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mzR docker build - r-base

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Oct 9th, 2015
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  1. Client:
  2. Version: 1.8.1
  3. API version: 1.20
  4. Go version: go1.4.2
  5. Git commit: d12ea79
  6. Built: Thu Aug 13 02:49:29 UTC 2015
  7. OS/Arch: linux/amd64
  8.  
  9. Server:
  10. Version: 1.8.3-rc4
  11. API version: 1.20
  12. Go version: go1.4.2
  13. Git commit: 9f1606a
  14. Built: Fri Oct 2 23:36:50 UTC 2015
  15. OS/Arch: linux/amd64
  16. Step 0 : FROM r-base:latest
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  807. e10b2d7fae0e Extracting
  808. e10b2d7fae0e Extracting
  809. e10b2d7fae0e Extracting
  810. e10b2d7fae0e Extracting
  811. e10b2d7fae0e Extracting
  812. e10b2d7fae0e Extracting
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  814. e10b2d7fae0e Extracting
  815. e10b2d7fae0e Extracting
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  817. e10b2d7fae0e Extracting
  818. e10b2d7fae0e Extracting
  819. e10b2d7fae0e Extracting
  820. e10b2d7fae0e Extracting
  821. e10b2d7fae0e Extracting
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  823. e10b2d7fae0e Extracting
  824. e10b2d7fae0e Extracting
  825. e10b2d7fae0e Extracting
  826. e10b2d7fae0e Extracting
  827. e10b2d7fae0e Extracting
  828. e10b2d7fae0e Extracting
  829. e10b2d7fae0e Extracting
  830. e10b2d7fae0e Extracting
  831. e10b2d7fae0e Extracting
  832. e10b2d7fae0e Extracting
  833. e10b2d7fae0e Extracting
  834. e10b2d7fae0e Extracting
  835. e10b2d7fae0e Extracting
  836. e10b2d7fae0e Extracting
  837. e10b2d7fae0e Extracting
  838. e10b2d7fae0e Extracting
  839. e10b2d7fae0e Extracting
  840. e10b2d7fae0e Extracting
  841. e10b2d7fae0e Extracting
  842. e10b2d7fae0e Extracting
  843. e10b2d7fae0e Extracting
  844. e10b2d7fae0e Extracting
  845. e10b2d7fae0e Extracting
  846. e10b2d7fae0e Extracting
  847. e10b2d7fae0e Extracting
  848. e10b2d7fae0e Extracting
  849. e10b2d7fae0e Extracting
  850. e10b2d7fae0e Extracting
  851. e10b2d7fae0e Extracting
  852. e10b2d7fae0e Extracting
  853. e10b2d7fae0e Pull complete
  854. 5075b0c23e12 Extracting
  855. 5075b0c23e12 Extracting
  856. 5075b0c23e12 Extracting
  857. 5075b0c23e12 Pull complete
  858. Digest: sha256:c12c1f5a5d1db5a7f38f95e751133cfca9a3d1c052c861228310eaa7b1337e2d
  859. Status: Downloaded newer image for r-base:latest
  860. ---> 5075b0c23e12
  861. Step 1 : RUN apt-get update -qq && apt-get dist-upgrade -y
  862. Reading package lists...
  863.  
  864. Building dependency tree...
  865. Reading state information...
  866.  
  867. The following NEW packages will be installed:
  868. libnghttp2-14
  869. The following packages will be upgraded:
  870. binutils bsdutils cpp-5 diffutils dpkg dpkg-dev g++-5 gcc-4.8-base gcc-5
  871. gcc-5-base gfortran-5 libasan2 libatomic1 libaudit-common libaudit1
  872. libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap2 libcap2-bin libcc1-0
