sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on gcc131.bak.milne.osuosl.org +==============================================================================+ | rna-star 2.7.1a+dfsg-1 (mips64el) Sun, 14 Jul 2019 05:24:45 +0000 | +==============================================================================+ Package: rna-star Version: 2.7.1a+dfsg-1 Source Version: 2.7.1a+dfsg-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-95e07f66-b357-4d8f-914a-a14c71fec2b2' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [149 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-07-13-0819.55.pdiff [3381 B] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2019-07-13-1430.24.pdiff [11.0 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2019-07-13-2016.13.pdiff [10.9 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main Sources 2019-07-14-0215.59.pdiff [5928 B] Get:7 http://debian.oregonstate.edu/debian unstable/main Sources 2019-07-14-0215.59.pdiff [5928 B] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-07-13-0819.55.pdiff [3123 B] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-07-13-1430.24.pdiff [21.1 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-07-13-2016.13.pdiff [13.2 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-07-14-0215.59.pdiff [7040 B] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-07-14-0215.59.pdiff [7040 B] Get:12 http://debian.oregonstate.edu/debian unstable/main mips64el Packages [8066 kB] Fetched 8346 kB in 2s (4171 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libsystemd0 libtasn1-6 libudev1 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 532 kB of archives. After this operation, 2048 B of additional disk space will be used. Get:1 http://debian.oregonstate.edu/debian unstable/main amd64 libsystemd0 amd64 241-6+b1 [330 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libtasn1-6 amd64 4.13-4 [52.1 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libudev1 amd64 241-6+b1 [149 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 532 kB in 0s (9225 kB/s) (Reading database ... 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Processing triggers for libc-bin (2.28-10) ... +------------------------------------------------------------------------------+ | 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 749 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main rna-star 2.7.1a+dfsg-1 (dsc) [2142 B] Get:2 http://debian.oregonstate.edu/debian unstable/main rna-star 2.7.1a+dfsg-1 (tar) [372 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main rna-star 2.7.1a+dfsg-1 (diff) [375 kB] Fetched 749 kB in 0s (32.2 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/rna-star-1zB0lY/rna-star-2.7.1a+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/rna-star-1zB0lY' with '<>' +------------------------------------------------------------------------------+ | Install crossbuild-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-mips64el:amd64 Filtered Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-mips64el:amd64 dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-tTzhBa/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-tTzhBa/apt_archive ./ InRelease Get:2 copy:/<>/resolver-tTzhBa/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-tTzhBa/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-tTzhBa/apt_archive ./ Sources [364 B] Get:5 copy:/<>/resolver-tTzhBa/apt_archive ./ Packages [452 B] Fetched 1773 B in 0s (84.3 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: binutils-mips64el-linux-gnuabi64 cpp-8-mips64el-linux-gnuabi64 cpp-mips64el-linux-gnuabi64 cross-config crossbuild-essential-mips64el dpkg-cross file g++-8-mips64el-linux-gnuabi64 g++-mips64el-linux-gnuabi64 gcc-8-cross-base gcc-8-mips64el-linux-gnuabi64 gcc-8-mips64el-linux-gnuabi64-base gcc-9-cross-base gcc-mips64el-linux-gnuabi64 libatomic1-mips64el-cross libc6-dev-mips64el-cross libc6-mips64el-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-mips64el-cross libgcc1-mips64el-cross libgomp1-mips64el-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libstdc++-8-dev-mips64el-cross libstdc++6-mips64el-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-mips64el-cross sensible-utils ucf Suggested packages: binutils-doc gcc-8-locales cpp-doc binutils-multiarch g++-8-multilib-mips64el-linux-gnuabi64 gcc-8-doc libstdc++6-8-dbg-mips64el-cross gcc-8-multilib-mips64el-linux-gnuabi64 libgcc1-dbg-mips64el-cross libgomp1-dbg-mips64el-cross libitm1-dbg-mips64el-cross libatomic1-dbg-mips64el-cross libasan5-dbg-mips64el-cross liblsan0-dbg-mips64el-cross libtsan0-dbg-mips64el-cross libubsan1-dbg-mips64el-cross libmpx2-dbg-mips64el-cross libquadmath0-dbg-mips64el-cross manpages-dev autoconf automake libtool flex bison gdb-mips64el-linux-gnuabi64 gcc-doc libyaml-shell-perl Recommended packages: libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl The following NEW packages will be installed: binutils-mips64el-linux-gnuabi64 cpp-8-mips64el-linux-gnuabi64 cpp-mips64el-linux-gnuabi64 cross-config crossbuild-essential-mips64el dpkg-cross file g++-8-mips64el-linux-gnuabi64 g++-mips64el-linux-gnuabi64 gcc-8-cross-base gcc-8-mips64el-linux-gnuabi64 gcc-8-mips64el-linux-gnuabi64-base gcc-9-cross-base gcc-mips64el-linux-gnuabi64 libatomic1-mips64el-cross libc6-dev-mips64el-cross libc6-mips64el-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-mips64el-cross libgcc1-mips64el-cross libgomp1-mips64el-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libstdc++-8-dev-mips64el-cross libstdc++6-mips64el-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-mips64el-cross sbuild-build-depends-core-dummy:mips64el sensible-utils ucf 0 upgraded, 43 newly installed, 0 to remove and 0 not upgraded. Need to get 40.8 MB of archives. After this operation, 151 MB of additional disk space will be used. Get:1 copy:/<>/resolver-tTzhBa/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [880 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.35-4 [242 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.35-4 [117 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.35-4 [66.3 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-mips64el-linux-gnuabi64 amd64 2.32.51.20190707-1 [2530 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-mips64el-linux-gnuabi64-base amd64 8.3.0-19cross1 [192 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-8-mips64el-linux-gnuabi64 amd64 8.3.0-19cross1 [6278 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-mips64el-linux-gnuabi64 amd64 4:8.3.0-1 [16.5 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-cross-base all 8.3.0-19cross1 [187 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.1.0-8cross1 [185 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-mips64el-cross all 2.28-10cross3 [1354 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-mips64el-cross all 1:9.1.0-8cross1 [69.2 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-mips64el-cross all 9.1.0-8cross1 [76.7 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-mips64el-cross all 9.1.0-8cross1 [7448 B] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-8-dev-mips64el-cross all 8.3.0-19cross1 [235 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-mips64el-linux-gnuabi64 amd64 8.3.0-19cross1 [6698 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-mips64el-linux-gnuabi64 amd64 4:8.3.0-1 [1472 B] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-mips64el-cross