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- Client:
- Version: 1.8.1
- API version: 1.20
- Go version: go1.4.2
- Git commit: d12ea79
- Built: Thu Aug 13 02:49:29 UTC 2015
- OS/Arch: linux/amd64
- Server:
- Version: 1.8.3-rc4
- API version: 1.20
- Go version: go1.4.2
- Git commit: 9f1606a
- Built: Fri Oct 2 23:36:50 UTC 2015
- OS/Arch: linux/amd64
- Step 0 : FROM r-base:latest
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- 5075b0c23e12 Pull complete
- Digest: sha256:c12c1f5a5d1db5a7f38f95e751133cfca9a3d1c052c861228310eaa7b1337e2d
- Status: Downloaded newer image for r-base:latest
- ---> 5075b0c23e12
- Step 1 : RUN apt-get update -qq && apt-get dist-upgrade -y
- Reading package lists...
- Building dependency tree...
- Reading state information...
- The following NEW packages will be installed:
- libnghttp2-14
- The following packages will be upgraded:
- binutils bsdutils cpp-5 diffutils dpkg dpkg-dev g++-5 gcc-4.8-base gcc-5
- gcc-5-base gfortran-5 libasan2 libatomic1 libaudit-common libaudit1
- libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap2 libcap2-bin libcc1-0
- libcilkrts5 libcurl3 libdb5.3 libdpkg-perl libfdisk1 libfreetype6
- libgcc-5-dev libgcc1 libgfortran-5-dev libgfortran3 libglib2.0-0
- libgnutls-deb0-28 libgomp1 libgpg-error0 libgraphite2-3 libicu55 libidn11
- libitm1 libldap-2.4-2 liblocale-gettext-perl liblsan0 libmount1 libmpx0
- libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpcre16-3 libpcre3
- libpcre3-dev libpcre32-3 libpcrecpp0v5 libpixman-1-0 libpsl0 libquadmath0
- libsasl2-2 libsasl2-modules-db libsmartcols1 libstdc++-5-dev libstdc++6
- libsystemd0 libtasn1-6 libtsan0 libubsan0 libudev1 libuuid1 linux-libc-dev
- locales lsb-base mount multiarch-support systemd systemd-sysv udev
- util-linux xdg-utils
- 78 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
- Need to get 168 MB of archives.
- After this operation, 10.8 MB of additional disk space will be used.
- Get:1 http://httpredir.debian.org/debian/ testing/main dpkg amd64 1.18.3 [2,912 kB]
- Get:2 http://httpredir.debian.org/debian/ testing/main bsdutils amd64 1:2.27-3 [104 kB]
- Get:3 http://httpredir.debian.org/debian/ testing/main diffutils amd64 1:3.3-2 [266 kB]
- Get:4 http://httpredir.debian.org/debian/ testing/main libc-dev-bin amd64 2.19-22 [237 kB]
- Get:5 http://httpredir.debian.org/debian/ testing/main libc6-dev amd64 2.19-22 [1,997 kB]
- Get:6 http://httpredir.debian.org/debian/ testing/main liblsan0 amd64 5.2.1-21 [109 kB]
- Get:7 http://httpredir.debian.org/debian/ testing/main libcilkrts5 amd64 5.2.1-21 [39.6 kB]
- Get:8 http://httpredir.debian.org/debian/ testing/main linux-libc-dev amd64 4.2.1-2 [1,047 kB]
- Get:9 http://httpredir.debian.org/debian/ testing/main g++-5 amd64 5.2.1-21 [37.2 MB]
- Get:10 http://httpredir.debian.org/debian/ testing/main libcap2 amd64 1:2.24-12 [16.4 kB]
- Get:11 http://httpredir.debian.org/debian/ testing/main libc-bin amd64 2.19-22 [1,285 kB]
- Get:12 http://httpredir.debian.org/debian/ testing/main libgcc1 amd64 1:5.2.1-21 [38.7 kB]
- Get:13 http://httpredir.debian.org/debian/ testing/main libtsan0 amd64 5.2.1-21 [245 kB]
- Get:14 http://httpredir.debian.org/debian/ testing/main libquadmath0 amd64 5.2.1-21 [131 kB]
- Get:15 http://httpredir.debian.org/debian/ testing/main libcc1-0 amd64 5.2.1-21 [30.4 kB]
- Get:16 http://httpredir.debian.org/debian/ testing/main libgomp1 amd64 5.2.1-21 [54.2 kB]
- Get:17 http://httpredir.debian.org/debian/ testing/main libgfortran-5-dev amd64 5.2.1-21 [285 kB]
- Get:18 http://httpredir.debian.org/debian/ testing/main gcc-5 amd64 5.2.1-21 [26.1 MB]
- Get:19 http://httpredir.debian.org/debian/ testing/main libitm1 amd64 5.2.1-21 [26.7 kB]
- Get:20 http://httpredir.debian.org/debian/ testing/main libatomic1 amd64 5.2.1-21 [8,730 B]
