r-bioc-bitseq →
1.24.0+dfsg-1 →
armhf → 2018-05-15 07:25:01
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| r-bioc-bitseq 1.24.0+dfsg-1 (armhf) Tue, 15 May 2018 06:58:43 +0000 |
+==============================================================================+
Package: r-bioc-bitseq
Version: 1.24.0+dfsg-1
Source Version: 1.24.0+dfsg-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-712b3e15-9d74-4d4b-b9d7-edc050e2dfc3' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.7 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.5 MB]
Fetched 23.3 MB in 28s (841 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'r-bioc-bitseq' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/r-pkg-team/r-bioc-bitseq.git
Please use:
git clone https://salsa.debian.org/r-pkg-team/r-bioc-bitseq.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 757 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main r-bioc-bitseq 1.24.0+dfsg-1 (dsc) [2156 B]
Get:2 http://172.17.0.1/private buster-staging/main r-bioc-bitseq 1.24.0+dfsg-1 (tar) [750 kB]
Get:3 http://172.17.0.1/private buster-staging/main r-bioc-bitseq 1.24.0+dfsg-1 (diff) [5492 B]
Fetched 757 kB in 0s (2165 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-bitseq-eXs8ke/r-bioc-bitseq-1.24.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-bitseq-eXs8ke' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-OHjZ7L/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.
gpg: keybox '/<<BUILDDIR>>/resolver-OHjZ7L/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-OHjZ7L/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-OHjZ7L/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-OHjZ7L/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-OHjZ7L/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-OHjZ7L/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-OHjZ7L/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (3202 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libssl1.1 openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 38 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-OHjZ7L/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13964 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), dh-r, r-base-dev, r-bioc-rsamtools, r-bioc-s4vectors, r-bioc-iranges, libboost-dev, zlib1g-dev
Filtered Build-Depends: debhelper (>= 11~), dh-r, r-base-dev, r-bioc-rsamtools, r-bioc-s4vectors, r-bioc-iranges, libboost-dev, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-r-bioc-bitseq-dummy' in '/<<BUILDDIR>>/resolver-OHjZ7L/apt_archive/sbuild-build-depends-r-bioc-bitseq-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-r-bioc-bitseq-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-OHjZ7L/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-OHjZ7L/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-OHjZ7L/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-OHjZ7L/apt_archive ./ Sources [542 B]
Get:5 copy:/<<BUILDDIR>>/resolver-OHjZ7L/apt_archive ./ Packages [625 B]
Fetched 2500 B in 1s (3795 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install r-bioc-bitseq build dependencies (apt-based resolver)
-------------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
dbus dbus-user-session e2fsprogs-l10n libnss-systemd libpam-systemd
systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cdbs dctrl-tools
debhelper dh-autoreconf dh-r dh-strip-nondeterminism file fontconfig
fontconfig-config fonts-dejavu-core gettext gettext-base gfortran gfortran-7
groff-base icu-devtools intltool-debian libarchive-zip-perl libblas-dev
libblas3 libboost-dev libboost1.62-dev libbsd0 libbz2-dev libcairo2
libcroco3 libcurl3 libdatrie1 libfile-stripnondeterminism-perl
libfontconfig1 libfreetype6 libfribidi0 libgfortran-7-dev libgfortran4
libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6
libicu-dev libicu57 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3
liblzma-dev libmagic-mgc libmagic1 libncurses-dev libncurses5-dev
libncurses6 libncursesw6 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0
libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3 libpcre3-dev
libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng-dev libpsl5
libreadline-dev libreadline7 librtmp1 libsigsegv2 libsm6 libssh2-1
libssl1.0.2 libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl
libtinfo6 libtk8.6 libtool libx11-6 libx11-data libxau6 libxcb-render0
libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxmuu1 libxrender1
libxss1 libxt6 m4 man-db pkg-config po-debconf r-base-core r-base-dev
r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings
r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicranges
r-bioc-iranges r-bioc-rsamtools r-bioc-s4vectors r-bioc-xvector
r-cran-bitops r-cran-formatr r-cran-futile.logger r-cran-futile.options
r-cran-lambda.r r-cran-rcurl r-cran-snow ucf unzip x11-common xauth
xdg-utils zip zlib1g zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation devscripts debtags dh-make dwz gettext-doc libasprintf-dev
libgettextpo-dev gfortran-doc gfortran-7-doc libgfortran4-dbg
libcoarrays-dev groff liblapack-doc libboost-doc libboost1.62-doc
libboost-atomic1.62-dev libboost-chrono1.62-dev libboost-context1.62-dev
libboost-coroutine1.62-dev libboost-date-time1.62-dev
libboost-exception1.62-dev libboost-fiber1.62-dev
libboost-filesystem1.62-dev libboost-graph1.62-dev
libboost-graph-parallel1.62-dev libboost-iostreams1.62-dev
libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev
libboost-mpi1.62-dev libboost-mpi-python1.62-dev
libboost-program-options1.62-dev libboost-python1.62-dev
libboost-random1.62-dev libboost-regex1.62-dev
libboost-serialization1.62-dev libboost-signals1.62-dev
libboost-system1.62-dev libboost-test1.62-dev libboost-thread1.62-dev
libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev
libboost1.62-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user icu-doc
liblzma-doc readline-doc tcl8.6 tk8.6 libtool-doc gcj-jdk m4-doc apparmor
less www-browser libmail-box-perl ess r-doc-info | r-doc-pdf r-mathlib
r-base-html texlive-base texlive-latex-base texlive-generic-recommended
texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils
texlive-latex-recommended texlive-latex-extra texinfo r-bioc-biobase
r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-runit
r-cran-foreach r-cran-batchjobs r-cran-bbmisc r-cran-doparallel r-cran-rmpi
r-bioc-variantannotation r-bioc-genomicalignments r-bioc-shortread
r-cran-codetools r-cran-knitr r-bioc-bsgenome r-bioc-genomicfeatures
r-bioc-summarizedexperiment r-cran-matrix r-bioc-rtracklayer r-bioc-gviz
r-bioc-annotationhub r-bioc-edger r-cran-digest r-bioc-graph
r-cran-data.table r-cran-shiny r-cran-testit r-cran-testthat r-cran-jsonlite
r-cran-xml r-cran-rsprng r-cran-rlecuyer
Recommended packages:
curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales libgpm2 libpng-tools
publicsuffix libltdl-dev libmail-sendmail-perl r-recommended r-doc-html
libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils
x11-xserver-utils
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cdbs dctrl-tools
debhelper dh-autoreconf dh-r dh-strip-nondeterminism file fontconfig
fontconfig-config fonts-dejavu-core gettext gettext-base gfortran gfortran-7
groff-base icu-devtools intltool-debian libarchive-zip-perl libblas-dev
libblas3 libboost-dev libboost1.62-dev libbsd0 libbz2-dev libcairo2
libcroco3 libcurl3 libdatrie1 libfile-stripnondeterminism-perl
libfontconfig1 libfreetype6 libfribidi0 libgfortran-7-dev libgfortran4
libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6
libicu-dev libicu57 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3
liblzma-dev libmagic-mgc libmagic1 libncurses-dev libncurses5-dev
libncurses6 libncursesw6 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0
libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3 libpcre3-dev
libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng-dev libpsl5
libreadline-dev librtmp1 libsigsegv2 libsm6 libssh2-1 libssl1.0.2 libtcl8.6
libthai-data libthai0 libtiff5 libtimedate-perl libtinfo6 libtk8.6 libtool
libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6
libxext6 libxft2 libxml2 libxmuu1 libxrender1 libxss1 libxt6 m4 man-db
pkg-config po-debconf r-base-core r-base-dev r-bioc-biocgenerics
r-bioc-biocparallel r-bioc-biostrings r-bioc-genomeinfodb
r-bioc-genomeinfodbdata r-bioc-genomicranges r-bioc-iranges r-bioc-rsamtools
r-bioc-s4vectors r-bioc-xvector r-cran-bitops r-cran-formatr
r-cran-futile.logger r-cran-futile.options r-cran-lambda.r r-cran-rcurl
r-cran-snow sbuild-build-depends-r-bioc-bitseq-dummy ucf unzip x11-common
xauth xdg-utils zip zlib1g-dev
The following packages will be upgraded:
libreadline7 zlib1g
2 upgraded, 136 newly installed, 0 to remove and 36 not upgraded.
Need to get 95.4 MB/125 MB of archives.