  873. libcilkrts5 libcurl3 libdb5.3 libdpkg-perl libfdisk1 libfreetype6
  874. libgcc-5-dev libgcc1 libgfortran-5-dev libgfortran3 libglib2.0-0
  875. libgnutls-deb0-28 libgomp1 libgpg-error0 libgraphite2-3 libicu55 libidn11
  876. libitm1 libldap-2.4-2 liblocale-gettext-perl liblsan0 libmount1 libmpx0
  877. libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpcre16-3 libpcre3
  878. libpcre3-dev libpcre32-3 libpcrecpp0v5 libpixman-1-0 libpsl0 libquadmath0
  879. libsasl2-2 libsasl2-modules-db libsmartcols1 libstdc++-5-dev libstdc++6
  880. libsystemd0 libtasn1-6 libtsan0 libubsan0 libudev1 libuuid1 linux-libc-dev
  881. locales lsb-base mount multiarch-support systemd systemd-sysv udev
  882. util-linux xdg-utils
  883. 78 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
  884. Need to get 168 MB of archives.
  885. After this operation, 10.8 MB of additional disk space will be used.
  886. Get:1 http://httpredir.debian.org/debian/ testing/main dpkg amd64 1.18.3 [2,912 kB]
  887. Get:2 http://httpredir.debian.org/debian/ testing/main bsdutils amd64 1:2.27-3 [104 kB]
  888. Get:3 http://httpredir.debian.org/debian/ testing/main diffutils amd64 1:3.3-2 [266 kB]
  889. Get:4 http://httpredir.debian.org/debian/ testing/main libc-dev-bin amd64 2.19-22 [237 kB]
  890. Get:5 http://httpredir.debian.org/debian/ testing/main libc6-dev amd64 2.19-22 [1,997 kB]
  891. Get:6 http://httpredir.debian.org/debian/ testing/main liblsan0 amd64 5.2.1-21 [109 kB]
  892. Get:7 http://httpredir.debian.org/debian/ testing/main libcilkrts5 amd64 5.2.1-21 [39.6 kB]
  893. Get:8 http://httpredir.debian.org/debian/ testing/main linux-libc-dev amd64 4.2.1-2 [1,047 kB]
  894. Get:9 http://httpredir.debian.org/debian/ testing/main g++-5 amd64 5.2.1-21 [37.2 MB]
  895. Get:10 http://httpredir.debian.org/debian/ testing/main libcap2 amd64 1:2.24-12 [16.4 kB]
  896. Get:11 http://httpredir.debian.org/debian/ testing/main libc-bin amd64 2.19-22 [1,285 kB]
  897. Get:12 http://httpredir.debian.org/debian/ testing/main libgcc1 amd64 1:5.2.1-21 [38.7 kB]
  898. Get:13 http://httpredir.debian.org/debian/ testing/main libtsan0 amd64 5.2.1-21 [245 kB]
  899. Get:14 http://httpredir.debian.org/debian/ testing/main libquadmath0 amd64 5.2.1-21 [131 kB]
  900. Get:15 http://httpredir.debian.org/debian/ testing/main libcc1-0 amd64 5.2.1-21 [30.4 kB]
  901. Get:16 http://httpredir.debian.org/debian/ testing/main libgomp1 amd64 5.2.1-21 [54.2 kB]
  902. Get:17 http://httpredir.debian.org/debian/ testing/main libgfortran-5-dev amd64 5.2.1-21 [285 kB]
  903. Get:18 http://httpredir.debian.org/debian/ testing/main gcc-5 amd64 5.2.1-21 [26.1 MB]
  904. Get:19 http://httpredir.debian.org/debian/ testing/main libitm1 amd64 5.2.1-21 [26.7 kB]
  905. Get:20 http://httpredir.debian.org/debian/ testing/main libatomic1 amd64 5.2.1-21 [8,730 B]
  906. Get:21 http://httpredir.debian.org/debian/ testing/main gcc-5-base amd64 5.2.1-21 [167 kB]
  907. Get:22 http://httpredir.debian.org/debian/ testing/main libubsan0 amd64 5.2.1-21 [98.9 kB]
  908. Get:23 http://httpredir.debian.org/debian/ testing/main libgfortran3 amd64 5.2.1-21 [253 kB]
  909. Get:24 http://httpredir.debian.org/debian/ testing/main lsb-base all 9.20150917 [27.3 kB]
  910. Get:25 http://httpredir.debian.org/debian/ testing/main binutils amd64 2.25.1-3 [3,612 kB]
  911. Get:26 http://httpredir.debian.org/debian/ testing/main gfortran-5 amd64 5.2.1-21 [27.0 MB]
  912. Get:27 http://httpredir.debian.org/debian/ testing/main systemd amd64 226-4 [3,422 kB]
  913. Get:28 http://httpredir.debian.org/debian/ testing/main libgcc-5-dev amd64 5.2.1-21 [2,223 kB]
  914. Get:29 http://httpredir.debian.org/debian/ testing/main libc6 amd64 2.19-22 [4,790 kB]
  915. Get:30 http://httpredir.debian.org/debian/ testing/main libasan2 amd64 5.2.1-21 [265 kB]
  916. Get:31 http://httpredir.debian.org/debian/ testing/main libsmartcols1 amd64 2.27-3 [115 kB]
  917. Get:32 http://httpredir.debian.org/debian/ testing/main libfdisk1 amd64 2.27-3 [193 kB]
  918. Get:33 http://httpredir.debian.org/debian/ testing/main libmpx0 amd64 5.2.1-21 [9,504 B]
  919. Get:34 http://httpredir.debian.org/debian/ testing/main cpp-5 amd64 5.2.1-21 [26.2 MB]
  920. Get:35 http://httpredir.debian.org/debian/ testing/main udev amd64 226-4 [1,034 kB]
  921. Get:36 http://httpredir.debian.org/debian/ testing/main libsystemd0 amd64 226-4 [242 kB]
  922. Get:37 http://httpredir.debian.org/debian/ testing/main libaudit-common all 1:2.4.4-3 [14.8 kB]
  923. Get:38 http://httpredir.debian.org/debian/ testing/main libmount1 amd64 2.27-3 [170 kB]
  924. Get:39 http://httpredir.debian.org/debian/ testing/main libblkid1 amd64 2.27-3 [161 kB]
  925. Get:40 http://httpredir.debian.org/debian/ testing/main liblocale-gettext-perl amd64 1.07-1 [19.0 kB]
  926. Get:41 http://httpredir.debian.org/debian/ testing/main libcap2-bin amd64 1:2.24-12 [25.9 kB]
  927. Get:42 http://httpredir.debian.org/debian/ testing/main libgnutls-deb0-28 amd64 3.3.18-1 [717 kB]
  928. Get:43 http://httpredir.debian.org/debian/ testing/main systemd-sysv amd64 226-4 [53.6 kB]
  929. Get:44 http://httpredir.debian.org/debian/ testing/main dpkg-dev all 1.18.3 [1,432 kB]
  930. Get:45 http://httpredir.debian.org/debian/ testing/main libpcrecpp0v5 amd64 2:8.35-7.2 [142 kB]
  931. Get:46 http://httpredir.debian.org/debian/ testing/main libnghttp2-14 amd64 1.3.2-0.1 [75.6 kB]
  932. Get:47 http://httpredir.debian.org/debian/ testing/main multiarch-support amd64 2.19-22 [180 kB]
  933. Get:48 http://httpredir.debian.org/debian/ testing/main libpsl0 amd64 0.11.0-1 [40.5 kB]
  934. Get:49 http://httpredir.debian.org/debian/ testing/main xdg-utils all 1.1.0~rc3+git20150922-1 [69.2 kB]