- Get:21 http://httpredir.debian.org/debian/ testing/main gcc-5-base amd64 5.2.1-21 [167 kB]
- Get:22 http://httpredir.debian.org/debian/ testing/main libubsan0 amd64 5.2.1-21 [98.9 kB]
- Get:23 http://httpredir.debian.org/debian/ testing/main libgfortran3 amd64 5.2.1-21 [253 kB]
- Get:24 http://httpredir.debian.org/debian/ testing/main lsb-base all 9.20150917 [27.3 kB]
- Get:25 http://httpredir.debian.org/debian/ testing/main binutils amd64 2.25.1-3 [3,612 kB]
- Get:26 http://httpredir.debian.org/debian/ testing/main gfortran-5 amd64 5.2.1-21 [27.0 MB]
- Get:27 http://httpredir.debian.org/debian/ testing/main systemd amd64 226-4 [3,422 kB]
- Get:28 http://httpredir.debian.org/debian/ testing/main libgcc-5-dev amd64 5.2.1-21 [2,223 kB]
- Get:29 http://httpredir.debian.org/debian/ testing/main libc6 amd64 2.19-22 [4,790 kB]
- Get:30 http://httpredir.debian.org/debian/ testing/main libasan2 amd64 5.2.1-21 [265 kB]
- Get:31 http://httpredir.debian.org/debian/ testing/main libsmartcols1 amd64 2.27-3 [115 kB]
- Get:32 http://httpredir.debian.org/debian/ testing/main libfdisk1 amd64 2.27-3 [193 kB]
- Get:33 http://httpredir.debian.org/debian/ testing/main libmpx0 amd64 5.2.1-21 [9,504 B]
- Get:34 http://httpredir.debian.org/debian/ testing/main cpp-5 amd64 5.2.1-21 [26.2 MB]
- Get:35 http://httpredir.debian.org/debian/ testing/main udev amd64 226-4 [1,034 kB]
- Get:36 http://httpredir.debian.org/debian/ testing/main libsystemd0 amd64 226-4 [242 kB]
- Get:37 http://httpredir.debian.org/debian/ testing/main libaudit-common all 1:2.4.4-3 [14.8 kB]
- Get:38 http://httpredir.debian.org/debian/ testing/main libmount1 amd64 2.27-3 [170 kB]
- Get:39 http://httpredir.debian.org/debian/ testing/main libblkid1 amd64 2.27-3 [161 kB]
- Get:40 http://httpredir.debian.org/debian/ testing/main liblocale-gettext-perl amd64 1.07-1 [19.0 kB]
- Get:41 http://httpredir.debian.org/debian/ testing/main libcap2-bin amd64 1:2.24-12 [25.9 kB]
- Get:42 http://httpredir.debian.org/debian/ testing/main libgnutls-deb0-28 amd64 3.3.18-1 [717 kB]
- Get:43 http://httpredir.debian.org/debian/ testing/main systemd-sysv amd64 226-4 [53.6 kB]
- Get:44 http://httpredir.debian.org/debian/ testing/main dpkg-dev all 1.18.3 [1,432 kB]
- Get:45 http://httpredir.debian.org/debian/ testing/main libpcrecpp0v5 amd64 2:8.35-7.2 [142 kB]
- Get:46 http://httpredir.debian.org/debian/ testing/main libnghttp2-14 amd64 1.3.2-0.1 [75.6 kB]
- Get:47 http://httpredir.debian.org/debian/ testing/main multiarch-support amd64 2.19-22 [180 kB]
- Get:48 http://httpredir.debian.org/debian/ testing/main libpsl0 amd64 0.11.0-1 [40.5 kB]
- Get:49 http://httpredir.debian.org/debian/ testing/main xdg-utils all 1.1.0~rc3+git20150922-1 [69.2 kB]
- Get:50 http://httpredir.debian.org/debian/ testing/main libgpg-error0 amd64 1.20-1 [103 kB]
- Get:51 http://httpredir.debian.org/debian/ testing/main gcc-4.8-base amd64 4.8.5-1 [156 kB]
- Get:52 http://httpredir.debian.org/debian/ testing/main libtasn1-6 amd64 4.7-2 [50.1 kB]
- Get:53 http://httpredir.debian.org/debian/ testing/main libidn11 amd64 1.32-3 [113 kB]
- Get:54 http://httpredir.debian.org/debian/ testing/main libsasl2-modules-db amd64 2.1.26.dfsg1-14 [67.0 kB]
- Get:55 http://httpredir.debian.org/debian/ testing/main libaudit1 amd64 1:2.4.4-3+b1 [47.5 kB]
- Get:56 http://httpredir.debian.org/debian/ testing/main libsasl2-2 amd64 2.1.26.dfsg1-14 [104 kB]
- Get:57 http://httpredir.debian.org/debian/ testing/main libldap-2.4-2 amd64 2.4.42+dfsg-2 [224 kB]
- Get:58 http://httpredir.debian.org/debian/ testing/main libpcre3-dev amd64 2:8.35-7.2 [623 kB]
- Get:59 http://httpredir.debian.org/debian/ testing/main locales all 2.19-22 [3,969 kB]
- Get:60 http://httpredir.debian.org/debian/ testing/main libglib2.0-0 amd64 2.46.0-2 [2,534 kB]
