sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +=================================================================================+ | rna-star 2.7.5a+20200629git1552aa0-1 (mips64el) Wed, 08 Jul 2020 07:35:51 +0000 | +=================================================================================+ Package: rna-star Version: 2.7.5a+20200629git1552aa0-1 Source Version: 2.7.5a+20200629git1552aa0-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: mips64el Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-66bfb700-63cc-4a08-bf09-a4d19233a87c' with '<>' I: NOTICE: Log filtering will replace 'build/rna-star-EzIIJt/resolver-kuiHMA' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://debian.oregonstate.edu/debian unstable InRelease Get:2 http://debian.oregonstate.edu/debian unstable/main mips64el Packages [7953 kB] Fetched 7953 kB in 2s (4540 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 821 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main rna-star 2.7.5a+20200629git1552aa0-1 (dsc) [2275 B] Get:2 http://debian.oregonstate.edu/debian unstable/main rna-star 2.7.5a+20200629git1552aa0-1 (tar) [443 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main rna-star 2.7.5a+20200629git1552aa0-1 (diff) [376 kB] Fetched 821 kB in 0s (41.6 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/rna-star-EzIIJt/rna-star-2.7.5a+20200629git1552aa0' with '<>' I: NOTICE: Log filtering will replace 'build/rna-star-EzIIJt' 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-mips64el:amd64, libc-dev:mips64el, libstdc++-dev:mips64el Filtered Build-Depends: debhelper-compat (= 13), libhts-dev, vim-common, xxd, zlib1g-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-mips64el:amd64, libc-dev:mips64el, libstdc++-dev:mips64el 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 [428 B] Get:5 copy:/<>/apt_archive ./ Packages [518 B] Fetched 1903 B in 0s (72.9 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-mips64el-linux-gnuabi64 bsdextrautils build-essential cpp-9-mips64el-linux-gnuabi64 cpp-mips64el-linux-gnuabi64 cross-config crossbuild-essential-mips64el debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-9 g++-9-mips64el-linux-gnuabi64 g++-mips64el-linux-gnuabi64 gcc-10-base:mips64el gcc-10-cross-base-mipsen gcc-9-base:mips64el gcc-9-cross-base-mipsen gcc-9-mips64el-linux-gnuabi64 gcc-9-mips64el-linux-gnuabi64-base gcc-mips64el-linux-gnuabi64 gettext gettext-base groff-base intltool-debian libarchive-zip-perl libatomic1:mips64el libatomic1-mips64el-cross libbrotli1:mips64el libbz2-1.0:mips64el libc6:mips64el libc6-dev libc6-dev:mips64el libc6-dev-mips64el-cross libc6-mips64el-cross libcom-err2:mips64el libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:mips64el libcrypt1:mips64el libcurl3-gnutls:mips64el libdb5.3:mips64el libdebhelper-perl libdebian-dpkgcross-perl libdeflate0:mips64el libdpkg-perl libelf1 libffi7:mips64el libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:mips64el libgcc-9-dev-mips64el-cross libgcc-s1:mips64el libgcc-s1-mips64el-cross libgcrypt20:mips64el libglib2.0-0 libgmp10:mips64el libgnutls30:mips64el libgomp1:mips64el libgomp1-mips64el-cross libgpg-error0:mips64el libgssapi-krb5-2:mips64el libhogweed5:mips64el libhts-dev:mips64el libhts3:mips64el libicu67 libidn2-0:mips64el libio-string-perl libk5crypto3:mips64el libkeyutils1:mips64el libkrb5-3:mips64el libkrb5support0:mips64el libldap-2.4-2:mips64el libldap-common liblocale-gettext-perl liblzma-dev:mips64el liblzma5:mips64el libmagic-mgc libmagic1 libnettle7:mips64el libnghttp2-14:mips64el libp11-kit0:mips64el libperl5.30 libpipeline1 libpsl5:mips64el librtmp1:mips64el libsasl2-2:mips64el libsasl2-modules-db:mips64el libsigsegv2 libssh2-1:mips64el libssl1.1:mips64el libstdc++-9-dev libstdc++-9-dev:mips64el libstdc++-9-dev-mips64el-cross libstdc++6:mips64el libstdc++6-mips64el-cross libsub-override-perl libtasn1-6:mips64el libtool libuchardet0 libunistring2:mips64el libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:mips64el linux-libc-dev-mips64el-cross m4 man-db perl perl-modules-5.30 po-debconf sensible-utils ucf vim-common xxd zlib1g:mips64el zlib1g-dev:mips64el Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-9-locales cpp-doc dh-make binutils-multiarch debian-keyring g++-multilib g++-9-multilib gcc-9-doc g++-9-multilib-mips64el-linux-gnuabi64 gcc-9-multilib-mips64el-linux-gnuabi64 manpages-dev flex bison gdb-mips64el-linux-gnuabi64 gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:mips64el libc-l10n:mips64el locales:mips64el glibc-doc manpages-dev:mips64el gnupg git bzr rng-tools:mips64el gnutls-bin:mips64el krb5-doc:mips64el krb5-user:mips64el liblzma-doc:mips64el libstdc++-9-doc libstdc++-9-doc:mips64el 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 libalgorithm-merge-perl curl | wget | lynx ca-certificates:mips64el libfile-fcntllock-perl libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libgpg-error-l10n:mips64el krb5-locales:mips64el publicsuffix:mips64el libsasl2-modules:mips64el 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-mips64el-linux-gnuabi64 bsdextrautils build-essential cpp-9-mips64el-linux-gnuabi64 cpp-mips64el-linux-gnuabi64 cross-config crossbuild-essential-mips64el debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-9 g++-9-mips64el-linux-gnuabi64 g++-mips64el-linux-gnuabi64 gcc-10-base:mips64el gcc-10-cross-base-mipsen gcc-9-base:mips64el gcc-9-cross-base-mipsen gcc-9-mips64el-linux-gnuabi64 gcc-9-mips64el-linux-gnuabi64-base gcc-mips64el-linux-gnuabi64 gettext gettext-base groff-base intltool-debian libarchive-zip-perl libatomic1:mips64el libatomic1-mips64el-cross libbrotli1:mips64el libbz2-1.0:mips64el libc6:mips64el libc6-dev libc6-dev:mips64el libc6-dev-mips64el-cross libc6-mips64el-cross libcom-err2:mips64el libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:mips64el libcrypt1:mips64el libcurl3-gnutls:mips64el libdb5.3:mips64el libdebhelper-perl libdebian-dpkgcross-perl libdeflate0:mips64el libdpkg-perl libelf1 libffi7:mips64el libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:mips64el libgcc-9-dev-mips64el-cross libgcc-s1:mips64el libgcc-s1-mips64el-cross libgcrypt20:mips64el libglib2.0-0 libgmp10:mips64el libgnutls30:mips64el libgomp1:mips64el libgomp1-mips64el-cross libgpg-error0:mips64el libgssapi-krb5-2:mips64el libhogweed5:mips64el libhts-dev:mips64el libhts3:mips64el libicu67 libidn2-0:mips64el libio-string-perl libk5crypto3:mips64el libkeyutils1:mips64el libkrb5-3:mips64el libkrb5support0:mips64el libldap-2.4-2:mips64el libldap-common liblocale-gettext-perl liblzma-dev:mips64el liblzma5:mips64el libmagic-mgc libmagic1 libnettle7:mips64el libnghttp2-14:mips64el libp11-kit0:mips64el libperl5.30 libpipeline1 libpsl5:mips64el librtmp1:mips64el libsasl2-2:mips64el libsasl2-modules-db:mips64el libsigsegv2 libssh2-1:mips64el libssl1.1:mips64el libstdc++-9-dev libstdc++-9-dev:mips64el libstdc++-9-dev-mips64el-cross libstdc++6:mips64el libstdc++6-mips64el-cross libsub-override-perl libtasn1-6:mips64el libtool libuchardet0 libunistring2:mips64el libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:mips64el linux-libc-dev-mips64el-cross m4 man-db perl perl-modules-5.30 po-debconf sbuild-build-depends-main-dummy:mips64el sensible-utils ucf vim-common xxd zlib1g:mips64el zlib1g-dev:mips64el 0 upgraded, 133 newly installed, 0 to remove and 0 not upgraded. Need to get 99.4 MB of archives. After this operation, 399 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [944 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 bsdextrautils amd64 2.35.2-7 [139 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-5 [920 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.3-2 [1314 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 perl-modules-5.30 all 5.30.3-4 [2806 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libperl5.30 amd64 5.30.3-4 [4019 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 perl amd64 5.30.3-4 [290 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main mips64el gcc-10-base mips64el 10.1.0-4 [198 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main mips64el gcc-9-base mips64el 9.3.0-14 [197 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 xxd amd64 2:8.2.0716-3 [157 