  935. Get:50 http://httpredir.debian.org/debian/ testing/main libgpg-error0 amd64 1.20-1 [103 kB]
  936. Get:51 http://httpredir.debian.org/debian/ testing/main gcc-4.8-base amd64 4.8.5-1 [156 kB]
  937. Get:52 http://httpredir.debian.org/debian/ testing/main libtasn1-6 amd64 4.7-2 [50.1 kB]
  938. Get:53 http://httpredir.debian.org/debian/ testing/main libidn11 amd64 1.32-3 [113 kB]
  939. Get:54 http://httpredir.debian.org/debian/ testing/main libsasl2-modules-db amd64 2.1.26.dfsg1-14 [67.0 kB]
  940. Get:55 http://httpredir.debian.org/debian/ testing/main libaudit1 amd64 1:2.4.4-3+b1 [47.5 kB]
  941. Get:56 http://httpredir.debian.org/debian/ testing/main libsasl2-2 amd64 2.1.26.dfsg1-14 [104 kB]
  942. Get:57 http://httpredir.debian.org/debian/ testing/main libldap-2.4-2 amd64 2.4.42+dfsg-2 [224 kB]
  943. Get:58 http://httpredir.debian.org/debian/ testing/main libpcre3-dev amd64 2:8.35-7.2 [623 kB]
  944. Get:59 http://httpredir.debian.org/debian/ testing/main locales all 2.19-22 [3,969 kB]
  945. Get:60 http://httpredir.debian.org/debian/ testing/main libglib2.0-0 amd64 2.46.0-2 [2,534 kB]
  946. Get:61 http://httpredir.debian.org/debian/ testing/main libpcre16-3 amd64 2:8.35-7.2 [242 kB]
  947. Get:62 http://httpredir.debian.org/debian/ testing/main libicu55 amd64 55.1-5 [7,651 kB]
  948. Get:63 http://httpredir.debian.org/debian/ testing/main libpcre3 amd64 2:8.35-7.2 [321 kB]
  949. Get:64 http://httpredir.debian.org/debian/ testing/main libdb5.3 amd64 5.3.28-11 [680 kB]
  950. Get:65 http://httpredir.debian.org/debian/ testing/main libcurl3 amd64 7.44.0-2 [272 kB]
  951. Get:66 http://httpredir.debian.org/debian/ testing/main libpango-1.0-0 amd64 1.38.0-3 [307 kB]
  952. Get:67 http://httpredir.debian.org/debian/ testing/main libpangocairo-1.0-0 amd64 1.38.0-3 [220 kB]
  953. Get:68 http://httpredir.debian.org/debian/ testing/main libpixman-1-0 amd64 0.33.2-2 [523 kB]
  954. Get:69 http://httpredir.debian.org/debian/ testing/main libstdc++-5-dev amd64 5.2.1-21 [1,366 kB]
  955. Get:70 http://httpredir.debian.org/debian/ testing/main libstdc++6 amd64 5.2.1-21 [388 kB]
  956. Get:71 http://httpredir.debian.org/debian/ testing/main libuuid1 amd64 2.27-3 [67.2 kB]
  957. Get:72 http://httpredir.debian.org/debian/ testing/main libudev1 amd64 226-4 [95.5 kB]
  958. Get:73 http://httpredir.debian.org/debian/ testing/main util-linux amd64 2.27-3 [897 kB]
  959. Get:74 http://httpredir.debian.org/debian/ testing/main mount amd64 2.27-3 [175 kB]
  960. Get:75 http://httpredir.debian.org/debian/ testing/main libpcre32-3 amd64 2:8.35-7.2 [234 kB]
  961. Get:76 http://httpredir.debian.org/debian/ testing/main libdpkg-perl all 1.18.3 [1,137 kB]
  962. Get:77 http://httpredir.debian.org/debian/ testing/main libfreetype6 amd64 2.6-2 [449 kB]
  963. Get:78 http://httpredir.debian.org/debian/ testing/main libgraphite2-3 amd64 1.3.3-1 [74.7 kB]
  964. Get:79 http://httpredir.debian.org/debian/ testing/main libpangoft2-1.0-0 amd64 1.38.0-3 [233 kB]
  965. debconf: delaying package configuration, since apt-utils is not installed
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  1848. Preparing to unpack .../libpangoft2-1.0-0_1.38.0-3_amd64.deb ...
  1849. Unpacking libpangoft2-1.0-0:amd64 (1.38.0-3) over (1.36.8-3) ...
  1850. Preparing to unpack .../libpangocairo-1.0-0_1.38.0-3_amd64.deb ...
  1851. Unpacking libpangocairo-1.0-0:amd64 (1.38.0-3) over (1.36.8-3) ...
  1852. Preparing to unpack .../libpixman-1-0_0.33.2-2_amd64.deb ...
  1853. Unpacking libpixman-1-0:amd64 (0.33.2-2) over (0.32.6-3) ...
  1854. Preparing to unpack .../libpsl0_0.11.0-1_amd64.deb ...
  1855. Unpacking libpsl0:amd64 (0.11.0-1) over (0.8.0-1) ...
  1856. Preparing to unpack .../xdg-utils_1.1.0~rc3+git20150922-1_all.deb ...
  1857. Unpacking xdg-utils (1.1.0~rc3+git20150922-1) over (1.1.0~rc3+git20150907-1) ...
  1858. Setting up libc-dev-bin (2.19-22) ...
  1859. Setting up linux-libc-dev:amd64 (4.2.1-2) ...
  1860. Setting up libc6-dev:amd64 (2.19-22) ...
  1861. Setting up libgomp1:amd64 (5.2.1-21) ...
  1862. Setting up libitm1:amd64 (5.2.1-21) ...
  1863. Setting up libatomic1:amd64 (5.2.1-21) ...
  1864. Setting up libasan2:amd64 (5.2.1-21) ...
  1865. Setting up liblsan0:amd64 (5.2.1-21) ...
  1866. Setting up libtsan0:amd64 (5.2.1-21) ...
  1867. Setting up libubsan0:amd64 (5.2.1-21) ...
  1868. Setting up libcilkrts5:amd64 (5.2.1-21) ...
  1869. Setting up libmpx0:amd64 (5.2.1-21) ...
  1870. Setting up libquadmath0:amd64 (5.2.1-21) ...
  1871. Setting up cpp-5 (5.2.1-21) ...
  1872. Setting up libcc1-0:amd64 (5.2.1-21) ...
  1873. Setting up binutils (2.25.1-3) ...
  1874. Setting up libgcc-5-dev:amd64 (5.2.1-21) ...
  1875. Setting up gcc-5 (5.2.1-21) ...
  1876. Setting up libstdc++-5-dev:amd64 (5.2.1-21) ...
  1877. Setting up g++-5 (5.2.1-21) ...
  1878. Setting up libgfortran3:amd64 (5.2.1-21) ...
  1879. Setting up libgfortran-5-dev:amd64 (5.2.1-21) ...
  1880. Setting up gfortran-5 (5.2.1-21) ...
  1881. Setting up libpcre16-3:amd64 (2:8.35-7.2) ...
  1882. Setting up libpcre32-3:amd64 (2:8.35-7.2) ...
  1883. Setting up libpcrecpp0v5:amd64 (2:8.35-7.2) ...
  1884. Setting up libpcre3-dev:amd64 (2:8.35-7.2) ...
  1885. Setting up liblocale-gettext-perl (1.07-1) ...
  1886. Setting up gcc-4.8-base:amd64 (4.8.5-1) ...
  1887. Setting up libtasn1-6:amd64 (4.7-2) ...
  1888. Setting up libgnutls-deb0-28:amd64 (3.3.18-1) ...
  1889. Setting up libidn11:amd64 (1.32-3) ...
  1890. Setting up libsasl2-modules-db:amd64 (2.1.26.dfsg1-14) ...
  1891. Setting up libsasl2-2:amd64 (2.1.26.dfsg1-14) ...
  1892. Setting up libldap-2.4-2:amd64 (2.4.42+dfsg-2) ...
  1893. Setting up locales (2.19-22) ...
  1894. debconf: unable to initialize frontend: Dialog
  1895. debconf: (TERM is not set, so the dialog frontend is not usable.)
