dh-autoreconf (19) ... Setting up libc6:arm64 (2.30-8) ... Setting up libnettle7:arm64 (3.5.1+really3.5.1-2) ... Setting up libcrypt-dev:arm64 (1:4.4.16-1) ... Setting up libtasn1-6:arm64 (4.16.0-2) ... Setting up libc6-dev:arm64 (2.30-8) ... Setting up libbz2-1.0:arm64 (1.0.8-3) ... Setting up libdb5.3:arm64 (5.3.28+dfsg1-0.6) ... Setting up libstdc++6:arm64 (10.1.0-3) ... Setting up liblsan0:arm64 (10.1.0-3) ... Setting up libitm1:arm64 (10.1.0-3) ... Setting up libtsan0:arm64 (10.1.0-3) ... Setting up libkeyutils1:arm64 (1.6.1-2) ... Setting up liblzma5:arm64 (5.2.4-1+b1) ... Setting up libgpg-error0:arm64 (1.38-1) ... Setting up libssl1.1:arm64 (1.1.1g-1) ... Setting up libbrotli1:arm64 (1.0.7-6.1) ... Setting up libffi7:arm64 (3.3-4) ... Setting up libnghttp2-14:arm64 (1.41.0-2) ... Setting up libunistring2:arm64 (0.9.10-4) ... Setting up libdeflate0:arm64 (1.6-1) ... Setting up libgcrypt20:arm64 (1.8.5-5) ... Setting up debhelper (13.1) ... Setting up zlib1g:arm64 (1:1.2.11.dfsg-2) ... Setting up libidn2-0:arm64 (2.3.0-1) ... Setting up libcom-err2:arm64 (1.45.6-1) ... Setting up libgomp1:arm64 (10.1.0-3) ... Setting up libkrb5support0:arm64 (1.17-10) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-2) ... Setting up libasan5:arm64 (9.3.0-13) ... Setting up libgmp10:arm64 (2:6.2.0+dfsg-4) ... Setting up libp11-kit0:arm64 (0.23.20-1) ... Setting up libatomic1:arm64 (10.1.0-3) ... Setting up libk5crypto3:arm64 (1.17-10) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2) ... Setting up liblzma-dev:arm64 (5.2.4-1+b1) ... Setting up libubsan1:arm64 (10.1.0-3) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2) ... Setting up libssh2-1:arm64 (1.8.0-2.1) ... Setting up libkrb5-3:arm64 (1.17-10) ... Setting up libpsl5:arm64 (0.21.0-1.1) ... Setting up libhogweed5:arm64 (3.5.1+really3.5.1-2) ... Setting up libgcc-9-dev:arm64 (9.3.0-13) ... Setting up libgnutls30:arm64 (3.6.14-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b1) ... Setting up libgssapi-krb5-2:arm64 (1.17-10) ... Setting up libstdc++-9-dev:arm64 (9.3.0-13) ... Setting up libldap-2.4-2:arm64 (2.4.50+dfsg-1) ... Setting up libcurl3-gnutls:arm64 (7.68.0-1) ... Setting up libhts3:arm64 (1.10.2-3) ... Setting up libhts-dev:arm64 (1.10.2-3) ... Setting up sbuild-build-depends-main-dummy:arm64 (0.invalid.0) ... Processing triggers for libc-bin (2.30-8) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in amd64 arm64 ppc64el mips64el) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-9-amd64 #1 SMP Debian 4.19.118-2 (2020-04-29) amd64 (x86_64) Toolchain package versions: binutils_2.34-8 dpkg-dev_1.19.7 g++-9_9.3.0-13 gcc-9_9.3.0-13 libc6-dev_2.30-8 libstdc++-9-dev_9.3.0-13 libstdc++-9-dev-arm64-cross_9.3.0-13cross1 libstdc++6_10.1.0-3 libstdc++6-arm64-cross_10.1.0-3cross1 linux-libc-dev_5.6.14-1 Package versions: adduser_3.118 apt_2.1.6 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-8 binutils-aarch64-linux-gnu_2.34-8 binutils-common_2.34-8 binutils-x86-64-linux-gnu_2.34-8 bsdmainutils_11.1.2+b1 bsdutils_1:2.35.2-2 build-essential_12.8 bzip2_1.0.8-3 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-8_8.4.0-4 cpp-9_9.3.0-13 cpp-9-aarch64-linux-gnu_9.3.0-13cross1 cpp-aarch64-linux-gnu_4:9.2.1-3.1 cross-config_2.6.15-3 crossbuild-essential-arm64_12.8 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.1 debian-archive-keyring_2019.1 debianutils_4.11 dh-autoreconf_19 dh-strip-nondeterminism_1.8.1-1 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.35.2-2 file_1:5.38-5 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-9_9.3.0-13 g++-9-aarch64-linux-gnu_9.3.0-13cross1 g++-aarch64-linux-gnu_4:9.2.1-3.1 gcc_4:9.2.1-3.1 gcc-10-base_10.1.0-3 gcc-10-cross-base_10.1.0-3cross1 gcc-8-base_8.4.0-4 gcc-9_9.3.0-13 gcc-9-aarch64-linux-gnu_9.3.0-13cross1 gcc-9-aarch64-linux-gnu-base_9.3.0-13cross1 gcc-9-base_9.3.0-13 gcc-9-cross-base_9.3.0-13cross1 gcc-aarch64-linux-gnu_4:9.2.1-3.1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapt-pkg5.0_1.8.4 libapt-pkg6.0_2.1.6 libarchive-zip-perl_1.68-1 libasan5_9.3.0-13 libasan5-arm64-cross_9.3.0-13cross1 libatomic1_10.1.0-3 libatomic1-arm64-cross_10.1.0-3cross1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3+b1 libbinutils_2.34-8 libblkid1_2.35.2-2 libbrotli1_1.0.7-6.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-3 libc-bin_2.30-8 libc-dev-bin_2.30-8 libc6_2.30-8 libc6-arm64-cross_2.30-2cross1 libc6-dev_2.30-8 libc6-dev-arm64-cross_2.30-2cross1 libcap-ng0_0.7.9-2.2 libcc1-0_10.1.0-3 libcom-err2_1.45.6-1 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000003-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-8 libctf0_2.34-8 libcurl3-gnutls_7.68.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.252 libdebhelper-perl_13.1 libdebian-dpkgcross-perl_2.6.15-3 libdeflate0_1.6-1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.35.2-2 libffi6_3.2.1-9 libffi7_3.3-4 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.8.1-1 libfile-which-perl_1.23-1 libgcc-9-dev_9.3.0-13 libgcc-9-dev-arm64-cross_9.3.0-13cross1 libgcc-s1_10.1.0-3 libgcc-s1-arm64-cross_10.1.0-3cross1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.3-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.14-1 libgomp1_10.1.0-3 libgomp1-arm64-cross_10.1.0-3cross1 libgpg-error0_1.38-1 libgssapi-krb5-2_1.17-10 libhogweed4_3.5.1+really3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.10.2-3 libhts3_1.10.2-3 libicu67_67.1-2 libidn2-0_2.3.0-1 libio-string-perl_1.08-3 libisl19_0.20-2 libisl22_0.22.1-1 libitm1_10.1.0-3 libitm1-arm64-cross_10.1.0-3cross1 