- Get:61 http://httpredir.debian.org/debian/ testing/main libpcre16-3 amd64 2:8.35-7.2 [242 kB]
- Get:62 http://httpredir.debian.org/debian/ testing/main libicu55 amd64 55.1-5 [7,651 kB]
- Get:63 http://httpredir.debian.org/debian/ testing/main libpcre3 amd64 2:8.35-7.2 [321 kB]
- Get:64 http://httpredir.debian.org/debian/ testing/main libdb5.3 amd64 5.3.28-11 [680 kB]
- Get:65 http://httpredir.debian.org/debian/ testing/main libcurl3 amd64 7.44.0-2 [272 kB]
- Get:66 http://httpredir.debian.org/debian/ testing/main libpango-1.0-0 amd64 1.38.0-3 [307 kB]
- Get:67 http://httpredir.debian.org/debian/ testing/main libpangocairo-1.0-0 amd64 1.38.0-3 [220 kB]
- Get:68 http://httpredir.debian.org/debian/ testing/main libpixman-1-0 amd64 0.33.2-2 [523 kB]
- Get:69 http://httpredir.debian.org/debian/ testing/main libstdc++-5-dev amd64 5.2.1-21 [1,366 kB]
- Get:70 http://httpredir.debian.org/debian/ testing/main libstdc++6 amd64 5.2.1-21 [388 kB]
- Get:71 http://httpredir.debian.org/debian/ testing/main libuuid1 amd64 2.27-3 [67.2 kB]
- Get:72 http://httpredir.debian.org/debian/ testing/main libudev1 amd64 226-4 [95.5 kB]
- Get:73 http://httpredir.debian.org/debian/ testing/main util-linux amd64 2.27-3 [897 kB]
- Get:74 http://httpredir.debian.org/debian/ testing/main mount amd64 2.27-3 [175 kB]
- Get:75 http://httpredir.debian.org/debian/ testing/main libpcre32-3 amd64 2:8.35-7.2 [234 kB]
- Get:76 http://httpredir.debian.org/debian/ testing/main libdpkg-perl all 1.18.3 [1,137 kB]
- Get:77 http://httpredir.debian.org/debian/ testing/main libfreetype6 amd64 2.6-2 [449 kB]
- Get:78 http://httpredir.debian.org/debian/ testing/main libgraphite2-3 amd64 1.3.3-1 [74.7 kB]
- Get:79 http://httpredir.debian.org/debian/ testing/main libpangoft2-1.0-0 amd64 1.38.0-3 [233 kB]
- [91mdebconf: delaying package configuration, since apt-utils is not installed
- [0m
- Fetched 168 MB in 27s (6,201 kB/s)
- (Reading database ...
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- Setting up binutils (2.25.1-3) ...
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- Setting up libpcrecpp0v5:amd64 (2:8.35-7.2) ...
- Setting up libpcre3-dev:amd64 (2:8.35-7.2) ...
- Setting up liblocale-gettext-perl (1.07-1) ...
- Setting up gcc-4.8-base:amd64 (4.8.5-1) ...
- Setting up libtasn1-6:amd64 (4.7-2) ...
- Setting up libgnutls-deb0-28:amd64 (3.3.18-1) ...
- Setting up libidn11:amd64 (1.32-3) ...
- Setting up libsasl2-modules-db:amd64 (2.1.26.dfsg1-14) ...
- Setting up libsasl2-2:amd64 (2.1.26.dfsg1-14) ...
- Setting up libldap-2.4-2:amd64 (2.4.42+dfsg-2) ...
- Setting up locales (2.19-22) ...
- debconf: unable to initialize frontend: Dialog
- debconf: (TERM is not set, so the dialog frontend is not usable.)
- debconf: falling back to frontend: Readline
- Generating locales (this might take a while)...
- en_US.UTF-8
- ...
- done
- Generation complete.
- Setting up libdpkg-perl (1.18.3) ...
- Setting up dpkg-dev (1.18.3) ...
- Setting up libnghttp2-14:amd64 (1.3.2-0.1) ...
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- Setting up libfreetype6:amd64 (2.6-2) ...
- Setting up libglib2.0-0:amd64 (2.46.0-2) ...
- No schema files found: doing nothing.
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- Setting up libicu55:amd64 (55.1-5) ...
- Setting up libpango-1.0-0:amd64 (1.38.0-3) ...
- Setting up libpangoft2-1.0-0:amd64 (1.38.0-3) ...
- Setting up libpangocairo-1.0-0:amd64 (1.38.0-3) ...
- Setting up libpixman-1-0:amd64 (0.33.2-2) ...
- Setting up libpsl0:amd64 (0.11.0-1) ...
- Setting up xdg-utils (1.1.0~rc3+git20150922-1) ...
- Processing triggers for libc-bin (2.19-22) ...
- ---> 5cd07b70e123
- Step 2 : RUN apt-get update -qq && apt-get install -y curl libnetcdf-dev libxml2-dev
- Reading package lists...
- Building dependency tree...
- Reading state information...
