Build log for r-bioc-bitseq (1.24.0+dfsg-1+b1) on armhf

r-bioc-bitseq → 1.24.0+dfsg-1+b1 → armhf → 2018-06-14 23:51:36

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03

+==============================================================================+
| r-bioc-bitseq 1.24.0+dfsg-1+b1 (armhf)       Thu, 14 Jun 2018 23:10:45 +0000 |
+==============================================================================+

Package: r-bioc-bitseq
Version: 1.24.0+dfsg-1+b1
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-8be79650-d967-414d-84eb-4ed9e1d11f7d' 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 [10.8 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.6 MB]
Fetched 23.4 MB in 27s (875 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 (1546 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-bitseq-0hwQMi/r-bioc-bitseq-1.24.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-bitseq-0hwQMi' 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-CEiBwp/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-CEiBwp/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-CEiBwp/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-CEiBwp/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-CEiBwp/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-CEiBwp/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-CEiBwp/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-CEiBwp/apt_archive ./ Packages [434 B]
Fetched 2110 B in 1s (3219 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 49 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-CEiBwp/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 ... 14002 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-CEiBwp/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-CEiBwp/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-CEiBwp/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-CEiBwp/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-CEiBwp/apt_archive ./ Sources [542 B]
Get:5 copy:/<<BUILDDIR>>/resolver-CEiBwp/apt_archive ./ Packages [626 B]
Fetched 2501 B in 1s (3481 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 cpp cpp-7 dctrl-tools
  debhelper default-libmysqlclient-dev dh-autoreconf dh-r
  dh-strip-nondeterminism dwz file fontconfig fontconfig-config
  fonts-dejavu-core g++-7 gcc gcc-7 gcc-7-base gdal-data gettext gettext-base
  gfortran gfortran-7 gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 groff-base
  hdf5-helpers icu-devtools intltool-debian libaec-dev libaec0
  libarchive-zip-perl libarmadillo-dev libarmadillo8 libarpack2 libarpack2-dev
  libasan4 libblas-dev libblas3 libboost-dev libboost1.62-dev libbsd0
  libbz2-dev libcairo2 libcharls-dev libcharls1 libcilkrts5 libcroco3
  libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdap-dev libdap25
  libdapclient6v5 libdapserver7v5 libdatrie1 libelf1 libepsilon-dev
  libepsilon1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1
  libfreetype6 libfreexl-dev libfreexl1 libfribidi0 libfyba-dev libfyba0
  libgcc-7-dev libgdal-dev libgdal20 libgeos-3.6.2 libgeos-c1v5 libgeos-dev
  libgeotiff-dev libgeotiff2 libgfortran-7-dev libgfortran4 libgif-dev libgif7
  libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin libglib2.0-data
  libglib2.0-dev libglib2.0-dev-bin libgraphite2-3 libgraphite2-dev
  libgssapi-krb5-2 libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0
  libharfbuzz0b libhdf4-0-alt libhdf4-alt-dev libhdf5-100 libhdf5-cpp-100
  libhdf5-dev libice6 libicu-dev libicu-le-hb-dev libicu-le-hb0 libicu60
  libisl19 libjbig-dev libjbig0 libjpeg-dev libjpeg62-turbo
  libjpeg62-turbo-dev libjson-c-dev libk5crypto3 libkeyutils1 libkml-dev
  libkmlbase1 libkmlconvenience1 libkmldom1 libkmlengine1 libkmlregionator1
  libkmlxsd1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblcms2-2
  libltdl-dev libltdl7 liblzma-dev libmagic-mgc libmagic1 libmariadbclient-dev
  libmariadbclient-dev-compat libmariadbclient18 libminizip-dev libminizip1
  libmpdec2 libncurses-dev libncurses5-dev libnetcdf-dev libnetcdf13
  libnghttp2-14 libnspr4 libnss3 libodbc1 libogdi3.2 libogdi3.2-dev
  libopenjp2-7 libopenjp2-7-dev 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
  libpoppler-dev libpoppler-private-dev libpoppler74 libpopt0 libpq-dev libpq5
  libproj-dev libproj13 libpsl5 libpython3-stdlib libpython3.6-minimal
  libpython3.6-stdlib libqhull-dev libqhull-r7 libqhull7 libreadline-dev
  libreadline7 librtmp1 libsigsegv2 libsm6 libspatialite-dev libspatialite7
  libsqlite3-0 libsqlite3-dev libssh2-1 libstdc++-7-dev libsuperlu-dev
  libsuperlu5 libsz2 libtcl8.6 libthai-data libthai0 libtiff-dev libtiff5
  libtiff5-dev libtiffxx5 libtimedate-perl libtk8.6 libtool libubsan0
  liburiparser-dev liburiparser1 libwebp-dev libwebp6 libwebpdemux2
  libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1
  libxdmcp6 libxerces-c-dev libxerces-c3.2 libxext6 libxft2 libxml2
  libxml2-dev libxmuu1 libxrender1 libxss1 libxt6 libzstd-dev m4 man-db
  mime-support mysql-common odbcinst odbcinst1debian2 pkg-config po-debconf
  proj-data python3 python3-distutils python3-lib2to3 python3-minimal
  python3.6 python3.6-minimal 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 unixodbc-dev unzip uuid-dev x11-common xauth xdg-utils zip
  zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
  vacation cpp-doc gcc-7-locales debtags dh-make gcc-7-doc libstdc++6-7-dbg
  gcc-multilib manpages-dev flex bison gdb gcc-doc libgcc1-dbg libgomp1-dbg
  libitm1-dbg libatomic1-dbg libasan4-dbg liblsan0-dbg libtsan0-dbg
  libubsan0-dbg libcilkrts5-dbg libmpx2-dbg libquadmath0-dbg gettext-doc
  libasprintf-dev libgettextpo-dev gfortran-doc gfortran-7-doc
  libgfortran4-dbg libcoarrays-dev groff libitpp-dev 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 libcurl4-doc
  libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev
  libssh2-1-dev libgdal-doc libgeotiff-epsg geotiff-bin gdal-bin
  libglib2.0-doc libgraphite2-utils krb5-doc krb5-user libhdf4-doc hdf4-tools
  libhdf5-doc icu-doc liblcms2-utils libtool-doc liblzma-doc ncurses-doc
  netcdf-bin netcdf-doc libmyodbc odbc-postgresql tdsodbc unixodbc-bin
  ogdi-bin libfreetype6-dev postgresql-doc-10 proj-bin readline-doc
  sqlite3-doc libstdc++-7-doc libsuperlu-doc tcl8.6 tk8.6 gcj-jdk
  libxerces-c-doc m4-doc apparmor less www-browser libmail-box-perl
  python3-doc python3-tk python3-venv python3.6-venv python3.6-doc
  binfmt-support 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-foreach r-cran-bbmisc 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-bioc-delayedarray r-bioc-graph
  r-cran-data.table r-cran-shiny r-cran-rmarkdown r-cran-jsonlite r-cran-xml
  r-cran-rsprng r-cran-rlecuyer
Recommended packages:
  curl | wget | lynx bzip2-doc libarchive-cpio-perl proj-bin shared-mime-info
  xdg-user-dirs krb5-locales libpng-tools poppler-data publicsuffix
  libmail-sendmail-perl r-recommended r-doc-html r-cran-runit r-cran-batchjobs
  r-cran-doparallel r-cran-digest r-bioc-annotate r-bioc-summarizedexperiment
  r-bioc-shortread r-cran-testit r-cran-codetools r-cran-survival
  r-cran-testthat 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 dctrl-tools debhelper
  default-libmysqlclient-dev dh-autoreconf dh-r dh-strip-nondeterminism dwz
  file fontconfig fontconfig-config fonts-dejavu-core gdal-data gettext
  gettext-base gfortran gfortran-7 gir1.2-glib-2.0 gir1.2-harfbuzz-0.0
  groff-base hdf5-helpers icu-devtools intltool-debian libaec-dev libaec0
  libarchive-zip-perl libarmadillo-dev libarmadillo8 libarpack2 libarpack2-dev
  libblas-dev libblas3 libboost-dev libboost1.62-dev libbsd0 libbz2-dev
  libcairo2 libcharls-dev libcharls1 libcroco3 libcurl3-gnutls libcurl4
  libcurl4-gnutls-dev libdap-dev libdap25 libdapclient6v5 libdapserver7v5
  libdatrie1 libelf1 libepsilon-dev libepsilon1 libexpat1-dev
  libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfreexl-dev
  libfreexl1 libfribidi0 libfyba-dev libfyba0 libgdal-dev libgdal20
  libgeos-3.6.2 libgeos-c1v5 libgeos-dev libgeotiff-dev libgeotiff2
  libgfortran-7-dev libgfortran4 libgif-dev libgif7 libgirepository-1.0-1
  libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev
  libglib2.0-dev-bin libgraphite2-3 libgraphite2-dev libgssapi-krb5-2
  libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b
  libhdf4-0-alt libhdf4-alt-dev libhdf5-100 libhdf5-cpp-100 libhdf5-dev
  libice6 libicu-dev libicu-le-hb-dev libicu-le-hb0 libicu60 libisl19
  libjbig-dev libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
  libjson-c-dev libk5crypto3 libkeyutils1 libkml-dev libkmlbase1
  libkmlconvenience1 libkmldom1 libkmlengine1 libkmlregionator1 libkmlxsd1
  libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblcms2-2 libltdl-dev
  libltdl7 liblzma-dev libmagic-mgc libmagic1 libmariadbclient-dev
  libmariadbclient-dev-compat libmariadbclient18 libminizip-dev libminizip1
  libmpdec2 libncurses-dev libncurses5-dev libnetcdf-dev libnetcdf13
  libnghttp2-14 libnspr4 libnss3 libodbc1 libogdi3.2 libogdi3.2-dev
  libopenjp2-7 libopenjp2-7-dev 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
  libpoppler-dev libpoppler-private-dev libpoppler74 libpopt0 libpq-dev libpq5
  libproj-dev libproj13 libpsl5 libpython3-stdlib libpython3.6-minimal
  libpython3.6-stdlib libqhull-dev libqhull-r7 libqhull7 libreadline-dev
  librtmp1 libsigsegv2 libsm6 libspatialite-dev libspatialite7 libsqlite3-dev
  libssh2-1 libsuperlu-dev libsuperlu5 libsz2 libtcl8.6 libthai-data libthai0
  libtiff-dev libtiff5 libtiff5-dev libtiffxx5 libtimedate-perl libtk8.6