all 9.1.0-8cross1 [396 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-mips64el-cross all 4.19.37-5cross3 [1266 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-mips64el-cross all 2.28-10cross3 [2513 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-8-dev-mips64el-cross all 8.3.0-19cross1 [1563 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 g++-8-mips64el-linux-gnuabi64 amd64 8.3.0-19cross1 [6859 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 g++-mips64el-linux-gnuabi64 amd64 4:8.3.0-1 [1192 B] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000001-1 [51.9 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-2 [8301 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.00+dfsg-1 [58.6 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1 [344 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.27-1 [66.8 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-mips64el all 12.6 [6584 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 40.8 MB in 1s (62.2 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 11957 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-3+b4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.35-4_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../03-libmagic1_1%3a5.35-4_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.35-4_amd64.deb ... Unpacking file (1:5.35-4) ... Selecting previously unselected package ucf. Preparing to unpack .../05-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package binutils-mips64el-linux-gnuabi64. Preparing to unpack .../06-binutils-mips64el-linux-gnuabi64_2.32.51.20190707-1_amd64.deb ... Unpacking binutils-mips64el-linux-gnuabi64 (2.32.51.20190707-1) ... Selecting previously unselected package gcc-8-mips64el-linux-gnuabi64-base:amd64. Preparing to unpack .../07-gcc-8-mips64el-linux-gnuabi64-base_8.3.0-19cross1_amd64.deb ... Unpacking gcc-8-mips64el-linux-gnuabi64-base:amd64 (8.3.0-19cross1) ... Selecting previously unselected package cpp-8-mips64el-linux-gnuabi64. Preparing to unpack .../08-cpp-8-mips64el-linux-gnuabi64_8.3.0-19cross1_amd64.deb ... Unpacking cpp-8-mips64el-linux-gnuabi64 (8.3.0-19cross1) ... Selecting previously unselected package cpp-mips64el-linux-gnuabi64. Preparing to unpack .../09-cpp-mips64el-linux-gnuabi64_4%3a8.3.0-1_amd64.deb ... Unpacking cpp-mips64el-linux-gnuabi64 (4:8.3.0-1) ... Selecting previously unselected package cross-config. Preparing to unpack .../10-cross-config_2.6.15-3_all.deb ... Unpacking cross-config (2.6.15-3) ... Selecting previously unselected package gcc-8-cross-base. Preparing to unpack .../11-gcc-8-cross-base_8.3.0-19cross1_all.deb ... Unpacking gcc-8-cross-base (8.3.0-19cross1) ... Selecting previously unselected package gcc-9-cross-base. Preparing to unpack .../12-gcc-9-cross-base_9.1.0-8cross1_all.deb ... Unpacking gcc-9-cross-base (9.1.0-8cross1) ... Selecting previously unselected package libc6-mips64el-cross. Preparing to unpack .../13-libc6-mips64el-cross_2.28-10cross3_all.deb ... Unpacking libc6-mips64el-cross (2.28-10cross3) ... Selecting previously unselected package libgcc1-mips64el-cross. Preparing to unpack .../14-libgcc1-mips64el-cross_1%3a9.1.0-8cross1_all.deb ... Unpacking libgcc1-mips64el-cross (1:9.1.0-8cross1) ... Selecting previously unselected package libgomp1-mips64el-cross. Preparing to unpack .../15-libgomp1-mips64el-cross_9.1.0-8cross1_all.deb ... Unpacking libgomp1-mips64el-cross (9.1.0-8cross1) ... Selecting previously unselected package libatomic1-mips64el-cross. Preparing to unpack .../16-libatomic1-mips64el-cross_9.1.0-8cross1_all.deb ... Unpacking libatomic1-mips64el-cross (9.1.0-8cross1) ... Selecting previously unselected package libgcc-8-dev-mips64el-cross. Preparing to unpack .../17-libgcc-8-dev-mips64el-cross_8.3.0-19cross1_all.deb ... Unpacking libgcc-8-dev-mips64el-cross (8.3.0-19cross1) ... Selecting previously unselected package gcc-8-mips64el-linux-gnuabi64. Preparing to unpack .../18-gcc-8-mips64el-linux-gnuabi64_8.3.0-19cross1_amd64.deb ... Unpacking gcc-8-mips64el-linux-gnuabi64 (8.3.0-19cross1) ... Selecting previously unselected package gcc-mips64el-linux-gnuabi64. Preparing to unpack .../19-gcc-mips64el-linux-gnuabi64_4%3a8.3.0-1_amd64.deb ... Unpacking gcc-mips64el-linux-gnuabi64 (4:8.3.0-1) ... Selecting previously unselected package libstdc++6-mips64el-cross. 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Selecting previously unselected package g++-mips64el-linux-gnuabi64. Preparing to unpack .../25-g++-mips64el-linux-gnuabi64_4%3a8.3.0-1_amd64.deb ... Unpacking g++-mips64el-linux-gnuabi64 (4:8.3.0-1) ... Selecting previously unselected package libconfig-inifiles-perl. Preparing to unpack .../26-libconfig-inifiles-perl_3.000001-1_all.deb ... Unpacking libconfig-inifiles-perl (3.000001-1) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../27-libio-string-perl_1.08-3_all.deb ... Unpacking libio-string-perl (1.08-3) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../28-libicu63_63.2-2_amd64.deb ... Unpacking libicu63:amd64 (63.2-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../29-libxml2_2.9.4+dfsg1-7+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libxml-namespacesupport-perl. Preparing to unpack .../30-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 .../31-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 .../32-libxml-sax-perl_1.00+dfsg-1_all.deb ... Unpacking libxml-sax-perl (1.00+dfsg-1) ... Selecting previously unselected package libxml-libxml-perl. Preparing to unpack .../33-libxml-libxml-perl_2.0134+dfsg-1_amd64.deb ... Unpacking libxml-libxml-perl (2.0134+dfsg-1) ... Selecting previously unselected package libxml-simple-perl. Preparing to unpack .../34-libxml-simple-perl_2.25-1_all.deb ... Unpacking libxml-simple-perl (2.25-1) ... Selecting previously unselected package libyaml-perl. Preparing to unpack .../35-libyaml-perl_1.27-1_all.deb ... Unpacking libyaml-perl (1.27-1) ... Selecting previously unselected package libconfig-auto-perl. Preparing to unpack .../36-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 .../37-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 .../38-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 .../39-libdebian-dpkgcross-perl_2.6.15-3_all.deb ... Unpacking libdebian-dpkgcross-perl (2.6.15-3) ... Selecting previously unselected package dpkg-cross. Preparing to unpack .../40-dpkg-cross_2.6.15-3_all.deb ... Unpacking dpkg-cross (2.6.15-3) ... Selecting previously unselected package crossbuild-essential-mips64el. Preparing to unpack .../41-crossbuild-essential-mips64el_12.6_all.deb ... Unpacking crossbuild-essential-mips64el (12.6) ... Selecting previously unselected package sbuild-build-depends-core-dummy:mips64el. Preparing to unpack .../42-sbuild-build-depends-core-dummy_0.invalid.0_mips64el.deb ... Unpacking sbuild-build-depends-core-dummy:mips64el (0.invalid.0) ... Setting up libconfig-inifiles-perl (3.000001-1) ... Setting up libfile-which-perl (1.23-1) ... Setting up libmagic-mgc (1:5.35-4) ... Setting up gcc-8-cross-base (8.3.0-19cross1) ... Setting up libmagic1:amd64 (1:5.35-4) ... Setting up libc6-mips64el-cross (2.28-10cross3) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up file (1:5.35-4) ... Setting up libyaml-perl (1.27-1) ... Setting up binutils-mips64el-linux-gnuabi64 (2.32.51.20190707-1) ... Setting up libicu63:amd64 (63.2-2) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up cross-config (2.6.15-3) ... Setting up gcc-9-cross-base (9.1.0-8cross1) ... Setting up gcc-8-mips64el-linux-gnuabi64-base:amd64 (8.3.0-19cross1) ... Setting up sensible-utils (0.0.12) ... Setting up linux-libc-dev-mips64el-cross (4.19.37-5cross3) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libgomp1-mips64el-cross (9.1.0-8cross1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up cpp-8-mips64el-linux-gnuabi64 (8.3.0-19cross1) ... Setting up libatomic1-mips64el-cross (9.1.0-8cross1) ... Setting up libgcc1-mips64el-cross (1:9.1.0-8cross1) ... Setting up libc6-dev-mips64el-cross (2.28-10cross3) ... Setting up ucf (3.0038+nmu1) ... Setting up libstdc++6-mips64el-cross (9.1.0-8cross1) ... Setting up cpp-mips64el-linux-gnuabi64 (4:8.3.0-1) ... Setting up libgcc-8-dev-mips64el-cross (8.3.0-19cross1) ... Setting up libxml-sax-perl (1.00+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-1) ... 