- The following extra packages will be installed:
- hdf5-helpers icu-devtools libcurl3-gnutls libcurl4-gnutls-dev libhdf5-10
- libhdf5-8 libhdf5-cpp-10 libhdf5-dev libicu-dev libnetcdf7 libxml2
- pkg-config sgml-base xml-core
- Suggested packages:
- libcurl4-doc libcurl3-dbg libgnutls28-dev libidn11-dev libkrb5-dev
- libldap2-dev librtmp-dev libssh2-1-dev libhdf5-doc icu-doc netcdf-bin
- netcdf-doc sgml-base-doc debhelper
- The following NEW packages will be installed:
- curl hdf5-helpers icu-devtools libcurl3-gnutls libcurl4-gnutls-dev
- libhdf5-10 libhdf5-8 libhdf5-cpp-10 libhdf5-dev libicu-dev libnetcdf-dev
- libnetcdf7 libxml2 libxml2-dev pkg-config sgml-base xml-core
- 0 upgraded, 17 newly installed, 0 to remove and 0 not upgraded.
- Need to get 19.4 MB of archives.
- After this operation, 92.1 MB of additional disk space will be used.
- Get:1 http://httpredir.debian.org/debian/ testing/main sgml-base all 1.26+nmu4 [14.6 kB]
- Get:2 http://httpredir.debian.org/debian/ testing/main libcurl3-gnutls amd64 7.44.0-2 [270 kB]
- Get:3 http://httpredir.debian.org/debian/ testing/main curl amd64 7.44.0-2 [207 kB]
- Get:4 http://httpredir.debian.org/debian/ testing/main hdf5-helpers amd64 1.8.15-patch1+docs-4 [38.7 kB]
- Get:5 http://httpredir.debian.org/debian/ testing/main libxml2 amd64 2.9.2+zdfsg1-4 [911 kB]
- Get:6 http://httpredir.debian.org/debian/ testing/main libhdf5-8 amd64 1.8.13+docs-15.1 [1,060 kB]
- Get:7 http://httpredir.debian.org/debian/ testing/main libhdf5-10 amd64 1.8.15-patch1+docs-4 [1,068 kB]
- Get:8 http://httpredir.debian.org/debian/ testing/main libhdf5-dev amd64 1.8.15-patch1+docs-4 [5,330 kB]
- Get:9 http://httpredir.debian.org/debian/ testing/main icu-devtools amd64 55.1-5 [176 kB]
- Get:10 http://httpredir.debian.org/debian/ testing/main libcurl4-gnutls-dev amd64 7.44.0-2 [349 kB]
- Get:11 http://httpredir.debian.org/debian/ testing/main libhdf5-cpp-10 amd64 1.8.15-patch1+docs-4 [123 kB]
- Get:12 http://httpredir.debian.org/debian/ testing/main libnetcdf-dev amd64 1:4.4.0~rc2-1 [71.7 kB]
- Get:13 http://httpredir.debian.org/debian/ testing/main pkg-config amd64 0.28-1 [57.5 kB]
- Get:14 http://httpredir.debian.org/debian/ testing/main xml-core all 0.13+nmu2 [24.2 kB]
- Get:15 http://httpredir.debian.org/debian/ testing/main libnetcdf7 amd64 1:4.4.0~rc2-1 [313 kB]
- Get:16 http://httpredir.debian.org/debian/ testing/main libicu-dev amd64 55.1-5 [8,553 kB]
- Get:17 http://httpredir.debian.org/debian/ testing/main libxml2-dev amd64 2.9.2+zdfsg1-4 [804 kB]
- [91mdebconf: delaying package configuration, since apt-utils is not installed
- [0m
- Fetched 19.4 MB in 2s (8,839 kB/s)
- Selecting previously unselected package sgml-base.
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- (Reading database ... 16832 files and directories currently installed.)
- Preparing to unpack .../sgml-base_1.26+nmu4_all.deb ...
- Unpacking sgml-base (1.26+nmu4) ...
- Selecting previously unselected package libxml2:amd64.
- Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_amd64.deb ...
- Unpacking libxml2:amd64 (2.9.2+zdfsg1-4) ...
- Selecting previously unselected package libcurl3-gnutls:amd64.
- Preparing to unpack .../libcurl3-gnutls_7.44.0-2_amd64.deb ...
- Unpacking libcurl3-gnutls:amd64 (7.44.0-2) ...
- Selecting previously unselected package curl.
- Preparing to unpack .../curl_7.44.0-2_amd64.deb ...
- Unpacking curl (7.44.0-2) ...
- Selecting previously unselected package hdf5-helpers.
- Preparing to unpack .../hdf5-helpers_1.8.15-patch1+docs-4_amd64.deb ...
- Unpacking hdf5-helpers (1.8.15-patch1+docs-4) ...
- Selecting previously unselected package icu-devtools.
- Preparing to unpack .../icu-devtools_55.1-5_amd64.deb ...
- Unpacking icu-devtools (55.1-5) ...
- Selecting previously unselected package libcurl4-gnutls-dev:amd64.
- Preparing to unpack .../libcurl4-gnutls-dev_7.44.0-2_amd64.deb ...
- Unpacking libcurl4-gnutls-dev:amd64 (7.44.0-2) ...
- Selecting previously unselected package libhdf5-10:amd64.