After this operation, 405 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-OHjZ7L/apt_archive ./ sbuild-build-depends-r-bioc-bitseq-dummy 0.invalid.0 [916 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf zlib1g armhf 1:1.2.11.dfsg-1 [87.3 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.3-2 [1146 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libx11-data all 2:1.6.5-1 [292 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libx11-6 armhf 2:1.6.5-1 [683 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libtinfo6 armhf 6.1+20180210-2 [307 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libreadline7 armhf 7.0-5 [130 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libssl1.0.2 armhf 1.0.2o-1 [888 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.33-2 [234 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.33-2 [106 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.33-2 [64.7 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3.1 [736 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf cdbs all 0.4.156 [83.1 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf dctrl-tools armhf 2.24-2 [94.4 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 17 [16.5 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.041-1 [19.9 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.041-1 [12.0 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.2.1 [1013 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf zip armhf 3.0-11 [212 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf unzip armhf 6.0-21 [149 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libpaper1 armhf 1.1.24+nmu5 [20.8 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libpaper-utils armhf 1.1.24+nmu5 [17.2 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf xdg-utils all 1.1.2-2 [72.8 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.3.0-12 [191 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.8.0-1 [103 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf fontconfig-config all 2.13.0-4 [280 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libfontconfig1 armhf 2.13.0-4 [325 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libcairo2 armhf 1.15.10-3 [575 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.31.1-1 [69.4 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.1-1 [51.4 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libcurl3 armhf 7.58.0-2 [276 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.8.0-1 [1518 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf fontconfig armhf 2.13.0-4 [403 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libfribidi0 armhf 0.19.7-2 [44.1 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libdatrie1 armhf 0.2.11-1 [34.6 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libpango-1.0-0 armhf 1.42.0-1 [158 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.7.6-1 [799 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libpangoft2-1.0-0 armhf 1.42.0-1 [53.2 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libpangocairo-1.0-0 armhf 1.42.0-1 [43.3 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libtcl8.6 armhf 8.6.8+dfsg-4 [863 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libtiff5 armhf 4.0.9-5 [224 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libxft2 armhf 2.3.2-2 [49.3 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libtk8.6 armhf 8.6.8-4 [657 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf r-base-core armhf 3.4.4-1 [23.0 MB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libgfortran-7-dev armhf 7.3.0-12 [232 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf gfortran-7 armhf 7.3.0-12 [5454 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:7.2.0-1d1 [1352 B]
Get:64 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.8.0-1 [111 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.8.0-1 [1577 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libncurses6 armhf 6.1+20180210-2 [78.3 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libncursesw6 armhf 6.1+20180210-2 [103 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libncurses-dev armhf 6.1+20180210-2 [278 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.1+20180210-2 [920 B]
Get:70 http://172.17.0.1/private buster-staging/main armhf libreadline-dev armhf 7.0-5 [110 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libpcre16-3 armhf 2:8.39-9 [234 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libpcre32-3 armhf 2:8.39-9 [226 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libpcrecpp0v5 armhf 2:8.39-9 [150 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libpcre3-dev armhf 2:8.39-9 [561 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-8.1 [26.9 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libxmuu1 armhf 2:1.1.2-2 [23.0 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf xauth armhf 1:1.0.10-1 [36.4 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf r-base-dev all 3.4.4-1 [4488 B]
Get:80 http://172.17.0.1/private buster-staging/main armhf dh-r all 20180508 [14.7 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-5+b2 [7004 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.62.0.1+b8 [3918 B]
Get:83 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocgenerics all 0.26.0-2 [582 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf r-cran-formatr armhf 1.5-2 [126 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf r-cran-lambda.r all 1.2.2-2 [87.6 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.options all 1.0.1-1 [16.0 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.logger all 1.4.3-2 [93.8 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf r-cran-snow all 1:0.4.2-1.1 [65.4 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocparallel armhf 1.12.0-2 [765 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf r-bioc-s4vectors armhf 0.16.0-1 [1163 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf r-bioc-iranges armhf 2.12.0-2 [1467 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf r-bioc-xvector armhf 0.18.0-1 [367 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf r-bioc-biostrings armhf 2.46.0-1 [13.6 MB]
Get:94 http://172.17.0.1/private buster-staging/main armhf r-cran-bitops armhf 1.0-6-3 [22.5 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf r-cran-rcurl armhf 1.95-4.10-1 [618 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodbdata all 1.1.0-2 [8213 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodb all 1.14.0-1 [3529 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomicranges armhf 1.30.3-1 [1576 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf r-bioc-rsamtools armhf 1.30.0-1 [3278 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 95.4 MB in 10s (9120 kB/s)
Selecting previously unselected package libbsd0:armhf.
(Reading database ... 13964 files and directories currently installed.)
Preparing to unpack .../libbsd0_0.8.7-1_armhf.deb ...
Unpacking libbsd0:armhf (0.8.7-1) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../bsdmainutils_11.1.2_armhf.deb ...
Unpacking bsdmainutils (11.1.2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../groff-base_1.22.3-10_armhf.deb ...
Unpacking groff-base (1.22.3-10) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../libpipeline1_1.5.0-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.0-1) ...
Preparing to unpack .../zlib1g_1%3a1.2.11.dfsg-1_armhf.deb ...
Unpacking zlib1g:armhf (1:1.2.11.dfsg-1) over (1:1.2.8.dfsg-5) ...
Setting up zlib1g:armhf (1:1.2.11.dfsg-1) ...
Selecting previously unselected package man-db.
(Reading database ... 14281 files and directories currently installed.)
Preparing to unpack .../0-man-db_2.8.3-2_armhf.deb ...
Unpacking man-db (2.8.3-2) ...
Selecting previously unselected package libxau6:armhf.
Preparing to unpack .../1-libxau6_1%3a1.0.8-1+b2_armhf.deb ...
Unpacking libxau6:armhf (1:1.0.8-1+b2) ...
Selecting previously unselected package libxdmcp6:armhf.
Preparing to unpack .../2-libxdmcp6_1%3a1.1.2-3_armhf.deb ...
Unpacking libxdmcp6:armhf (1:1.1.2-3) ...
Selecting previously unselected package libxcb1:armhf.
Preparing to unpack .../3-libxcb1_1.13-1_armhf.deb ...
Unpacking libxcb1:armhf (1.13-1) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../4-libx11-data_2%3a1.6.5-1_all.deb ...
Unpacking libx11-data (2:1.6.5-1) ...
Selecting previously unselected package libx11-6:armhf.
Preparing to unpack .../5-libx11-6_2%3a1.6.5-1_armhf.deb ...
Unpacking libx11-6:armhf (2:1.6.5-1) ...
Selecting previously unselected package libxext6:armhf.
Preparing to unpack .../6-libxext6_2%3a1.3.3-1+b2_armhf.deb ...
Unpacking libxext6:armhf (2:1.3.3-1+b2) ...
Selecting previously unselected package x11-common.
Preparing to unpack .../7-x11-common_1%3a7.7+19_all.deb ...
Unpacking x11-common (1:7.7+19) ...
Selecting previously unselected package libxss1:armhf.
Preparing to unpack .../8-libxss1_1%3a1.2.2-1_armhf.deb ...
Unpacking libxss1:armhf (1:1.2.2-1) ...
Selecting previously unselected package libtinfo6:armhf.
Preparing to unpack .../9-libtinfo6_6.1+20180210-2_armhf.deb ...
Unpacking libtinfo6:armhf (6.1+20180210-2) ...
Setting up libtinfo6:armhf (6.1+20180210-2) ...
(Reading database ... 14897 files and directories currently installed.)
Preparing to unpack .../libreadline7_7.0-5_armhf.deb ...
Unpacking libreadline7:armhf (7.0-5) over (7.0-3) ...
Setting up libreadline7:armhf (7.0-5) ...
Selecting previously unselected package libssl1.0.2:armhf.
(Reading database ... 14897 files and directories currently installed.)
Preparing to unpack .../000-libssl1.0.2_1.0.2o-1_armhf.deb ...
Unpacking libssl1.0.2:armhf (1.0.2o-1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../001-libmagic-mgc_1%3a5.33-2_armhf.deb ...
Unpacking libmagic-mgc (1:5.33-2) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../002-libmagic1_1%3a5.33-2_armhf.deb ...
Unpacking libmagic1:armhf (1:5.33-2) ...
Selecting previously unselected package file.
Preparing to unpack .../003-file_1%3a5.33-2_armhf.deb ...
Unpacking file (1:5.33-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../004-gettext-base_0.19.8.1-6_armhf.deb ...
Unpacking gettext-base (0.19.8.1-6) ...
Selecting previously unselected package libkeyutils1:armhf.
Preparing to unpack .../005-libkeyutils1_1.5.9-9.2_armhf.deb ...
Unpacking libkeyutils1:armhf (1.5.9-9.2) ...
Selecting previously unselected package ucf.
Preparing to unpack .../006-ucf_3.0038_all.deb ...
Moving old data out of the way
Unpacking ucf (3.0038) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../007-libsigsegv2_2.12-2_armhf.deb ...
Unpacking libsigsegv2:armhf (2.12-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../008-m4_1.4.18-1_armhf.deb ...
Unpacking m4 (1.4.18-1) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../009-autoconf_2.69-11_all.deb ...
Unpacking autoconf (2.69-11) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../010-autotools-dev_20180224.1_all.deb ...
Unpacking autotools-dev (20180224.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../011-automake_1%3a1.15.1-3.1_all.deb ...
Unpacking automake (1:1.15.1-3.1) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../012-autopoint_0.19.8.1-6_all.deb ...
Unpacking autopoint (0.19.8.1-6) ...
Selecting previously unselected package cdbs.
Preparing to unpack .../013-cdbs_0.4.156_all.deb ...
Unpacking cdbs (0.4.156) ...
Selecting previously unselected package dctrl-tools.
Preparing to unpack .../014-dctrl-tools_2.24-2_armhf.deb ...
Unpacking dctrl-tools (2.24-2) ...
Selecting previously unselected package libtool.
Preparing to unpack .../015-libtool_2.4.6-2.1_all.deb ...
Unpacking libtool (2.4.6-2.1) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../016-dh-autoreconf_17_all.deb ...
Unpacking dh-autoreconf (17) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../017-libarchive-zip-perl_1.60-1_all.deb ...
Unpacking libarchive-zip-perl (1.60-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../018-libfile-stripnondeterminism-perl_0.041-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (0.041-1) ...
Selecting previously unselected package libtimedate-perl.
Preparing to unpack .../019-libtimedate-perl_2.3000-2_all.deb ...
Unpacking libtimedate-perl (2.3000-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../020-dh-strip-nondeterminism_0.041-1_all.deb ...
Unpacking dh-strip-nondeterminism (0.041-1) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../021-libglib2.0-0_2.56.1-2_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.56.1-2) ...
Selecting previously unselected package libicu57:armhf.
Preparing to unpack .../022-libicu57_57.1-9_armhf.deb ...
Unpacking libicu57:armhf (57.1-9) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../023-libxml2_2.9.4+dfsg1-6.1_armhf.deb ...
Unpacking libxml2:armhf (2.9.4+dfsg1-6.1) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../024-libcroco3_0.6.12-2_armhf.deb ...
Unpacking libcroco3:armhf (0.6.12-2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../025-gettext_0.19.8.1-6_armhf.deb ...
Unpacking gettext (0.19.8.1-6) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../026-intltool-debian_0.35.0+20060710.4_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.4) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../027-po-debconf_1.0.20_all.deb ...
Unpacking po-debconf (1.0.20) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../028-debhelper_11.2.1_all.deb ...
Unpacking debhelper (11.2.1) ...
Selecting previously unselected package zip.
Preparing to unpack .../029-zip_3.0-11_armhf.deb ...
Unpacking zip (3.0-11) ...
Selecting previously unselected package unzip.
Preparing to unpack .../030-unzip_6.0-21_armhf.deb ...
Unpacking unzip (6.0-21) ...
Selecting previously unselected package libpaper1:armhf.
Preparing to unpack .../031-libpaper1_1.1.24+nmu5_armhf.deb ...