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 libstdc++-8-dev-mips64el-cross (8.3.0-19cross1) ... Setting up gcc-8-mips64el-linux-gnuabi64 (8.3.0-19cross1) ... Setting up g++-8-mips64el-linux-gnuabi64 (8.3.0-19cross1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up gcc-mips64el-linux-gnuabi64 (4:8.3.0-1) ... Setting up g++-mips64el-linux-gnuabi64 (4:8.3.0-1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3) ... Setting up dpkg-cross (2.6.15-3) ... Setting up crossbuild-essential-mips64el (12.6) ... Setting up sbuild-build-depends-core-dummy:mips64el (0.invalid.0) ... Processing triggers for libc-bin (2.28-10) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (mips64el included in amd64 arm64 ppc64el mips64el) Setup apt archive ----------------- dpkg-deb: building package 'sbuild-build-depends-essential-dummy' in '/<>/resolver-tTzhBa/apt_archive/sbuild-build-depends-essential-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-tTzhBa/apt_archive ./ InRelease Get:2 copy:/<>/resolver-tTzhBa/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-tTzhBa/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-tTzhBa/apt_archive ./ Sources [484 B] Get:5 copy:/<>/resolver-tTzhBa/apt_archive ./ Packages [571 B] Fetched 2018 B in 0s (104 kB/s) Reading package lists... Reading package lists... Install essential build dependencies (apt-based resolver) --------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-essential-dummy:mips64el 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 848 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-tTzhBa/apt_archive ./ sbuild-build-depends-essential-dummy 0.invalid.0 [848 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 848 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-essential-dummy:mips64el. (Reading database ... 15135 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-essential-dummy_0.invalid.0_mips64el.deb ... Unpacking sbuild-build-depends-essential-dummy:mips64el (0.invalid.0) ... Setting up sbuild-build-depends-essential-dummy:mips64el (0.invalid.0) ... +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: libc-dev, libstdc++-dev, debhelper (>= 11), libhts-dev, vim-common, xxd, zlib1g-dev Filtered Build-Depends: libc-dev, libstdc++-dev, debhelper (>= 11), libhts-dev, vim-common, xxd, zlib1g-dev dpkg-deb: building package 'sbuild-build-depends-rna-star-dummy' in '/<>/resolver-tTzhBa/apt_archive/sbuild-build-depends-rna-star-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy sbuild-build-depends-rna-star-dummy dpkg-scanpackages: info: Wrote 3 entries to output Packages file. Ign:1 copy:/<>/resolver-tTzhBa/apt_archive ./ InRelease Get:2 copy:/<>/resolver-tTzhBa/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-tTzhBa/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-tTzhBa/apt_archive ./ Sources [658 B] Get:5 copy:/<>/resolver-tTzhBa/apt_archive ./ Packages [744 B] Fetched 2365 B in 0s (120 kB/s) Reading package lists... Reading package lists... Install rna-star 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 bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:mips64el gcc-9-base:mips64el gettext gettext-base groff-base intltool-debian libarchive-zip-perl libatomic1:mips64el libbsd0 libbz2-1.0:mips64el libc6:mips64el libc6-dev:mips64el libcom-err2:mips64el libcroco3 libcurl3-gnutls:mips64el libdb5.3:mips64el libdeflate0:mips64el libelf1 libffi6:mips64el libfile-stripnondeterminism-perl libgcc-8-dev:mips64el libgcc1:mips64el libgcrypt20:mips64el libglib2.0-0 libgmp10:mips64el libgnutls30:mips64el libgomp1:mips64el libgpg-error0:mips64el libgssapi-krb5-2:mips64el libhogweed4:mips64el libhts-dev:mips64el libhts2:mips64el libidn2-0:mips64el libk5crypto3:mips64el libkeyutils1:mips64el libkrb5-3:mips64el libkrb5support0:mips64el libldap-2.4-2:mips64el libldap-common liblzma-dev:mips64el liblzma5:mips64el libmonkey-patch-perl libncurses6 libnettle6:mips64el libnghttp2-14:mips64el libp11-kit0:mips64el libpipeline1 libpsl5:mips64el librtmp1:mips64el libsasl2-2:mips64el libsasl2-modules-db:mips64el libsigsegv2 libssh2-1:mips64el libssl1.1:mips64el libstdc++-8-dev:mips64el libstdc++6:mips64el libsub-delete-perl libsub-identify-perl libsuper-perl libtasn1-6:mips64el libtool libuchardet0 libunistring2:mips64el linux-libc-dev:mips64el m4 man-db po-debconf vim-common xxd zlib1g:mips64el zlib1g-dev:mips64el Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:mips64el libc-l10n:mips64el locales:mips64el manpages-dev:mips64el rng-tools:mips64el gnutls-bin:mips64el krb5-doc:mips64el krb5-user:mips64el liblzma-doc:mips64el libstdc++-8-doc:mips64el libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx ca-certificates:mips64el libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libgpg-error-l10n:mips64el krb5-locales:mips64el libgpm2 publicsuffix:mips64el libsasl2-modules:mips64el libltdl-dev libmail-sendmail-perl vim | vim-gtk | vim-gtk3 | vim-athena | vim-nox | vim-tiny The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:mips64el gcc-9-base:mips64el gettext gettext-base groff-base intltool-debian libarchive-zip-perl libatomic1:mips64el libbsd0 libbz2-1.0:mips64el libc6:mips64el libc6-dev:mips64el libcom-err2:mips64el libcroco3 libcurl3-gnutls:mips64el libdb5.3:mips64el libdeflate0:mips64el libelf1 libffi6:mips64el libfile-stripnondeterminism-perl libgcc-8-dev:mips64el libgcc1:mips64el libgcrypt20:mips64el libglib2.0-0 libgmp10:mips64el libgnutls30:mips64el libgomp1:mips64el libgpg-error0:mips64el libgssapi-krb5-2:mips64el libhogweed4:mips64el libhts-dev:mips64el libhts2:mips64el libidn2-0:mips64el libk5crypto3:mips64el libkeyutils1:mips64el libkrb5-3:mips64el libkrb5support0:mips64el libldap-2.4-2:mips64el libldap-common liblzma-dev:mips64el liblzma5:mips64el libmonkey-patch-perl libncurses6 libnettle6:mips64el libnghttp2-14:mips64el libp11-kit0:mips64el libpipeline1 libpsl5:mips64el librtmp1:mips64el libsasl2-2:mips64el libsasl2-modules-db:mips64el libsigsegv2 libssh2-1:mips64el libssl1.1:mips64el libstdc++-8-dev:mips64el libstdc++6:mips64el libsub-delete-perl libsub-identify-perl libsuper-perl libtasn1-6:mips64el libtool libuchardet0 libunistring2:mips64el linux-libc-dev:mips64el m4 man-db po-debconf sbuild-build-depends-rna-star-dummy:mips64el vim-common xxd zlib1g:mips64el zlib1g-dev:mips64el 0 upgraded, 81 newly installed, 0 to remove and 0 not upgraded. Need to get 30.9 MB of archives. After this operation, 119 MB of additional disk space will be used. Get:1 copy:/<>/resolver-tTzhBa/apt_archive ./ sbuild-build-depends-rna-star-dummy 0.invalid.0 [904 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.9.1-2 [99.5 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-3 [916 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main mips64el gcc-9-base mips64el 9.1.0-8 [190 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 xxd amd64 2:8.1.0875-5 [140 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 vim-common all 2:8.1.0875-5 [195 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-2 [203 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11 [341 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-10 [547 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-delete-perl all 1.00002-2 [7516 B] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-identify-perl amd64 0.14-1+b1 [12.0 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libsuper-perl all 1.20141117-1 [10.6 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libmonkey-patch-perl all 0.03-2 [11.4 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.2.0-2 [20.7 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.2.0-2 [13.4 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.12.20190711-1 [80.4 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.58.3-3 [1259 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.1+20181013-2 [102 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.1.1 [1016 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main mips64el gcc-8-base mips64el 8.3.0-19 [192 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main mips64el libgcc1 mips64el 1:9.1.0-8 [69.2 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main mips64el libc6 mips64el 2.28-10 [2562 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main mips64el libatomic1 mips64el 9.1.0-8 [7492 B] Get:40 http://debian.oregonstate.edu/debian unstable/main mips64el libbz2-1.0 mips64el 1.0.6-9.2 [46.6 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main mips64el linux-libc-dev mips64el 4.19.37-5 [1179 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main mips64el libc6-dev mips64el 2.28-10 [2513 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main mips64el libcom-err2 mips64el 1.45.2-1 [69.5 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main mips64el libgmp10 mips64el 2:6.1.2+dfsg-4 [237 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main mips64el libnettle6 mips64el 3.4.1-1 [227 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main mips64el libhogweed4 mips64el 3.4.1-1 [134 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main mips64el libunistring2 mips64el 0.9.10-2 [376 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main mips64el libidn2-0 mips64el 2.0.5-1 [75.5 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main mips64el libffi6 mips64el 3.2.1-9 [21.0 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main mips64el libp11-kit0 mips64el 0.23.15-2 [257 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main mips64el libtasn1-6 mips64el 4.13-4 [49.8 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main mips64el libgnutls30 mips64el 3.6.8-2 [993 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main mips64el libkeyutils1 mips64el 1.6-6 [14.5 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main mips64el libkrb5support0 mips64el 1.17-4 [62.4 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main mips64el libk5crypto3 mips64el 1.17-4 [120 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main mips64el libssl1.1 mips64el 1.1.1c-1 [1135 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main mips64el libkrb5-3 mips64el 1.17-4 [332 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main mips64el libgssapi-krb5-2 mips64el 1.17-4 [141 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main mips64el libdb5.3 mips64el 5.3.28+dfsg1-0.6 [597 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main mips64el libsasl2-modules-db mips64el 2.1.27+dfsg-1 [68.2 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main mips64el libsasl2-2 mips64el 2.1.27+dfsg-1 [102 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libldap-common all 2.4.47+dfsg-3 [89.4 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main mips64el libldap-2.4-2 mips64el 2.4.47+dfsg-3 [203 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main mips64el libnghttp2-14 mips64el 1.37.0-1 [78.8 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main mips64el libpsl5 mips64el 0.20.2-2 [53.5 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main mips64el zlib1g mips64el 1:1.2.11.dfsg-1 [91.1 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main mips64el librtmp1 mips64el 2.4+20151223.gitfa8646d.1-2 [55.9 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main mips64el libgpg-error0 mips64el 1.36-2 [68.0 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main mips64el libgcrypt20 mips64el 1.8.4-5 [496 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main mips64el libssh2-1 mips64el 1.8.0-2.1 [134 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main mips64el libcurl3-gnutls mips64el 7.65.1-1 [310 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main mips64el libdeflate0 mips64el 1.2-1 [49.6 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main mips64el libgomp1 mips64el 9.1.0-8 [78.4 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main mips64el libgcc-8-dev mips64el 8.3.0-19 [235 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main mips64el liblzma5 mips64el 5.2.4-1 [151 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main mips64el libhts2 mips64el 1.9-11 [279 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main mips64el liblzma-dev mips64el 5.2.4-1 [214 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main mips64el zlib1g-dev mips64el 1:1.2.11.dfsg-1 [215 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main mips64el libhts-dev mips64el 1.9-11 [4351 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main mips64el libstdc++6 mips64el 9.1.0-8 [436 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main mips64el libstdc++-8-dev mips64el 8.3.0-19 [1559 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 30.9 MB in 1s (55.2 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 15135 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_amd64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package gcc-9-base:mips64el. 