  1896. debconf: falling back to frontend: Readline
  1897. Generating locales (this might take a while)...
  1898. en_US.UTF-8
  1899. ...
  1900. done
  1901. Generation complete.
  1902. Setting up libdpkg-perl (1.18.3) ...
  1903. Setting up dpkg-dev (1.18.3) ...
  1904. Setting up libnghttp2-14:amd64 (1.3.2-0.1) ...
  1905. Setting up libcurl3:amd64 (7.44.0-2) ...
  1906. Setting up libfreetype6:amd64 (2.6-2) ...
  1907. Setting up libglib2.0-0:amd64 (2.46.0-2) ...
  1908. No schema files found: doing nothing.
  1909. Setting up libgraphite2-3:amd64 (1.3.3-1) ...
  1910. Setting up libicu55:amd64 (55.1-5) ...
  1911. Setting up libpango-1.0-0:amd64 (1.38.0-3) ...
  1912. Setting up libpangoft2-1.0-0:amd64 (1.38.0-3) ...
  1913. Setting up libpangocairo-1.0-0:amd64 (1.38.0-3) ...
  1914. Setting up libpixman-1-0:amd64 (0.33.2-2) ...
  1915. Setting up libpsl0:amd64 (0.11.0-1) ...
  1916. Setting up xdg-utils (1.1.0~rc3+git20150922-1) ...
  1917. Processing triggers for libc-bin (2.19-22) ...
  1918. ---> 5cd07b70e123
  1919. Step 2 : RUN apt-get update -qq && apt-get install -y curl libnetcdf-dev libxml2-dev
  1920. Reading package lists...
  1921.  
  1922. Building dependency tree...
  1923. Reading state information...
  1924.  
  1925. The following extra packages will be installed:
  1926. hdf5-helpers icu-devtools libcurl3-gnutls libcurl4-gnutls-dev libhdf5-10
  1927. libhdf5-8 libhdf5-cpp-10 libhdf5-dev libicu-dev libnetcdf7 libxml2
  1928. pkg-config sgml-base xml-core
  1929. Suggested packages:
  1930. libcurl4-doc libcurl3-dbg libgnutls28-dev libidn11-dev libkrb5-dev
  1931. libldap2-dev librtmp-dev libssh2-1-dev libhdf5-doc icu-doc netcdf-bin
  1932. netcdf-doc sgml-base-doc debhelper
  1933. The following NEW packages will be installed:
  1934. curl hdf5-helpers icu-devtools libcurl3-gnutls libcurl4-gnutls-dev
  1935. libhdf5-10 libhdf5-8 libhdf5-cpp-10 libhdf5-dev libicu-dev libnetcdf-dev
  1936. libnetcdf7 libxml2 libxml2-dev pkg-config sgml-base xml-core
  1937. 0 upgraded, 17 newly installed, 0 to remove and 0 not upgraded.
  1938. Need to get 19.4 MB of archives.
  1939. After this operation, 92.1 MB of additional disk space will be used.
  1940. Get:1 http://httpredir.debian.org/debian/ testing/main sgml-base all 1.26+nmu4 [14.6 kB]
  1941. Get:2 http://httpredir.debian.org/debian/ testing/main libcurl3-gnutls amd64 7.44.0-2 [270 kB]
  1942. Get:3 http://httpredir.debian.org/debian/ testing/main curl amd64 7.44.0-2 [207 kB]
  1943. Get:4 http://httpredir.debian.org/debian/ testing/main hdf5-helpers amd64 1.8.15-patch1+docs-4 [38.7 kB]
  1944. Get:5 http://httpredir.debian.org/debian/ testing/main libxml2 amd64 2.9.2+zdfsg1-4 [911 kB]
  1945. Get:6 http://httpredir.debian.org/debian/ testing/main libhdf5-8 amd64 1.8.13+docs-15.1 [1,060 kB]
  1946. Get:7 http://httpredir.debian.org/debian/ testing/main libhdf5-10 amd64 1.8.15-patch1+docs-4 [1,068 kB]
  1947. Get:8 http://httpredir.debian.org/debian/ testing/main libhdf5-dev amd64 1.8.15-patch1+docs-4 [5,330 kB]
  1948. Get:9 http://httpredir.debian.org/debian/ testing/main icu-devtools amd64 55.1-5 [176 kB]
  1949. Get:10 http://httpredir.debian.org/debian/ testing/main libcurl4-gnutls-dev amd64 7.44.0-2 [349 kB]
  1950. Get:11 http://httpredir.debian.org/debian/ testing/main libhdf5-cpp-10 amd64 1.8.15-patch1+docs-4 [123 kB]
  1951. Get:12 http://httpredir.debian.org/debian/ testing/main libnetcdf-dev amd64 1:4.4.0~rc2-1 [71.7 kB]
  1952. Get:13 http://httpredir.debian.org/debian/ testing/main pkg-config amd64 0.28-1 [57.5 kB]
  1953. Get:14 http://httpredir.debian.org/debian/ testing/main xml-core all 0.13+nmu2 [24.2 kB]
  1954. Get:15 http://httpredir.debian.org/debian/ testing/main libnetcdf7 amd64 1:4.4.0~rc2-1 [313 kB]
  1955. Get:16 http://httpredir.debian.org/debian/ testing/main libicu-dev amd64 55.1-5 [8,553 kB]
  1956. Get:17 http://httpredir.debian.org/debian/ testing/main libxml2-dev amd64 2.9.2+zdfsg1-4 [804 kB]
  1957. debconf: delaying package configuration, since apt-utils is not installed
  1958. 