libk5crypto3_1.17-10 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10 libkrb5support0_1.17-10 libldap-2.4-2_2.4.50+dfsg-1 libldap-common_2.4.50+dfsg-1 liblocale-gettext-perl_1.07-4 liblsan0_10.1.0-3 liblsan0-arm64-cross_10.1.0-3cross1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1+b1 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.2-2 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.4.0-4 libncursesw6_6.2-1 libnettle6_3.5.1+really3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.41.0-2 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12+b1 libperl5.28_5.28.1-6 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2 libpsl5_0.21.0-1.1 libquadmath0_10.1.0-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+b1 libselinux1_3.0-1+b3 libsemanage-common_3.0-1 libsemanage1_3.0-1+b3 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.35.2-2 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1g-1 libstdc++-9-dev_9.3.0-13 libstdc++-9-dev-arm64-cross_9.3.0-13cross1 libstdc++6_10.1.0-3 libstdc++6-arm64-cross_10.1.0-3cross1 libsub-override-perl_0.09-2 libsystemd0_245.6-1 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libtsan0_10.1.0-3 libtsan0-arm64-cross_10.1.0-3cross1 libubsan1_10.1.0-3 libubsan1-arm64-cross_10.1.0-3cross1 libuchardet0_0.0.7-1 libudev1_245.6-1 libunistring2_0.9.10-4 libuuid1_2.35.2-2 libxml-libxml-perl_2.0134+dfsg-2 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.02+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.10+dfsg-5+b1 libyaml-perl_1.30-1 libzstd1_1.4.5+dfsg-2 linux-libc-dev_5.6.14-1 linux-libc-dev-arm64-cross_5.4.19-1cross1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0 m4_1.4.18-4 make_4.3-3 man-db_2.9.2-1 mawk_1.3.4.20200120-2 mount_2.35.2-2 ncurses-base_6.2-1 ncurses-bin_6.2-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.28_5.28.1-6 perl-modules-5.30_5.30.3-4 po-debconf_1.0.21 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 ucf_3.0042 util-linux_2.35.2-2 vim-common_2:8.2.0716-3 xxd_2:8.2.0716-3 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: rna-star Binary: rna-star Architecture: amd64 arm64 ppc64el mips64el Version: 2.7.4a+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Sascha Steinbiss Homepage: https://github.com/alexdobin/STAR/ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/rna-star Vcs-Git: https://salsa.debian.org/med-team/rna-star.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libhts-dev, vim-common, xxd, zlib1g-dev Package-List: rna-star deb science optional arch=amd64,arm64,ppc64el,mips64el Checksums-Sha1: d900558312c0d6d119341ddab01842faa90c265e 413556 rna-star_2.7.4a+dfsg.orig.tar.xz b93cce1b81398de62fd4100c230245b9533db93d 375352 rna-star_2.7.4a+dfsg-1.debian.tar.xz Checksums-Sha256: 299f775649fe45c876a905f7d4f5ca321a83b7fac15b2f0688aacf6741b87a38 413556 rna-star_2.7.4a+dfsg.orig.tar.xz 1cade98271e54035f64d694b0eaaf2c1e82a73ca1e4d2256fb48a4f98269a1cb 375352 rna-star_2.7.4a+dfsg-1.debian.tar.xz Files: c8be1ca4fc91473ec0bb39bfcb49f6e0 413556 rna-star_2.7.4a+dfsg.orig.tar.xz e272129e2c1488568af7860983a17010 375352 rna-star_2.7.4a+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJHBAEBCAAxFiEEhMGXeonn7+0+XKYuL9i+2sAg7tEFAl7b4csTHG1vZWxsZXJA ZGViaWFuLm9yZwAKCRAv2L7awCDu0UOcEAC9KQu99hfxGid/9XQrelsNg8pj/X6Z 5R2nhwSzfXe2+gFe1bM086ZbYiDyYyXfAzYgXMpaiqYDI58AokIK2Ne1ne453ZT4 qJndK8yIC35rK1itrvKjwanGJ8RCQFfHorMnnJIfEA+Vwb+9qTf1SkpARzj8ixhD 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extracting rna-star in /<> dpkg-source: info: unpacking rna-star_2.7.4a+dfsg.orig.tar.xz dpkg-source: info: unpacking rna-star_2.7.4a+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying donotuse_own_htslib.patch dpkg-source: info: applying mips_shm_noreserve.patch dpkg-source: info: applying reproducible.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.arm64 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-12f7141f-0b84-471a-b16c-5a5db9e69359 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aarm64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package rna-star dpkg-buildpackage: info: source version 2.7.4a+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steffen Moeller dpkg-architecture: warning: specified GNU system type aarch64-linux-gnu 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 arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' cd source && /usr/bin/make clean make[2]: Entering directory '/<>/source' rm -f *.o STAR STARstatic STARlong Depend.list make[2]: Leaving directory '/<>/source' rm -f source/parametersDefault.xxd make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build --sourcedirectory=source -- CCFLAGS_common_add="-flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CCFLAGS="-flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" LDFLAGS_add="-Wl,-z,relro -Wl,-z,now" cd source && make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=aarch64-linux-gnu-pkg-config CXX=aarch64-linux-gnu-g\+\+ CC=aarch64-linux-gnu-gcc "CCFLAGS_common_add=-flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "CCFLAGS=-flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" "LDFLAGS_add=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/<>/source' xxd -i parametersDefault > parametersDefault.xxd echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ErrorWarning.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_insertSequences.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readSAMheader.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countVelocyto.