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Setting up libsub-identify-perl (0.14-1+b1) ... Setting up libglib2.0-0:amd64 (2.58.3-3) ... No schema files found: doing nothing. Setting up linux-libc-dev:mips64el (4.19.37-5) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libldap-common (2.4.47+dfsg-3) ... Setting up xxd (2:8.1.0875-5) ... Setting up autotools-dev (20180224.1) ... Setting up vim-common (2:8.1.0875-5) ... Setting up libncurses6:amd64 (6.1+20181013-2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up gcc-8-base:mips64el (8.3.0-19) ... Setting up autopoint (0.19.8.1-9) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up libsub-delete-perl (1.00002-2) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libbsd0:amd64 (0.9.1-2) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up gcc-9-base:mips64el (9.1.0-8) ... Setting up libsuper-perl (1.20141117-1) ... Setting up gettext (0.19.8.1-9) ... Setting up libtool (2.4.6-10) ... Setting up m4 (1.4.18-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up autoconf (2.69-11) ... Setting up dwz (0.12.20190711-1) ... Setting up groff-base (1.22.4-3) ... Setting up libmonkey-patch-perl (0.03-2) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.2.0-2) ... Setting up po-debconf (1.0.21) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libc6:mips64el (2.28-10) ... Setting up libtasn1-6:mips64el (4.13-4) ... Setting up libc6-dev:mips64el (2.28-10) ... Setting up libbz2-1.0:mips64el (1.0.6-9.2) ... Setting up libdb5.3:mips64el (5.3.28+dfsg1-0.6) ... Setting up libkeyutils1:mips64el (1.6-6) ... Setting up liblzma5:mips64el (5.2.4-1) ... Setting up libgpg-error0:mips64el (1.36-2) ... Setting up libgcc1:mips64el (1:9.1.0-8) ... Setting up libssl1.1:mips64el (1.1.1c-1) ... Setting up libnghttp2-14:mips64el (1.37.0-1) ... Setting up libunistring2:mips64el (0.9.10-2) ... Setting up libdeflate0:mips64el (1.2-1) ... Setting up libgcrypt20:mips64el (1.8.4-5) ... Setting up zlib1g:mips64el (1:1.2.11.dfsg-1) ... Setting up libffi6:mips64el (3.2.1-9) ... Setting up libidn2-0:mips64el (2.0.5-1) ... Setting up libcom-err2:mips64el (1.45.2-1) ... Setting up libgomp1:mips64el (9.1.0-8) ... Setting up libkrb5support0:mips64el (1.17-4) ... Setting up libsasl2-modules-db:mips64el (2.1.27+dfsg-1) ... Setting up dh-autoreconf (19) ... Setting up libgmp10:mips64el (2:6.1.2+dfsg-4) ... Setting up libp11-kit0:mips64el (0.23.15-2) ... Setting up libatomic1:mips64el (9.1.0-8) ... Setting up libk5crypto3:mips64el (1.17-4) ... Setting up libnettle6:mips64el (3.4.1-1) ... Setting up libgcc-8-dev:mips64el (8.3.0-19) ... Setting up libsasl2-2:mips64el (2.1.27+dfsg-1) ... Setting up liblzma-dev:mips64el (5.2.4-1) ... Setting up dh-strip-nondeterminism (1.2.0-2) ... Setting up zlib1g-dev:mips64el (1:1.2.11.dfsg-1) ... Setting up libssh2-1:mips64el (1.8.0-2.1) ... Setting up libkrb5-3:mips64el (1.17-4) ... Setting up libstdc++6:mips64el (9.1.0-8) ... Setting up libstdc++-8-dev:mips64el (8.3.0-19) ... Setting up libpsl5:mips64el (0.20.2-2) ... Setting up libhogweed4:mips64el (3.4.1-1) ... Setting up debhelper (12.1.1) ... Setting up libgnutls30:mips64el (3.6.8-2) ... Setting up librtmp1:mips64el (2.4+20151223.gitfa8646d.1-2) ... Setting up libgssapi-krb5-2:mips64el (1.17-4) ... Setting up libldap-2.4-2:mips64el (2.4.47+dfsg-3) ... Setting up libcurl3-gnutls:mips64el (7.65.1-1) ... Setting up libhts2:mips64el (1.9-11) ... Setting up libhts-dev:mips64el (1.9-11) ... Setting up sbuild-build-depends-rna-star-dummy:mips64el (0.invalid.0) ... Processing triggers for libc-bin (2.28-10) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.32.51.20190707-1 dpkg-dev_1.19.7 g++-8_8.3.0-19 gcc-8_8.3.0-19 libc6-dev_2.28-10 libstdc++-8-dev_8.3.0-19 libstdc++-8-dev-mips64el-cross_8.3.0-19cross1 libstdc++6_9.1.0-8 libstdc++6-mips64el-cross_9.1.0-8cross1 linux-libc-dev_4.19.37-5 Package versions: adduser_3.118 apt_1.8.2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.46 bash_5.0-4 binutils_2.32.51.20190707-1 binutils-common_2.32.51.20190707-1 binutils-mips64el-linux-gnuabi64_2.32.51.20190707-1 binutils-x86-64-linux-gnu_2.32.51.20190707-1 bsdmainutils_11.1.2+b1 bsdutils_1:2.33.1-0.1 build-essential_12.6 bzip2_1.0.6-9.2 coreutils_8.30-3 cpp_4:8.3.0-1 cpp-8_8.3.0-19 cpp-8-mips64el-linux-gnuabi64_8.3.0-19cross1 cpp-mips64el-linux-gnuabi64_4:8.3.0-1 cross-config_2.6.15-3 crossbuild-essential-mips64el_12.6 dash_0.5.10.2-5 debconf_1.5.72 debhelper_12.1.1 debian-archive-keyring_2019.1 debianutils_4.8.6.2 dh-autoreconf_19 dh-strip-nondeterminism_1.2.0-2 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.12.20190711-1 e2fsprogs_1.45.2-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-4 findutils_4.6.0+git+20190510-2 g++_4:8.3.0-1 g++-8_8.3.0-19 g++-8-mips64el-linux-gnuabi64_8.3.0-19cross1 g++-mips64el-linux-gnuabi64_4:8.3.0-1 gcc_4:8.3.0-1 gcc-8_8.3.0-19 gcc-8-base_8.3.0-19 gcc-8-cross-base_8.3.0-19cross1 gcc-8-mips64el-linux-gnuabi64_8.3.0-19cross1 gcc-8-mips64el-linux-gnuabi64-base_8.3.0-19cross1 gcc-9-base_9.1.0-8 gcc-9-cross-base_9.1.0-8cross1 gcc-mips64el-linux-gnuabi64_4:8.3.0-1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.17-1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.21 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapt-pkg5.0_1.8.2 libarchive-zip-perl_1.64-1 libasan5_9.1.0-8 libatomic1_9.1.0-8 libatomic1-mips64el-cross_9.1.0-8cross1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.5-1 libaudit1_1:2.8.5-1 libbinutils_2.32.51.20190707-1 libblkid1_2.33.1-0.1 libbsd0_0.9.1-2 libbz2-1.0_1.0.6-9.2 libc-bin_2.28-10 libc-dev-bin_2.28-10 libc6_2.28-10 libc6-dev_2.28-10 libc6-dev-mips64el-cross_2.28-10cross3 libc6-mips64el-cross_2.28-10cross3 libcap-ng0_0.7.9-2 libcc1-0_9.1.0-8 libcom-err2_1.45.2-1 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000001-1 libcroco3_0.6.12-3 libcurl3-gnutls_7.65.1-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.249 libdebian-dpkgcross-perl_2.6.15-3 libdeflate0_1.2-1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.2-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.2.0-2 libfile-which-perl_1.23-1 libgcc-8-dev_8.3.0-19 libgcc-8-dev-mips64el-cross_8.3.0-19cross1 libgcc1_1:9.1.0-8 libgcc1-mips64el-cross_1:9.1.0-8cross1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-4 libgdbm6_1.18.1-4 libglib2.0-0_2.58.3-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.8-2 libgomp1_9.1.0-8 libgomp1-mips64el-cross_9.1.0-8cross1 libgpg-error0_1.36-2 libgssapi-krb5-2_1.17-4 libhogweed4_3.4.1-1 libhts-dev_1.9-11 libhts2_1.9-11 libicu63_63.2-2 libidn2-0_2.0.5-1 libio-string-perl_1.08-3 libisl19_0.20-2 libitm1_9.1.0-8 libk5crypto3_1.17-4 libkeyutils1_1.6-6 libkrb5-3_1.17-4 libkrb5support0_1.17-4 libldap-2.4-2_2.4.47+dfsg-3 libldap-common_2.4.47+dfsg-3 liblocale-gettext-perl_1.07-3+b4 liblsan0_9.1.0-8 liblz4-1_1.8.3-1 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-4 libmagic1_1:5.35-4 libmonkey-patch-perl_0.03-2 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.3.0-19 libncurses6_6.1+20181013-2 libncursesw6_6.1+20181013-2 libnettle6_3.4.1-1 libnghttp2-14_1.37.0-1 libp11-kit0_0.23.15-2 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_10.32-5 libpcre3_2:8.39-12 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libpsl5_0.20.2-2 libquadmath0_9.1.0-8 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1 libsasl2-modules-db_2.1.27+dfsg-1 libseccomp2_2.3.3-4 libselinux1_2.9-2 libsemanage-common_2.9-2 libsemanage1_2.9-2 libsepol1_2.9-2 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libss2_1.45.2-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1c-1 libstdc++-8-dev_8.3.0-19 libstdc++-8-dev-mips64el-cross_8.3.0-19cross1 libstdc++6_9.1.0-8 libstdc++6-mips64el-cross_9.1.0-8cross1 libsub-delete-perl_1.00002-2 libsub-identify-perl_0.14-1+b1 libsuper-perl_1.20141117-1 libsystemd0_241-6+b1 libtasn1-6_4.13-4 libtinfo6_6.1+20181013-2 libtool_2.4.6-10 libtsan0_9.1.0-8 libubsan1_9.1.0-8 libuchardet0_0.0.6-3 libudev1_241-6+b1 libunistring2_0.9.10-2 libuuid1_2.33.1-0.1 libxml-libxml-perl_2.0134+dfsg-1 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.00+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.4+dfsg1-7+b3 libyaml-perl_1.27-1 libzstd1_1.3.8+dfsg-3 linux-libc-dev_4.19.37-5 linux-libc-dev-mips64el-cross_4.19.37-5cross3 login_1:4.7-1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-2 mawk_1.3.3-17+b3 mount_2.33.1-0.1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 passwd_1:4.7-1 patch_2.7.6-4 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 po-debconf_1.0.21 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-essential-dummy_0.invalid.0 sbuild-build-depends-rna-star-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-8 tar_1.30+dfsg-6 tzdata_2019b-1 ucf_3.0038+nmu1 util-linux_2.33.1-0.1 vim-common_2:8.1.0875-5 xxd_2:8.1.0875-5 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Mon Jul 8 15:36:31 2019 UTC gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./rna-star_2.7.1a+dfsg-1.dsc dpkg-source: info: extracting rna-star in /<>/rna-star-2.7.1a+dfsg dpkg-source: info: unpacking rna-star_2.7.1a+dfsg.orig.tar.xz dpkg-source: info: unpacking rna-star_2.7.1a+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying donotuse_own_htslib.patch dpkg-source: info: applying mips_shm_noreserve.patch dpkg-source: info: applying reproducible.