  1959. Fetched 19.4 MB in 2s (8,839 kB/s)
  1960. Selecting previously unselected package sgml-base.
  1961. (Reading database ...
  1962. (Reading database ... 5%
  1963. (Reading database ... 10%
  1964. (Reading database ... 15%
  1965. (Reading database ... 20%
  1966. (Reading database ... 25%
  1967. (Reading database ... 30%
  1968. (Reading database ... 35%
  1969. (Reading database ... 40%
  1970. (Reading database ... 45%
  1971. (Reading database ... 50%
  1972. (Reading database ... 55%
  1973. (Reading database ... 60%
  1974. (Reading database ... 65%
  1975. (Reading database ... 70%
  1976. (Reading database ... 75%
  1977. (Reading database ... 80%
  1978. (Reading database ... 85%
  1979. (Reading database ... 90%
  1980. (Reading database ... 95%
  1981. (Reading database ... 100%
  1982. (Reading database ... 16832 files and directories currently installed.)
  1983. Preparing to unpack .../sgml-base_1.26+nmu4_all.deb ...
  1984. Unpacking sgml-base (1.26+nmu4) ...
  1985. Selecting previously unselected package libxml2:amd64.
  1986.  
  1987. Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_amd64.deb ...
  1988. Unpacking libxml2:amd64 (2.9.2+zdfsg1-4) ...
  1989. Selecting previously unselected package libcurl3-gnutls:amd64.
  1990. Preparing to unpack .../libcurl3-gnutls_7.44.0-2_amd64.deb ...
  1991. Unpacking libcurl3-gnutls:amd64 (7.44.0-2) ...
  1992. Selecting previously unselected package curl.
  1993. Preparing to unpack .../curl_7.44.0-2_amd64.deb ...
  1994. Unpacking curl (7.44.0-2) ...
  1995. Selecting previously unselected package hdf5-helpers.
  1996. Preparing to unpack .../hdf5-helpers_1.8.15-patch1+docs-4_amd64.deb ...
  1997. Unpacking hdf5-helpers (1.8.15-patch1+docs-4) ...
  1998. Selecting previously unselected package icu-devtools.
  1999. Preparing to unpack .../icu-devtools_55.1-5_amd64.deb ...
  2000. Unpacking icu-devtools (55.1-5) ...
  2001. Selecting previously unselected package libcurl4-gnutls-dev:amd64.
  2002. Preparing to unpack .../libcurl4-gnutls-dev_7.44.0-2_amd64.deb ...
  2003. Unpacking libcurl4-gnutls-dev:amd64 (7.44.0-2) ...
  2004. Selecting previously unselected package libhdf5-10:amd64.
  2005. Preparing to unpack .../libhdf5-10_1.8.15-patch1+docs-4_amd64.deb ...
  2006. Unpacking libhdf5-10:amd64 (1.8.15-patch1+docs-4) ...
  2007. Selecting previously unselected package libhdf5-8:amd64.
  2008. Preparing to unpack .../libhdf5-8_1.8.13+docs-15.1_amd64.deb ...
  2009. Unpacking libhdf5-8:amd64 (1.8.13+docs-15.1) ...
  2010. Selecting previously unselected package libhdf5-cpp-10:amd64.
  2011. Preparing to unpack .../libhdf5-cpp-10_1.8.15-patch1+docs-4_amd64.deb ...
  2012. Unpacking libhdf5-cpp-10:amd64 (1.8.15-patch1+docs-4) ...
  2013. Selecting previously unselected package libhdf5-dev.
  2014. Preparing to unpack .../libhdf5-dev_1.8.15-patch1+docs-4_amd64.deb ...
  2015. Unpacking libhdf5-dev (1.8.15-patch1+docs-4) ...
  2016. Selecting previously unselected package libicu-dev:amd64.
  2017. Preparing to unpack .../libicu-dev_55.1-5_amd64.deb ...
  2018. Unpacking libicu-dev:amd64 (55.1-5) ...
  2019. Selecting previously unselected package libnetcdf7.
  2020. Preparing to unpack .../libnetcdf7_1%3a4.4.0~rc2-1_amd64.deb ...
  2021. Unpacking libnetcdf7 (1:4.4.0~rc2-1) ...
  2022. Selecting previously unselected package libnetcdf-dev.
  2023. Preparing to unpack .../libnetcdf-dev_1%3a4.4.0~rc2-1_amd64.deb ...
  2024. Unpacking libnetcdf-dev (1:4.4.0~rc2-1) ...
  2025. Selecting previously unselected package libxml2-dev:amd64.
  2026. Preparing to unpack .../libxml2-dev_2.9.2+zdfsg1-4_amd64.deb ...
  2027. Unpacking libxml2-dev:amd64 (2.9.2+zdfsg1-4) ...
  2028. Selecting previously unselected package pkg-config.
  2029. Preparing to unpack .../pkg-config_0.28-1_amd64.deb ...
  2030. Unpacking pkg-config (0.28-1) ...
  2031. Selecting previously unselected package xml-core.
  2032. Preparing to unpack .../xml-core_0.13+nmu2_all.deb ...
  2033. Unpacking xml-core (0.13+nmu2) ...
  2034. Setting up sgml-base (1.26+nmu4) ...
  2035. Setting up libxml2:amd64 (2.9.2+zdfsg1-4) ...
  2036.  
  2037. Setting up libcurl3-gnutls:amd64 (7.44.0-2) ...
  2038. Setting up curl (7.44.0-2) ...
  2039. Setting up hdf5-helpers (1.8.15-patch1+docs-4) ...
  2040. Setting up icu-devtools (55.1-5) ...
  2041. Setting up libcurl4-gnutls-dev:amd64 (7.44.0-2) ...
  2042. Setting up libhdf5-10:amd64 (1.8.15-patch1+docs-4) ...
  2043. Setting up libhdf5-8:amd64 (1.8.13+docs-15.1) ...
  2044. Setting up libhdf5-cpp-10:amd64 (1.8.15-patch1+docs-4) ...
  2045. Setting up libhdf5-dev (1.8.15-patch1+docs-4) ...
  2046. 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
  2047.  