Unpacking libpaper1:armhf (1.1.24+nmu5) ...
Selecting previously unselected package libpaper-utils.
Preparing to unpack .../032-libpaper-utils_1.1.24+nmu5_armhf.deb ...
Unpacking libpaper-utils (1.1.24+nmu5) ...
Selecting previously unselected package xdg-utils.
Preparing to unpack .../033-xdg-utils_1.1.2-2_all.deb ...
Unpacking xdg-utils (1.1.2-2) ...
Selecting previously unselected package libgfortran4:armhf.
Preparing to unpack .../034-libgfortran4_7.3.0-12_armhf.deb ...
Unpacking libgfortran4:armhf (7.3.0-12) ...
Selecting previously unselected package libblas3:armhf.
Preparing to unpack .../035-libblas3_3.8.0-1_armhf.deb ...
Unpacking libblas3:armhf (3.8.0-1) ...
Selecting previously unselected package libfreetype6:armhf.
Preparing to unpack .../036-libfreetype6_2.8.1-2_armhf.deb ...
Unpacking libfreetype6:armhf (2.8.1-2) ...
Selecting previously unselected package fonts-dejavu-core.
Preparing to unpack .../037-fonts-dejavu-core_2.37-1_all.deb ...
Unpacking fonts-dejavu-core (2.37-1) ...
Selecting previously unselected package fontconfig-config.
Preparing to unpack .../038-fontconfig-config_2.13.0-4_all.deb ...
Unpacking fontconfig-config (2.13.0-4) ...
Selecting previously unselected package libfontconfig1:armhf.
Preparing to unpack .../039-libfontconfig1_2.13.0-4_armhf.deb ...
Unpacking libfontconfig1:armhf (2.13.0-4) ...
Selecting previously unselected package libpixman-1-0:armhf.
Preparing to unpack .../040-libpixman-1-0_0.34.0-2_armhf.deb ...
Unpacking libpixman-1-0:armhf (0.34.0-2) ...
Selecting previously unselected package libxcb-render0:armhf.
Preparing to unpack .../041-libxcb-render0_1.13-1_armhf.deb ...
Unpacking libxcb-render0:armhf (1.13-1) ...
Selecting previously unselected package libxcb-shm0:armhf.
Preparing to unpack .../042-libxcb-shm0_1.13-1_armhf.deb ...
Unpacking libxcb-shm0:armhf (1.13-1) ...
Selecting previously unselected package libxrender1:armhf.
Preparing to unpack .../043-libxrender1_1%3a0.9.10-1_armhf.deb ...
Unpacking libxrender1:armhf (1:0.9.10-1) ...
Selecting previously unselected package libcairo2:armhf.
Preparing to unpack .../044-libcairo2_1.15.10-3_armhf.deb ...
Unpacking libcairo2:armhf (1.15.10-3) ...
Selecting previously unselected package libkrb5support0:armhf.
Preparing to unpack .../045-libkrb5support0_1.16-2_armhf.deb ...
Unpacking libkrb5support0:armhf (1.16-2) ...
Selecting previously unselected package libk5crypto3:armhf.
Preparing to unpack .../046-libk5crypto3_1.16-2_armhf.deb ...
Unpacking libk5crypto3:armhf (1.16-2) ...
Selecting previously unselected package libkrb5-3:armhf.
Preparing to unpack .../047-libkrb5-3_1.16-2_armhf.deb ...
Unpacking libkrb5-3:armhf (1.16-2) ...
Selecting previously unselected package libgssapi-krb5-2:armhf.
Preparing to unpack .../048-libgssapi-krb5-2_1.16-2_armhf.deb ...
Unpacking libgssapi-krb5-2:armhf (1.16-2) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../049-libnghttp2-14_1.31.1-1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.31.1-1) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../050-libpsl5_0.20.1-1_armhf.deb ...
Unpacking libpsl5:armhf (0.20.1-1) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../051-librtmp1_2.4+20151223.gitfa8646d.1-1_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../052-libssh2-1_1.8.0-1_armhf.deb ...
Unpacking libssh2-1:armhf (1.8.0-1) ...
Selecting previously unselected package libcurl3:armhf.
Preparing to unpack .../053-libcurl3_7.58.0-2_armhf.deb ...
Unpacking libcurl3:armhf (7.58.0-2) ...
Selecting previously unselected package libice6:armhf.
Preparing to unpack .../054-libice6_2%3a1.0.9-2_armhf.deb ...
Unpacking libice6:armhf (2:1.0.9-2) ...
Selecting previously unselected package libjpeg62-turbo:armhf.
Preparing to unpack .../055-libjpeg62-turbo_1%3a1.5.2-2+b1_armhf.deb ...
Unpacking libjpeg62-turbo:armhf (1:1.5.2-2+b1) ...
Selecting previously unselected package liblapack3:armhf.
Preparing to unpack .../056-liblapack3_3.8.0-1_armhf.deb ...
Unpacking liblapack3:armhf (3.8.0-1) ...
Selecting previously unselected package fontconfig.
Preparing to unpack .../057-fontconfig_2.13.0-4_armhf.deb ...
Unpacking fontconfig (2.13.0-4) ...
Selecting previously unselected package libfribidi0:armhf.
Preparing to unpack .../058-libfribidi0_0.19.7-2_armhf.deb ...
Unpacking libfribidi0:armhf (0.19.7-2) ...
Selecting previously unselected package libthai-data.
Preparing to unpack .../059-libthai-data_0.1.27-2_all.deb ...
Unpacking libthai-data (0.1.27-2) ...
Selecting previously unselected package libdatrie1:armhf.
Preparing to unpack .../060-libdatrie1_0.2.11-1_armhf.deb ...
Unpacking libdatrie1:armhf (0.2.11-1) ...
Selecting previously unselected package libthai0:armhf.
Preparing to unpack .../061-libthai0_0.1.27-2_armhf.deb ...
Unpacking libthai0:armhf (0.1.27-2) ...
Selecting previously unselected package libpango-1.0-0:armhf.
Preparing to unpack .../062-libpango-1.0-0_1.42.0-1_armhf.deb ...
Unpacking libpango-1.0-0:armhf (1.42.0-1) ...
Selecting previously unselected package libgraphite2-3:armhf.
Preparing to unpack .../063-libgraphite2-3_1.3.11-2_armhf.deb ...
Unpacking libgraphite2-3:armhf (1.3.11-2) ...
Selecting previously unselected package libharfbuzz0b:armhf.
Preparing to unpack .../064-libharfbuzz0b_1.7.6-1_armhf.deb ...
Unpacking libharfbuzz0b:armhf (1.7.6-1) ...
Selecting previously unselected package libpangoft2-1.0-0:armhf.
Preparing to unpack .../065-libpangoft2-1.0-0_1.42.0-1_armhf.deb ...
Unpacking libpangoft2-1.0-0:armhf (1.42.0-1) ...
Selecting previously unselected package libpangocairo-1.0-0:armhf.
Preparing to unpack .../066-libpangocairo-1.0-0_1.42.0-1_armhf.deb ...
Unpacking libpangocairo-1.0-0:armhf (1.42.0-1) ...
Selecting previously unselected package libsm6:armhf.
Preparing to unpack .../067-libsm6_2%3a1.2.2-1+b3_armhf.deb ...
Unpacking libsm6:armhf (2:1.2.2-1+b3) ...
Selecting previously unselected package libtcl8.6:armhf.
Preparing to unpack .../068-libtcl8.6_8.6.8+dfsg-4_armhf.deb ...
Unpacking libtcl8.6:armhf (8.6.8+dfsg-4) ...
Selecting previously unselected package libjbig0:armhf.
Preparing to unpack .../069-libjbig0_2.1-3.1+b2_armhf.deb ...
Unpacking libjbig0:armhf (2.1-3.1+b2) ...
Selecting previously unselected package libtiff5:armhf.
Preparing to unpack .../070-libtiff5_4.0.9-5_armhf.deb ...
Unpacking libtiff5:armhf (4.0.9-5) ...
Selecting previously unselected package libxft2:armhf.
Preparing to unpack .../071-libxft2_2.3.2-2_armhf.deb ...
Unpacking libxft2:armhf (2.3.2-2) ...
Selecting previously unselected package libtk8.6:armhf.
Preparing to unpack .../072-libtk8.6_8.6.8-4_armhf.deb ...
Unpacking libtk8.6:armhf (8.6.8-4) ...
Selecting previously unselected package libxt6:armhf.
Preparing to unpack .../073-libxt6_1%3a1.1.5-1_armhf.deb ...
Unpacking libxt6:armhf (1:1.1.5-1) ...
Selecting previously unselected package r-base-core.
Preparing to unpack .../074-r-base-core_3.4.4-1_armhf.deb ...
Unpacking r-base-core (3.4.4-1) ...
Selecting previously unselected package libgfortran-7-dev:armhf.
Preparing to unpack .../075-libgfortran-7-dev_7.3.0-12_armhf.deb ...
Unpacking libgfortran-7-dev:armhf (7.3.0-12) ...
Selecting previously unselected package gfortran-7.
Preparing to unpack .../076-gfortran-7_7.3.0-12_armhf.deb ...
Unpacking gfortran-7 (7.3.0-12) ...
Selecting previously unselected package gfortran.
Preparing to unpack .../077-gfortran_4%3a7.2.0-1d1_armhf.deb ...
Unpacking gfortran (4:7.2.0-1d1) ...
Selecting previously unselected package libblas-dev:armhf.
Preparing to unpack .../078-libblas-dev_3.8.0-1_armhf.deb ...
Unpacking libblas-dev:armhf (3.8.0-1) ...
Selecting previously unselected package liblapack-dev:armhf.
Preparing to unpack .../079-liblapack-dev_3.8.0-1_armhf.deb ...
Unpacking liblapack-dev:armhf (3.8.0-1) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../080-libncurses6_6.1+20180210-2_armhf.deb ...
Unpacking libncurses6:armhf (6.1+20180210-2) ...
Selecting previously unselected package libncursesw6:armhf.
Preparing to unpack .../081-libncursesw6_6.1+20180210-2_armhf.deb ...
Unpacking libncursesw6:armhf (6.1+20180210-2) ...
Selecting previously unselected package libncurses-dev:armhf.
Preparing to unpack .../082-libncurses-dev_6.1+20180210-2_armhf.deb ...