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp Stats.cpp SuffixArrayFuns.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_generateCigarP.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_quantAlign.cpp Variation.cpp alignSmithWaterman.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp loadGTF.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp bam_cat.c BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ErrorWarning.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_insertSequences.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readSAMheader.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countVelocyto.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp Stats.cpp SuffixArrayFuns.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_generateCigarP.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_quantAlign.cpp Variation.cpp alignSmithWaterman.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp loadGTF.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp bam_cat.c 'rm' -f ./Depend.list aarch64-linux-gnu-g++ -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ErrorWarning.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_insertSequences.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readSAMheader.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countVelocyto.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp Stats.cpp SuffixArrayFuns.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_generateCigarP.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_quantAlign.cpp Variation.cpp alignSmithWaterman.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp loadGTF.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp bam_cat.c parametersDefault.xxd >> Depend.list aarch64-linux-gnu-g++: warning: parametersDefault.xxd: linker input file unused because linking not done aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_sumThreads.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_countVelocyto.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_countCBgeneUMI.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_classifyAlign.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_cellFiltering.cpp SoloFeature_cellFiltering.cpp: In member function ‘void SoloFeature::cellFiltering()’: SoloFeature_cellFiltering.cpp:27:50: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct SoloFeature::’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 27 | memset(&filteredCells,0,sizeof(filteredCells)); | ^ In file included from SoloFeature_cellFiltering.cpp:1: SoloFeature.h:48:12: note: ‘struct SoloFeature::’ declared here 48 | struct { | ^ aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_statsOutput.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' bamSortByCoordinate.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloBarcode.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ParametersSolo.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloRead.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloRead_record.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadBarcode.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadBarcode_getCBandUMI.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloBarcode_extractBarcode.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadFeature.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadFeature_record.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadFeature_inputRecords.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Solo.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_collapseUMI.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_outputResults.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_processRecords.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_addBAMtags.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputAlignments.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' STAR.cpp STAR.cpp: In function ‘int main(int, char**)’: STAR.cpp:344:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] 344 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:348:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] 348 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SharedMemory.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' PackedArray.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SuffixArrayFuns.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Parameters.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' InOutStreams.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SequenceFuns.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Stats.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_alignScore.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_generateCigarP.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Chain.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_variationAdjust.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Variation.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_waspMap.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_storeAligns.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_stitchPieces.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_multMapSelect.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_mapOneRead.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' readLoad.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlignChunk.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlignChunk_processChunks.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlignChunk_mapChunk.