  libtool liburiparser-dev liburiparser1 libwebp-dev libwebp6 libwebpdemux2
  libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1
  libxdmcp6 libxerces-c-dev libxerces-c3.2 libxext6 libxft2 libxml2
  libxml2-dev libxmuu1 libxrender1 libxss1 libxt6 libzstd-dev m4 man-db
  mime-support mysql-common odbcinst odbcinst1debian2 pkg-config po-debconf
  proj-data python3 python3-distutils python3-lib2to3 python3-minimal
  python3.6 python3.6-minimal 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 unixodbc-dev unzip
  uuid-dev x11-common xauth xdg-utils zip zlib1g-dev
The following packages will be upgraded:
  cpp cpp-7 g++-7 gcc gcc-7 gcc-7-base libasan4 libcilkrts5 libgcc-7-dev
  libreadline7 libsqlite3-0 libstdc++-7-dev libubsan0
13 upgraded, 258 newly installed, 0 to remove and 36 not upgraded.
Need to get 191 MB/202 MB of archives.
After this operation, 615 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-CEiBwp/apt_archive ./ sbuild-build-depends-r-bioc-bitseq-dummy 0.invalid.0 [908 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 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 libpython3.6-minimal armhf 3.6.5-9 [565 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf python3.6-minimal armhf 3.6.5-9 [1374 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf python3-minimal armhf 3.6.5-3 [36.2 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libreadline7 armhf 7.0-5 [130 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libsqlite3-0 armhf 3.24.0-1 [521 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libpython3.6-stdlib armhf 3.6.5-9 [1651 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf python3.6 armhf 3.6.5-9 [229 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.6.5-3 [19.7 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.6.5-3 [24.1 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libisl19 armhf 0.19-1 [427 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf g++-7 armhf 7.3.0-19 [5593 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf gcc-7 armhf 7.3.0-19 [5488 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf cpp-7 armhf 7.3.0-19 [5139 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libasan4 armhf 7.3.0-19 [301 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libubsan0 armhf 7.3.0-19 [106 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libcilkrts5 armhf 7.3.0-19 [35.2 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libstdc++-7-dev armhf 7.3.0-19 [1506 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libgcc-7-dev armhf 7.3.0-19 [671 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf gcc-7-base armhf 7.3.0-19 [187 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.33-3 [234 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.33-3 [106 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.33-3 [64.7 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3.1 [736 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf cpp armhf 4:7.3.0-3+rpi1 [19.2 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf dctrl-tools armhf 2.24-2 [94.4 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf gcc armhf 4:7.3.0-3+rpi1 [5192 B]
Get:42 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.041-2 [20.0 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.041-2 [12.0 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.4 [160 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.7.6-1+b1 [799 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7 [602 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.3.2 [994 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libmariadbclient-dev armhf 1:10.1.29-6+b1 [1528 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libmariadbclient-dev-compat armhf 1:10.1.29-6+b1 [27.6 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf default-libmysqlclient-dev armhf 1.0.4 [3708 B]
Get:63 http://172.17.0.1/private buster-staging/main armhf zip armhf 3.0-11 [212 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf unzip armhf 6.0-21 [149 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libpaper1 armhf 1.1.24+nmu5 [20.8 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libpaper-utils armhf 1.1.24+nmu5 [17.2 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf xdg-utils all 1.1.3-1 [73.3 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.3.0-19 [191 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.8.0-1 [103 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf fontconfig-config all 2.13.0-5 [280 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libfontconfig1 armhf 2.13.0-5 [325 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libcairo2 armhf 1.15.10-3 [575 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.32.0-1 [71.7 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-1 [52.5 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libcurl4 armhf 7.60.0-2 [281 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.8.0-1 [1518 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf fontconfig armhf 2.13.0-5 [403 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libfribidi0 armhf 0.19.7-2 [44.1 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libdatrie1 armhf 0.2.11-1 [34.6 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libpango-1.0-0 armhf 1.42.0-1 [158 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libpangoft2-1.0-0 armhf 1.42.0-1 [53.2 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libpangocairo-1.0-0 armhf 1.42.0-1 [43.3 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libtcl8.6 armhf 8.6.8+dfsg-4 [863 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libtiff5 armhf 4.0.9-5 [224 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libxft2 armhf 2.3.2-2 [49.3 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libtk8.6 armhf 8.6.8-4 [657 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf r-base-core armhf 3.5.0-5 [23.6 MB]
Get:89 http://172.17.0.1/private buster-staging/main armhf libgfortran-7-dev armhf 7.3.0-19 [232 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf gfortran-7 armhf 7.3.0-19 [5459 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:7.3.0-3+rpi1 [1436 B]
Get:92 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.8.0-1 [111 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.8.0-1 [1577 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf libncurses-dev armhf 6.1+20180210-4 [278 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.1+20180210-4 [936 B]
Get:96 http://172.17.0.1/private buster-staging/main armhf libreadline-dev armhf 7.0-5 [110 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf libpcre16-3 armhf 2:8.39-9 [234 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf libpcre32-3 armhf 2:8.39-9 [226 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf libpcrecpp0v5 armhf 2:8.39-9 [150 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf libpcre3-dev armhf 2:8.39-9 [561 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-8.1 [26.9 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf icu-devtools armhf 60.2-6 [166 kB]
Get:103 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-icu0 armhf 1.7.6-1+b1 [584 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-gobject0 armhf 1.7.6-1+b1 [591 kB]
Get:105 http://172.17.0.1/private buster-staging/main armhf libgirepository-1.0-1 armhf 1.56.1-1 [77.6 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf gir1.2-glib-2.0 armhf 1.56.1-1 [142 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf gir1.2-harfbuzz-0.0 armhf 1.7.6-1+b1 [597 kB]
Get:108 http://172.17.0.1/private buster-staging/main armhf libglib2.0-data all 2.56.1-2 [2671 kB]
Get:109 http://172.17.0.1/private buster-staging/main armhf libglib2.0-bin armhf 2.56.1-2 [1694 kB]
Get:110 http://172.17.0.1/private buster-staging/main armhf python3-lib2to3 all 3.6.5-4 [79.0 kB]
Get:111 http://172.17.0.1/private buster-staging/main armhf python3-distutils all 3.6.5-4 [144 kB]
Get:112 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev-bin armhf 2.56.1-2 [1733 kB]
Get:113 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev armhf 2.56.1-2 [2807 kB]
Get:114 http://172.17.0.1/private buster-staging/main armhf libgraphite2-dev armhf 1.3.11-2 [22.2 kB]
Get:115 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-dev armhf 1.7.6-1+b1 [879 kB]
Get:116 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb-dev armhf 1.0.3+git161113-5 [28.3 kB]
Get:117 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 60.2-6 [8643 kB]
Get:118 http://172.17.0.1/private buster-staging/main armhf libxmuu1 armhf 2:1.1.2-2 [23.0 kB]
Get:119 http://172.17.0.1/private buster-staging/main armhf xauth armhf 1:1.0.10-1 [36.4 kB]
Get:120 http://172.17.0.1/private buster-staging/main armhf r-base-dev all 3.5.0-5 [4484 B]
Get:121 http://172.17.0.1/private buster-staging/main armhf dh-r all 20180601 [32.0 kB]
Get:122 http://172.17.0.1/private buster-staging/main armhf gdal-data all 2.3.0+dfsg-1 [729 kB]
Get:123 http://172.17.0.1/private buster-staging/main armhf hdf5-helpers armhf 1.10.0-patch1+docs-4+b2 [36.4 kB]
Get:124 http://172.17.0.1/private buster-staging/main armhf libaec-dev armhf 1.0.2-1 [19.1 kB]
Get:125 http://172.17.0.1/private buster-staging/main armhf libarpack2 armhf 3.5.0+real-2+b2 [80.6 kB]
Get:126 http://172.17.0.1/private buster-staging/main armhf libarmadillo8 armhf 1:8.400.0+dfsg-3 [83.7 kB]
Get:127 http://172.17.0.1/private buster-staging/main armhf libarpack2-dev armhf 3.5.0+real-2+b2 [87.0 kB]
Get:128 http://172.17.0.1/private buster-staging/main armhf libhdf5-100 armhf 1.10.0-patch1+docs-4+b2 [1216 kB]