  2048. Setting up libicu-dev:amd64 (55.1-5) ...
  2049. Setting up libnetcdf7 (1:4.4.0~rc2-1) ...
  2050. Setting up libnetcdf-dev (1:4.4.0~rc2-1) ...
  2051. Setting up libxml2-dev:amd64 (2.9.2+zdfsg1-4) ...
  2052. Setting up pkg-config (0.28-1) ...
  2053. Setting up xml-core (0.13+nmu2) ...
  2054. Processing triggers for libc-bin (2.19-22) ...
  2055. Processing triggers for sgml-base (1.26+nmu4) ...
  2056. ---> 47acfcf714e1
  2057. Step 3 : RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile
  2058. ---> 34010b913c12
  2059. Step 4 : RUN Rscript -e "source('https://bioconductor.org/biocLite.R'); biocLite('mzR')"
  2060. Installing package into ‘/usr/local/lib/R/site-library’
  2061. (as ‘lib’ is unspecified)
  2062. 
  2063. trying URL 'https://bioconductor.org/packages/3.1/bioc/src/contrib/BiocInstaller_1.18.4.tar.gz'
  2064. 
  2065. Content type 'application/x-gzip' length 14977 bytes (14 KB)
  2066. ======
  2067. ==================================
  2068. ==========
  2069. downloaded 14 KB
  2070.  
  2071. 
  2072. * installing *source* package ‘BiocInstaller’ ...
  2073. 
  2074. ** R
  2075. 
  2076. ** inst
  2077. 
  2078. ** preparing package for lazy loading
  2079. 
  2080. ** help
  2081. 
  2082. *** installing help indices
  2083. 
  2084. ** building package indices
  2085. 
  2086. ** testing if installed package can be loaded
  2087. 
  2088. Bioconductor version 3.1 (BiocInstaller 1.18.4), ?biocLite for help
  2089. * DONE (BiocInstaller)
  2090. 
  2091. The downloaded source packages are in
  2092. ‘/tmp/RtmppcQqr5/downloaded_packages’
  2093. Bioconductor version 3.1 (BiocInstaller 1.18.4), ?biocLite for help
  2094. 
  2095. BioC_mirror: http://bioconductor.org
  2096. 
  2097. Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.2.
  2098. 
  2099. Installing package(s) ‘mzR’
  2100. 
  2101. also installing the dependencies ‘Rcpp’, ‘Biobase’, ‘BiocGenerics’, ‘ProtGenerics’, ‘zlibbioc’
  2102.  
  2103. 
  2104. trying URL 'http://cran.us.r-project.org/src/contrib/Rcpp_0.12.1.tar.gz'
  2105. 
  2106. Content type 'application/x-gzip'
  2107.  length 2366386 bytes (2.3 MB)
  2108. 
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  2159. downloaded 2.3 MB
  2160.  
  2161. 
  2162. trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/Biobase_2.28.0.tar.gz'
  2163. 
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  2217. downloaded 1.6 MB
  2218.  
  2219. 
  2220. trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/BiocGenerics_0.14.0.tar.gz'
  2221. 
  2222. Content type 'application/x-gzip' length 36236 bytes (35 KB)
  2223. ===
  2224. ==============
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  2244. 
  2245. downloaded 35 KB
  2246.  
  2247. 
  2248. trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/ProtGenerics_1.0.0.tar.gz'
  2249. 
  2250. Content type 'application/x-gzip' length 3135 bytes
  2251. ====
  2252. ==========================================
  2253. ====
  2254. downloaded 3135 bytes
  2255.  
  2256. 
  2257. trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/zlibbioc_1.14.0.tar.gz'
  2258. 
  2259. Content type 'application/x-gzip' length 257607 bytes (251 KB)
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  2285. downloaded 251 KB
  2286.  
  2287. 
  2288. trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/mzR_2.2.2.tar.gz'
  2289. 
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  2343. downloaded 14.0 MB
  2344.  
  2345. 
  2346. * installing *source* package ‘Rcpp’ ...
  2347. 
  2348. ** package ‘Rcpp’ successfully unpacked and MD5 sums checked
  2349. 
  2350. ** libs
  2351. 
  2352. 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
  2353. 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
  2354. 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
  2355. 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
  2356. 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
  2357. 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
  2358. 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
  2359. installing to /usr/local/lib/R/site-library/Rcpp/libs
  2360. 
  2361. ** R
  2362. 
  2363. ** inst
  2364. 
  2365. ** preparing package for lazy loading
  2366. 
  2367. ** help
  2368. 
  2369. *** installing help indices
  2370. 
  2371. ** building package indices
  2372. 
  2373. ** installing vignettes
  2374. 
  2375. ** testing if installed package can be loaded
  2376. 
  2377. * DONE (Rcpp)
  2378. 
  2379. * installing *source* package ‘BiocGenerics’ ...
  2380. 
  2381. ** R
  2382. 
  2383. ** inst
  2384. 
  2385. ** preparing package for lazy loading
  2386. 
  2387. Creating a new generic function for ‘append’ in package ‘BiocGenerics’
  2388. 
  2389. Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’
  2390. 
  2391. Creating a new generic function for ‘as.vector’ in package ‘BiocGenerics’
  2392. 
  2393. Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’
  2394. 
  2395. Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’
  2396. 
  2397. Creating a new generic function for ‘do.call’ in package ‘BiocGenerics’
  2398. 
  2399. Creating a new generic function for ‘duplicated’ in package ‘BiocGenerics’
  2400. 
  2401. Creating a new generic function for ‘anyDuplicated’ in package ‘BiocGenerics’
  2402. 
  2403. Creating a new generic function for ‘eval’ in package ‘BiocGenerics’
  2404. 
  2405. Creating a new generic function for ‘pmax’ in package ‘BiocGenerics’
  2406. 
  2407. Creating a new generic function for ‘pmin’ in package ‘BiocGenerics’
  2408. 
  2409. Creating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’
  2410. 
  2411. Creating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’
  2412. 
  2413. Creating a new generic function for ‘Reduce’ in package ‘BiocGenerics’
  2414. 