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' OutSJ.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' outputSJ.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' blocksOverlap.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ThreadControl.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sysRemoveDir.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_maxMappableLength2strands.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' binarySearch2.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputTranscriptSAM.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputTranscriptSJ.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputTranscriptCIGARp.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_createExtendWindowsWithAlign.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_assignAlignToWindow.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_oneRead.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_stitchWindowSeeds.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_peOverlapMergeMap.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_mappedFilter.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ParametersChimeric_initialize.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetection.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetectionOld.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetectionOldOutput.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericDetection.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericDetection_chimericDetectionMult.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetectionPEmerged.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericAlign_chimericJunctionOutput.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericAlign_chimericStitching.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' stitchWindowAligns.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' extendAlign.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' stitchAlignToTranscript.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' alignSmithWaterman.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome_genomeGenerate.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeParametersWrite.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeScanFastaFiles.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeSAindex.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome_insertSequences.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' insertSeqSA.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' funCompareUintAndSuffixes.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' funCompareUintAndSuffixesMemcmp.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' TimeFunctions.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ErrorWarning.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' loadGTF.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' streamFuns.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' stringSubstituteAll.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_quantAlign.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_geneFullAlignOverlap.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_quantTranscriptome.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Quantifications.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_geneCountsAddAlign.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbLoadFromFiles.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbLoadFromStream.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbPrepare.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbBuildIndex.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbInsertJunctions.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' mapThreadsSpawn.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Parameters_readSAMheader.cpp Parameters_readSAMheader.cpp: In member function ‘void Parameters::readSAMheader(std::string, std::vector >)’: Parameters_readSAMheader.cpp:26:15: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 26 | system(com1.c_str()); | ~~~~~~^~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' bam_cat.c bam_cat.c: In function ‘int bam_cat(int, char* const*, const bam_hdr_t*, const char*)’: bam_cat.c:80:25: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result] 80 | if (h) bam_hdr_write(fp, h); | ~~~~~~~~~~~~~^~~~~~~ bam_cat.c:96:44: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result] 96 | if (h == 0 && i == 0) bam_hdr_write(fp, old); | ~~~~~~~~~~~~~^~~~~~~~~ bam_cat.c:99:23: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] 99 | bgzf_write(fp, (void*)((char*)in->uncompressed_block + in->block_offset), in->block_length - in->block_offset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_cat.c:100:23: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] 100 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ bam_cat.c:111:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] 111 | bgzf_raw_write(fp, ebuf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bam_cat.c:115:40: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] 115 | if(j!=0) bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:118:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] 118 | bgzf_raw_write(fp, buf, len); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ bam_cat.c:131:31: warning: ignoring return value of ‘ssize_t bgzf_raw_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] 131 | bgzf_raw_write(fp, ebuf, es); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' serviceFuns.