Get:129 http://172.17.0.1/private buster-staging/main armhf libhdf5-cpp-100 armhf 1.10.0-patch1+docs-4+b2 [117 kB]
Get:130 http://172.17.0.1/private buster-staging/main armhf libhdf5-dev armhf 1.10.0-patch1+docs-4+b2 [2150 kB]
Get:131 http://172.17.0.1/private buster-staging/main armhf libsuperlu-dev armhf 5.2.1+dfsg1-3 [18.2 kB]
Get:132 http://172.17.0.1/private buster-staging/main armhf libarmadillo-dev armhf 1:8.400.0+dfsg-3 [344 kB]
Get:133 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-5.1 [7003 kB]
Get:134 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.62.0.1+b8 [3918 B]
Get:135 http://172.17.0.1/private buster-staging/main armhf libcharls-dev armhf 1.1.0+dfsg-2 [21.6 kB]
Get:136 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.60.0-2 [279 kB]
Get:137 http://172.17.0.1/private buster-staging/main armhf libcurl4-gnutls-dev armhf 7.60.0-2 [352 kB]
Get:138 http://172.17.0.1/private buster-staging/main armhf libxml2-dev armhf 2.9.4+dfsg1-7 [672 kB]
Get:139 http://172.17.0.1/private buster-staging/main armhf uuid-dev armhf 2.32-0.1 [91.3 kB]
Get:140 http://172.17.0.1/private buster-staging/main armhf libdap-dev armhf 3.19.1-2 [760 kB]
Get:141 http://172.17.0.1/private buster-staging/main armhf libpopt0 armhf 1.16-11 [45.9 kB]
Get:142 http://172.17.0.1/private buster-staging/main armhf libepsilon-dev armhf 0.9.2+dfsg-2 [46.8 kB]
Get:143 http://172.17.0.1/private buster-staging/main armhf libfreexl-dev armhf 1.0.5-1 [30.2 kB]
Get:144 http://172.17.0.1/private buster-staging/main armhf libfyba-dev armhf 4.1.1-3 [425 kB]
Get:145 http://172.17.0.1/private buster-staging/main armhf proj-data all 5.1.0-1 [7002 kB]
Get:146 http://172.17.0.1/private buster-staging/main armhf libproj13 armhf 5.1.0-1 [182 kB]
Get:147 http://172.17.0.1/private buster-staging/main armhf libgif7 armhf 5.1.4-3 [41.0 kB]
Get:148 http://172.17.0.1/private buster-staging/main armhf liburiparser1 armhf 0.8.5-1 [34.7 kB]
Get:149 http://172.17.0.1/private buster-staging/main armhf libnetcdf13 armhf 1:4.6.1-1 [344 kB]
Get:150 http://172.17.0.1/private buster-staging/main armhf libltdl7 armhf 2.4.6-2.1 [386 kB]
Get:151 http://172.17.0.1/private buster-staging/main armhf libodbc1 armhf 2.3.6-0.1 [186 kB]
Get:152 http://172.17.0.1/private buster-staging/main armhf libnspr4 armhf 2:4.19-3+rpi1 [90.0 kB]
Get:153 http://172.17.0.1/private buster-staging/main armhf libnss3 armhf 2:3.37.1-1 [933 kB]
Get:154 http://172.17.0.1/private buster-staging/main armhf libpoppler74 armhf 0.63.0-2 [1225 kB]
Get:155 http://172.17.0.1/private buster-staging/main armhf libpq5 armhf 10.4-2 [148 kB]
Get:156 http://172.17.0.1/private buster-staging/main armhf libxerces-c3.2 armhf 3.2.1+debian-2+b2 [710 kB]
Get:157 http://172.17.0.1/private buster-staging/main armhf odbcinst armhf 2.3.6-0.1 [47.6 kB]
Get:158 http://172.17.0.1/private buster-staging/main armhf odbcinst1debian2 armhf 2.3.6-0.1 [70.8 kB]
Get:159 http://172.17.0.1/private buster-staging/main armhf libgdal20 armhf 2.3.0+dfsg-1 [4842 kB]
Get:160 http://172.17.0.1/private buster-staging/main armhf libgeos-dev armhf 3.6.2-1 [282 kB]
Get:161 http://172.17.0.1/private buster-staging/main armhf libtiffxx5 armhf 4.0.9-5 [100 kB]
Get:162 http://172.17.0.1/private buster-staging/main armhf libtiff5-dev armhf 4.0.9-5 [337 kB]
Get:163 http://172.17.0.1/private buster-staging/main armhf libtiff-dev armhf 4.0.9-5 [96.3 kB]
Get:164 http://172.17.0.1/private buster-staging/main armhf libgeotiff-dev armhf 1.4.2-2+b2 [93.5 kB]
Get:165 http://172.17.0.1/private buster-staging/main armhf libgif-dev armhf 5.1.4-3 [43.4 kB]
Get:166 http://172.17.0.1/private buster-staging/main armhf libnetcdf-dev armhf 1:4.6.1-1 [80.5 kB]
Get:167 http://172.17.0.1/private buster-staging/main armhf libhdf4-alt-dev armhf 4.2.13-2 [310 kB]
Get:168 http://172.17.0.1/private buster-staging/main armhf libjson-c-dev armhf 0.12.1-1.3 [34.6 kB]
Get:169 http://172.17.0.1/private buster-staging/main armhf libminizip-dev armhf 1.1-8 [25.6 kB]
Get:170 http://172.17.0.1/private buster-staging/main armhf liburiparser-dev armhf 0.8.5-1 [17.8 kB]
Get:171 http://172.17.0.1/private buster-staging/main armhf libkml-dev armhf 1.3.0-5 [940 kB]
Get:172 http://172.17.0.1/private buster-staging/main armhf libltdl-dev armhf 2.4.6-2.1 [158 kB]
Get:173 http://172.17.0.1/private buster-staging/main armhf libproj-dev armhf 5.1.0-1 [225 kB]
Get:174 http://172.17.0.1/private buster-staging/main armhf libogdi3.2-dev armhf 3.2.1+ds-1+b1 [38.3 kB]
Get:175 http://172.17.0.1/private buster-staging/main armhf libopenjp2-7-dev armhf 2.3.0-1 [43.7 kB]
Get:176 http://172.17.0.1/private buster-staging/main armhf libpoppler-dev armhf 0.63.0-2 [22.5 kB]
Get:177 http://172.17.0.1/private buster-staging/main armhf libpoppler-private-dev armhf 0.63.0-2 [187 kB]