  2415. Creating a new generic function for ‘Filter’ in package ‘BiocGenerics’
  2416. 
  2417. Creating a new generic function for ‘Find’ in package ‘BiocGenerics’
  2418. 
  2419. Creating a new generic function for ‘Map’ in package ‘BiocGenerics’
  2420. 
  2421. Creating a new generic function for ‘Position’ in package ‘BiocGenerics’
  2422. 
  2423. Creating a new generic function for ‘get’ in package ‘BiocGenerics’
  2424. 
  2425. Creating a new generic function for ‘mget’ in package ‘BiocGenerics’
  2426. 
  2427. Creating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’
  2428. 
  2429. Creating a new generic function for ‘lapply’ in package ‘BiocGenerics’
  2430. 
  2431. Creating a new generic function for ‘sapply’ in package ‘BiocGenerics’
  2432. 
  2433. Creating a new generic function for ‘mapply’ in package ‘BiocGenerics’
  2434. 
  2435. Creating a new generic function for ‘match’ in package ‘BiocGenerics’
  2436. 
  2437. Creating a new generic function for ‘order’ in package ‘BiocGenerics’
  2438. 
  2439. Creating a new generic function for ‘paste’ in package ‘BiocGenerics’
  2440. 
  2441. Creating a new generic function for ‘rank’ in package ‘BiocGenerics’
  2442. 
  2443. Creating a new generic function for ‘rep.int’ in package ‘BiocGenerics’
  2444. 
  2445. Creating a new generic function for ‘rownames’ in package ‘BiocGenerics’
  2446. 
  2447. Creating a new generic function for ‘colnames’ in package ‘BiocGenerics’
  2448. 
  2449. Creating a new generic function for ‘union’ in package ‘BiocGenerics’
  2450. 
  2451. Creating a new generic function for ‘intersect’ in package ‘BiocGenerics’
  2452. 
  2453. Creating a new generic function for ‘setdiff’ in package ‘BiocGenerics’
  2454. 
  2455. Creating a new generic function for ‘sort’ in package ‘BiocGenerics’
  2456. 
  2457. Creating a new generic function for ‘table’ in package ‘BiocGenerics’
  2458. 
  2459. Creating a new generic function for ‘tapply’ in package ‘BiocGenerics’
  2460. 
  2461. Creating a new generic function for ‘unique’ in package ‘BiocGenerics’
  2462. 
  2463. Creating a new generic function for ‘unlist’ in package ‘BiocGenerics’
  2464. 
  2465. Creating a new generic function for ‘unsplit’ in package ‘BiocGenerics’
  2466. 
  2467. Creating a new generic function for ‘xtabs’ in package ‘BiocGenerics’
  2468. 
  2469. Creating a new generic function for ‘clusterCall’ in package ‘BiocGenerics’
  2470. 
  2471. Creating a new generic function for ‘clusterApply’ in package ‘BiocGenerics’
  2472. 
  2473. Creating a new generic function for ‘clusterApplyLB’ in package ‘BiocGenerics’
  2474. 
  2475. Creating a new generic function for ‘clusterEvalQ’ in package ‘BiocGenerics’
  2476. 
  2477. Creating a new generic function for ‘clusterExport’ in package ‘BiocGenerics’
  2478. 
  2479. Creating a new generic function for ‘clusterMap’ in package ‘BiocGenerics’
  2480. 
  2481. Creating a new generic function for ‘parLapply’ in package ‘BiocGenerics’
  2482. 
  2483. Creating a new generic function for ‘parSapply’ in package ‘BiocGenerics’
  2484. 
  2485. Creating a new generic function for ‘parApply’ in package ‘BiocGenerics’
  2486. 
  2487. Creating a new generic function for ‘parRapply’ in package ‘BiocGenerics’
  2488. 
  2489. Creating a new generic function for ‘parCapply’ in package ‘BiocGenerics’
  2490. 
  2491. Creating a new generic function for ‘parLapplyLB’ in package ‘BiocGenerics’
  2492. 
  2493. Creating a new generic function for ‘parSapplyLB’ in package ‘BiocGenerics’
  2494. 
  2495. ** help
  2496. 
  2497. *** installing help indices
  2498. 
  2499. ** building package indices
  2500. 
  2501. ** testing if installed package can be loaded
  2502. 
  2503. * DONE (BiocGenerics)
  2504. 
  2505. * installing *source* package ‘zlibbioc’ ...
  2506. 
  2507. configure: creating ./config.status
  2508. config.status: creating src/Makevars
  2509. ** libs
  2510. 
  2511. mkdir -p "/usr/local/lib/R/site-library/zlibbioc/include"
  2512. 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
  2513. 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
  2514. installing to /usr/local/lib/R/site-library/zlibbioc/libs
  2515. 
  2516. ** R
  2517. 
  2518. ** inst
  2519. 
  2520. ** preparing package for lazy loading
  2521. 
  2522. ** help
  2523. 
  2524. *** installing help indices
  2525. 
  2526. ** building package indices
  2527. 
  2528. ** installing vignettes
  2529. 
  2530. ** testing if installed package can be loaded
  2531. 
  2532. * DONE (zlibbioc)
  2533. 
  2534. * installing *source* package ‘Biobase’ ...
  2535. 
  2536. ** libs
  2537. 
  2538. 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
  2539. 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
  2540. 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
  2541. 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
  2542. 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
  2543. 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
  2544. 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
  2545. installing to /usr/local/lib/R/site-library/Biobase/libs
  2546. 
  2547. ** R
  2548. 
  2549. ** data
  2550. 
  2551. ** inst
  2552. 
  2553. ** preparing package for lazy loading
  2554. 
  2555. ** help
  2556. 
  2557. *** installing help indices
  2558. 
  2559. ** building package indices
  2560. 
  2561. ** installing vignettes
  2562. 
  2563. ** testing if installed package can be loaded
  2564. 
  2565. * DONE (Biobase)
  2566. 
  2567. * installing *source* package ‘ProtGenerics’ ...
  2568. 
  2569. ** R
  2570. 
  2571. ** preparing package for lazy loading
  2572. 
  2573. ** help
  2574. 
  2575. *** installing help indices
  2576. 
  2577. ** building package indices
  2578. 
  2579. ** testing if installed package can be loaded
  2580. 