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMoutput.cpp BAMoutput.cpp: In member function ‘void BAMoutput::unsortedOneAlign(char*, long long unsigned int, long long unsigned int)’: BAMoutput.cpp:59:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] 59 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMoutput.cpp: In member function ‘void BAMoutput::unsortedFlush()’: BAMoutput.cpp:72:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] 72 | bgzf_write(bgzfBAM,bamArray,binBytes1); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMfunctions.cpp BAMfunctions.cpp: In function ‘std::string bam_cigarString(bam1_t*)’: BAMfunctions.cpp:12:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 12 | for (int i = 0; i < c->n_cigar; ++i) { | ~~^~~~~~~~~~~~ BAMfunctions.cpp: In function ‘int bam_read1_fromArray(char*, bam1_t*)’: BAMfunctions.cpp:59:16: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 59 | if (b->m_data < b->l_data) { | ~~~~~~~~~~^~~~~~~~~~~ BAMfunctions.cpp: In function ‘void outBAMwriteHeader(BGZF*, const string&, const std::vector >&, const std::vector&)’: BAMfunctions.cpp:76:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] 76 | bgzf_write(fp,"BAM\001",4); | ~~~~~~~~~~^~~~~~~~~~~~~~~~ BAMfunctions.cpp:78:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] 78 | bgzf_write(fp,(char*) &hlen,sizeof(hlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:79:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] 79 | bgzf_write(fp,samh.c_str(),hlen); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:81:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] 81 | bgzf_write(fp,(char*) &nchr,sizeof(nchr)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:85:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] 85 | bgzf_write(fp,(char*) &rlen,sizeof(rlen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:86:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] 86 | bgzf_write(fp,chrn.at(ii).data(),rlen); //this includes \0 at the end of the string | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:87:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] 87 | bgzf_write(fp,(char*) &slen,sizeof(slen)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMfunctions.cpp:89:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] 89 | bgzf_flush(fp); | ~~~~~~~~~~^~~~ aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_alignBAM.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMbinSortByCoordinate.cpp BAMbinSortByCoordinate.cpp: In function ‘void BAMbinSortByCoordinate(unsigned int, long long unsigned int, long long unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)’: BAMbinSortByCoordinate.cpp:73:19: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] 73 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp:76:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] 76 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' signalFromBAM.cpp aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' bamRemoveDuplicates.cpp bamRemoveDuplicates.cpp: In function ‘void bamRemoveDuplicates(std::string, std::string, Parameters&)’: bamRemoveDuplicates.cpp:125:18: warning: ignoring return value of ‘int bam_hdr_write(BGZF*, const sam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result] 125 | bam_hdr_write(bgzfOut, bamHeader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:152:27: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] 152 | bgzf_write(bgzfOut,bamRaw,bamS); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:248:15: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] 248 | bgzf_write(bgzfOut,bamRaw,bamLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bamRemoveDuplicates.cpp:249:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] 249 | bgzf_flush(bgzfOut); | ~~~~~~~~~~^~~~~~~~~ aarch64-linux-gnu-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMbinSortUnmapped.cpp BAMbinSortUnmapped.cpp: In function ‘void BAMbinSortUnmapped(unsigned int, long long unsigned int, std::string, Parameters&, Genome&, Solo&)’: BAMbinSortUnmapped.cpp:62:23: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] 62 | bgzf_write(bgzfBin, bam0, size0); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BAMbinSortUnmapped.cpp:80:15: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] 80 | bgzf_flush(bgzfBin); | ~~~~~~~~~~^~~~~~~~~ aarch64-linux-gnu-g++ -o STAR -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_collapseUMI.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o InOutStreams.o SequenceFuns.o Genome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericStitching.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o alignSmithWaterman.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o loadGTF.