- Preparing to unpack .../libhdf5-10_1.8.15-patch1+docs-4_amd64.deb ...
- Unpacking libhdf5-10:amd64 (1.8.15-patch1+docs-4) ...
- Selecting previously unselected package libhdf5-8:amd64.
- Preparing to unpack .../libhdf5-8_1.8.13+docs-15.1_amd64.deb ...
- Unpacking libhdf5-8:amd64 (1.8.13+docs-15.1) ...
- Selecting previously unselected package libhdf5-cpp-10:amd64.
- Preparing to unpack .../libhdf5-cpp-10_1.8.15-patch1+docs-4_amd64.deb ...
- Unpacking libhdf5-cpp-10:amd64 (1.8.15-patch1+docs-4) ...
- Selecting previously unselected package libhdf5-dev.
- Preparing to unpack .../libhdf5-dev_1.8.15-patch1+docs-4_amd64.deb ...
- Unpacking libhdf5-dev (1.8.15-patch1+docs-4) ...
- Selecting previously unselected package libicu-dev:amd64.
- Preparing to unpack .../libicu-dev_55.1-5_amd64.deb ...
- Unpacking libicu-dev:amd64 (55.1-5) ...
- Selecting previously unselected package libnetcdf7.
- Preparing to unpack .../libnetcdf7_1%3a4.4.0~rc2-1_amd64.deb ...
- Unpacking libnetcdf7 (1:4.4.0~rc2-1) ...
- Selecting previously unselected package libnetcdf-dev.
- Preparing to unpack .../libnetcdf-dev_1%3a4.4.0~rc2-1_amd64.deb ...
- Unpacking libnetcdf-dev (1:4.4.0~rc2-1) ...
- Selecting previously unselected package libxml2-dev:amd64.
- Preparing to unpack .../libxml2-dev_2.9.2+zdfsg1-4_amd64.deb ...
- Unpacking libxml2-dev:amd64 (2.9.2+zdfsg1-4) ...
- Selecting previously unselected package pkg-config.
- Preparing to unpack .../pkg-config_0.28-1_amd64.deb ...
- Unpacking pkg-config (0.28-1) ...
- Selecting previously unselected package xml-core.
- Preparing to unpack .../xml-core_0.13+nmu2_all.deb ...
- Unpacking xml-core (0.13+nmu2) ...
- Setting up sgml-base (1.26+nmu4) ...
- Setting up libxml2:amd64 (2.9.2+zdfsg1-4) ...
- Setting up libcurl3-gnutls:amd64 (7.44.0-2) ...
- Setting up curl (7.44.0-2) ...
- Setting up hdf5-helpers (1.8.15-patch1+docs-4) ...
- Setting up icu-devtools (55.1-5) ...
- Setting up libcurl4-gnutls-dev:amd64 (7.44.0-2) ...
- Setting up libhdf5-10:amd64 (1.8.15-patch1+docs-4) ...
- Setting up libhdf5-8:amd64 (1.8.13+docs-15.1) ...
- Setting up libhdf5-cpp-10:amd64 (1.8.15-patch1+docs-4) ...
- Setting up libhdf5-dev (1.8.15-patch1+docs-4) ...
- update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
- Setting up libicu-dev:amd64 (55.1-5) ...
- Setting up libnetcdf7 (1:4.4.0~rc2-1) ...
- Setting up libnetcdf-dev (1:4.4.0~rc2-1) ...
- Setting up libxml2-dev:amd64 (2.9.2+zdfsg1-4) ...
- Setting up pkg-config (0.28-1) ...
- Setting up xml-core (0.13+nmu2) ...
- Processing triggers for libc-bin (2.19-22) ...
- Processing triggers for sgml-base (1.26+nmu4) ...