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.mips64el DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=POSIX 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-95e07f66-b357-4d8f-914a-a14c71fec2b2 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package rna-star dpkg-buildpackage: info: source version 2.7.1a+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss 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 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/rna-star-2.7.1a+dfsg' cd source && /usr/bin/make clean make[2]: Entering directory '/<>/rna-star-2.7.1a+dfsg/source' rm -f *.o STAR STARstatic STARlong Depend.list make[2]: Leaving directory '/<>/rna-star-2.7.1a+dfsg/source' rm -f source/parametersDefault.xxd make[1]: Leaving directory '/<>/rna-star-2.7.1a+dfsg' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>/rna-star-2.7.1a+dfsg' cd source && /usr/bin/make CCFLAGS_common_add="-flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x" CCFLAGS="-flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -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 '/<>/rna-star-2.7.1a+dfsg/source' xxd -i parametersDefault > parametersDefault.xxd echo Transcriptome.cpp Genome.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Stats.cpp blocksOverlap.cpp SoloReadFeature_record.cpp ChimericDetection_chimericDetectionMult.cpp outputSJ.cpp Quantifications.cpp ReadAlignChunk.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp SoloReadBarcode_getCBandUMI.cpp signalFromBAM.cpp Chain.cpp ReadAlign_calcCIGAR.cpp sjdbLoadFromStream.cpp sjAlignSplit.cpp SoloReadFeature_inputRecords.cpp Parameters_closeReadsFiles.cpp ReadAlign_CIGAR.cpp SoloFeature_collapseUMI.cpp stitchWindowAligns.cpp GlobalVariables.cpp Parameters.cpp ReadAlign_chimericDetection.cpp Transcriptome_geneFullAlignOverlap.cpp BAMfunctions.cpp ReadAlign.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp Transcript_generateCigarP.cpp ThreadControl.cpp BAMbinSortUnmapped.cpp ReadAlign_chimericDetectionOld.cpp sjdbInsertJunctions.cpp InOutStreams.cpp ReadAlign_chimericDetectionPEmerged.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp BAMoutput.cpp SoloReadBarcode.cpp genomeParametersWrite.cpp ParametersSolo.cpp ChimericAlign.cpp ReadAlign_outputTranscriptSJ.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign_chimericDetectionOldOutput.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_alignBAM.cpp ChimericAlign_chimericJunctionOutput.cpp genomeSAindex.cpp stringSubstituteAll.cpp ChimericDetection.cpp Transcript_variationOutput.cpp SharedMemory.cpp sysRemoveDir.cpp Transcript_variationAdjust.cpp ReadAlign_waspMap.cpp bamRemoveDuplicates.cpp ReadAlign_stitchWindowSeeds.cpp SoloRead_record.cpp ReadAlign_storeAligns.cpp ReadAlign_oneRead.cpp ReadAlign_mappedFilter.cpp ReadAlign_outputVariation.cpp Parameters_readSAMheader.cpp Transcript.cpp SuffixArrayFuns.cpp alignSmithWaterman.cpp SequenceFuns.cpp extendAlign.cpp ChimericAlign_chimericStitching.cpp OutSJ.cpp sjdbLoadFromFiles.cpp ReadAlign_peOverlapMergeMap.cpp genomeScanFastaFiles.cpp ReadAlign_mapOneRead.cpp sjdbBuildIndex.cpp ReadAlign_quantTranscriptome.cpp Genome_genomeGenerate.cpp Variation.cpp Parameters_openReadsFiles.cpp ReadAlign_outputTranscriptSAM.cpp PackedArray.cpp readLoad.cpp binarySearch2.cpp SoloReadFeature.cpp Solo.cpp Transcriptome_geneCountsAddAlign.cpp sjdbPrepare.cpp ChimericSegment.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp SoloFeature.cpp BAMbinSortByCoordinate.cpp Genome_insertSequences.cpp Transcriptome_quantAlign.cpp ReadAlign_outputAlignments.cpp STAR.cpp SoloFeature_outputResults.cpp SoloRead.cpp SoloFeature_processRecords.cpp bam_cat.c Transcriptome.cpp Genome.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Stats.cpp blocksOverlap.cpp SoloReadFeature_record.cpp ChimericDetection_chimericDetectionMult.cpp outputSJ.cpp Quantifications.cpp ReadAlignChunk.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp SoloReadBarcode_getCBandUMI.cpp signalFromBAM.cpp Chain.cpp ReadAlign_calcCIGAR.cpp sjdbLoadFromStream.cpp sjAlignSplit.cpp SoloReadFeature_inputRecords.cpp Parameters_closeReadsFiles.cpp ReadAlign_CIGAR.cpp SoloFeature_collapseUMI.cpp stitchWindowAligns.cpp GlobalVariables.cpp Parameters.cpp ReadAlign_chimericDetection.cpp Transcriptome_geneFullAlignOverlap.cpp BAMfunctions.cpp ReadAlign.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp Transcript_generateCigarP.cpp ThreadControl.cpp BAMbinSortUnmapped.cpp ReadAlign_chimericDetectionOld.cpp sjdbInsertJunctions.cpp InOutStreams.cpp ReadAlign_chimericDetectionPEmerged.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp BAMoutput.cpp SoloReadBarcode.cpp genomeParametersWrite.cpp ParametersSolo.cpp ChimericAlign.cpp ReadAlign_outputTranscriptSJ.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign_chimericDetectionOldOutput.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_alignBAM.cpp ChimericAlign_chimericJunctionOutput.cpp genomeSAindex.cpp stringSubstituteAll.cpp ChimericDetection.cpp Transcript_variationOutput.cpp SharedMemory.cpp sysRemoveDir.cpp Transcript_variationAdjust.cpp ReadAlign_waspMap.cpp bamRemoveDuplicates.cpp ReadAlign_stitchWindowSeeds.cpp SoloRead_record.cpp ReadAlign_storeAligns.cpp ReadAlign_oneRead.cpp ReadAlign_mappedFilter.cpp ReadAlign_outputVariation.cpp Parameters_readSAMheader.cpp Transcript.cpp SuffixArrayFuns.cpp alignSmithWaterman.cpp SequenceFuns.cpp extendAlign.cpp ChimericAlign_chimericStitching.cpp OutSJ.cpp sjdbLoadFromFiles.cpp ReadAlign_peOverlapMergeMap.cpp genomeScanFastaFiles.cpp ReadAlign_mapOneRead.cpp sjdbBuildIndex.cpp ReadAlign_quantTranscriptome.cpp Genome_genomeGenerate.cpp Variation.cpp Parameters_openReadsFiles.cpp ReadAlign_outputTranscriptSAM.cpp PackedArray.cpp readLoad.cpp binarySearch2.cpp SoloReadFeature.cpp Solo.cpp Transcriptome_geneCountsAddAlign.cpp sjdbPrepare.cpp ChimericSegment.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp SoloFeature.cpp BAMbinSortByCoordinate.cpp Genome_insertSequences.cpp Transcriptome_quantAlign.cpp ReadAlign_outputAlignments.cpp STAR.cpp SoloFeature_outputResults.cpp SoloRead.cpp SoloFeature_processRecords.cpp bam_cat.c 'rm' -f ./Depend.list g++ -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -MM Transcriptome.cpp Genome.cpp ReadAlign_outputTranscriptCIGARp.cpp ErrorWarning.cpp Stats.cpp blocksOverlap.cpp SoloReadFeature_record.cpp ChimericDetection_chimericDetectionMult.cpp outputSJ.cpp Quantifications.cpp ReadAlignChunk.cpp stitchAlignToTranscript.cpp TimeFunctions.cpp stitchGapIndel.cpp SoloReadBarcode_getCBandUMI.cpp signalFromBAM.cpp Chain.cpp ReadAlign_calcCIGAR.cpp sjdbLoadFromStream.cpp sjAlignSplit.cpp SoloReadFeature_inputRecords.cpp Parameters_closeReadsFiles.cpp ReadAlign_CIGAR.cpp SoloFeature_collapseUMI.cpp stitchWindowAligns.cpp GlobalVariables.cpp Parameters.cpp ReadAlign_chimericDetection.cpp Transcriptome_geneFullAlignOverlap.cpp BAMfunctions.cpp ReadAlign.