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 vim-common all 2:8.2.0716-3 [192 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.38-5 [262 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.38-5 [120 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.38-5 [67.9 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0043 [74.0 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11.1 [341 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.2-3 [801 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-mips64el-linux-gnuabi64 amd64 2.34-5cross6 [2310 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.16-1 [104 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.30-8 [2631 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev amd64 9.3.0-14 [1701 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9 amd64 9.3.0-14 [10.7 MB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:9.2.1-3.1 [1644 B] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libdpkg-perl all 1.20.4 [1471 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-dev all 1.20.4 [1907 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.8 [7640 B] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-mips64el-linux-gnuabi64-base amd64 9.3.0-8cross1 [196 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-mips64el-linux-gnuabi64 amd64 9.3.0-8cross1 [6468 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-mips64el-linux-gnuabi64 amd64 4:9.2.1-4.1 [16.7 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3.1 [39.9 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base-mipsen all 9.3.0-8cross1 [192 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-cross-base-mipsen all 10-20200324-1cross1 [192 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-mips64el-cross all 2.30-2cross1 [1327 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-mips64el-cross all 10-20200324-1cross1 [69.8 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-mips64el-cross all 10-20200324-1cross1 [87.5 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-mips64el-cross all 10-20200324-1cross1 [7388 B] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-mips64el-cross all 9.3.0-8cross1 [248 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-mips64el-linux-gnuabi64 amd64 9.3.0-8cross1 [6825 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-mips64el-linux-gnuabi64 amd64 4:9.2.1-4.1 [1484 B] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-mips64el-cross all 10-20200324-1cross1 [393 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-mips64el-cross all 5.4.19-1cross1 [1166 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-mips64el-cross all 2.30-2cross1 [2476 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-mips64el-cross all 9.3.0-8cross1 [1726 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-mips64el-linux-gnuabi64 amd64 9.3.0-8cross1 [7050 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 g++-mips64el-linux-gnuabi64 amd64 4:9.2.1-4.1 [1192 B] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libicu67 amd64 67.1-2 [8610 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.10+dfsg-5+b1 [710 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-2 [343 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3.1 [38.9 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3.1 [49.9 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-mips64el all 12.8 [6704 B] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-14 [513 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 13.2 [187 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.8.1-2 [38.2 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.8.1-2 [15.1 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-5 [151 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.64.4-1 [1341 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 13.2 [1007 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main mips64el libgcc-s1 mips64el 10.1.0-4 [69.4 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main mips64el libcrypt1 mips64el 1:4.4.16-1 [95.5 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main mips64el libc6 mips64el 2.30-8 [2554 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main mips64el libatomic1 mips64el 10.1.0-4 [7480 B] Get:90 http://debian.oregonstate.edu/debian unstable/main mips64el libbrotli1 mips64el 1.0.7-6.1 [271 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main mips64el libbz2-1.0 mips64el 1.0.8-3 [47.4 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main mips64el linux-libc-dev mips64el 5.7.6-1 [1120 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main mips64el libcrypt-dev mips64el 1:4.4.16-1 [118 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main mips64el libc6-dev mips64el 2.30-8 [2476 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main mips64el libcom-err2 mips64el 1.45.6-1 [71.5 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main mips64el libgmp10 mips64el 2:6.2.0+dfsg-6 [241 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main mips64el libnettle7 mips64el 3.5.1+really3.5.1-2 [236 kB] Get:98 http://debian.oregonstate.edu/debian unstable/main mips64el libhogweed5 mips64el 3.5.1+really3.5.1-2 [132 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main mips64el libunistring2 mips64el 0.9.10-4 [371 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main mips64el libidn2-0 mips64el 2.3.0-1 [84.5 kB] Get:101 http://debian.oregonstate.edu/debian unstable/main mips64el libffi7 mips64el 3.3-4 [22.6 kB] Get:102 http://debian.oregonstate.edu/debian unstable/main mips64el libp11-kit0 mips64el 0.23.20-1 [269 kB] Get:103 http://debian.oregonstate.edu/debian unstable/main mips64el libtasn1-6 mips64el 4.16.0-2 [52.6 kB] Get:104 http://debian.oregonstate.edu/debian unstable/main mips64el libgnutls30 mips64el 3.6.14-2 [1089 kB] Get:105 http://debian.oregonstate.edu/debian unstable/main mips64el libkrb5support0 mips64el 1.17-10 [62.7 kB] Get:106 http://debian.oregonstate.edu/debian unstable/main mips64el libk5crypto3 mips64el 1.17-10 [121 kB] Get:107 http://debian.oregonstate.edu/debian unstable/main mips64el libkeyutils1 mips64el 1.6.1-2 [15.0 kB] Get:108 http://debian.oregonstate.edu/debian unstable/main mips64el libssl1.1 mips64el 1.1.1g-1 [1143 kB] Get:109 http://debian.oregonstate.edu/debian unstable/main mips64el libkrb5-3 mips64el 1.17-10 [333 kB] Get:110 http://debian.oregonstate.edu/debian unstable/main mips64el libgssapi-krb5-2 mips64el 1.17-10 [142 kB] Get:111 http://debian.oregonstate.edu/debian unstable/main mips64el libdb5.3 mips64el 5.3.28+dfsg1-0.6 [597 kB] Get:112 http://debian.oregonstate.edu/debian unstable/main mips64el libsasl2-modules-db mips64el 2.1.27+dfsg-2 [68.3 kB] Get:113 http://debian.oregonstate.edu/debian unstable/main mips64el libsasl2-2 mips64el 2.1.27+dfsg-2 [102 kB] Get:114 http://debian.oregonstate.edu/debian unstable/main amd64 libldap-common all 2.4.50+dfsg-1 [92.9 kB] Get:115 http://debian.oregonstate.edu/debian unstable/main mips64el libldap-2.4-2 mips64el 2.4.50+dfsg-1 [207 kB] Get:116 http://debian.oregonstate.edu/debian unstable/main mips64el libnghttp2-14 mips64el 1.41.0-2 [68.2 kB] Get:117 http://debian.oregonstate.edu/debian unstable/main mips64el libpsl5 mips64el 0.21.0-1.1 [55.0 kB] Get:118 http://debian.oregonstate.edu/debian unstable/main mips64el zlib1g mips64el 1:1.2.11.dfsg-2 [88.2 kB] Get:119 http://debian.oregonstate.edu/debian unstable/main mips64el librtmp1 mips64el 2.4+20151223.gitfa8646d.1-2+b1 [56.0 kB] Get:120 http://debian.oregonstate.edu/debian unstable/main mips64el libgpg-error0 mips64el 1.38-2 [74.2 kB] Get:121 http://debian.oregonstate.edu/debian unstable/main mips64el libgcrypt20 mips64el 1.8.5-5 [497 kB] Get:122 http://debian.oregonstate.edu/debian unstable/main mips64el libssh2-1 mips64el 1.8.0-2.1 [134 kB] Get:123 http://debian.oregonstate.edu/debian unstable/main mips64el libcurl3-gnutls mips64el 7.68.0-1 [296 kB] Get:124 http://debian.oregonstate.edu/debian unstable/main mips64el libdeflate0 mips64el 1.6-1 [50.6 kB] Get:125 http://debian.oregonstate.edu/debian unstable/main mips64el libgomp1 mips64el 10.1.0-4 [89.6 kB] Get:126 http://debian.oregonstate.edu/debian unstable/main mips64el libgcc-9-dev mips64el 9.3.0-14 [248 kB] Get:127 http://debian.oregonstate.edu/debian unstable/main mips64el liblzma5 mips64el 5.2.4-1+b1 [151 kB] Get:128 http://debian.oregonstate.edu/debian unstable/main mips64el libhts3 mips64el 1.10.2-4 [346 kB] Get:129 http://debian.oregonstate.edu/debian unstable/main mips64el liblzma-dev mips64el 5.2.4-1+b1 [214 kB] Get:130 http://debian.oregonstate.edu/debian unstable/main mips64el zlib1g-dev mips64el 1:1.2.11.dfsg-2 [191 kB] Get:131 http://debian.oregonstate.edu/debian unstable/main mips64el libhts-dev mips64el 1.10.2-4 [4865 kB] Get:132 http://debian.oregonstate.edu/debian unstable/main mips64el libstdc++6 mips64el 10.1.0-4 [432 kB] Get:133 http://debian.oregonstate.edu/debian unstable/main mips64el libstdc++-9-dev mips64el 9.3.0-14 [1736 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 99.4 MB in 1s (114 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 10428 files and directories currently installed.) Preparing to unpack .../000-bsdextrautils_2.35.2-7_amd64.deb ... Unpacking bsdextrautils (2.35.2-7) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../001-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../002-groff-base_1.22.4-5_amd64.