- ---> 47acfcf714e1
- Step 3 : RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile
- ---> 34010b913c12
- Step 4 : RUN Rscript -e "source('https://bioconductor.org/biocLite.R'); biocLite('mzR')"
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- g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Date.cpp -o Date.o
- g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Module.cpp -o Module.o
- g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Rcpp_init.cpp -o Rcpp_init.o
- g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c api.cpp -o api.o
- g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c attributes.cpp -o attributes.o
- g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c barrier.cpp -o barrier.o
- g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -L/usr/lib/R/lib -lR
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- mkdir -p "/usr/local/lib/R/site-library/zlibbioc/include"
- gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c R_init_zlibbioc.c -o R_init_zlibbioc.o
- gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o zlibbioc.so R_init_zlibbioc.o -L/usr/lib/R/lib -lR
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- gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Rinit.c -o Rinit.o
- gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c anyMissing.c -o anyMissing.o
- gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c envir.c -o envir.o
- gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c matchpt.c -o matchpt.o
- gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rowMedians.c -o rowMedians.o
- gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c sublist_extract.c -o sublist_extract.o
- gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/usr/lib/R/lib -lR
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- find . -name \*~ -exec rm {} \; ## from cleanup
- find . -name \*.o -exec rm {} \; ## from cleanup
- find . -name "#*#" -exec rm {} \; ## from cleanup
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c cramp.cpp -o cramp.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ramp_base64.cpp -o ramp_base64.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ramp.cpp -o ramp.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppRamp.cpp -o RcppRamp.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppRampModule.cpp -o RcppRampModule.o
- gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rnetCDF.c -o rnetCDF.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppPwiz.cpp -o RcppPwiz.o
- [91mIn file included from ./boost/format/alt_sstream.hpp:20:0,
- from ./boost/format/internals.hpp:23,
- from ./boost/format.hpp:38,
- from ./pwiz/utility/misc/String.hpp:30,
- from pwiz/utility/misc/Std.hpp:31,
- from RcppPwiz.h:19,
- from RcppPwiz.cpp:1:
- ./boost/utility/base_from_member.hpp:100:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template<typename ...T>
- ^
- [0m
- [91m./boost/utility/base_from_member.hpp:105:43: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template<typename T, typename U, typename ...U2>
- ^
- [0m
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppPwizModule.cpp -o RcppPwizModule.o
- [91mIn file included from ./boost/format/alt_sstream.hpp:20:0,
- from ./boost/format/internals.hpp:23,
- from ./boost/format.hpp:38,
- from ./pwiz/utility/misc/String.hpp:30,
- from pwiz/utility/misc/Std.hpp:31,
- from RcppPwiz.h:19,
- from RcppPwizModule.cpp:2:
- ./boost/utility/base_from_member.hpp:100:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template<typename ...T>
- ^
- [0m
- [91m./boost/utility/base_from_member.hpp:105:43: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template<typename T, typename U, typename ...U2>
- ^
- [0m
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppIdent.cpp -o RcppIdent.o
- [91mIn file included from ./boost/format/alt_sstream.hpp:20:0,
- from ./boost/format/internals.hpp:23,
- from ./boost/format.hpp:38,
- from ./pwiz/utility/misc/String.hpp:30,
- from pwiz/utility/misc/Std.hpp:31,
- from RcppIdent.h:14,
- from RcppIdent.cpp:1:
- ./boost/utility/base_from_member.hpp:100:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template<typename ...T>
- ^
- [0m
- [91m./boost/utility/base_from_member.hpp:105:43: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template<typename T, typename U, typename ...U2>
- ^
- [0m
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppIdentModule.cpp -o RcppIdentModule.o
- [91mIn file included from ./boost/format/alt_sstream.hpp:20:0,
- from ./boost/format/internals.hpp:23,
- from ./boost/format.hpp:38,
- from ./pwiz/utility/misc/String.hpp:30,
- from pwiz/utility/misc/Std.hpp:31,
- from RcppIdent.h:14,
- from RcppIdentModule.cpp:2:
- ./boost/utility/base_from_member.hpp:100:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template<typename ...T>
- ^
- [0m
- [91m./boost/utility/base_from_member.hpp:105:43: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template<typename T, typename U, typename ...U2>
- ^
- [0m
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/system/src/error_code.cpp -o boost/system/src/error_code.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/fileiter.cpp -o boost/regex/src/fileiter.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/regex_raw_buffer.cpp -o boost/regex/src/regex_raw_buffer.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/cregex.cpp -o boost/regex/src/cregex.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/regex_debug.cpp -o boost/regex/src/regex_debug.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/instances.cpp -o boost/regex/src/instances.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/icu.cpp -o boost/regex/src/icu.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/usinstances.cpp -o boost/regex/src/usinstances.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/regex.cpp -o boost/regex/src/regex.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/wide_posix_api.cpp -o boost/regex/src/wide_posix_api.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/regex_traits_defaults.cpp -o boost/regex/src/regex_traits_defaults.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/winstances.cpp -o boost/regex/src/winstances.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/wc_regex_traits.cpp -o boost/regex/src/wc_regex_traits.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/c_regex_traits.cpp -o boost/regex/src/c_regex_traits.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/cpp_regex_traits.cpp -o boost/regex/src/cpp_regex_traits.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/static_mutex.cpp -o boost/regex/src/static_mutex.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/regex/src/w32_regex_traits.cpp -o boost/regex/src/w32_regex_traits.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/iostreams/src/zlib.cpp -o boost/iostreams/src/zlib.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/iostreams/src/file_descriptor.cpp -o boost/iostreams/src/file_descriptor.o