Unpacking libncurses-dev:armhf (6.1+20180210-2) ...
Selecting previously unselected package libncurses5-dev:armhf.
Preparing to unpack .../083-libncurses5-dev_6.1+20180210-2_armhf.deb ...
Unpacking libncurses5-dev:armhf (6.1+20180210-2) ...
Selecting previously unselected package libreadline-dev:armhf.
Preparing to unpack .../084-libreadline-dev_7.0-5_armhf.deb ...
Unpacking libreadline-dev:armhf (7.0-5) ...
Selecting previously unselected package libjpeg62-turbo-dev:armhf.
Preparing to unpack .../085-libjpeg62-turbo-dev_1%3a1.5.2-2+b1_armhf.deb ...
Unpacking libjpeg62-turbo-dev:armhf (1:1.5.2-2+b1) ...
Selecting previously unselected package libjpeg-dev.
Preparing to unpack .../086-libjpeg-dev_1%3a1.5.2-2_all.deb ...
Unpacking libjpeg-dev (1:1.5.2-2) ...
Selecting previously unselected package libpcre16-3:armhf.
Preparing to unpack .../087-libpcre16-3_2%3a8.39-9_armhf.deb ...
Unpacking libpcre16-3:armhf (2:8.39-9) ...
Selecting previously unselected package libpcre32-3:armhf.
Preparing to unpack .../088-libpcre32-3_2%3a8.39-9_armhf.deb ...
Unpacking libpcre32-3:armhf (2:8.39-9) ...
Selecting previously unselected package libpcrecpp0v5:armhf.
Preparing to unpack .../089-libpcrecpp0v5_2%3a8.39-9_armhf.deb ...
Unpacking libpcrecpp0v5:armhf (2:8.39-9) ...
Selecting previously unselected package libpcre3-dev:armhf.
Preparing to unpack .../090-libpcre3-dev_2%3a8.39-9_armhf.deb ...
Unpacking libpcre3-dev:armhf (2:8.39-9) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../091-zlib1g-dev_1%3a1.2.11.dfsg-1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Selecting previously unselected package libpng-dev:armhf.
Preparing to unpack .../092-libpng-dev_1.6.34-1_armhf.deb ...
Unpacking libpng-dev:armhf (1.6.34-1) ...
Selecting previously unselected package libbz2-dev:armhf.
Preparing to unpack .../093-libbz2-dev_1.0.6-8.1_armhf.deb ...
Unpacking libbz2-dev:armhf (1.0.6-8.1) ...
Selecting previously unselected package liblzma-dev:armhf.
Preparing to unpack .../094-liblzma-dev_5.2.2-1.3_armhf.deb ...
Unpacking liblzma-dev:armhf (5.2.2-1.3) ...
Selecting previously unselected package icu-devtools.
Preparing to unpack .../095-icu-devtools_57.1-9_armhf.deb ...
Unpacking icu-devtools (57.1-9) ...
Selecting previously unselected package libicu-dev.
Preparing to unpack .../096-libicu-dev_57.1-9_armhf.deb ...
Unpacking libicu-dev (57.1-9) ...
Selecting previously unselected package libxmuu1:armhf.
Preparing to unpack .../097-libxmuu1_2%3a1.1.2-2_armhf.deb ...
Unpacking libxmuu1:armhf (2:1.1.2-2) ...
Selecting previously unselected package xauth.
Preparing to unpack .../098-xauth_1%3a1.0.10-1_armhf.deb ...
Unpacking xauth (1:1.0.10-1) ...
Selecting previously unselected package pkg-config.
Preparing to unpack .../099-pkg-config_0.29-4_armhf.deb ...
Unpacking pkg-config (0.29-4) ...
Selecting previously unselected package r-base-dev.
Preparing to unpack .../100-r-base-dev_3.4.4-1_all.deb ...
Unpacking r-base-dev (3.4.4-1) ...
Selecting previously unselected package dh-r.
Preparing to unpack .../101-dh-r_20180508_all.deb ...
Unpacking dh-r (20180508) ...
Selecting previously unselected package libboost1.62-dev:armhf.
Preparing to unpack .../102-libboost1.62-dev_1.62.0+dfsg-5+b2_armhf.deb ...
Unpacking libboost1.62-dev:armhf (1.62.0+dfsg-5+b2) ...
Selecting previously unselected package libboost-dev:armhf.
Preparing to unpack .../103-libboost-dev_1.62.0.1+b8_armhf.deb ...
Unpacking libboost-dev:armhf (1.62.0.1+b8) ...
Selecting previously unselected package r-bioc-biocgenerics.
Preparing to unpack .../104-r-bioc-biocgenerics_0.26.0-2_all.deb ...
Unpacking r-bioc-biocgenerics (0.26.0-2) ...
Selecting previously unselected package r-cran-formatr.
Preparing to unpack .../105-r-cran-formatr_1.5-2_armhf.deb ...
Unpacking r-cran-formatr (1.5-2) ...
Selecting previously unselected package r-cran-lambda.r.
Preparing to unpack .../106-r-cran-lambda.r_1.2.2-2_all.deb ...
Unpacking r-cran-lambda.r (1.2.2-2) ...
Selecting previously unselected package r-cran-futile.options.
Preparing to unpack .../107-r-cran-futile.options_1.0.1-1_all.deb ...
Unpacking r-cran-futile.options (1.0.1-1) ...
Selecting previously unselected package r-cran-futile.logger.
Preparing to unpack .../108-r-cran-futile.logger_1.4.3-2_all.deb ...
Unpacking r-cran-futile.logger (1.4.3-2) ...
Selecting previously unselected package r-cran-snow.
Preparing to unpack .../109-r-cran-snow_1%3a0.4.2-1.1_all.deb ...
Unpacking r-cran-snow (1:0.4.2-1.1) ...
Selecting previously unselected package r-bioc-biocparallel.
Preparing to unpack .../110-r-bioc-biocparallel_1.12.0-2_armhf.deb ...
Unpacking r-bioc-biocparallel (1.12.0-2) ...
Selecting previously unselected package r-bioc-s4vectors.
Preparing to unpack .../111-r-bioc-s4vectors_0.16.0-1_armhf.deb ...
Unpacking r-bioc-s4vectors (0.16.0-1) ...
Selecting previously unselected package r-bioc-iranges.
Preparing to unpack .../112-r-bioc-iranges_2.12.0-2_armhf.deb ...
Unpacking r-bioc-iranges (2.12.0-2) ...
Selecting previously unselected package r-bioc-xvector.
Preparing to unpack .../113-r-bioc-xvector_0.18.0-1_armhf.deb ...
Unpacking r-bioc-xvector (0.18.0-1) ...
Selecting previously unselected package r-bioc-biostrings.
Preparing to unpack .../114-r-bioc-biostrings_2.46.0-1_armhf.deb ...
Unpacking r-bioc-biostrings (2.46.0-1) ...
Selecting previously unselected package r-cran-bitops.
Preparing to unpack .../115-r-cran-bitops_1.0-6-3_armhf.deb ...
Unpacking r-cran-bitops (1.0-6-3) ...
Selecting previously unselected package r-cran-rcurl.
Preparing to unpack .../116-r-cran-rcurl_1.95-4.10-1_armhf.deb ...
Unpacking r-cran-rcurl (1.95-4.10-1) ...
Selecting previously unselected package r-bioc-genomeinfodbdata.
Preparing to unpack .../117-r-bioc-genomeinfodbdata_1.1.0-2_all.deb ...
Unpacking r-bioc-genomeinfodbdata (1.1.0-2) ...
Selecting previously unselected package r-bioc-genomeinfodb.
Preparing to unpack .../118-r-bioc-genomeinfodb_1.14.0-1_all.deb ...
Unpacking r-bioc-genomeinfodb (1.14.0-1) ...
Selecting previously unselected package r-bioc-genomicranges.
Preparing to unpack .../119-r-bioc-genomicranges_1.30.3-1_armhf.deb ...
Unpacking r-bioc-genomicranges (1.30.3-1) ...
Selecting previously unselected package r-bioc-rsamtools.
Preparing to unpack .../120-r-bioc-rsamtools_1.30.0-1_armhf.deb ...
Unpacking r-bioc-rsamtools (1.30.0-1) ...
Selecting previously unselected package sbuild-build-depends-r-bioc-bitseq-dummy.
Preparing to unpack .../121-sbuild-build-depends-r-bioc-bitseq-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-r-bioc-bitseq-dummy (0.invalid.0) ...
Setting up cdbs (0.4.156) ...
Setting up libbz2-dev:armhf (1.0.6-8.1) ...
Setting up libjpeg62-turbo:armhf (1:1.5.2-2+b1) ...
Setting up libarchive-zip-perl (1.60-1) ...
Setting up libnghttp2-14:armhf (1.31.1-1) ...
Setting up libgfortran4:armhf (7.3.0-12) ...
Setting up libboost1.62-dev:armhf (1.62.0+dfsg-5+b2) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libjbig0:armhf (2.1-3.1+b2) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up fonts-dejavu-core (2.37-1) ...
Setting up libpsl5:armhf (0.20.1-1) ...
Setting up groff-base (1.22.3-10) ...
Setting up libglib2.0-0:armhf (2.56.1-2) ...
No schema files found: removed existing output file.
Setting up libncursesw6:armhf (6.1+20180210-2) ...
Setting up unzip (6.0-21) ...
Setting up dctrl-tools (2.24-2) ...
Setting up libdatrie1:armhf (0.2.11-1) ...
Setting up libtiff5:armhf (4.0.9-5) ...
Setting up gettext-base (0.19.8.1-6) ...
Setting up libpipeline1:armhf (1.5.0-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-9) ...
Setting up libbsd0:armhf (0.8.7-1) ...
Setting up ucf (3.0038) ...
Setting up libxml2:armhf (2.9.4+dfsg1-6.1) ...
Setting up zip (3.0-11) ...
Setting up libfreetype6:armhf (2.8.1-2) ...
Setting up libmagic-mgc (1:5.33-2) ...
Setting up libmagic1:armhf (1:5.33-2) ...
Setting up libgraphite2-3:armhf (1.3.11-2) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up libssl1.0.2:armhf (1.0.2o-1) ...
Setting up pkg-config (0.29-4) ...