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../003-libpipeline1_1.5.2-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.2-2) ... Selecting previously unselected package man-db. Preparing to unpack .../004-man-db_2.9.3-2_amd64.deb ... Unpacking man-db (2.9.3-2) ... Selecting previously unselected package perl-modules-5.30. Preparing to unpack .../005-perl-modules-5.30_5.30.3-4_all.deb ... Unpacking perl-modules-5.30 (5.30.3-4) ... Selecting previously unselected package libperl5.30:amd64. Preparing to unpack .../006-libperl5.30_5.30.3-4_amd64.deb ... Unpacking libperl5.30:amd64 (5.30.3-4) ... Selecting previously unselected package perl. Preparing to unpack .../007-perl_5.30.3-4_amd64.deb ... Unpacking perl (5.30.3-4) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../008-liblocale-gettext-perl_1.07-4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-4) ... Selecting previously unselected package gcc-10-base:mips64el. Preparing to unpack .../009-gcc-10-base_10.1.0-4_mips64el.deb ... Unpacking gcc-10-base:mips64el (10.1.0-4) ... Selecting previously unselected package gcc-9-base:mips64el. Preparing to unpack .../010-gcc-9-base_9.3.0-14_mips64el.deb ... Unpacking gcc-9-base:mips64el (9.3.0-14) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../011-sensible-utils_0.0.12+nmu1_all.deb ... Unpacking sensible-utils (0.0.12+nmu1) ... Selecting previously unselected package xxd. Preparing to unpack .../012-xxd_2%3a8.2.0716-3_amd64.deb ... Unpacking xxd (2:8.2.0716-3) ... Selecting previously unselected package vim-common. Preparing to unpack .../013-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 .../014-libmagic-mgc_1%3a5.38-5_amd64.deb ... Unpacking libmagic-mgc (1:5.38-5) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../015-libmagic1_1%3a5.38-5_amd64.deb ... Unpacking libmagic1:amd64 (1:5.38-5) ... Selecting previously unselected package file. Preparing to unpack .../016-file_1%3a5.38-5_amd64.deb ... Unpacking file (1:5.38-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../017-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 .../018-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../019-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../020-m4_1.4.18-4_amd64.deb ... Unpacking m4 (1.4.18-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../021-autoconf_2.69-11.1_all.deb ... Unpacking autoconf (2.69-11.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../022-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../023-automake_1%3a1.16.2-3_all.deb ... Unpacking automake (1:1.16.2-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../024-autopoint_0.19.8.1-10_all.deb ... Unpacking autopoint (0.19.8.1-10) ... Selecting previously unselected package binutils-mips64el-linux-gnuabi64. Preparing to unpack .../025-binutils-mips64el-linux-gnuabi64_2.34-5cross6_amd64.deb ... Unpacking binutils-mips64el-linux-gnuabi64 (2.34-5cross6) ... Selecting previously unselected package libcrypt-dev:amd64. Preparing to unpack .../026-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 .../027-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 .../028-libstdc++-9-dev_9.3.0-14_amd64.deb ... Unpacking libstdc++-9-dev:amd64 (9.3.0-14) ... Selecting previously unselected package g++-9. Preparing to unpack .../029-g++-9_9.3.0-14_amd64.deb ... Unpacking g++-9 (9.3.0-14) ... Selecting previously unselected package g++. Preparing to unpack .../030-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 .../031-libdpkg-perl_1.20.4_all.deb ... Unpacking libdpkg-perl (1.20.4) ... Selecting previously unselected package dpkg-dev. Preparing to unpack .../032-dpkg-dev_1.20.4_all.deb ... Unpacking dpkg-dev (1.20.4) ... Selecting previously unselected package build-essential. Preparing to unpack .../033-build-essential_12.8_amd64.deb ... Unpacking build-essential (12.8) ... Selecting previously unselected package gcc-9-mips64el-linux-gnuabi64-base:amd64. Preparing to unpack .../034-gcc-9-mips64el-linux-gnuabi64-base_9.3.0-8cross1_amd64.deb ... Unpacking gcc-9-mips64el-linux-gnuabi64-base:amd64 (9.3.0-8cross1) ... Selecting previously unselected package cpp-9-mips64el-linux-gnuabi64. Preparing to unpack .../035-cpp-9-mips64el-linux-gnuabi64_9.3.0-8cross1_amd64.deb ... Unpacking cpp-9-mips64el-linux-gnuabi64 (9.3.0-8cross1) ... 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Selecting previously unselected package libgcc-s1-mips64el-cross. Preparing to unpack .../041-libgcc-s1-mips64el-cross_10-20200324-1cross1_all.deb ... Unpacking libgcc-s1-mips64el-cross (10-20200324-1cross1) ... Selecting previously unselected package libgomp1-mips64el-cross. Preparing to unpack .../042-libgomp1-mips64el-cross_10-20200324-1cross1_all.deb ... Unpacking libgomp1-mips64el-cross (10-20200324-1cross1) ... Selecting previously unselected package libatomic1-mips64el-cross. Preparing to unpack .../043-libatomic1-mips64el-cross_10-20200324-1cross1_all.deb ... Unpacking libatomic1-mips64el-cross (10-20200324-1cross1) ... Selecting previously unselected package libgcc-9-dev-mips64el-cross. Preparing to unpack .../044-libgcc-9-dev-mips64el-cross_9.3.0-8cross1_all.deb ... Unpacking libgcc-9-dev-mips64el-cross (9.3.0-8cross1) ... Selecting previously unselected package gcc-9-mips64el-linux-gnuabi64. Preparing to unpack .../045-gcc-9-mips64el-linux-gnuabi64_9.3.0-8cross1_amd64.deb ... Unpacking gcc-9-mips64el-linux-gnuabi64 (9.3.0-8cross1) ... Selecting previously unselected package gcc-mips64el-linux-gnuabi64. Preparing to unpack .../046-gcc-mips64el-linux-gnuabi64_4%3a9.2.1-4.1_amd64.deb ... Unpacking gcc-mips64el-linux-gnuabi64 (4:9.2.1-4.1) ... Selecting previously unselected package libstdc++6-mips64el-cross. Preparing to unpack .../047-libstdc++6-mips64el-cross_10-20200324-1cross1_all.deb ... Unpacking libstdc++6-mips64el-cross (10-20200324-1cross1) ... Selecting previously unselected package linux-libc-dev-mips64el-cross. Preparing to unpack .../048-linux-libc-dev-mips64el-cross_5.4.19-1cross1_all.deb ... Unpacking linux-libc-dev-mips64el-cross (5.4.19-1cross1) ... Selecting previously unselected package libc6-dev-mips64el-cross. Preparing to unpack .../049-libc6-dev-mips64el-cross_2.30-2cross1_all.deb ... Unpacking libc6-dev-mips64el-cross (2.30-2cross1) ... Selecting previously unselected package libstdc++-9-dev-mips64el-cross. Preparing to unpack .../050-libstdc++-9-dev-mips64el-cross_9.3.0-8cross1_all.deb ... Unpacking libstdc++-9-dev-mips64el-cross (9.3.0-8cross1) ... Selecting previously unselected package g++-9-mips64el-linux-gnuabi64. Preparing to unpack .../051-g++-9-mips64el-linux-gnuabi64_9.3.0-8cross1_amd64.deb ... Unpacking g++-9-mips64el-linux-gnuabi64 (9.3.0-8cross1) ... Selecting previously unselected package g++-mips64el-linux-gnuabi64. Preparing to unpack .../052-g++-mips64el-linux-gnuabi64_4%3a9.2.1-4.1_amd64.deb ... Unpacking g++-mips64el-linux-gnuabi64 (4:9.2.1-4.1) ... Selecting previously unselected package libconfig-inifiles-perl. Preparing to unpack .../053-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 .../054-libio-string-perl_1.08-3_all.deb ... Unpacking libio-string-perl (1.08-3) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../055-libicu67_67.1-2_amd64.deb ... Unpacking libicu67:amd64 (67.1-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../056-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 .../057-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 .../058-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 .../059-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 .../060-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 .../061-libxml-simple-perl_2.25-1_all.deb ... Unpacking libxml-simple-perl (2.25-1) ... Selecting previously unselected package libyaml-perl. Preparing to unpack .../062-libyaml-perl_1.30-1_all.deb ... Unpacking libyaml-perl (1.30-1) ... Selecting previously unselected package libconfig-auto-perl. Preparing to unpack .../063-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 .../064-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 .../065-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 .../066-libdebian-dpkgcross-perl_2.6.15-3.1_all.deb ... Unpacking libdebian-dpkgcross-perl (2.6.15-3.1) ... Selecting previously unselected package dpkg-cross. Preparing to unpack .../067-dpkg-cross_2.6.15-3.1_all.deb ... Unpacking dpkg-cross (2.6.15-3.1) ... Selecting previously unselected package crossbuild-essential-mips64el. Preparing to unpack .../068-crossbuild-essential-mips64el_12.8_all.deb ... Unpacking crossbuild-essential-mips64el (12.8) ... Selecting previously unselected package libtool. Preparing to unpack .../069-libtool_2.4.6-14_all.deb ... Unpacking libtool (2.4.6-14) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../070-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../071-libdebhelper-perl_13.2_all.deb ... Unpacking libdebhelper-perl (13.2) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../072-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 .../073-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../074-libfile-stripnondeterminism-perl_1.8.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.8.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../075-dh-strip-nondeterminism_1.8.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.8.1-2) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../076-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../077-dwz_0.13-5_amd64.deb ... Unpacking dwz (0.13-5) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../078-libglib2.0-0_2.64.4-1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.64.4-1) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../079-libcroco3_0.6.13-1_amd64.deb ... Unpacking libcroco3:amd64 (0.6.13-1) ... Selecting previously unselected package gettext. Preparing to unpack .../080-gettext_0.19.8.1-10_amd64.deb ... Unpacking gettext (0.19.8.1-10) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../081-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../082-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../083-debhelper_13.2_all.deb ... Unpacking debhelper (13.2) ... Selecting previously unselected package libgcc-s1:mips64el. 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Setting up perl-modules-5.30 (5.30.3-4) ... Setting up bsdextrautils (2.35.2-7) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-2) ... Setting up libmagic-mgc (1:5.38-5) ... Setting up libglib2.0-0:amd64 (2.64.4-1) ... No schema files found: doing nothing. Setting up libmagic1:amd64 (1:5.38-5) ... Setting up gcc-9-mips64el-linux-gnuabi64-base:amd64 (9.3.0-8cross1) ... Setting up linux-libc-dev:mips64el (5.7.6-1) ... Setting up libc6-mips64el-cross (2.30-2cross1) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.38-5) ... Setting up gcc-9-cross-base-mipsen (9.3.0-8cross1) ... Setting up libldap-common (2.4.50+dfsg-1) ... Setting up binutils-mips64el-linux-gnuabi64 (2.34-5cross6) ... Setting up xxd (2:8.2.0716-3) ... Setting up gcc-10-base:mips64el (10.1.0-4) ... Setting up autotools-dev (20180224.1) ... Setting up cross-config (2.6.15-3.1) ... Setting up vim-common (2:8.2.0716-3) ... Setting up gcc-10-cross-base-mipsen (10-20200324-1cross1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up autopoint (0.19.8.1-10) ... 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 linux-libc-dev-mips64el-cross (5.4.19-1cross1) ... Setting up cpp-9-mips64el-linux-gnuabi64 (9.3.0-8cross1) ... Setting up cpp-mips64el-linux-gnuabi64 (4:9.2.1-4.1) ... Setting up libgomp1-mips64el-cross (10-20200324-1cross1) ... Setting up libgcc-s1-mips64el-cross (10-20200324-1cross1) ... 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:mips64el (9.3.0-14) ... Setting up libatomic1-mips64el-cross (10-20200324-1cross1) ... Setting up libstdc++-9-dev:amd64 (9.3.0-14) ... Setting up libtool (2.4.6-14) ... Setting up m4 (1.4.18-4) ... Setting up perl (5.30.3-4) ... Setting up libc6-dev-mips64el-cross (2.30-2cross1) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up ucf (3.0043) ... Setting up g++-9 (9.3.0-14) ... Setting up libdpkg-perl (1.20.4) ... Setting up autoconf (2.69-11.1) ... Setting up libstdc++6-mips64el-cross (10-20200324-1cross1) ... 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 libgcc-9-dev-mips64el-cross (9.3.0-8cross1) ... Setting up libsub-override-perl (0.09-2) ... Setting up automake (1:1.16.2-3) ... 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 libarchive-zip-perl (1.68-1) ... Setting up libstdc++-9-dev-mips64el-cross (9.3.0-8cross1) ... Setting up libdebhelper-perl (13.2) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libyaml-perl (1.30-1) ... Setting up gcc-9-mips64el-linux-gnuabi64 (9.3.0-8cross1) ... Setting up dpkg-dev (1.20.4) ... 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-mips64el-linux-gnuabi64 (4:9.2.1-4.1) ... Setting up build-essential (12.8) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libfile-stripnondeterminism-perl (1.8.1-2) ... Setting up g++-9-mips64el-linux-gnuabi64 (9.3.0-8cross1) ... 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 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 (1.8.1-2) ... Setting up g++-mips64el-linux-gnuabi64 (4:9.2.1-4.1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3.1) ... Setting up dpkg-cross (2.6.15-3.1) ... Setting up crossbuild-essential-mips64el (12.8) ... Setting up libcrypt1:mips64el (1:4.4.16-1) ... Setting up libgcc-s1:mips64el (10.1.0-4) ... Setting up dh-autoreconf (19) ... Setting up libc6:mips64el (2.30-8) ... Setting up libnettle7:mips64el (3.5.1+really3.5.1-2) ... Setting up libcrypt-dev:mips64el (1:4.4.16-1) ... Setting up libtasn1-6:mips64el (4.16.0-2) ... Setting up libc6-dev:mips64el (2.30-8) ... Setting up libbz2-1.0:mips64el (1.0.8-3) ... Setting up libdb5.3:mips64el (5.3.28+dfsg1-0.6) ... Setting up libstdc++6:mips64el (10.1.0-4) ... Setting up libkeyutils1:mips64el (1.6.1-2) ... Setting up liblzma5:mips64el (5.2.4-1+b1) ... Setting up libgpg-error0:mips64el (1.38-2) ... Setting up libssl1.1:mips64el (1.1.1g-1) ... Setting up libbrotli1:mips64el (1.0.7-6.1) ... Setting up libffi7:mips64el (3.3-4) ... Setting up libnghttp2-14:mips64el (1.41.0-2) ... Setting up libunistring2:mips64el (0.9.10-4) ... Setting up libdeflate0:mips64el (1.6-1) ... Setting up libgcrypt20:mips64el (1.8.5-5) ... Setting up debhelper (13.2) ... Setting up zlib1g:mips64el (1:1.2.11.dfsg-2) ... Setting up libidn2-0:mips64el (2.3.0-1) ... Setting up libcom-err2:mips64el (1.45.6-1) ... Setting up libgomp1:mips64el (10.1.0-4) ... Setting up libkrb5support0:mips64el (1.17-10) ... Setting up libsasl2-modules-db:mips64el (2.1.27+dfsg-2) ... Setting up libgmp10:mips64el (2:6.2.0+dfsg-6) ... Setting up libp11-kit0:mips64el (0.23.20-1) ... Setting up libatomic1:mips64el (10.1.0-4) ... Setting up libk5crypto3:mips64el (1.17-10) ... Setting up libsasl2-2:mips64el (2.1.27+dfsg-2) ... Setting up liblzma-dev:mips64el (5.2.4-1+b1) ... Setting up zlib1g-dev:mips64el (1:1.2.11.dfsg-2) ... Setting up libssh2-1:mips64el (1.8.0-2.1) ... Setting up libkrb5-3:mips64el (1.17-10) ... Setting up libpsl5:mips64el (0.21.0-1.1) ... Setting up libhogweed5:mips64el (3.5.1+really3.5.1-2) ... Setting up libgcc-9-dev:mips64el (9.3.0-14) ... Setting up libgnutls30:mips64el (3.6.14-2) ... Setting up librtmp1:mips64el (2.4+20151223.gitfa8646d.1-2+b1) ... Setting up libgssapi-krb5-2:mips64el (1.17-10) ... Setting up libstdc++-9-dev:mips64el (9.3.0-14) ... Setting up libldap-2.4-2:mips64el (2.4.50+dfsg-1) ... Setting up libcurl3-gnutls:mips64el (7.68.0-1) ... Setting up libhts3:mips64el (1.10.2-4) ... Setting up libhts-dev:mips64el (1.10.2-4) ... Setting up sbuild-build-depends-main-dummy:mips64el (0.invalid.0) ... Processing triggers for libc-bin (2.30-8) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (mips64el 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_2.34.90.20200706-1 dpkg-dev_1.20.4 g++-9_9.3.0-14 gcc-9_9.3.0-14 libc6-dev_2.30-8 libstdc++-9-dev_9.3.0-14 libstdc++-9-dev-mips64el-cross_9.3.0-8cross1 libstdc++6_10.1.0-4 libstdc++6-mips64el-cross_10-20200324-1cross1 linux-libc-dev_5.7.6-1 Package versions: adduser_3.118 apt_2.1.6 autoconf_2.69-11.1 automake_1:1.16.2-3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-6 binutils_2.34.90.20200706-1 binutils-common_2.34.90.20200706-1 binutils-mips64el-linux-gnuabi64_2.34-5cross6 binutils-x86-64-linux-gnu_2.34.90.20200706-1 bsdextrautils_2.35.2-7 bsdutils_1:2.35.2-7 build-essential_12.8 bzip2_1.0.8-3 coreutils_8.32-2 cpp_4:9.2.1-3.1 cpp-8_8.4.0-4 cpp-9_9.3.0-14 cpp-9-mips64el-linux-gnuabi64_9.3.0-8cross1 cpp-mips64el-linux-gnuabi64_4:9.2.1-4.1 cross-config_2.6.15-3.1 crossbuild-essential-mips64el_12.8 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2 debian-archive-keyring_2019.1 debianutils_4.11 dh-autoreconf_19 dh-strip-nondeterminism_1.8.1-2 diffutils_1:3.7-3 dpkg_1.20.4 dpkg-cross_2.6.15-3.1 dpkg-dev_1.20.4 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.35.2-7 file_1:5.38-5 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-9_9.3.0-14 g++-9-mips64el-linux-gnuabi64_9.3.0-8cross1 g++-mips64el-linux-gnuabi64_4:9.2.1-4.1 gcc_4:9.2.1-3.1 gcc-10-base_10.1.0-4 gcc-10-cross-base-mipsen_10-20200324-1cross1 gcc-8-base_8.4.0-4 gcc-9_9.3.0-14 gcc-9-base_9.3.0-14 gcc-9-cross-base-mipsen_9.3.0-8cross1 gcc-9-mips64el-linux-gnuabi64_9.3.0-8cross1 gcc-9-mips64el-linux-gnuabi64-base_9.3.0-8cross1 gcc-mips64el-linux-gnuabi64_4:9.2.1-4.1 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_1.58 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_9.3.0-14 libatomic1_10.1.0-4 libatomic1-mips64el-cross_10-20200324-1cross1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3+b1 libbinutils_2.34.90.20200706-1 libblkid1_2.35.2-7 libbrotli1_1.0.7-6.1 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 libc6-dev-mips64el-cross_2.30-2cross1 libc6-mips64el-cross_2.30-2cross1 libcap-ng0_0.7.9-2.2 libcc1-0_10.1.0-4 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_2.34.90.20200706-1 libctf0_2.34.90.20200706-1 libcurl3-gnutls_7.68.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.253 libdebhelper-perl_13.2 libdebian-dpkgcross-perl_2.6.15-3.1 libdeflate0_1.6-1 libdpkg-perl_1.20.4 libelf1_0.176-1.1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.35.2-7 libffi6_3.2.1-9 libffi7_3.3-4 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.8.1-2 libfile-which-perl_1.23-1 libgcc-9-dev_9.3.0-14 libgcc-9-dev-mips64el-cross_9.3.0-8cross1 libgcc-s1_10.1.0-4 libgcc-s1-mips64el-cross_10-20200324-1cross1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.4-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2 libgomp1_10.1.0-4 libgomp1-mips64el-cross_10-20200324-1cross1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10 libhogweed4_3.5.1+really3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.10.2-4 libhts3_1.10.2-4 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_10.1.0-4 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_10.1.0-4 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_2.35.2-7 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_2:8.39-13 libperl5.28_5.28.1-6 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2 libpsl5_0.21.0-1.1 libquadmath0_10.1.0-4 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_2.35.2-7 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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_3.0043 util-linux_2.35.2-7 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: 2.7.5a+20200629git1552aa0-1 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: 07a7305fadc11a4e554de9074e8ed706814ce02f 442872 rna-star_2.7.5a+20200629git1552aa0.orig.tar.xz 9dd76d7b6d130dc12e435921639a014d929e0db5 375748 rna-star_2.7.5a+20200629git1552aa0-1.debian.tar.xz Checksums-Sha256: 51cd546d04b387740f339b61e44bf68841e2da21fa1e5fdfffa76bb3b51fe762 442872 rna-star_2.7.5a+20200629git1552aa0.orig.tar.xz 3f1021fc020fe53b452cd2511daac4410fbe213bba20053d40354b52961d81a6 375748 rna-star_2.7.5a+20200629git1552aa0-1.debian.tar.xz Files: 0645a97dd3ff4dda32a31e9aef7d9fe1 442872 rna-star_2.7.5a+20200629git1552aa0.orig.tar.xz 97c32e5166ecf5f8acf97bed5d77c10d 375748 rna-star_2.7.5a+20200629git1552aa0-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJHBAEBCAAxFiEEhMGXeonn7+0+XKYuL9i+2sAg7tEFAl8ErSsTHG1vZWxsZXJA ZGViaWFuLm9yZwAKCRAv2L7awCDu0VyOD/0YPREzP4z6WI63k1pZzIESnF991PcR 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check signature: No public key dpkg-source: warning: failed to verify signature on ./rna-star_2.7.5a+20200629git1552aa0-1.dsc dpkg-source: info: extracting rna-star in /<> dpkg-source: info: unpacking rna-star_2.7.5a+20200629git1552aa0.orig.tar.xz dpkg-source: info: unpacking rna-star_2.7.5a+20200629git1552aa0-1.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 dpkg-source: info: applying mathRoutinesNotInScope.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.mips64el 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-66bfb700-63cc-4a08-bf09-a4d19233a87c SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -amips64el -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package rna-star dpkg-buildpackage: info: source version 2.7.5a+20200629git1552aa0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steffen Moeller dpkg-architecture: warning: specified GNU system type mips64el-linux-gnuabi64 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 mips64el 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=mips64el-linux-gnuabi64-pkg-config CXX=mips64el-linux-gnuabi64-g\+\+ CC=mips64el-linux-gnuabi64-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 GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_consensusSequence.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.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_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.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_transformGenome.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_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.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 SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp twoPassRunPass1.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 GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_consensusSequence.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.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_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.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_transformGenome.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_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.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 SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp twoPassRunPass1.cpp bam_cat.c 'rm' -f ./Depend.list mips64el-linux-gnuabi64-g++ -std=c++11 -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 GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_consensusSequence.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.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_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.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_transformGenome.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_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.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 SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd >> Depend.list mips64el-linux-gnuabi64-g++: warning: parametersDefault.xxd: linker input file unused because linking not done mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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=""' soloInputFeatureUMI.