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/thread/src/pthread/once.cpp -o boost/thread/src/pthread/once.o
- [91mIn file included from ./boost/thread/pthread/once_atomic.hpp:17:0,
- from ./boost/thread/once.hpp:20,
- from boost/thread/src/pthread/./once_atomic.cpp:9,
- from boost/thread/src/pthread/once.cpp:8:
- ./boost/thread/detail/invoke.hpp:242:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <class Ret, class A, class A0, class ...Args>
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:249:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- ./boost/thread/detail/invoke.hpp:249:91: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:254:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <class Ret, class A, class A0, class ...Args>
- ^
- ./boost/thread/detail/invoke.hpp:261:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- ./boost/thread/detail/invoke.hpp:261:97: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:266:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <class Ret, class A, class A0, class ...Args>
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:273:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:273:100: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:278:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <class Ret, class A, class A0, class ...Args>
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:285:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:285:106: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:293:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <class Ret, class A, class A0, class ...Args>
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:300:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:300:91: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:305:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <class Ret, class A, class A0, class ...Args>
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:312:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:312:97: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:317:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <class Ret, class A, class A0, class ...Args>
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:324:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:324:100: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- ./boost/thread/detail/invoke.hpp:329:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <class Ret, class A, class A0, class ...Args>
- ^
- ./boost/thread/detail/invoke.hpp:336:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- ./boost/thread/detail/invoke.hpp:336:106: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:398:42: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <class Ret, class Fp, class ...Args>
- ^
- ./boost/thread/detail/invoke.hpp:405:68: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(BOOST_THREAD_RV_REF(Fp) f, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- ./boost/thread/detail/invoke.hpp:409:32: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <class Ret, class ...Args>
- ^
- ./boost/thread/detail/invoke.hpp:411:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret(*f)(Args... ), BOOST_THREAD_RV_REF(Args) ...args)
- ^
- ./boost/thread/detail/invoke.hpp:411:60: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret(*f)(Args... ), BOOST_THREAD_RV_REF(Args) ...args)
- ^
- [0m
- [91mIn file included from ./boost/thread/once.hpp:20:0,
- from boost/thread/src/pthread/./once_atomic.cpp:9,
- from boost/thread/src/pthread/once.cpp:8:
- ./boost/thread/pthread/once_atomic.hpp:120:37: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template<typename Function, class ...ArgTypes>
- ^
- [0m
- [91m./boost/thread/pthread/once_atomic.hpp:121:108: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args)
- ^
- [0m
- g++ -I/usr/share/R/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c boost/thread/src/pthread/thread.cpp -o boost/thread/src/pthread/thread.o
- [91mIn file included from ./boost/chrono/duration.hpp:42:0,
- from ./boost/chrono/time_point.hpp:33,
- from ./boost/thread/lock_types.hpp:22,
- from ./boost/thread/pthread/thread_data.hpp:12,
- from ./boost/thread/thread_only.hpp:17,
- from boost/thread/src/pthread/thread.cpp:11:
- ./boost/type_traits/common_type.hpp:69:22: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template<typename... T>
- ^
- [0m
- [91m./boost/type_traits/common_type.hpp:149:46: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template<typename T, typename U, typename... V>
- ^
- [0m
- [91mIn file included from ./boost/thread/detail/thread.hpp:21:0,
- from ./boost/thread/thread_only.hpp:22,
- from boost/thread/src/pthread/thread.cpp:11:
- ./boost/thread/detail/make_tuple_indices.hpp:35:26: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <std::size_t...> struct tuple_indices
- ^
- [0m
- [91m./boost/thread/detail/make_tuple_indices.hpp:41:46: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <std::size_t Sp, std::size_t ...Indices, std::size_t Ep>
- ^
- ./boost/thread/detail/make_tuple_indices.hpp:47:46: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <std::size_t Ep, std::size_t ...Indices>
- ^
- [0m
- [91mIn file included from ./boost/thread/detail/thread.hpp:22:0,
- from ./boost/thread/thread_only.hpp:22,
- from boost/thread/src/pthread/thread.cpp:11:
- ./boost/thread/detail/invoke.hpp:242:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <class Ret, class A, class A0, class ...Args>
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:249:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- ./boost/thread/detail/invoke.hpp:249:91: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:254:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <class Ret, class A, class A0, class ...Args>
- ^
- ./boost/thread/detail/invoke.hpp:261:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- ./boost/thread/detail/invoke.hpp:261:97: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- ./boost/thread/detail/invoke.hpp:266:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <class Ret, class A, class A0, class ...Args>
- ^
- ./boost/thread/detail/invoke.hpp:273:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- ./boost/thread/detail/invoke.hpp:273:100: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:278:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <class Ret, class A, class A0, class ...Args>