Setting up libpixman-1-0:armhf (0.34.0-2) ...
Setting up libblas3:armhf (3.8.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libssh2-1:armhf (1.8.0-1) ...
Processing triggers for libc-bin (2.27-3+rpi1) ...
Setting up autotools-dev (20180224.1) ...
Processing triggers for systemd (238-4) ...
Setting up libgfortran-7-dev:armhf (7.3.0-12) ...
Setting up libfribidi0:armhf (0.19.7-2) ...
Setting up gfortran-7 (7.3.0-12) ...
Setting up libpcrecpp0v5:armhf (2:8.39-9) ...
Setting up libpcre32-3:armhf (2:8.39-9) ...
Setting up icu-devtools (57.1-9) ...
Setting up libpcre16-3:armhf (2:8.39-9) ...
Setting up libboost-dev:armhf (1.62.0.1+b8) ...
Setting up libtcl8.6:armhf (8.6.8+dfsg-4) ...
Setting up libthai-data (0.1.27-2) ...
Setting up libjpeg62-turbo-dev:armhf (1:1.5.2-2+b1) ...
Setting up liblzma-dev:armhf (5.2.2-1.3) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libkeyutils1:armhf (1.5.9-9.2) ...
Setting up bsdmainutils (11.1.2) ...
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 x11-common (1:7.7+19) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
Running in chroot, ignoring request.
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of restart.
Setting up xdg-utils (1.1.2-2) ...
Setting up libncurses6:armhf (6.1+20180210-2) ...
Setting up libx11-data (2:1.6.5-1) ...
Setting up libxau6:armhf (1:1.0.8-1+b2) ...
Setting up autopoint (0.19.8.1-6) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (0.041-1) ...
Setting up libpaper1:armhf (1.1.24+nmu5) ...
Creating config file /etc/papersize with new version
Setting up gfortran (4:7.2.0-1d1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libpaper-utils (1.1.24+nmu5) ...
Setting up libpcre3-dev:armhf (2:8.39-9) ...
Setting up fontconfig-config (2.13.0-4) ...
Installing new version of config file /etc/fonts/fonts.conf ...
Setting up gettext (0.19.8.1-6) ...
Setting up libblas-dev:armhf (3.8.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up liblapack3:armhf (3.8.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libharfbuzz0b:armhf (1.7.6-1) ...
Setting up autoconf (2.69-11) ...
Setting up libthai0:armhf (0.1.27-2) ...
Setting up libicu-dev (57.1-9) ...
Setting up file (1:5.33-2) ...
Setting up libkrb5support0:armhf (1.16-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libjpeg-dev (1:1.5.2-2) ...
Setting up automake (1:1.15.1-3.1) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up libice6:armhf (2:1.0.9-2) ...
Setting up man-db (2.8.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libpng-dev:armhf (1.6.34-1) ...
Setting up libncurses-dev:armhf (6.1+20180210-2) ...
Setting up libxcb1:armhf (1.13-1) ...
Setting up liblapack-dev:armhf (3.8.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libtool (2.4.6-2.1) ...
Setting up libfontconfig1:armhf (2.13.0-4) ...
Setting up libsm6:armhf (2:1.2.2-1+b3) ...
Setting up libk5crypto3:armhf (1.16-2) ...
Setting up libxcb-render0:armhf (1.13-1) ...
Setting up po-debconf (1.0.20) ...
Setting up libx11-6:armhf (2:1.6.5-1) ...
Setting up libxmuu1:armhf (2:1.1.2-2) ...
Setting up libncurses5-dev:armhf (6.1+20180210-2) ...
Setting up libreadline-dev:armhf (7.0-5) ...
Setting up libxcb-shm0:armhf (1.13-1) ...
Setting up libxt6:armhf (1:1.1.5-1) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up libkrb5-3:armhf (1.16-2) ...
Setting up libxft2:armhf (2.3.2-2) ...
Setting up fontconfig (2.13.0-4) ...
Regenerating fonts cache... done.
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up libxss1:armhf (1:1.2.2-1) ...
Setting up libgssapi-krb5-2:armhf (1.16-2) ...
Setting up xauth (1:1.0.10-1) ...
Setting up libpango-1.0-0:armhf (1.42.0-1) ...
Setting up libcairo2:armhf (1.15.10-3) ...
Setting up libcurl3:armhf (7.58.0-2) ...
Setting up libtk8.6:armhf (8.6.8-4) ...
Setting up libpangoft2-1.0-0:armhf (1.42.0-1) ...
Setting up libpangocairo-1.0-0:armhf (1.42.0-1) ...
Setting up r-base-core (3.4.4-1) ...
Creating config file /etc/R/Renviron with new version
Setting up r-base-dev (3.4.4-1) ...
Setting up r-bioc-biocgenerics (0.26.0-2) ...
Setting up r-cran-bitops (1.0-6-3) ...
Setting up r-cran-formatr (1.5-2) ...
Setting up r-cran-futile.options (1.0.1-1) ...
Setting up r-cran-rcurl (1.95-4.10-1) ...
Setting up r-cran-lambda.r (1.2.2-2) ...
Setting up r-cran-snow (1:0.4.2-1.1) ...
Setting up r-bioc-s4vectors (0.16.0-1) ...
Setting up r-bioc-genomeinfodbdata (1.1.0-2) ...
Setting up r-cran-futile.logger (1.4.3-2) ...
Setting up r-bioc-iranges (2.12.0-2) ...
Setting up r-bioc-biocparallel (1.12.0-2) ...
Setting up r-bioc-genomeinfodb (1.14.0-1) ...
Setting up r-bioc-xvector (0.18.0-1) ...
Setting up r-bioc-biostrings (2.46.0-1) ...
Setting up r-bioc-genomicranges (1.30.3-1) ...
Setting up r-bioc-rsamtools (1.30.0-1) ...
Setting up dh-autoreconf (17) ...
Setting up dh-strip-nondeterminism (0.041-1) ...
Setting up debhelper (11.2.1) ...
Setting up dh-r (20180508) ...
Setting up sbuild-build-depends-r-bioc-bitseq-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.30-15+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-12 gcc-7_7.3.0-12 libc6-dev_2.27-3+rpi1 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180414-1+rpi1 linux-libc-dev_4.15.17-1+rpi1
Package versions: adduser_3.117 apt_1.6.1 autoconf_2.69-11 automake_1:1.15.1-3.1 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-2+b1 binutils_2.30-15+rpi1 binutils-arm-linux-gnueabihf_2.30-15+rpi1 binutils-common_2.30-15+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.31.1-0.5 build-essential_12.4+b1 bzip2_1.0.6-8.1 ca-certificates_20170717 cdbs_0.4.156 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.3.0-12 dash_0.5.8-2.10 dbus_1.12.6-2 dbus-user-session_1.12.6-2 dctrl-tools_2.24-2 debconf_1.5.66 debhelper_11.2.1 debianutils_4.8.4 dh-autoreconf_17 dh-r_20180508 dh-strip-nondeterminism_0.041-1 diffutils_1:3.6-1 dirmngr_2.2.5-1 dmsetup_2:1.02.145-4.1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 e2fslibs_1.44.1-2 e2fsprogs_1.44.1-2 e2fsprogs-l10n_1.44.1-2 fakeroot_1.22-2 fdisk_2.31.1-0.5 file_1:5.33-2 findutils_4.6.0+git+20171230-2 fontconfig_2.13.0-4 fontconfig-config_2.13.0-4 fonts-dejavu-core_2.37-1 g++_4:7.2.0-1d1 g++-7_7.3.0-12 gcc_4:7.2.0-1d1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1 gcc-5-base_5.5.0-8 gcc-6-base_6.4.0-12+rpi1 gcc-7_7.3.0-12 gcc-7-base_7.3.0-12 gcc-8-base_8-20180414-1+rpi1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gfortran_4:7.2.0-1d1 gfortran-7_7.3.0-12 gnupg_2.2.5-1 gnupg-l10n_2.2.5-1 gnupg-utils_2.2.5-1 gpg_2.2.5-1 gpg-agent_2.2.5-1 gpg-wks-client_2.2.5-1 gpg-wks-server_2.2.5-1 gpgconf_2.2.5-1 gpgsm_2.2.5-1 gpgv_2.2.5-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 hostname_3.20 icu-devtools_57.1-9 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.12-4 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-2 libasan4_7.3.0-12 libassuan0_2.5.1-2 libatomic1_8-20180414-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.2-1 libaudit1_1:2.8.2-1 libbinutils_2.30-15+rpi1 libblas-dev_3.8.0-1 libblas3_3.8.0-1 libblkid1_2.31.1-0.5 libboost-dev_1.62.0.1+b8 libboost1.62-dev_1.62.0+dfsg-5+b2 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libbz2-dev_1.0.6-8.1 libc-bin_2.27-3+rpi1 libc-dev-bin_2.27-3+rpi1 libc6_2.27-3+rpi1 libc6-dev_2.27-3+rpi1 libcairo2_1.15.10-3 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.2 libcc1-0_8-20180414-1+rpi1 libcilkrts5_7.3.0-12 libcom-err2_1.44.1-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1 libcryptsetup4_2:1.7.5-1 libcurl3_7.58.0-2 libdatrie1_0.2.11-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.6-2 libdebconfclient0_0.243 libdevmapper1.02.1_2:1.02.145-4.1 libdpkg-perl_1.19.0.5 libdrm-common_2.4.91-2+rpi1 libdrm2_2.4.91-2+rpi1 libexpat1_2.2.5-3 libext2fs2_1.44.1-2 libfakeroot_1.22-2 libfdisk1_2.31.1-0.5 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.041-1 libfontconfig1_2.13.0-4 libfreetype6_2.8.1-2 libfribidi0_0.19.7-2 libgcc-7-dev_7.3.0-12 libgcc1_1:8-20180414-1+rpi1 libgcrypt20_1.8.2-2 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libgfortran-7-dev_7.3.0-12 libgfortran4_7.3.0-12 libglib2.0-0_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8-20180414-1+rpi1 libgpg-error0_1.29-4 libgraphite2-3_1.3.11-2 libgssapi-krb5-2_1.16-2 libharfbuzz0b_1.7.6-1 libhogweed4_3.4-1 libice6_2:1.0.9-2 libicu-dev_57.1-9 libicu57_57.1-9 libidn11_1.33-2.2 libidn2-0_2.0.4-1.1 libip4tc0_1.6.2-1 libisl15_0.18-4 libjbig0_2.1-3.1+b2 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2 libkeyutils1_1.5.9-9.2 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libkrb5-3_1.16-2 libkrb5support0_1.16-2 libksba8_1.3.5-2 liblapack-dev_3.8.0-1 liblapack3_3.8.0-1 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblocale-gettext-perl_1.07-3+b2 liblz4-1_1.8.1.2-1+rpi1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-2 libmagic1_1:5.33-2 libmount1_2.31.1-0.5 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses-dev_6.1+20180210-2 libncurses5_6.1-1 libncurses5-dev_6.1+20180210-2 libncurses6_6.1+20180210-2 libncursesw5_6.1-1 libncursesw6_6.1+20180210-2 libnettle6_3.4-1 libnghttp2-14_1.31.1-1 libnpth0_1.5-3 libnss-systemd_238-4 libp11-kit0_0.23.10-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_238-4 libpam0g_1.1.8-3.7 libpango-1.0-0_1.42.0-1 libpangocairo-1.0-0_1.42.0-1 libpangoft2-1.0-0_1.42.0-1 libpaper-utils_1.1.24+nmu5 libpaper1_1.1.24+nmu5 libpcre16-3_2:8.39-9 libpcre3_2:8.39-9 libpcre3-dev_2:8.39-9 libpcre32-3_2:8.39-9 libpcrecpp0v5_2:8.39-9 libperl5.26_5.26.2-2 libpipeline1_1.5.0-1 libpixman-1-0_0.34.0-2 libplymouth4_0.9.3-2 libpng-dev_1.6.34-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.14-1 libpsl5_0.20.1-1 libreadline-dev_7.0-5 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.12-2 libsm6_2:1.2.2-1+b3 libsmartcols1_2.31.1-0.5 libsqlite3-0_3.23.1-1 libss2_1.44.1-2 libssh2-1_1.8.0-1 libssl1.0.2_1.0.2o-1 libssl1.1_1.1.0h-2 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180414-1+rpi1 libsystemd0_238-4 libtasn1-6_4.13-2 libtcl8.6_8.6.8+dfsg-4 libtext-charwidth-perl_0.04-7.1 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libthai-data_0.1.27-2 libthai0_0.1.27-2 libtiff5_4.0.9-5 libtimedate-perl_2.3000-2 libtinfo5_6.1-1 libtinfo6_6.1+20180210-2 libtk8.6_8.6.8-4 libtool_2.4.6-2.1 libubsan0_7.3.0-12 libudev1_238-4 