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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_countSmartSeq.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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_redistributeReadsByCB.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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_quantTranscript.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 SoloFeature_outputResults.cpp: In member function ‘void SoloFeature::outputResults(bool)’: SoloFeature_outputResults.cpp:45:17: warning: ignoring return value of ‘int symlink(const char*, const char*)’, declared with attribute warn_unused_result [-Wunused-result] 45 | symlink("../../../SJ.out.tab", (outputPrefix1+pSolo.outFileNames[1]).c_str()); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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_transformGenome.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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_transformGenome.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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_convertGenomeCigar.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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=""' twoPassRunPass1.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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=""' samHeaders.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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_genomeLoad.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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_genomeOutLoad.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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_transformGenome.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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_outputSpliceGraphSAM.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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_mapOneReadSpliceGraph.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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=""' SpliceGraph.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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=""' SpliceGraph_swScoreSpliced.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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=""' SpliceGraph_swTraceBack.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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=""' SpliceGraph_findSuperTr.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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=""' sjAlignSplit.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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=""' GTF.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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=""' GTF_transcriptGeneSJ.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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=""' GTF_superTranscript.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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=""' SuperTranscriptome.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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:173:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] 173 | bgzf_flush(P.inOut->outBAMfileUnsorted); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:177:19: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result] 177 | bgzf_flush(P.inOut->outQuantBAMfile); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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_consensusSequence.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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_readFilesInit.cpp mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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()); | ~~~~~~^~~~~~~~~~~~~~ mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -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); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 ‘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); | ~~~~~~~~~~^~~~ mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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); | ~~~~~~~~~~^~~~~~~~~ mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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 mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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); | ~~~~~~~~~~^~~~~~~~~ mips64el-linux-gnuabi64-g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -std=c++11 -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); | ~~~~~~~~~~^~~~~~~~~ mips64el-linux-gnuabi64-g++ -o STAR -O3 -std=c++11 -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 soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o 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_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.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 Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o Genome_consensusSequence.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.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_readFilesInit.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 -lhts -Bdynamic -lz -Wl,-z,relro -Wl,-z,now Parameters_openReadsFiles.cpp: In member function ‘void Parameters::openReadsFiles()’: Parameters_openReadsFiles.cpp:46:23: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 46 | system(("ls -lL " + readFilesNames[imate][ifile] + " > "+ outFileTmp+"/readFilesIn.info 2>&1").c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/<>/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_2.7.5a+20200629git1552aa0-1_mips64el.deb'. dpkg-deb: building package 'rna-star-dbgsym' in '../rna-star-dbgsym_2.7.5a+20200629git1552aa0-1_mips64el.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../rna-star_2.7.5a+20200629git1552aa0-1_mips64el.changes dpkg-genchanges: warning: the current version (2.7.5a+20200629git1552aa0-1) is earlier than the previous one (2.7.5a+dfsg-1) 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 2020-07-08T07:40:55Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ rna-star_2.7.5a+20200629git1552aa0-1_mips64el.changes: ------------------------------------------------------ Format: 1.8 Date: Tue, 07 Jul 2020 19:09:25 +0200 Source: rna-star Binary: rna-star rna-star-dbgsym Built-For-Profiles: cross nocheck Architecture: mips64el Version: 2.7.5a+20200629git1552aa0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Steffen Moeller Description: rna-star - ultrafast universal RNA-seq aligner Changes: rna-star (2.7.5a+20200629git1552aa0-1) unstable; urgency=medium . * Upstream kindly fixed the FTBFS reported before 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rna-star_2.7.5a+20200629git1552aa0-1_mips64el.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Wed, 08 Jul 2020 07:40:55 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.69-11.1), automake (= 1:1.16.2-3), autopoint (= 0.19.8.1-10), autotools-dev (= 20180224.1), base-files (= 11), base-passwd (= 3.5.47), bash (= 5.0-6), binutils (= 2.34.90.20200706-1), binutils-common (= 2.34.90.20200706-1), binutils-x86-64-linux-gnu (= 2.34.90.20200706-1), bsdextrautils (= 2.35.2-7), bsdutils (= 1:2.35.2-7), build-essential (= 12.8), bzip2 (= 1.0.8-3), coreutils (= 8.32-2), cpp (= 4:9.2.1-3.1), cpp-9 (= 9.3.0-14), dash (= 0.5.10.2-7), debconf (= 1.5.74), debhelper (= 13.2), debianutils (= 4.11), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.8.1-2), diffutils (= 1:3.7-3), dpkg (= 1.20.4), dpkg-dev (= 1.20.4), dwz (= 0.13-5), file (= 1:5.38-5), findutils (= 4.7.0-1), g++ (= 4:9.2.1-3.1), g++-9 (= 9.3.0-14), gcc (= 4:9.2.1-3.1), gcc-10-base (= 10.1.0-4), gcc-9 (= 9.3.0-14), 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(= 1.4.18-4), make (= 4.3-4), man-db (= 2.9.3-2), 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 (= 2.35.2-7), 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="1594141765" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ rna-star-dbgsym_2.7.5a+20200629git1552aa0-1_mips64el.deb -------------------------------------------------------- new Debian package, version 2.0. size 6016148 bytes: control archive=552 bytes. 