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlignChunk_mapChunk.cpp serviceFuns.cpp Transcript_generateCigarP.cpp ThreadControl.cpp BAMbinSortUnmapped.cpp ReadAlign_chimericDetectionOld.cpp sjdbInsertJunctions.cpp InOutStreams.cpp ReadAlign_chimericDetectionPEmerged.cpp insertSeqSA.cpp streamFuns.cpp ReadAlignChunk_processChunks.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_multMapSelect.cpp Transcript_alignScore.cpp BAMoutput.cpp SoloReadBarcode.cpp genomeParametersWrite.cpp ParametersSolo.cpp ChimericAlign.cpp ReadAlign_outputTranscriptSJ.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign_chimericDetectionOldOutput.cpp mapThreadsSpawn.cpp loadGTF.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_alignBAM.cpp ChimericAlign_chimericJunctionOutput.cpp genomeSAindex.cpp stringSubstituteAll.cpp ChimericDetection.cpp Transcript_variationOutput.cpp SharedMemory.cpp sysRemoveDir.cpp Transcript_variationAdjust.cpp ReadAlign_waspMap.cpp bamRemoveDuplicates.cpp ReadAlign_stitchWindowSeeds.cpp SoloRead_record.cpp ReadAlign_storeAligns.cpp ReadAlign_oneRead.cpp ReadAlign_mappedFilter.cpp ReadAlign_outputVariation.cpp Parameters_readSAMheader.cpp Transcript.cpp SuffixArrayFuns.cpp alignSmithWaterman.cpp SequenceFuns.cpp extendAlign.cpp ChimericAlign_chimericStitching.cpp OutSJ.cpp sjdbLoadFromFiles.cpp ReadAlign_peOverlapMergeMap.cpp genomeScanFastaFiles.cpp ReadAlign_mapOneRead.cpp sjdbBuildIndex.cpp ReadAlign_quantTranscriptome.cpp Genome_genomeGenerate.cpp Variation.cpp Parameters_openReadsFiles.cpp ReadAlign_outputTranscriptSAM.cpp PackedArray.cpp readLoad.cpp binarySearch2.cpp SoloReadFeature.cpp Solo.cpp Transcriptome_geneCountsAddAlign.cpp sjdbPrepare.cpp ChimericSegment.cpp ReadAlign_stitchPieces.cpp funCompareUintAndSuffixes.cpp SoloFeature.cpp BAMbinSortByCoordinate.cpp Genome_insertSequences.cpp Transcriptome_quantAlign.cpp ReadAlign_outputAlignments.cpp STAR.cpp SoloFeature_outputResults.cpp SoloRead.cpp SoloFeature_processRecords.cpp bam_cat.c parametersDefault.xxd >> Depend.list g++: warning: parametersDefault.xxd: linker input file unused because linking not done g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ParametersSolo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloRead_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadBarcode.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadBarcode_getCBandUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadFeature_record.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloReadFeature_inputRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Solo.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_collapseUMI.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_outputResults.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SoloFeature_processRecords.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputAlignments.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' STAR.cpp STAR.cpp: In function 'int main(int, char**)': STAR.cpp:352:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)', declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(P.inOut->outBAMfileUnsorted); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STAR.cpp:356:19: warning: ignoring return value of 'int bgzf_flush(BGZF*)', declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(P.inOut->outQuantBAMfile); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SharedMemory.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' PackedArray.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SuffixArrayFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Parameters.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' InOutStreams.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' SequenceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Stats.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_alignScore.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_generateCigarP.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Chain.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcript_variationAdjust.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Variation.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_waspMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_storeAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_stitchPieces.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_multMapSelect.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_mapOneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' readLoad.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlignChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlignChunk_processChunks.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlignChunk_mapChunk.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' OutSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' outputSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' blocksOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ThreadControl.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sysRemoveDir.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_maxMappableLength2strands.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' binarySearch2.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputTranscriptSAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputTranscriptSJ.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_outputTranscriptCIGARp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_createExtendWindowsWithAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_assignAlignToWindow.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_oneRead.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_stitchWindowSeeds.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_peOverlapMergeMap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_mappedFilter.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetectionOld.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetectionOldOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericDetection.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericDetection_chimericDetectionMult.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_chimericDetectionPEmerged.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericAlign_chimericJunctionOutput.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ChimericAlign_chimericStitching.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' stitchWindowAligns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' extendAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' stitchAlignToTranscript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' alignSmithWaterman.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome_genomeGenerate.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeParametersWrite.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeScanFastaFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' genomeSAindex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Genome_insertSequences.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' insertSeqSA.