libunistring2_0.9.8-1 libuuid1_2.31.1-0.5 libx11-6_2:1.6.5-1 libx11-data_2:1.6.5-1 libxau6_1:1.0.8-1+b2 libxcb-render0_1.13-1 libxcb-shm0_1.13-1 libxcb1_1.13-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxft2_2.3.2-2 libxml2_2.9.4+dfsg1-6.1 libxmuu1_2:1.1.2-2 libxrender1_1:0.9.10-1 libxss1_1:1.2.2-1 libxt6_1:1.1.5-1 libzstd1_1.3.3+dfsg-2+rpi1 linux-base_4.5 linux-libc-dev_4.15.17-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.3-2 mawk_1.3.3-17 mount_2.31.1-0.5 multiarch-support_2.27-3+rpi1 nano_2.9.5-1 ncurses-base_6.1-1 ncurses-bin_6.1-1 netbase_5.4 openssl_1.1.0h-2 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-2 perl-base_5.26.2-2 perl-modules-5.26_5.26.2-3 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.3-2 po-debconf_1.0.20 procps_2:3.3.14-1 r-base-core_3.4.4-1 r-base-dev_3.4.4-1 r-bioc-biocgenerics_0.26.0-2 r-bioc-biocparallel_1.12.0-2 r-bioc-biostrings_2.46.0-1 r-bioc-genomeinfodb_1.14.0-1 r-bioc-genomeinfodbdata_1.1.0-2 r-bioc-genomicranges_1.30.3-1 r-bioc-iranges_2.12.0-2 r-bioc-rsamtools_1.30.0-1 r-bioc-s4vectors_0.16.0-1 r-bioc-xvector_0.18.0-1 r-cran-bitops_1.0-6-3 r-cran-formatr_1.5-2 r-cran-futile.logger_1.4.3-2 r-cran-futile.options_1.0.1-1 r-cran-lambda.r_1.2.2-2 r-cran-rcurl_1.95-4.10-1 r-cran-snow_1:0.4.2-1.1 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-bitseq-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_238-4 systemd-sysv_238-4 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2018d-1 ucf_3.0038 udev_238-4 unzip_6.0-21 util-linux_2.31.1-0.5 x11-common_1:7.7+19 xauth_1:1.0.10-1 xdg-utils_1.1.2-2 xz-utils_5.2.2-1.3 zip_3.0-11 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 Sat May 12 20:00:53 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./r-bioc-bitseq_1.24.0+dfsg-1.dsc
dpkg-source: info: extracting r-bioc-bitseq in /<<BUILDDIR>>/r-bioc-bitseq-1.24.0+dfsg
dpkg-source: info: unpacking r-bioc-bitseq_1.24.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking r-bioc-bitseq_1.24.0+dfsg-1.debian.tar.xz
dpkg-source: info: applying use_debian_packaged_zlib.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-712b3e15-9d74-4d4b-b9d7-edc050e2dfc3
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package r-bioc-bitseq
dpkg-buildpackage: info: source version 1.24.0+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build r-bioc-bitseq-1.24.0+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --buildsystem R
dh_testdir -O--buildsystem=R
dh_auto_clean -O--buildsystem=R
dh_autoreconf_clean -O--buildsystem=R
dh_clean -O--buildsystem=R
debian/rules build-arch
dh build-arch --buildsystem R
dh_testdir -a -O--buildsystem=R
dh_update_autotools_config -a -O--buildsystem=R
dh_autoreconf -a -O--buildsystem=R
dh_auto_configure -a -O--buildsystem=R
dh_auto_build -a -O--buildsystem=R
dh_auto_test -a -O--buildsystem=R
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --buildsystem R
dh_testroot -a -O--buildsystem=R
dh_prep -a -O--buildsystem=R
dh_installdirs -a -O--buildsystem=R
dh_auto_install -a -O--buildsystem=R
I: R Package: BitSeq Version: 1.24.0
I: Building using R version 3.4.4-1
I: R API version: r-api-3.4
I: Using built-time from d/changelog: Sat, 12 May 2018 21:41:33 +0200
mkdir -p /<<BUILDDIR>>/r-bioc-bitseq-1.24.0\+dfsg/debian/r-bioc-bitseq/usr/lib/R/site-library
R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-bitseq-1.24.0\+dfsg/debian/r-bioc-bitseq/usr/lib/R/site-library --clean . "--built-timestamp='Sat, 12 May 2018 21:41:33 +0200'"
* installing *source* package 'BitSeq' ...
configure: Version def: -DBS_VERSION=\"1.24.0\"
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for g++ option to support OpenMP... -fopenmp
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/Makevars.win
** libs
make[1]: Entering directory '/<<BUILDDIR>>/r-bioc-bitseq-1.24.0+dfsg/src'
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ArgumentParser.cpp -o ArgumentParser.o
In file included from /usr/include/c++/7/vector:69:0,
from ArgumentParser.h:6,
from ArgumentParser.cpp:5:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c CollapsedSampler.cpp -o CollapsedSampler.o
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c FileHeader.cpp -o FileHeader.o
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c GibbsParameters.cpp -o GibbsParameters.o
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c GibbsSampler.cpp -o GibbsSampler.o
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MyTimer.cpp -o MyTimer.o
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c PosteriorSamples.cpp -o PosteriorSamples.o
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_BitSeq.cpp -o R_init_BitSeq.o
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ReadDistribution.cpp -o ReadDistribution.o
In file included from /usr/include/c++/7/vector:69:0,
from ReadDistribution.h:4,
from ReadDistribution.cpp:7:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ReadDistribution.h:4,
from ReadDistribution.cpp:7:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void ReadDistribution::updateMismatchFreq(bam1_t*)':
/usr/include/c++/7/bits/stl_vector.h:712:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:712:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/map:60:0,
from ReadDistribution.h:5,
from ReadDistribution.cpp:7:
/usr/include/c++/7/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const long int&>, std::tuple<>}; _Key = long int; _Val = std::pair<const long int, double>; _KeyOfValue = std::_Select1st<std::pair<const long int, double> >; _Compare = std::less<long int>; _Alloc = std::allocator<std::pair<const long int, double> >]':
/usr/include/c++/7/bits/stl_tree.h:2395:7: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const long int, double> >}' changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/map:61:0,
from ReadDistribution.h:5,
from ReadDistribution.cpp:7:
/usr/include/c++/7/bits/stl_map.h: In member function 'double ReadDistribution::getWeightNorm(long int, ns_rD::readT, long int)':
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const long int, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const long int, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h: In member function 'bool ReadDistribution::observed(ns_rD::fragmentP)':
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const long int, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const long int, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const long int, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const long int, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const long int, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const long int, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const long int, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:493:4: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const long int, double> >}' changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
In file included from /usr/include/c++/7/vector:64:0,
from ReadDistribution.h:4,
from ReadDistribution.cpp:7:
/usr/include/c++/7/bits/stl_vector.h: In constructor 'ReadDistribution::ReadDistribution()':
/usr/include/c++/7/bits/stl_vector.h:712:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:712:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Sampler.cpp -o Sampler.o
In file included from /usr/include/c++/7/vector:69:0,
from Sampler.h:4,
from Sampler.cpp:5:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from Sampler.h:4,
from Sampler.cpp:5:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void Sampler::appendFile()':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SimpleSparse.cpp -o SimpleSparse.o
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c TagAlignments.cpp -o TagAlignments.o
In file included from /usr/include/c++/7/vector:69:0,
from TagAlignments.h:5,
from TagAlignments.cpp:3:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from TagAlignments.h:5,
from TagAlignments.cpp:3:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void TagAlignments::pushAlignmentL(long int, double)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c TranscriptExpression.cpp -o TranscriptExpression.o
In file included from /usr/include/c++/7/algorithm:62:0,
from TranscriptExpression.cpp:1:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from TranscriptExpression.cpp:1:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >; _Distance = int; _Tp = trExpInfoT; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from TranscriptExpression.cpp:1:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'void TranscriptExpression::doSort(bool)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c TranscriptInfo.cpp -o TranscriptInfo.o
In file included from /usr/include/c++/7/vector:69:0,
from TranscriptInfo.h:4,
from TranscriptInfo.cpp:4:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const transcriptT&}; _Tp = transcriptT; _Alloc = std::allocator<transcriptT>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<transcriptT>::iterator {aka __gnu_cxx::__normal_iterator<transcriptT*, std::vector<transcriptT> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from TranscriptInfo.h:4,
from TranscriptInfo.cpp:4:
/usr/include/c++/7/bits/stl_vector.h: In member function 'bool TranscriptInfo::setInfo(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<long int>)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<transcriptT*, std::vector<transcriptT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'bool TranscriptInfo::readInfo(std::__cxx11::string)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<transcriptT*, std::vector<transcriptT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c TranscriptSequence.cpp -o TranscriptSequence.o
In file included from /usr/include/c++/7/vector:69:0,
from TranscriptSequence.h:6,
from TranscriptSequence.cpp:6:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const trSeqInfoT&}; _Tp = trSeqInfoT; _Alloc = std::allocator<trSeqInfoT>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<trSeqInfoT>::iterator {aka __gnu_cxx::__normal_iterator<trSeqInfoT*, std::vector<trSeqInfoT> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from TranscriptSequence.h:6,
from TranscriptSequence.cpp:6:
/usr/include/c++/7/bits/stl_vector.h: In member function 'bool TranscriptSequence::readSequence(std::__cxx11::string, refFormatT)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trSeqInfoT*, std::vector<trSeqInfoT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c VariationalBayes.cpp -o VariationalBayes.o
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/boost/random/detail/polynomial.hpp:18,
from /usr/include/boost/random/mersenne_twister.hpp:32,
from VariationalBayes.h:4,
from VariationalBayes.cpp:12:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {boost::random::gamma_distribution<double>::param_type}; _Tp = boost::random::gamma_distribution<double>::param_type; _Alloc = std::allocator<boost::random::gamma_distribution<double>::param_type>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<boost::random::gamma_distribution<double>::param_type>::iterator {aka __gnu_cxx::__normal_iterator<boost::random::gamma_distribution<double>::param_type*, std::vector<boost::random::gamma_distribution<double>::param_type> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void VariationalBayes::generateSamples(long int, const string&, const std::vector<double>*, std::ofstream*)':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<boost::random::gamma_distribution<double>::param_type*, std::vector<boost::random::gamma_distribution<double>::param_type> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c common.cpp -o common.o
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c estimateDE.cpp -o estimateDE.o
estimateDE.cpp:57:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
estimateDE.cpp:57:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c estimateExpression.cpp -o estimateExpression.o
estimateExpression.cpp:532:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
estimateExpression.cpp:532:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from estimateExpression.cpp:1:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from estimateExpression.cpp:1:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from estimateExpression.cpp:1:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'void MCMC(TagAlignments*, gibbsParameters&, ArgumentParser&)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c estimateHyperPar.cpp -o estimateHyperPar.o
estimateHyperPar.cpp:62:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
estimateHyperPar.cpp:62:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/boost/random/detail/polynomial.hpp:18,
from /usr/include/boost/random/mersenne_twister.hpp:32,
from estimateHyperPar.cpp:10:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ns_params::paramT&}; _Tp = ns_params::paramT; _Alloc = std::allocator<ns_params::paramT>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<ns_params::paramT>::iterator {aka __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:153:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from estimateHyperPar.cpp:6:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from estimateHyperPar.cpp:6:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >; _Distance = int; _Tp = ns_params::paramT; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from estimateHyperPar.cpp:6:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/boost/random/detail/polynomial.hpp:18,
from /usr/include/boost/random/mersenne_twister.hpp:32,
from estimateHyperPar.cpp:10:
/usr/include/c++/7/bits/stl_vector.h: In function 'int estimateHyperPar(int*, char**)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from estimateHyperPar.cpp:6:
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/boost/random/detail/polynomial.hpp:18,
from /usr/include/boost/random/mersenne_twister.hpp:32,
from estimateHyperPar.cpp:10:
/usr/include/c++/7/bits/stl_vector.h:1180:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
{ return _M_erase(begin() + (__position - cbegin())); }
^
/usr/include/c++/7/bits/stl_vector.h:1180:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
{ return _M_erase(begin() + (__position - cbegin())); }
^
/usr/include/c++/7/bits/stl_vector.h:1180:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
{ return _M_erase(begin() + (__position - cbegin())); }
^
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c estimateVBExpression.cpp -o estimateVBExpression.o
estimateVBExpression.cpp:126:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
estimateVBExpression.cpp:126:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c getGeneExpression.cpp -o getGeneExpression.o
getGeneExpression.cpp:33:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
getGeneExpression.cpp:33:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c getVariance.cpp -o getVariance.o
getVariance.cpp:28:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
getVariance.cpp:28:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
getWithinGeneExpression.cpp:54:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
getWithinGeneExpression.cpp:54:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lowess.cpp -o lowess.o
In file included from /usr/include/c++/7/algorithm:62:0,
from lowess.cpp:17:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from lowess.cpp:17:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from lowess.cpp:17:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'void lowess(const std::vector<double>&, const std::vector<double>&, double, long int, double, std::vector<double>&, std::vector<double>&, std::vector<double>&)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c misc.cpp -o misc.o
In file included from /usr/include/c++/7/vector:69:0,
from ArgumentParser.h:6,
from misc.h:6,
from misc.cpp:5:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ns_params::paramT&}; _Tp = ns_params::paramT; _Alloc = std::allocator<ns_params::paramT>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<ns_params::paramT>::iterator {aka __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from misc.cpp:1:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from misc.cpp:1:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from misc.cpp:1:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'void ns_misc::computeCI(double, std::vector<double>*, double*, double*)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from misc.cpp:1:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >; _Distance = int; _Tp = ns_params::paramT; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from misc.cpp:1:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ArgumentParser.h:6,
from misc.h:6,
from misc.cpp:5:
/usr/include/c++/7/bits/stl_vector.h: In function 'bool ns_params::readParams(const string&, std::vector<ns_params::paramT>*, std::ofstream*)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from misc.cpp:1:
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c parseAlignment.cpp -o parseAlignment.o
parseAlignment.cpp:102:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
parseAlignment.cpp:102:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from ArgumentParser.h:6,
from parseAlignment.cpp:7:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {ns_parseAlignment::TagAlignment}; _Tp = ns_parseAlignment::TagAlignment; _Alloc = std::allocator<ns_parseAlignment::TagAlignment>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<ns_parseAlignment::TagAlignment>::iterator {aka __gnu_cxx::__normal_iterator<ns_parseAlignment::TagAlignment*, std::vector<ns_parseAlignment::TagAlignment> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In function 'int parseAlignment(int*, char**)':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_parseAlignment::TagAlignment*, std::vector<ns_parseAlignment::TagAlignment> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c transposeFiles.cpp -o transposeFiles.o
g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o BitSeq.so ArgumentParser.o CollapsedSampler.o FileHeader.o GibbsParameters.o GibbsSampler.o MyTimer.o PosteriorSamples.o R_init_BitSeq.o ReadDistribution.o Sampler.o SimpleSparse.o TagAlignments.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o VariationalBayes.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o estimateVBExpression.o getGeneExpression.o getVariance.o getWithinGeneExpression.o lowess.o misc.o parseAlignment.o transposeFiles.o /usr/lib/R/site-library/Rsamtools/usrlib//libbam.a /usr/lib/R/site-library/Rsamtools/usrlib//libbcf.a /usr/lib/R/site-library/Rsamtools/usrlib//libtabix.a -lz -pthread -fopenmp -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/<<BUILDDIR>>/r-bioc-bitseq-1.24.0+dfsg/src'
make[1]: Entering directory '/<<BUILDDIR>>/r-bioc-bitseq-1.24.0+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/r-bioc-bitseq-1.24.0+dfsg/src'
installing to /<<BUILDDIR>>/r-bioc-bitseq-1.24.0+dfsg/debian/r-bioc-bitseq/usr/lib/R/site-library/BitSeq/libs
** R
** inst
** preparing package for lazy loading
Warning: multiple methods tables found for 'pos'
Warning: replacing previous import 'BiocGenerics::pos' by 'IRanges::pos' when loading 'GenomeInfoDb'
Warning: replacing previous import 'BiocGenerics::pos' by 'IRanges::pos' when loading 'GenomicRanges'
Warning: replacing previous import 'BiocGenerics::pos' by 'IRanges::pos' when loading 'XVector'
Warning: multiple methods tables found for 'pos'
Warning: replacing previous import 'BiocGenerics::pos' by 'IRanges::pos' when loading 'Biostrings'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: multiple methods tables found for 'pos'
Warning: replacing previous import 'BiocGenerics::pos' by 'IRanges::pos' when loading 'GenomeInfoDb'
Warning: replacing previous import 'BiocGenerics::pos' by 'IRanges::pos' when loading 'GenomicRanges'
Warning: replacing previous import 'BiocGenerics::pos' by 'IRanges::pos' when loading 'XVector'
Warning: multiple methods tables found for 'pos'
Warning: replacing previous import 'BiocGenerics::pos' by 'IRanges::pos' when loading 'Biostrings'
* DONE (BitSeq)
rm -f /<<BUILDDIR>>/r-bioc-bitseq-1.24.0\+dfsg/debian/r-bioc-bitseq/usr/lib/R/site-library/BitSeq/LICENSE
Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 290.
Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 291.
Use of uninitialized value $dep_line in split at /usr/share/perl5/Dpkg/Deps.pm line 294.