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -Bstatic -lhts -Bdynamic -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now Parameters_openReadsFiles.cpp: In member function ‘void Parameters::openReadsFiles()’: Parameters_openReadsFiles.cpp:72:23: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 72 | system(("ls -lL " + rfName + " > "+ outFileTmp+"/readFilesIn.info 2>&1").c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Parameters_openReadsFiles.cpp: In member function ‘openReadsFiles’: Parameters_openReadsFiles.cpp:33:20: warning: variable ‘imate’ might be clobbered by ‘longjmp’ or ‘vfork’ [-Wclobbered] 33 | for (uint imate=0;imate>/source' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress --exclude=.pdf make[1]: Leaving directory '/<>' dh_fixperms -a dh_missing -a dh_dwz -a -a dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'rna-star' in '../rna-star_2.7.4a+dfsg-1_arm64.deb'. dpkg-deb: building package 'rna-star-dbgsym' in '../rna-star-dbgsym_2.7.4a+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../rna-star_2.7.4a+dfsg-1_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2020-06-09T22:13:46Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ rna-star_2.7.4a+dfsg-1_arm64.changes: ------------------------------------- Format: 1.8 Date: Sat, 06 Jun 2020 20:31:10 +0200 Source: rna-star Binary: rna-star rna-star-dbgsym Built-For-Profiles: cross nocheck Architecture: arm64 Version: 2.7.4a+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Steffen Moeller Description: rna-star - ultrafast universal RNA-seq aligner Changes: rna-star (2.7.4a+dfsg-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. 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+------------------------------------------------------------------------------+ Format: 1.0 Source: rna-star Binary: rna-star Architecture: arm64 Version: 2.7.4a+dfsg-1 Checksums-Md5: 936d3eaaff7e9831d1f9c47406b64d41 4423364 rna-star-dbgsym_2.7.4a+dfsg-1_arm64.deb 0c82da847b4c70fb0b03c00aadb22283 480944 rna-star_2.7.4a+dfsg-1_arm64.deb Checksums-Sha1: 5364e39bd0a3aae78ad839dd8a1be3bb6b29f404 4423364 rna-star-dbgsym_2.7.4a+dfsg-1_arm64.deb 0377974c301ffdf20b1bbe8c7b7613f482eae0c5 480944 rna-star_2.7.4a+dfsg-1_arm64.deb Checksums-Sha256: fad3a79ad1c548bf9b1a018d699a5083ce5b1c3a46996f5d54dff3585657b305 4423364 rna-star-dbgsym_2.7.4a+dfsg-1_arm64.deb c7ae9d69c4e17cbfacaf2bbbdb6a9b54610dd80ff15cb7c6b583996880aabace 480944 rna-star_2.7.4a+dfsg-1_arm64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Tue, 09 Jun 2020 22:13:46 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.69-11.1), automake (= 1:1.16.2-1), autopoint (= 0.19.8.1-10), autotools-dev (= 20180224.1), base-files (= 11), base-passwd (= 3.5.47), bash (= 5.0-6), binutils (= 2.34-8), binutils-common (= 2.34-8), binutils-x86-64-linux-gnu (= 2.34-8), bsdmainutils (= 11.1.2+b1), bsdutils (= 1:2.35.2-2), build-essential (= 12.8), bzip2 (= 1.0.8-3), coreutils (= 8.30-3+b1), cpp (= 4:9.2.1-3.1), cpp-9 (= 9.3.0-13), dash (= 0.5.10.2-7), debconf (= 1.5.74), debhelper (= 13.1), debianutils (= 4.11), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.8.1-1), diffutils (= 1:3.7-3), dpkg (= 1.19.7), dpkg-dev (= 1.19.7), dwz (= 0.13-5), file (= 1:5.38-5), findutils (= 4.7.0-1), g++ (= 4:9.2.1-3.1), g++-9 (= 9.3.0-13), gcc (= 4:9.2.1-3.1), gcc-10-base (= 10.1.0-3), gcc-9 (= 9.3.0-13), gcc-9-base (= 9.3.0-13), gettext (= 0.19.8.1-10), gettext-base (= 0.19.8.1-10), grep (= 3.4-1), groff-base (= 1.22.4-5), gzip (= 1.10-2), hostname (= 3.23), init-system-helpers (= 1.57), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-8), libarchive-zip-perl (= 1.68-1), libasan5 (= 9.3.0-13), libatomic1 (= 10.1.0-3), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-3), libaudit1 (= 1:2.8.5-3+b1), libbinutils (= 2.34-8), libblkid1 (= 2.35.2-2), libbrotli1 (= 1.0.7-6.1), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.8-3), libc-bin (= 2.30-8), libc-dev-bin (= 2.30-8), libc6 (= 2.30-8), libc6-dev (= 2.30-8), libcap-ng0 (= 0.7.9-2.2), libcc1-0 (= 10.1.0-3), libcom-err2 (= 1.45.6-1), libcroco3 (= 0.6.13-1), libcrypt-dev (= 1:4.4.16-1), libcrypt1 (= 1:4.4.16-1), libctf-nobfd0 (= 2.34-8), libctf0 (= 2.34-8), libcurl3-gnutls (= 7.68.0-1), libdb5.3 (= 5.3.28+dfsg1-0.6), libdebconfclient0 (= 0.252), libdebhelper-perl (= 13.1), libdeflate0 (= 1.6-1), libdpkg-perl (= 1.19.7), libelf1 (= 0.176-1.1), libffi7 (= 3.3-4), libfile-stripnondeterminism-perl (= 1.8.1-1), libgcc-9-dev (= 9.3.0-13), libgcc-s1 (= 10.1.0-3), libgcrypt20 (= 1.8.5-5), libgdbm-compat4 (= 1.18.1-5), libgdbm6 (= 1.18.1-5), libglib2.0-0 (= 2.64.3-1), libgmp10 (= 2:6.2.0+dfsg-4), libgnutls30 (= 3.6.14-1), libgomp1 (= 10.1.0-3), libgpg-error0 (= 1.38-1), libgssapi-krb5-2 (= 1.17-10), libhogweed5 (= 3.5.1+really3.5.1-2), libhts-dev (= 1.10.2-3), libhts3 (= 1.10.2-3), libicu67 (= 67.1-2), libidn2-0 (= 2.3.0-1), libisl22 (= 0.22.1-1), libitm1 (= 10.1.0-3), libk5crypto3 (= 1.17-10), libkeyutils1 (= 1.6.1-2), libkrb5-3 (= 1.17-10), libkrb5support0 (= 1.17-10), libldap-2.4-2 (= 2.4.50+dfsg-1), libldap-common (= 2.4.50+dfsg-1), liblsan0 (= 10.1.0-3), liblz4-1 (= 1.9.2-2), liblzma-dev (= 5.2.4-1+b1), liblzma5 (= 5.2.4-1+b1), libmagic-mgc (= 1:5.38-5), libmagic1 (= 1:5.38-5), libmount1 (= 2.35.2-2), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), libnettle7 (= 3.5.1+really3.5.1-2), libnghttp2-14 (= 1.41.0-2), libp11-kit0 (= 0.23.20-1), libpam-modules (= 1.3.1-5), libpam-modules-bin (= 1.3.1-5), libpam-runtime (= 1.3.1-5), libpam0g (= 1.3.1-5), libpcre2-8-0 (= 10.34-7), libpcre3 (= 2:8.39-12+b1), libperl5.30 (= 5.30.3-4), libpipeline1 (= 1.5.2-2), libpsl5 (= 0.21.0-1.1), libquadmath0 (= 10.1.0-3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b1), libsasl2-2 (= 2.1.27+dfsg-2), libsasl2-modules-db (= 2.1.27+dfsg-2), libseccomp2 (= 2.4.3-1+b1), libselinux1 (= 3.0-1+b3), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.35.2-2), libssh2-1 (= 1.8.0-2.1), libssl1.1 (= 1.1.1g-1), libstdc++-9-dev (= 9.3.0-13), libstdc++6 (= 10.1.0-3), libsub-override-perl (= 0.09-2), libsystemd0 (= 245.6-1), libtasn1-6 (= 4.16.0-2), libtinfo6 (= 6.2-1), libtool (= 2.4.6-14), libtsan0 (= 10.1.0-3), libubsan1 (= 10.1.0-3), libuchardet0 (= 0.0.7-1), libudev1 (= 245.6-1), libunistring2 (= 0.9.10-4), libuuid1 (= 2.35.2-2), libxml2 (= 2.9.10+dfsg-5+b1), linux-libc-dev (= 5.6.14-1), login (= 1:4.8.1-1), lsb-base (= 11.1.0), m4 (= 1.4.18-4), make (= 4.3-3), man-db (= 2.9.2-1), mawk (= 1.3.4.20200120-2), ncurses-base (= 6.2-1), ncurses-bin (= 6.2-1), patch (= 2.7.6-6), perl (= 5.30.3-4), perl-base (= 5.30.3-4), perl-modules-5.30 (= 5.30.3-4), po-debconf (= 1.0.21), sed (= 4.7-1), sensible-utils (= 0.0.12+nmu1), sysvinit-utils (= 2.96-3), tar (= 1.30+dfsg-7), util-linux (= 2.35.2-2), vim-common (= 2:8.2.0716-3), xxd (= 2:8.2.0716-3), xz-utils (= 5.2.4-1+b1), zlib1g (= 1:1.2.11.dfsg-2), zlib1g-dev (= 1:1.2.11.dfsg-2) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1591468270" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ rna-star-dbgsym_2.7.4a+dfsg-1_arm64.deb --------------------------------------- new Debian package, version 2.0. size 4423364 bytes: control archive=544 bytes. 387 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: rna-star-dbgsym Source: rna-star Version: 2.7.4a+dfsg-1 Auto-Built-Package: debug-symbols Architecture: arm64 Maintainer: Debian Med Packaging Team Installed-Size: 4649 Depends: rna-star (= 2.7.4a+dfsg-1) Section: debug Priority: optional Description: debug symbols for rna-star Build-Ids: c9ff3cd3548740f692eaa661342858799e449ad5 drwxr-xr-x root/root 0 2020-06-06 18:31 ./ drwxr-xr-x root/root 0 2020-06-06 18:31 ./usr/ drwxr-xr-x root/root 0 2020-06-06 18:31 ./usr/lib/ drwxr-xr-x root/root 0 2020-06-06 18:31 ./usr/lib/debug/ drwxr-xr-x root/root 0 2020-06-06 18:31 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2020-06-06 18:31 ./usr/lib/debug/.build-id/c9/ -rw-r--r-- root/root 4750216 2020-06-06 18:31 ./usr/lib/debug/.build-id/c9/ff3cd3548740f692eaa661342858799e449ad5.debug drwxr-xr-x root/root 0 2020-06-06 18:31 ./usr/share/ drwxr-xr-x root/root 0 2020-06-06 18:31 ./usr/share/doc/ lrwxrwxrwx root/root 0 2020-06-06 18:31 ./usr/share/doc/rna-star-dbgsym -> rna-star rna-star_2.7.4a+dfsg-1_arm64.deb -------------------------------- new Debian package, version 2.0. size 480944 bytes: control archive=1408 bytes. 1367 bytes, 24 lines control 672 bytes, 10 lines md5sums Package: rna-star Version: 2.7.4a+dfsg-1 Architecture: arm64 Maintainer: Debian Med Packaging Team Installed-Size: 961 Depends: libc6 (>= 2.29), libgcc-s1 (>= 4.2), libgomp1 (>= 6), libhts3 (>= 1.10), libstdc++6 (>= 9) Section: science Priority: optional Homepage: https://github.com/alexdobin/STAR/ Description: ultrafast universal RNA-seq aligner Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, the authors experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. drwxr-xr-x root/root 0 2020-06-06 18:31 ./ drwxr-xr-x root/root 0 2020-06-06 18:31 ./usr/ drwxr-xr-x root/root 0 2020-06-06 18:31 ./usr/bin/ -rwxr-xr-x root/root 728640 2020-06-06 18:31 ./usr/bin/STAR drwxr-xr-x root/root 0 2020-06-06 18:31 ./usr/share/ drwxr-xr-x root/root 0 2020-06-06 18:31 ./usr/share/doc-base/ -rw-r--r-- root/root 1179 2020-06-06 18:30 ./usr/share/doc-base/rna-star drwxr-xr-x root/root 0 2020-06-06 18:31 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-06-06 18:31 ./usr/share/doc/rna-star/ -rw-r--r-- root/root 220 2020-06-06 18:30 ./usr/share/doc/rna-star/README.Debian -rw-r--r-- root/root 3240 2020-06-01 19:08 ./usr/share/doc/rna-star/README.md -rw-r--r-- root/root 5788 2020-06-01 19:08 ./usr/share/doc/rna-star/RELEASEnotes.md.gz -rw-r--r-- root/root 212272 2020-06-01 19:08 ./usr/share/doc/rna-star/STARmanual.pdf -rw-r--r-- root/root 2112 2020-06-06 18:31 ./usr/share/doc/rna-star/changelog.Debian.gz -rw-r--r-- root/root 10714 2020-06-01 19:08 ./usr/share/doc/rna-star/changelog.gz -rw-r--r-- root/root 2565 2020-06-06 18:31 ./usr/share/doc/rna-star/copyright drwxr-xr-x root/root 0 2020-06-06 18:31 ./usr/share/man/ drwxr-xr-x root/root 0 2020-06-06 18:31 ./usr/share/man/man1/ -rw-r--r-- root/root 824 2020-06-06 18:31 ./usr/share/man/man1/STAR.1.gz lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [555 B] Get:5 copy:/<>/apt_archive ./ Packages [641 B] Fetched 2159 B in 0s (82.5 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libcpanel-json-xs-perl libdevel-callchecker-perl libdevel-size-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-address-xs-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-socket-ssl-perl libipc-system-simple-perl libjson-maybexs-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl liblist-utilsby-perl libmailtools-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libnamespace-clean-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsqlite3-0 libssl1.1 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libxml-writer-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common t1utils Suggested packages: libxml-parser-perl libdata-dump-perl ca-certificates libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libdevel-lexalias-perl libdevel-stacktrace-perl libwww-perl binutils-multiarch libtext-template-perl readline-doc Recommended packages: gnupg libhttp-message-perl libasync-mergepoint-perl libsereal-perl libtest-fatal-perl libtest-refcount-perl libdigest-bubblebabble-perl libnet-dns-sec-perl libnet-libidn-perl libperl4-corelibs-perl libauthen-sasl-perl libpackage-stash-xs-perl libref-util-perl libtype-tiny-xs-perl libperlio-gzip-perl The following NEW packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libcpanel-json-xs-perl libdevel-callchecker-perl libdevel-size-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-address-xs-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-socket-ssl-perl libipc-system-simple-perl libjson-maybexs-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl liblist-utilsby-perl libmailtools-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libnamespace-clean-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsqlite3-0 libssl1.1 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libxml-writer-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common sbuild-build-depends-lintian-dummy:arm64 t1utils 0 upgraded, 81 newly installed, 0 to remove and 0 not upgraded. Need to get 9378 kB of archives. After this operation, 26.6 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [844 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 8.0-4 [72.5 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline8 amd64 8.0-4 [160 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 netbase all 6.1 [19.