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' funCompareUintAndSuffixes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' funCompareUintAndSuffixesMemcmp.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' TimeFunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ErrorWarning.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' loadGTF.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' streamFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' stringSubstituteAll.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_quantAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_geneFullAlignOverlap.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_quantTranscriptome.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Quantifications.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Transcriptome_geneCountsAddAlign.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbLoadFromFiles.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbLoadFromStream.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbPrepare.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbBuildIndex.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' sjdbInsertJunctions.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' mapThreadsSpawn.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' Parameters_readSAMheader.cpp Parameters_readSAMheader.cpp: In member function 'void Parameters::readSAMheader(std::__cxx11::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] system(com1.c_str()); ~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -Wall -Wextra -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -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 bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result] if (h) bam_hdr_write(fp, h); ~~~~~~~~~~~~~^~~~~~~ bam_cat.c:96:44: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result] 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] 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] 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] 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] 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] 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] bgzf_raw_write(fp, ebuf, es); ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' serviceFuns.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -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] 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] bgzf_write(bgzfBAM,bamArray,binBytes1); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' BAMfunctions.cpp BAMfunctions.cpp: In function 'std::__cxx11::string bam_cigarString(bam1_t*)': BAMfunctions.cpp:12:25: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] for (int i = 0; i < c->n_cigar; ++i) { ~~^~~~~~~~~~~~ BAMfunctions.cpp: In function 'int bam_read1_fromArray(char*, bam1_t*)': BAMfunctions.cpp:59:16: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (b->m_data < b->l_data) { ~~~~~~~~~~^~~~~~~~~~~ BAMfunctions.cpp: In function 'void outBAMwriteHeader(BGZF*, const string&, const std::vector >&, const std::vector&)': BAMfunctions.cpp:76:15: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)', declared with attribute warn_unused_result [-Wunused-result] 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] 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] 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] 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] 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] 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] 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] bgzf_flush(fp); ~~~~~~~~~~^~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' ReadAlign_alignBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -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::__cxx11::string, Parameters&, Genome&)': BAMbinSortByCoordinate.cpp:66:19: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)', declared with attribute warn_unused_result [-Wunused-result] bgzf_write(bgzfBin,ib, *((uint32*) ib)+sizeof(uint32) ); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMbinSortByCoordinate.cpp:69:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)', declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(bgzfBin); ~~~~~~~~~~^~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' signalFromBAM.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D'COMPILATION_TIME_PLACE=""' bamRemoveDuplicates.cpp bamRemoveDuplicates.cpp: In function 'void bamRemoveDuplicates(std::__cxx11::string, std::__cxx11::string, Parameters&)': bamRemoveDuplicates.cpp:125:18: warning: ignoring return value of 'int bam_hdr_write(BGZF*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result] 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] 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] 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] bgzf_flush(bgzfOut); ~~~~~~~~~~^~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -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::__cxx11::string, Parameters&, Genome&)': BAMbinSortUnmapped.cpp:52:23: warning: ignoring return value of 'ssize_t bgzf_write(BGZF*, const void*, size_t)', declared with attribute warn_unused_result [-Wunused-result] bgzf_write(bgzfBin, bamIn[it], bamSize.at(it)); ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BAMbinSortUnmapped.cpp:69:15: warning: ignoring return value of 'int bgzf_flush(BGZF*)', declared with attribute warn_unused_result [-Wunused-result] bgzf_flush(bgzfBin); ~~~~~~~~~~^~~~~~~~~ g++ -o STAR -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE=""' -flto -flto -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -g -O2 -fdebug-prefix-map=/<>/rna-star-2.7.1a+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_collapseUMI.o SoloFeature_outputResults.o SoloFeature_processRecords.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 ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericStitching.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o alignSmithWaterman.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o loadGTF.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o -pthread -Bstatic -lhts -Bdynamic -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now Parameters_openReadsFiles.cpp: In member function 'void Parameters::openReadsFiles()': Parameters_openReadsFiles.cpp:61:23: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(("ls -lL " + rfName + " > "+ outFileTmp+"/readFilesIn.info 2>&1").c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/ld: cannot find -lhts collect2: error: ld returned 1 exit status make[2]: *** [Makefile:108: STAR] Error 1 make[2]: Leaving directory '/<>/rna-star-2.7.1a+dfsg/source' make[1]: *** [debian/rules:18: override_dh_auto_build] Error 2 make[1]: Leaving directory '/<>/rna-star-2.7.1a+dfsg' make: *** [debian/rules:15: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2019-07-14T05:27:13Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 61080 Build-Time: 109 Distribution: unstable Fail-Stage: build Foreign Architectures: mips64el Host Architecture: mips64el Install-Time: 27 Job: rna-star_2.7.1a+dfsg-1 Machine Architecture: amd64 Package: rna-star Package-Time: 148 Source-Version: 2.7.1a+dfsg-1 Space: 61080 Status: attempted Version: 2.7.1a+dfsg-1 -------------------------------------------------------------------------------- Finished at 2019-07-14T05:27:13Z Build needed 00:02:28, 61080k disk space