I: Using r-bioc-rsamtools for Depends:Rsamtools
I: Using r-bioc-edger for Suggests:edgeR
W: Cannot find a debian package for Suggests:DESeq
W: Cannot find a debian package for Suggests:BiocStyle
I: Using r-bioc-s4vectors for Imports:S4Vectors
I: Using r-bioc-iranges for Imports:IRanges
dh_install -a -O--buildsystem=R
dh_installdocs -a -O--buildsystem=R
dh_installchangelogs -a -O--buildsystem=R
dh_installexamples -a -O--buildsystem=R
dh_installman -a -O--buildsystem=R
dh_installcatalogs -a -O--buildsystem=R
dh_installcron -a -O--buildsystem=R
dh_installdebconf -a -O--buildsystem=R
dh_installemacsen -a -O--buildsystem=R
dh_installifupdown -a -O--buildsystem=R
dh_installinfo -a -O--buildsystem=R
dh_installinit -a -O--buildsystem=R
dh_installsystemd -a -O--buildsystem=R
dh_installmenu -a -O--buildsystem=R
dh_installmime -a -O--buildsystem=R
dh_installmodules -a -O--buildsystem=R
dh_installlogcheck -a -O--buildsystem=R
dh_installlogrotate -a -O--buildsystem=R
dh_installpam -a -O--buildsystem=R
dh_installppp -a -O--buildsystem=R
dh_installudev -a -O--buildsystem=R
dh_installgsettings -a -O--buildsystem=R
dh_bugfiles -a -O--buildsystem=R
dh_ucf -a -O--buildsystem=R
dh_lintian -a -O--buildsystem=R
dh_gconf -a -O--buildsystem=R
dh_icons -a -O--buildsystem=R
dh_perl -a -O--buildsystem=R
dh_usrlocal -a -O--buildsystem=R
dh_link -a -O--buildsystem=R
dh_installwm -a -O--buildsystem=R
dh_installxfonts -a -O--buildsystem=R
dh_strip_nondeterminism -a -O--buildsystem=R
dh_compress -a -O--buildsystem=R
dh_fixperms -a -O--buildsystem=R
dh_missing -a -O--buildsystem=R
dh_strip -a -O--buildsystem=R
dh_makeshlibs -a -O--buildsystem=R
dh_shlibdeps -a -O--buildsystem=R
dh_installdeb -a -O--buildsystem=R
dh_gencontrol -a -O--buildsystem=R
dh_md5sums -a -O--buildsystem=R
dh_builddeb -a -O--buildsystem=R
dpkg-deb: building package 'r-bioc-bitseq' in '../r-bioc-bitseq_1.24.0+dfsg-1_armhf.deb'.
dpkg-deb: building package 'r-bioc-bitseq-dbgsym' in '../r-bioc-bitseq-dbgsym_1.24.0+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../r-bioc-bitseq_1.24.0+dfsg-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build r-bioc-bitseq-1.24.0+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-05-15T07:24:49Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
r-bioc-bitseq_1.24.0+dfsg-1_armhf.changes:
------------------------------------------
Format: 1.8
Date: Sat, 12 May 2018 21:41:33 +0200
Source: r-bioc-bitseq
Binary: r-bioc-bitseq
Architecture: armhf
Version: 1.24.0+dfsg-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
r-bioc-bitseq - transcript expression inference and analysis for RNA-seq data
Closes: 892522
Changes:
r-bioc-bitseq (1.24.0+dfsg-1) unstable; urgency=medium
.
* Initial release (closes: #892522)
Checksums-Sha1:
86f7913a583ffcbdc041235fdaaa65e82d56bd4b 2350900 r-bioc-bitseq-dbgsym_1.24.0+dfsg-1_armhf.deb
0a17632192fb67c69fb2383cc8988e95663c19a0 8143 r-bioc-bitseq_1.24.0+dfsg-1_armhf.buildinfo
a7361a11f6087a9d9fa990d7c2fb2c3f1cd7f592 910972 r-bioc-bitseq_1.24.0+dfsg-1_armhf.deb
Checksums-Sha256:
55b8b3c9f43e43ea73d228d7f32c992df691d9824d4d7801a75a06b87834a657 2350900 r-bioc-bitseq-dbgsym_1.24.0+dfsg-1_armhf.deb
c54ecf7ce8005c1428fbec577405644430f4b645f39a8d07bdfd37b129f53be6 8143 r-bioc-bitseq_1.24.0+dfsg-1_armhf.buildinfo
e52bbb16cc9944b74be690e35bf2e79963a9705742cd57a5325bd3c24837f441 910972 r-bioc-bitseq_1.24.0+dfsg-1_armhf.deb
Files:
4f252fa88514d11cc5584229e499132f 2350900 debug optional r-bioc-bitseq-dbgsym_1.24.0+dfsg-1_armhf.deb
ad1347ce6a6304c34d1e725bb8440fb2 8143 gnu-r optional r-bioc-bitseq_1.24.0+dfsg-1_armhf.buildinfo
ddafe16cd24016f777d80175255c2f65 910972 gnu-r optional r-bioc-bitseq_1.24.0+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
r-bioc-bitseq-dbgsym_1.24.0+dfsg-1_armhf.deb
--------------------------------------------
new Debian package, version 2.0.
size 2350900 bytes: control archive=540 bytes.
401 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: r-bioc-bitseq-dbgsym
Source: r-bioc-bitseq
Version: 1.24.0+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 2381
Depends: r-bioc-bitseq (= 1.24.0+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for r-bioc-bitseq
Build-Ids: 06d0ec82acfc1e8fd3455830c964eb51e75a8551
drwxr-xr-x root/root 0 2018-05-12 19:41 ./
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/lib/
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/lib/debug/.build-id/06/
-rw-r--r-- root/root 2427232 2018-05-12 19:41 ./usr/lib/debug/.build-id/06/d0ec82acfc1e8fd3455830c964eb51e75a8551.debug
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/share/
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-05-12 19:41 ./usr/share/doc/r-bioc-bitseq-dbgsym -> r-bioc-bitseq
r-bioc-bitseq_1.24.0+dfsg-1_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 910972 bytes: control archive=1896 bytes.
1187 bytes, 22 lines control
2861 bytes, 36 lines md5sums
Package: r-bioc-bitseq
Version: 1.24.0+dfsg-1
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 5454
Depends: r-base-core (>= 3.4.4-1), r-api-3.4, r-bioc-rsamtools, r-bioc-s4vectors, r-bioc-iranges, libc6 (>= 2.23), libgcc1 (>= 1:3.5), libgomp1 (>= 4.9), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3)
Suggests: r-bioc-edger
Section: gnu-r
Priority: optional
Homepage: https://bioconductor.org/packages/BitSeq/
Description: transcript expression inference and analysis for RNA-seq data
The BitSeq package is targeted for transcript expression
analysis and differential expression analysis of RNA-seq data
in two stage process. In the first stage it uses Bayesian
inference methodology to infer expression of individual
transcripts from individual RNA-seq experiments. The second
stage of BitSeq embraces the differential expression analysis
of transcript expression. Providing expression estimates from
replicates of multiple conditions, Log-Normal model of the
estimates is used for inferring the condition mean transcript
expression and ranking the transcripts based on the likelihood
of differential expression.
drwxr-xr-x root/root 0 2018-05-12 19:41 ./
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/lib/
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/lib/R/
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/lib/R/site-library/
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/
-rw-r--r-- root/root 697 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/CITATION
-rw-r--r-- root/root 1518 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/DESCRIPTION
-rw-r--r-- root/root 1159 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/INDEX
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/Meta/
-rw-r--r-- root/root 845 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/Meta/Rd.rds
-rw-r--r-- root/root 112 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/Meta/features.rds
-rw-r--r-- root/root 838 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/Meta/hsearch.rds
-rw-r--r-- root/root 374 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/Meta/links.rds
-rw-r--r-- root/root 365 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/Meta/nsInfo.rds
-rw-r--r-- root/root 1165 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/Meta/package.rds
-rw-r--r-- root/root 239 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/Meta/vignette.rds
-rw-r--r-- root/root 383 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/NAMESPACE
-rw-r--r-- root/root 4127 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/NEWS
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/R/
-rw-r--r-- root/root 1056 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/R/BitSeq
-rw-r--r-- root/root 16670 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/R/BitSeq.rdb
-rw-r--r-- root/root 621 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/R/BitSeq.rdx
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/doc/
-rw-r--r-- root/root 6530 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/doc/BitSeq.R
-rw-r--r-- root/root 17972 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/doc/BitSeq.Rnw
-rw-r--r-- root/root 215750 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/doc/BitSeq.pdf
-rw-r--r-- root/root 1316 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/doc/index.html
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/extdata/
-rw-r--r-- root/root 4070127 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/extdata/data-c0b0.sam
-rw-r--r-- root/root 176210 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/extdata/data-c0b1.rpkm
-rw-r--r-- root/root 176210 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/extdata/data-c1b0.rpkm
-rw-r--r-- root/root 176210 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/extdata/data-c1b1.rpkm
-rw-r--r-- root/root 87197 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/extdata/ensSelect1.fasta
-rw-r--r-- root/root 2009 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/extdata/ensSelect1.tr
-rw-r--r-- root/root 636 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/extdata/parameters1.txt
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/help/
-rw-r--r-- root/root 655 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/help/AnIndex
-rw-r--r-- root/root 42086 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/help/BitSeq.rdb
-rw-r--r-- root/root 470 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/help/BitSeq.rdx
-rw-r--r-- root/root 289 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/help/aliases.rds
-rw-r--r-- root/root 272 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/help/paths.rds
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/html/
-rw-r--r-- root/root 4296 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/html/00Index.html
-rw-r--r-- root/root 1335 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/html/R.css
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/libs/
-rw-r--r-- root/root 525248 2018-05-12 19:41 ./usr/lib/R/site-library/BitSeq/libs/BitSeq.so
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/share/
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-05-12 19:41 ./usr/share/doc/r-bioc-bitseq/
-rw-r--r-- root/root 162 2018-05-12 19:41 ./usr/share/doc/r-bioc-bitseq/changelog.Debian.gz
-rw-r--r-- root/root 10115 2018-05-12 19:41 ./usr/share/doc/r-bioc-bitseq/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 16768
Build-Time: 625
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 890
Job: r-bioc-bitseq_1.24.0+dfsg-1
Machine Architecture: armhf
Package: r-bioc-bitseq
Package-Time: 1566
Source-Version: 1.24.0+dfsg-1
Space: 16768
Status: successful
Version: 1.24.0+dfsg-1
--------------------------------------------------------------------------------
Finished at 2018-05-15T07:24:49Z
Build needed 00:26:06, 16768k disc space