Get:178 http://172.17.0.1/private buster-staging/main armhf libpq-dev armhf 10.4-2 [145 kB]
Get:179 http://172.17.0.1/private buster-staging/main armhf libqhull-r7 armhf 2015.2-4 [171 kB]
Get:180 http://172.17.0.1/private buster-staging/main armhf libqhull-dev armhf 2015.2-4 [346 kB]
Get:181 http://172.17.0.1/private buster-staging/main armhf libsqlite3-dev armhf 3.24.0-1 [655 kB]
Get:182 http://172.17.0.1/private buster-staging/main armhf libspatialite-dev armhf 4.3.0a-5+b2 [1460 kB]
Get:183 http://172.17.0.1/private buster-staging/main armhf libwebpdemux2 armhf 0.6.1-2 [86.7 kB]
Get:184 http://172.17.0.1/private buster-staging/main armhf libwebp-dev armhf 0.6.1-2 [304 kB]
Get:185 http://172.17.0.1/private buster-staging/main armhf libxerces-c-dev armhf 3.2.1+debian-2+b2 [1486 kB]
Get:186 http://172.17.0.1/private buster-staging/main armhf libzstd-dev armhf 1.3.4+dfsg-3+rpi1 [209 kB]
Get:187 http://172.17.0.1/private buster-staging/main armhf unixodbc-dev armhf 2.3.6-0.1 [232 kB]
Get:188 http://172.17.0.1/private buster-staging/main armhf libgdal-dev armhf 2.3.0+dfsg-1 [6211 kB]
Get:189 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocgenerics all 0.26.0-3 [641 kB]
Get:190 http://172.17.0.1/private buster-staging/main armhf r-cran-formatr armhf 1.5-2+b1 [149 kB]
Get:191 http://172.17.0.1/private buster-staging/main armhf r-cran-lambda.r all 1.2.3-2 [117 kB]
Get:192 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.options all 1.0.1-2 [19.8 kB]
Get:193 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.logger all 1.4.3-3 [102 kB]
Get:194 http://172.17.0.1/private buster-staging/main armhf r-cran-snow all 1:0.4.2-2 [108 kB]
Get:195 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocparallel armhf 1.14.1-1+b1 [1051 kB]
Get:196 http://172.17.0.1/private buster-staging/main armhf r-bioc-s4vectors armhf 0.18.2-1+b1 [1802 kB]
Get:197 http://172.17.0.1/private buster-staging/main armhf r-bioc-iranges armhf 2.14.10-1+b1 [2127 kB]
Get:198 http://172.17.0.1/private buster-staging/main armhf r-bioc-xvector armhf 0.20.0-2+b1 [592 kB]
Get:199 http://172.17.0.1/private buster-staging/main armhf r-bioc-biostrings armhf 2.48.0-2+b1 [14.1 MB]
Get:200 http://172.17.0.1/private buster-staging/main armhf r-cran-bitops armhf 1.0-6-3+b1 [24.0 kB]
Get:201 http://172.17.0.1/private buster-staging/main armhf r-cran-rcurl armhf 1.95-4.10-1+b2 [712 kB]
Get:202 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodbdata all 1.1.0-3 [8213 kB]
Get:203 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodb all 1.16.0-3 [3687 kB]
Get:204 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomicranges armhf 1.32.3-1+b1 [1938 kB]
Get:205 http://172.17.0.1/private buster-staging/main armhf r-bioc-rsamtools armhf 1.32.0-2+b1 [3489 kB]
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Setting up fontconfig (2.13.0-5) ...
Regenerating fonts cache... done.
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 gfortran (4:7.3.0-3+rpi1) ...
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 libhdf5-cpp-100:armhf (1.10.0-patch1+docs-4+b2) ...
Setting up libpoppler-dev:armhf (0.63.0-2) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up libglib2.0-dev-bin (2.56.1-2) ...
Setting up libxss1:armhf (1:1.2.2-1) ...
Setting up libhdf5-dev (1.10.0-patch1+docs-4+b2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
Setting up libkmlconvenience1:armhf (1.3.0-5) ...
Setting up libglib2.0-dev:armhf (2.56.1-2) ...
Setting up libgssapi-krb5-2:armhf (1.16-2) ...
Setting up xauth (1:1.0.10-1) ...
Setting up libarmadillo8 (1:8.400.0+dfsg-3) ...
Setting up libpq5:armhf (10.4-2) ...
Setting up libkmlregionator1:armhf (1.3.0-5) ...
Setting up libpango-1.0-0:armhf (1.42.0-1) ...
Setting up libarpack2-dev:armhf (3.5.0+real-2+b2) ...
Setting up libarmadillo-dev (1:8.400.0+dfsg-3) ...
Setting up libcairo2:armhf (1.15.10-3) ...
Setting up libpoppler-private-dev:armhf (0.63.0-2) ...
Setting up libpq-dev (10.4-2) ...
Setting up libcurl3-gnutls:armhf (7.60.0-2) ...
Setting up libtk8.6:armhf (8.6.8-4) ...
Setting up libcurl4:armhf (7.60.0-2) ...
Setting up libkml-dev:armhf (1.3.0-5) ...
Setting up libpangoft2-1.0-0:armhf (1.42.0-1) ...
Setting up libnetcdf13:armhf (1:4.6.1-1) ...
Setting up libcurl4-gnutls-dev:armhf (7.60.0-2) ...
Setting up libnetcdf-dev (1:4.6.1-1) ...
Setting up libpangocairo-1.0-0:armhf (1.42.0-1) ...
Setting up libhdf4-alt-dev (4.2.13-2) ...
Setting up dh-autoreconf (19) ...
Setting up odbcinst (2.3.6-0.1) ...
Setting up libicu-le-hb0:armhf (1.0.3+git161113-5) ...
Setting up dh-strip-nondeterminism (0.041-2) ...
Setting up odbcinst1debian2:armhf (2.3.6-0.1) ...
Setting up libicu60:armhf (60.2-6) ...
Setting up unixodbc-dev:armhf (2.3.6-0.1) ...
Setting up libharfbuzz-icu0:armhf (1.7.6-1+b1) ...
Setting up r-base-core (3.5.0-5) ...