418 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: rna-star-dbgsym Source: rna-star Version: 2.7.5a+20200629git1552aa0-1 Auto-Built-Package: debug-symbols Architecture: mips64el Maintainer: Debian Med Packaging Team Installed-Size: 6320 Depends: rna-star (= 2.7.5a+20200629git1552aa0-1) Section: debug Priority: optional Description: debug symbols for rna-star Build-Ids: 1e2d3bd5a9cc18423320a5ddeab358e89673f649 drwxr-xr-x root/root 0 2020-07-07 17:09 ./ drwxr-xr-x root/root 0 2020-07-07 17:09 ./usr/ drwxr-xr-x root/root 0 2020-07-07 17:09 ./usr/lib/ drwxr-xr-x root/root 0 2020-07-07 17:09 ./usr/lib/debug/ drwxr-xr-x root/root 0 2020-07-07 17:09 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2020-07-07 17:09 ./usr/lib/debug/.build-id/1e/ -rw-r--r-- root/root 6460512 2020-07-07 17:09 ./usr/lib/debug/.build-id/1e/2d3bd5a9cc18423320a5ddeab358e89673f649.debug drwxr-xr-x root/root 0 2020-07-07 17:09 ./usr/share/ drwxr-xr-x root/root 0 2020-07-07 17:09 ./usr/share/doc/ lrwxrwxrwx root/root 0 2020-07-07 17:09 ./usr/share/doc/rna-star-dbgsym -> rna-star rna-star_2.7.5a+20200629git1552aa0-1_mips64el.deb ------------------------------------------------- new Debian package, version 2.0. size 539888 bytes: control archive=1420 bytes. 1385 bytes, 24 lines control 672 bytes, 10 lines md5sums Package: rna-star Version: 2.7.5a+20200629git1552aa0-1 Architecture: mips64el Maintainer: Debian Med Packaging Team Installed-Size: 1305 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 2020-07-07 17:09 ./ drwxr-xr-x root/root 0 2020-07-07 17:09 ./usr/ drwxr-xr-x root/root 0 2020-07-07 17:09 ./usr/bin/ -rwxr-xr-x root/root 1074960 2020-07-07 17:09 ./usr/bin/STAR drwxr-xr-x root/root 0 2020-07-07 17:09 ./usr/share/ drwxr-xr-x root/root 0 2020-07-07 17:09 ./usr/share/doc-base/ -rw-r--r-- root/root 1179 2020-06-27 15:10 ./usr/share/doc-base/rna-star drwxr-xr-x root/root 0 2020-07-07 17:09 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-07-07 17:09 ./usr/share/doc/rna-star/ -rw-r--r-- root/root 220 2020-06-27 15:10 ./usr/share/doc/rna-star/README.Debian -rw-r--r-- root/root 3240 2020-07-07 16:47 ./usr/share/doc/rna-star/README.md -rw-r--r-- root/root 6368 2020-07-07 16:47 ./usr/share/doc/rna-star/RELEASEnotes.md.gz -rw-r--r-- root/root 217311 2020-07-07 16:47 ./usr/share/doc/rna-star/STARmanual.pdf -rw-r--r-- root/root 2257 2020-07-07 17:09 ./usr/share/doc/rna-star/changelog.Debian.gz -rw-r--r-- root/root 11036 2020-07-07 16:47 ./usr/share/doc/rna-star/changelog.gz -rw-r--r-- root/root 2565 2020-06-27 15:10 ./usr/share/doc/rna-star/copyright drwxr-xr-x root/root 0 2020-07-07 17:09 ./usr/share/man/ drwxr-xr-x root/root 0 2020-07-07 17:09 ./usr/share/man/man1/ -rw-r--r-- root/root 824 2020-07-07 17:09 ./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 [558 B] Get:5 copy:/<>/apt_archive ./ Packages [650 B] Fetched 2171 B in 0s (85.0 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 libdata-messagepack-perl libdata-validate-domain-perl libdevel-callchecker-perl libdevel-size-perl libdynaloader-functions-perl libemail-address-xs-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 libipc-system-simple-perl libjson-maybexs-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl liblist-utilsby-perl libmetrics-any-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-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 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-name-perl libsub-quote-perl libtest-metrics-any-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-xslate-perl libtime-duration-perl libtime-moment-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 patchutils readline-common t1utils Suggested packages: libxml-parser-perl libdata-dump-perl 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 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 libdata-messagepack-perl libdata-validate-domain-perl libdevel-callchecker-perl libdevel-size-perl libdynaloader-functions-perl libemail-address-xs-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 libipc-system-simple-perl libjson-maybexs-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl liblist-utilsby-perl libmetrics-any-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-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 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-name-perl libsub-quote-perl libtest-metrics-any-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-xslate-perl libtime-duration-perl libtime-moment-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 patchutils readline-common sbuild-build-depends-lintian-dummy:mips64el t1utils 0 upgraded, 78 newly installed, 0 to remove and 0 not upgraded. Need to get 7310 kB of archives. After this operation, 20.7 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [852 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 diffstat amd64 1.63-1 [35.6 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.3-7.1 [50.5 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.20-1 [532 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.32.3-1 [753 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.20-1 [894 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.36+b3 [71.0 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b2 [11.3 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libdynaloader-functions-perl all 0.003-1 [12.6 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.008-1+b1 [15.9 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libparams-classify-perl amd64 0.015-1+b2 [25.6 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-implementation-perl all 0.09-1 [12.9 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libvariable-magic-perl amd64 0.62-1+b2 [46.0 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-endofscope-perl all 0.24-1 [18.6 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-method-modifiers-perl all 2.13-1 [19.2 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-xsaccessor-perl amd64 1.19-3+b5 [38.4 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libclone-perl amd64 0.45-1 [15.1 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-tiny-perl all 2.24-1 [16.2 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libcpanel-json-xs-perl amd64 4.19-1 [126 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libdata-messagepack-perl amd64 1.00-2+b2 [38.2 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-1 [33.3 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libdata-validate-domain-perl all 0.10-1 [12.3 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-size-perl amd64 0.83-1+b1 [26.0 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libemail-address-xs-perl amd64 1.04-1+b2 [28.1 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libexporter-tiny-perl all 1.002002-1 [37.8 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-system-simple-perl all 1.30-1 [28.2 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libnumber-compare-perl all 0.03-1 [7642 B] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-glob-perl all 0.11-1 [8888 B] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libfont-ttf-perl all 1.06-1 [317 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libfuture-perl all 0.45-1 [84.4 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-tagset-perl all 3.20-4 [13.0 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 1.76-2 [90.2 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-parser-perl amd64 3.72-5 [105 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libstruct-dumb-perl all 0.12-1 [12.9 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libmetrics-any-perl all 0.06-1 [41.8 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libtest-metrics-any-perl all 0.01-2 [7060 B] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-perl all 0.77-3 [274 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 liblinux-epoll-perl amd64 0.017-1 [16.8 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-loop-epoll-perl all 0.21-1 [12.1 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libjson-maybexs-perl all 1.004002-1 [13.1 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-compare-perl