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.63-1 [35.6 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.3-7 [50.4 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.20-1 [532 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.32.2-2 [752 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.20-1 [894 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.36+b3 [71.0 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b2 [11.3 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libdynaloader-functions-perl all 0.003-1 [12.6 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.008-1+b1 [15.9 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libparams-classify-perl amd64 0.015-1+b2 [25.6 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-implementation-perl all 0.09-1 [12.9 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libvariable-magic-perl amd64 0.62-1+b2 [46.0 kB] Get:20 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Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libfuture-perl all 0.45-1 [84.4 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-tagset-perl all 3.20-4 [13.0 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 1.76-2 [90.2 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-parser-perl amd64 3.72-5 [105 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libstruct-dumb-perl all 0.12-1 [12.9 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-perl all 0.75-1 [269 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 liblinux-epoll-perl amd64 0.017-1 [16.8 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-loop-epoll-perl all 0.20-1 [11.9 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libjson-maybexs-perl all 1.004002-1 [13.1 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-compare-perl all 0.53-1 [68.9 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl amd64 0.416-1+b5 [63.6 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-utilsby-perl all 0.11-1 [15.4 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 librole-tiny-perl all 2.001004-1 [20.8 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libmoo-perl all 2.004000-1 [59.4 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libmoox-aliases-perl all 0.001006-1 [10.2 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libpackage-stash-perl all 0.38-1 [21.7 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-identify-perl amd64 0.14-1+b2 [12.0 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.26-1 [13.5 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.114-1 [53.6 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-decoder-perl amd64 4.011+ds-1 [106 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-encoder-perl amd64 4.011+ds-1 [108 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libtype-tiny-perl all 1.010001-1 [338 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libunicode-utf8-perl amd64 0.62-1+b1 [20.2 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-writer-perl all 0.625-1 [29.7 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.82+repack-1 [35.6 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.3.4-3 [89.9 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.80.0 [1286 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 9378 kB in 0s (47.8 MB/s) Selecting previously unselected package readline-common. (Reading database ... 20639 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.0-4_all.deb ... Unpacking readline-common (8.0-4) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../01-libreadline8_8.0-4_amd64.deb ... Unpacking libreadline8:amd64 (8.0-4) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.1_all.deb ... Unpacking netbase (6.1) ... Selecting previously unselected package diffstat. Preparing to unpack .../03-diffstat_1.63-1_amd64.deb ... Unpacking diffstat (1.63-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../04-libassuan0_2.5.3-7_amd64.deb ... Unpacking libassuan0:amd64 (2.5.3-7) ... Selecting previously unselected package gpgconf. Preparing to unpack .../05-gpgconf_2.2.20-1_amd64.deb ... Unpacking gpgconf (2.2.20-1) ... Selecting previously unselected package libsqlite3-0:amd64. 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I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 129900 Build-Time: 196 Distribution: unstable Foreign Architectures: arm64 Host Architecture: arm64 Install-Time: 22 Job: rna-star_2.7.4a+dfsg-1 Lintian: pass Machine Architecture: amd64 Package: rna-star Package-Time: 233 Source-Version: 2.7.4a+dfsg-1 Space: 129900 Status: successful Version: 2.7.4a+dfsg-1 -------------------------------------------------------------------------------- Finished at 2020-06-09T22:13:46Z Build needed 00:03:53, 129900k disk space