Creating config file /etc/R/Renviron with new version
Setting up r-bioc-biocgenerics (0.26.0-3) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up r-cran-bitops (1.0-6-3+b1) ...
Setting up r-cran-formatr (1.5-2+b1) ...
Setting up r-cran-futile.options (1.0.1-2) ...
Setting up libspatialite7:armhf (4.3.0a-5+b2) ...
Setting up icu-devtools (60.2-6) ...
Setting up r-cran-rcurl (1.95-4.10-1+b2) ...
Setting up libspatialite-dev:armhf (4.3.0a-5+b2) ...
Setting up libharfbuzz-dev:armhf (1.7.6-1+b1) ...
Setting up libxerces-c3.2:armhf (3.2.1+debian-2+b2) ...
Setting up r-cran-lambda.r (1.2.3-2) ...
Setting up r-cran-snow (1:0.4.2-2) ...
Setting up libdap25:armhf (3.19.1-2) ...
Setting up libicu-le-hb-dev:armhf (1.0.3+git161113-5) ...
Setting up gettext (0.19.8.1-6) ...
Setting up r-bioc-genomeinfodbdata (1.1.0-3) ...
Setting up libicu-dev (60.2-6) ...
Setting up r-base-dev (3.5.0-5) ...
Setting up libxml2-dev:armhf (2.9.4+dfsg1-7) ...
Setting up libdapclient6v5:armhf (3.19.1-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libdapserver7v5:armhf (3.19.1-2) ...
Setting up r-cran-futile.logger (1.4.3-3) ...
Setting up libxerces-c-dev (3.2.1+debian-2+b2) ...
Setting up libdap-dev:armhf (3.19.1-2) ...
Setting up r-bioc-biocparallel (1.14.1-1+b1) ...
Setting up po-debconf (1.0.20) ...
Setting up libgdal20 (2.3.0+dfsg-1) ...
Setting up debhelper (11.3.2) ...
Setting up dh-r (20180601) ...
Setting up libgdal-dev (2.3.0+dfsg-1) ...
Setting up r-bioc-s4vectors (0.18.2-1+b1) ...
Setting up r-bioc-iranges (2.14.10-1+b1) ...
Setting up r-bioc-genomeinfodb (1.16.0-3) ...
Setting up r-bioc-xvector (0.20.0-2+b1) ...
Setting up r-bioc-biostrings (2.48.0-2+b1) ...
Setting up r-bioc-genomicranges (1.32.3-1+b1) ...
Setting up r-bioc-rsamtools (1.32.0-2+b1) ...
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_7.3.0-19 gcc-7_7.3.0-19 libc6-dev_2.27-3+rpi1 libstdc++-7-dev_7.3.0-19 libstdc++6_8.1.0-3+rpi1 linux-libc-dev_4.16.5-1+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_1:2.32-0.1 build-essential_12.4+b1 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.3.0-3+rpi1 cpp-7_7.3.0-19 dash_0.5.8-2.10 dbus_1.12.8-2 dbus-user-session_1.12.8-2 dctrl-tools_2.24-2 debconf_1.5.66 debhelper_11.3.2 debianutils_4.8.6 default-libmysqlclient-dev_1.0.4 dh-autoreconf_19 dh-r_20180601 dh-strip-nondeterminism_0.041-2 diffutils_1:3.6-1 dirmngr_2.2.5-1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.2-1 e2fsprogs_1.44.2-1 e2fsprogs-l10n_1.44.2-1 fakeroot_1.22-2 fdisk_2.31.1-0.5 file_1:5.33-3 findutils_4.6.0+git+20171230-2 fontconfig_2.13.0-5 fontconfig-config_2.13.0-5 fonts-dejavu-core_2.37-1 g++_4:7.2.0-1d1 g++-7_7.3.0-19 gcc_4:7.3.0-3+rpi1 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_7.3.0-19 gcc-7-base_7.3.0-19 gcc-8-base_8.1.0-3+rpi1 gdal-data_2.3.0+dfsg-1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gfortran_4:7.3.0-3+rpi1 gfortran-7_7.3.0-19 gir1.2-glib-2.0_1.56.1-1 gir1.2-harfbuzz-0.0_1.7.6-1+b1 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 hdf5-helpers_1.10.0-patch1+docs-4+b2 hostname_3.20 icu-devtools_60.2-6 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 libaec-dev_1.0.2-1 libaec0_1.0.2-1 libapparmor1_2.12-4 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 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libqhull-r7_2015.2-4 libqhull7_2015.2-4 libreadline-dev_7.0-5 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-2 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-2 libsigsegv2_2.12-2 libsm6_2:1.2.2-1+b3 libsmartcols1_2.32-0.1 libspatialite-dev_4.3.0a-5+b2 libspatialite7_4.3.0a-5+b2 libsqlite3-0_3.24.0-1 libsqlite3-dev_3.24.0-1 libss2_1.44.2-1 libssh2-1_1.8.0-1 libssl1.1_1.1.0h-4 libstdc++-7-dev_7.3.0-19 libstdc++6_8.1.0-3+rpi1 libsuperlu-dev_5.2.1+dfsg1-3 libsuperlu5_5.2.1+dfsg1-3 libsystemd0_238-4 libsz2_1.0.2-1 libtasn1-6_4.13-3 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 libtiff-dev_4.0.9-5 libtiff5_4.0.9-5 libtiff5-dev_4.0.9-5 libtiffxx5_4.0.9-5 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180210-4 libtinfo6_6.1+20180210-4 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odbcinst1debian2_2.3.6-0.1 openssl_1.1.0h-4 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-5 perl-base_5.26.2-5 perl-modules-5.26_5.26.2-5 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-1 proj-data_5.1.0-1 python3_3.6.5-3 python3-distutils_3.6.5-4 python3-lib2to3_3.6.5-4 python3-minimal_3.6.5-3 python3.6_3.6.5-9 python3.6-minimal_3.6.5-9 r-base-core_3.5.0-5 r-base-dev_3.5.0-5 r-bioc-biocgenerics_0.26.0-3 r-bioc-biocparallel_1.14.1-1+b1 r-bioc-biostrings_2.48.0-2+b1 r-bioc-genomeinfodb_1.16.0-3 r-bioc-genomeinfodbdata_1.1.0-3 r-bioc-genomicranges_1.32.3-1+b1 r-bioc-iranges_2.14.10-1+b1 r-bioc-rsamtools_1.32.0-2+b1 r-bioc-s4vectors_0.18.2-1+b1 r-bioc-xvector_0.20.0-2+b1 r-cran-bitops_1.0-6-3+b1 r-cran-formatr_1.5-2+b1 r-cran-futile.logger_1.4.3-3 r-cran-futile.options_1.0.1-2 r-cran-lambda.r_1.2.3-2 r-cran-rcurl_1.95-4.10-1+b2 r-cran-snow_1:0.4.2-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 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_1.30+dfsg-2 tzdata_2018e-1 ucf_3.0038 udev_238-4 unixodbc-dev_2.3.6-0.1 unzip_6.0-21 util-linux_2.31.1-0.5 uuid-dev_2.32-0.1 x11-common_1:7.7+19 xauth_1:1.0.10-1 xdg-utils_1.1.3-1 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