all 0.53-1 [68.9 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl amd64 0.416-1+b5 [63.6 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-utilsby-perl all 0.11-1 [15.4 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 librole-tiny-perl all 2.001004-1 [20.8 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libmoo-perl all 2.004000-1 [59.4 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libmoox-aliases-perl all 0.001006-1 [10.2 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libmouse-perl amd64 2.5.10-1 [173 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libpackage-stash-perl all 0.38-1 [21.7 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-identify-perl amd64 0.14-1+b2 [12.0 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.26-1 [13.5 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.114-1 [53.6 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-decoder-perl amd64 4.014+ds-1 [106 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-encoder-perl amd64 4.014+ds-1 [108 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshteinxs-perl amd64 0.03-4+b7 [8696 B] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-xslate-perl amd64 3.5.8-1 [198 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libtime-duration-perl all 1.21-1 [13.7 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libtime-moment-perl amd64 0.44-1+b2 [75.1 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3300-1 [39.2 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libtype-tiny-perl all 1.010002-1 [338 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libunicode-utf8-perl amd64 0.62-1+b1 [20.2 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-writer-perl all 0.625-1 [29.7 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.82+repack-1 [35.6 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.3.4-3 [89.9 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.83.0 [1296 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7310 kB in 0s (32.4 MB/s) Selecting previously unselected package readline-common. (Reading database ... 20526 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 diffstat. Preparing to unpack .../02-diffstat_1.63-1_amd64.deb ... Unpacking diffstat (1.63-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../03-libassuan0_2.5.3-7.1_amd64.deb ... Unpacking libassuan0:amd64 (2.5.3-7.1) ... Selecting previously unselected package gpgconf. Preparing to unpack .../04-gpgconf_2.2.20-1_amd64.deb ... Unpacking gpgconf (2.2.20-1) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../05-libsqlite3-0_3.32.3-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.32.3-1) ... Selecting previously unselected package gpg. Preparing to unpack .../06-gpg_2.2.20-1_amd64.deb ... Unpacking gpg (2.2.20-1) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../07-libapt-pkg-perl_0.1.36+b3_amd64.deb ... Unpacking libapt-pkg-perl (0.1.36+b3) ... Selecting previously unselected package libb-hooks-op-check-perl. Preparing to unpack .../08-libb-hooks-op-check-perl_0.22-1+b2_amd64.deb ... Unpacking libb-hooks-op-check-perl (0.22-1+b2) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../09-libdynaloader-functions-perl_0.003-1_all.deb ... Unpacking libdynaloader-functions-perl (0.003-1) ... Selecting previously unselected package libdevel-callchecker-perl. Preparing to unpack .../10-libdevel-callchecker-perl_0.008-1+b1_amd64.deb ... Unpacking libdevel-callchecker-perl (0.008-1+b1) ... Selecting previously unselected package libparams-classify-perl. Preparing to unpack .../11-libparams-classify-perl_0.015-1+b2_amd64.deb ... 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Preparing to unpack .../22-libconfig-tiny-perl_2.24-1_all.deb ... Unpacking libconfig-tiny-perl (2.24-1) ... Selecting previously unselected package libcpanel-json-xs-perl. Preparing to unpack .../23-libcpanel-json-xs-perl_4.19-1_amd64.deb ... Unpacking libcpanel-json-xs-perl (4.19-1) ... Selecting previously unselected package libdata-messagepack-perl. Preparing to unpack .../24-libdata-messagepack-perl_1.00-2+b2_amd64.deb ... Unpacking libdata-messagepack-perl (1.00-2+b2) ... Selecting previously unselected package libnet-domain-tld-perl. Preparing to unpack .../25-libnet-domain-tld-perl_1.75-1_all.deb ... Unpacking libnet-domain-tld-perl (1.75-1) ... Selecting previously unselected package libdata-validate-domain-perl. Preparing to unpack .../26-libdata-validate-domain-perl_0.10-1_all.deb ... Unpacking libdata-validate-domain-perl (0.10-1) ... Selecting previously unselected package libdevel-size-perl. Preparing to unpack .../27-libdevel-size-perl_0.83-1+b1_amd64.deb ... Unpacking libdevel-size-perl (0.83-1+b1) ... Selecting previously unselected package libemail-address-xs-perl. Preparing to unpack .../28-libemail-address-xs-perl_1.04-1+b2_amd64.deb ... Unpacking libemail-address-xs-perl (1.04-1+b2) ... Selecting previously unselected package libexporter-tiny-perl. Preparing to unpack .../29-libexporter-tiny-perl_1.002002-1_all.deb ... Unpacking libexporter-tiny-perl (1.002002-1) ... Selecting previously unselected package libipc-system-simple-perl. Preparing to unpack .../30-libipc-system-simple-perl_1.30-1_all.deb ... Unpacking libipc-system-simple-perl (1.30-1) ... Selecting previously unselected package libfile-basedir-perl. Preparing to unpack .../31-libfile-basedir-perl_0.08-1_all.deb ... Unpacking libfile-basedir-perl (0.08-1) ... Selecting previously unselected package libnumber-compare-perl. Preparing to unpack .../32-libnumber-compare-perl_0.03-1_all.deb ... Unpacking libnumber-compare-perl (0.03-1) ... 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Selecting previously unselected package libhtml-parser-perl. Preparing to unpack .../39-libhtml-parser-perl_3.72-5_amd64.deb ... Unpacking libhtml-parser-perl (3.72-5) ... Selecting previously unselected package libimport-into-perl. Preparing to unpack .../40-libimport-into-perl_1.002005-1_all.deb ... Unpacking libimport-into-perl (1.002005-1) ... Selecting previously unselected package libstruct-dumb-perl. Preparing to unpack .../41-libstruct-dumb-perl_0.12-1_all.deb ... Unpacking libstruct-dumb-perl (0.12-1) ... Selecting previously unselected package libmetrics-any-perl. Preparing to unpack .../42-libmetrics-any-perl_0.06-1_all.deb ... Unpacking libmetrics-any-perl (0.06-1) ... Selecting previously unselected package libtest-metrics-any-perl. Preparing to unpack .../43-libtest-metrics-any-perl_0.01-2_all.deb ... Unpacking libtest-metrics-any-perl (0.01-2) ... Selecting previously unselected package libio-async-perl. Preparing to unpack .../44-libio-async-perl_0.77-3_all.deb ... Unpacking libio-async-perl (0.77-3) ... Selecting previously unselected package liblinux-epoll-perl. Preparing to unpack .../45-liblinux-epoll-perl_0.017-1_amd64.deb ... Unpacking liblinux-epoll-perl (0.017-1) ... Selecting previously unselected package libio-async-loop-epoll-perl. Preparing to unpack .../46-libio-async-loop-epoll-perl_0.21-1_all.deb ... Unpacking libio-async-loop-epoll-perl (0.21-1) ... Selecting previously unselected package libjson-maybexs-perl. Preparing to unpack .../47-libjson-maybexs-perl_1.004002-1_all.deb ... Unpacking libjson-maybexs-perl (1.004002-1) ... Selecting previously unselected package liblist-compare-perl. Preparing to unpack .../48-liblist-compare-perl_0.53-1_all.deb ... Unpacking liblist-compare-perl (0.53-1) ... Selecting previously unselected package liblist-moreutils-perl. Preparing to unpack .../49-liblist-moreutils-perl_0.416-1+b5_amd64.deb ... Unpacking liblist-moreutils-perl (0.416-1+b5) ... 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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: 193404 Build-Time: 274 Distribution: unstable Foreign Architectures: mips64el Host Architecture: mips64el Install-Time: 20 Job: rna-star_2.7.5a+20200629git1552aa0-1 Lintian: pass Machine Architecture: amd64 Package: rna-star Package-Time: 304 Source-Version: 2.7.5a+20200629git1552aa0-1 Space: 193404 Status: successful Version: 2.7.5a+20200629git1552aa0-1 -------------------------------------------------------------------------------- Finished at 2020-07-08T07:40:55Z Build needed 00:05:04, 193404k disk space