- ^
- ./boost/thread/detail/invoke.hpp:285:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- ./boost/thread/detail/invoke.hpp:285:106: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- ./boost/thread/detail/invoke.hpp:293:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <class Ret, class A, class A0, class ...Args>
- ^
- ./boost/thread/detail/invoke.hpp:300:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- ./boost/thread/detail/invoke.hpp:300:91: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:305:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <class Ret, class A, class A0, class ...Args>
- ^
- ./boost/thread/detail/invoke.hpp:312:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- ./boost/thread/detail/invoke.hpp:312:97: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- ./boost/thread/detail/invoke.hpp:317:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <class Ret, class A, class A0, class ...Args>
- ^
- ./boost/thread/detail/invoke.hpp:324:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- ./boost/thread/detail/invoke.hpp:324:100: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- [0m
- [91m./boost/thread/detail/invoke.hpp:329:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <class Ret, class A, class A0, class ...Args>
- ^
- ./boost/thread/detail/invoke.hpp:336:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- ./boost/thread/detail/invoke.hpp:336:106: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- ./boost/thread/detail/invoke.hpp:398:42: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <class Ret, class Fp, class ...Args>
- ^
- ./boost/thread/detail/invoke.hpp:405:68: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(BOOST_THREAD_RV_REF(Fp) f, BOOST_THREAD_RV_REF(Args) ...args)
- ^
- ./boost/thread/detail/invoke.hpp:409:32: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template <class Ret, class ...Args>
- ^
- ./boost/thread/detail/invoke.hpp:411:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret(*f)(Args... ), BOOST_THREAD_RV_REF(Args) ...args)
- ^
- ./boost/thread/detail/invoke.hpp:411:60: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- invoke(Ret(*f)(Args... ), BOOST_THREAD_RV_REF(Args) ...args)
- ^
- [0m
- [91mIn file included from ./boost/thread/once.hpp:20:0,
- from boost/thread/src/pthread/thread.cpp:17:
- ./boost/thread/pthread/once_atomic.hpp:120:37: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- template<typename Function, class ...ArgTypes>
- ^
- [0m
- [91m./boost/thread/pthread/once_atomic.hpp:121:108: warning: variadic templates only available with -std=c++11 or -std=gnu++11
- inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args)
- ^
- [0m
- [91mboost/thread/src/pthread/thread.cpp: In function ‘boost::detail::thread_data_base* boost::detail::get_current_thread_data()’:
- boost/thread/src/pthread/thread.cpp:140:88: error: no matching function for call to ‘call_once(boost::once_flag&, void (&)())’
- boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key);
- ^
- In file included from ./boost/thread/once.hpp:20:0,
- from boost/thread/src/pthread/thread.cpp:17:
- ./boost/thread/pthread/once_atomic.hpp:121:15: note: candidate: template<class Function, class ... ArgTypes> void boost::call_once(boost::once_flag&, boost::detail::thread_move_t<T>, boost::detail::thread_move_t<Args>...)
- inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args)
- ^
- [0m
- [91m./boost/thread/pthread/once_atomic.hpp:121:15: note: template argument deduction/substitution failed:
- boost/thread/src/pthread/thread.cpp:140:88: note: mismatched types ‘boost::detail::thread_move_t<T>’ and ‘void (*)()’
- boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key);
- ^
- In file included from boost/thread/src/pthread/thread.cpp:17:0:
- ./boost/thread/once.hpp:35:13: note: candidate: template<class Function> void boost::call_once(Function, boost::once_flag&)
- inline void call_once(Function func,once_flag& flag)
- ^
- ./boost/thread/once.hpp:35:13: note: template argument deduction/substitution failed:
- boost/thread/src/pthread/thread.cpp:140:88: note: cannot convert ‘boost::detail::{anonymous}::create_current_thread_tls_key’ (type ‘void()’) to type ‘boost::once_flag&’
- boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key);
- ^
- [0m
- [91mboost/thread/src/pthread/thread.cpp: In function ‘void boost::detail::set_current_thread_data(boost::detail::thread_data_base*)’:
- boost/thread/src/pthread/thread.cpp:146:88: error: no matching function for call to ‘call_once(boost::once_flag&, void (&)())’
- boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key);
- ^
- In file included from ./boost/thread/once.hpp:20:0,
- from boost/thread/src/pthread/thread.cpp:17:
- ./boost/thread/pthread/once_atomic.hpp:121:15: note: candidate: template<class Function, class ... ArgTypes> void boost::call_once(boost::once_flag&, boost::detail::thread_move_t<T>, boost::detail::thread_move_t<Args>...)
- inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args)
- ^
- ./boost/thread/pthread/once_atomic.hpp:121:15: note: template argument deduction/substitution failed:
- boost/thread/src/pthread/thread.cpp:146:88: note: mismatched types ‘boost::detail::thread_move_t<T>’ and ‘void (*)()’
- boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key);
- ^
- In file included from boost/thread/src/pthread/thread.cpp:17:0:
- ./boost/thread/once.hpp:35:13: note: candidate: template<class Function> void boost::call_once(Function, boost::once_flag&)
- inline void call_once(Function func,once_flag& flag)
- ^
- ./boost/thread/once.hpp:35:13: note: template argument deduction/substitution failed:
- boost/thread/src/pthread/thread.cpp:146:88: note: cannot convert ‘boost::detail::{anonymous}::create_current_thread_tls_key’ (type ‘void()’) to type ‘boost::once_flag&’
- boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key);
- ^
- [0m
- /usr/lib/R/etc/Makeconf:143: recipe for target 'boost/thread/src/pthread/thread.o' failed
- [91mmake: *** [boost/thread/src/pthread/thread.o] Error 1
- [0m
- [91mERROR: compilation failed for package ‘mzR’
- [0m
- [91m* removing ‘/usr/local/lib/R/site-library/mzR’
- [0m
- The downloaded source packages are in
- ‘/tmp/RtmppcQqr5/downloaded_packages’
- [91mWarning message:
- [0m
- [91mIn install.packages(pkgs = doing, lib = lib, ...) :[0m
- [91m
- installation of package ‘mzR’ had non-zero exit status
- [0m
- ---> 10aae02c3a0b
- Successfully built 10aae02c3a0b
- 10aae02c3a0b Image successfully pushed
- 34010b913c12 Image successfully pushed
- 47acfcf714e1 Image successfully pushed
- 5cd07b70e123 Image successfully pushed
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