Hack binNMU version
-------------------

Created changelog entry for binNMU version 1.24.0+dfsg-1+b1

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-8be79650-d967-414d-84eb-4ed9e1d11f7d
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+b1
dpkg-buildpackage: info: source distribution buster-staging
 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 3.5.0-5
I: R API version: r-api-3.5
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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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-iXuhKy/r-base-3.5.0=. -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
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* 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
I: Using libgdal-dev for Suggests:DESeq
W: Cannot find a debian package for Suggests:BiocStyle
I: Using libgdal-dev 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
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   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
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   dh_installinit -a -O--buildsystem=R
   dh_installsystemd -a -O--buildsystem=R
   dh_installmenu -a -O--buildsystem=R
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   dh_installpam -a -O--buildsystem=R
   dh_installppp -a -O--buildsystem=R
   dh_installudev -a -O--buildsystem=R
   dh_installgsettings -a -O--buildsystem=R
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   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+b1_armhf.deb'.
dpkg-deb: building package 'r-bioc-bitseq-dbgsym' in '../r-bioc-bitseq-dbgsym_1.24.0+dfsg-1+b1_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+b1_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 2018-06-14T23:50:57Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Post Build Chroot                                                            |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


r-bioc-bitseq_1.24.0+dfsg-1+b1_armhf.changes:
---------------------------------------------

Format: 1.8
Date: Sat, 12 May 2018 21:41:33 +0200
Source: r-bioc-bitseq (1.24.0+dfsg-1)
Binary: r-bioc-bitseq
Binary-Only: yes
Architecture: armhf
Version: 1.24.0+dfsg-1+b1
Distribution: buster-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
 r-bioc-bitseq - transcript expression inference and analysis for RNA-seq data
Changes:
 r-bioc-bitseq (1.24.0+dfsg-1+b1) buster-staging; urgency=low, binary-only=yes
 .
   * Binary-only non-maintainer upload for armhf; no source changes.
   * rebuild due to debcheck failure
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Files:
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+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


r-bioc-bitseq-dbgsym_1.24.0+dfsg-1+b1_armhf.deb
-----------------------------------------------

 new Debian package, version 2.0.
 size 2350056 bytes: control archive=548 bytes.
     423 bytes,    12 lines      control              
     106 bytes,     1 lines      md5sums              
 Package: r-bioc-bitseq-dbgsym
 Source: r-bioc-bitseq (1.24.0+dfsg-1)
 Version: 1.24.0+dfsg-1+b1
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
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drwxr-xr-x root/root         0 2018-05-12 19:41 ./
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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+b1_armhf.deb
----------------------------------------

 new Debian package, version 2.0.
 size 935104 bytes: control archive=1940 bytes.
    1241 bytes,    23 lines      control              
    2949 bytes,    37 lines      md5sums              
 Package: r-bioc-bitseq
 Source: r-bioc-bitseq (1.24.0+dfsg-1)
 Version: 1.24.0+dfsg-1+b1
 Architecture: armhf
 Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
 Installed-Size: 5478
 Depends: r-base-core (>= 3.5.0-5), r-api-3.5, 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, libgdal-dev
 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.

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| Post Build                                                                   |
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| Cleanup                                                                      |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

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| Summary                                                                      |
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Build Architecture: armhf
Build-Space: 16820
Build-Time: 650
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 1709
Job: r-bioc-bitseq_1.24.0+dfsg-1
Machine Architecture: armhf
Package: r-bioc-bitseq
Package-Time: 2412
Source-Version: 1.24.0+dfsg-1
Space: 16820
Status: successful
Version: 1.24.0+dfsg-1+b1
--------------------------------------------------------------------------------
Finished at 2018-06-14T23:50:57Z
Build needed 00:40:12, 16820k disc space
Raspbian Package Auto-Building

Build log for r-bioc-bitseq (1.24.0+dfsg-1+b1) on armhf