  2581. * DONE (ProtGenerics)
  2582. 
  2583. * installing *source* package ‘mzR’ ...
  2584. 
  2585. ** libs
  2586. 
  2587. rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/thread/src/pthread/once.o ./boost/thread/src/pthread/thread.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/utf8_codecvt_facet.o ./pwiz/data/msdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/RAMPAdapter.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/Version.o ./pwiz/data/identdata/References.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./random_access_gzFile.o rampR.o R_init_mzR.o
  2588. find . -name \*~ -exec rm {} \; ## from cleanup
  2589. find . -name \*.o -exec rm {} \; ## from cleanup
  2590. find . -name "#*#" -exec rm {} \; ## from cleanup
  2591. 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
  2592. 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
  2593. 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
  2594. 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
  2595. 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
  2596. 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
  2597. 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
  2598. In file included from ./boost/format/alt_sstream.hpp:20:0,
  2599. from ./boost/format/internals.hpp:23,
  2600. from ./boost/format.hpp:38,
  2601. from ./pwiz/utility/misc/String.hpp:30,
  2602. from pwiz/utility/misc/Std.hpp:31,
  2603. from RcppPwiz.h:19,
  2604. from RcppPwiz.cpp:1:
  2605. ./boost/utility/base_from_member.hpp:100:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2606. template<typename ...T>
  2607. ^
  2608. 
  2609. ./boost/utility/base_from_member.hpp:105:43: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2610. template<typename T, typename U, typename ...U2>
  2611. ^
  2612. 
  2613. 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
  2614. In file included from ./boost/format/alt_sstream.hpp:20:0,
  2615. from ./boost/format/internals.hpp:23,
  2616. from ./boost/format.hpp:38,
  2617. from ./pwiz/utility/misc/String.hpp:30,
  2618. from pwiz/utility/misc/Std.hpp:31,
  2619. from RcppPwiz.h:19,
  2620. from RcppPwizModule.cpp:2:
  2621. ./boost/utility/base_from_member.hpp:100:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2622. template<typename ...T>
  2623. ^
  2624. 
  2625. ./boost/utility/base_from_member.hpp:105:43: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2626. template<typename T, typename U, typename ...U2>
  2627. ^
  2628. 
  2629. 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
  2630. In file included from ./boost/format/alt_sstream.hpp:20:0,
  2631. from ./boost/format/internals.hpp:23,
  2632. from ./boost/format.hpp:38,
  2633. from ./pwiz/utility/misc/String.hpp:30,
  2634. from pwiz/utility/misc/Std.hpp:31,
  2635. from RcppIdent.h:14,
  2636. from RcppIdent.cpp:1:
  2637. ./boost/utility/base_from_member.hpp:100:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2638. template<typename ...T>
  2639. ^
  2640. 
  2641. ./boost/utility/base_from_member.hpp:105:43: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2642. template<typename T, typename U, typename ...U2>
  2643. ^
  2644. 
  2645. 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
  2646. In file included from ./boost/format/alt_sstream.hpp:20:0,
  2647. from ./boost/format/internals.hpp:23,
  2648. from ./boost/format.hpp:38,
  2649. from ./pwiz/utility/misc/String.hpp:30,
  2650. from pwiz/utility/misc/Std.hpp:31,
  2651. from RcppIdent.h:14,
  2652. from RcppIdentModule.cpp:2:
  2653. ./boost/utility/base_from_member.hpp:100:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2654. template<typename ...T>
  2655. ^
  2656. 
  2657. ./boost/utility/base_from_member.hpp:105:43: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2658. template<typename T, typename U, typename ...U2>
  2659. ^
  2660. 
  2661. 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
  2662. 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
  2663. 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
  2664. 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
  2665. 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
  2666. 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
  2667. 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
  2668. 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
  2669. 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
  2670. 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
  2671. 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
  2672. 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
  2673. 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
  2674. 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
  2675. 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
  2676. 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
  2677. 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
  2678. 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
  2679. 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
  2680. 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
  2681. 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
  2682. In file included from ./boost/thread/pthread/once_atomic.hpp:17:0,
  2683. from ./boost/thread/once.hpp:20,
  2684. from boost/thread/src/pthread/./once_atomic.cpp:9,
  2685. from boost/thread/src/pthread/once.cpp:8:
  2686. ./boost/thread/detail/invoke.hpp:242:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2687. template <class Ret, class A, class A0, class ...Args>
  2688. ^
  2689. 
  2690. ./boost/thread/detail/invoke.hpp:249:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2691. invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2692. ^
  2693. ./boost/thread/detail/invoke.hpp:249:91: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2694. invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2695. ^
  2696. 
  2697. ./boost/thread/detail/invoke.hpp:254:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2698. template <class Ret, class A, class A0, class ...Args>
  2699. ^
  2700. ./boost/thread/detail/invoke.hpp:261:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2701. invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2702. ^
  2703. ./boost/thread/detail/invoke.hpp:261:97: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2704. invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2705. ^
  2706. 
  2707. ./boost/thread/detail/invoke.hpp:266:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2708. template <class Ret, class A, class A0, class ...Args>
  2709. ^
  2710. 
  2711. ./boost/thread/detail/invoke.hpp:273:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2712. invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2713. ^
  2714. 
  2715. ./boost/thread/detail/invoke.hpp:273:100: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2716. invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2717. ^
  2718. 
  2719. ./boost/thread/detail/invoke.hpp:278:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2720. template <class Ret, class A, class A0, class ...Args>
  2721. ^
  2722. 
  2723. ./boost/thread/detail/invoke.hpp:285:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2724. invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2725. ^
  2726. 
  2727. ./boost/thread/detail/invoke.hpp:285:106: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2728. invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2729. ^
  2730. 
  2731. ./boost/thread/detail/invoke.hpp:293:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2732. template <class Ret, class A, class A0, class ...Args>
  2733. ^
  2734. 
  2735. ./boost/thread/detail/invoke.hpp:300:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2736. invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2737. ^
  2738. 
  2739. ./boost/thread/detail/invoke.hpp:300:91: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2740. invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2741. ^
  2742. 
  2743. ./boost/thread/detail/invoke.hpp:305:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2744. template <class Ret, class A, class A0, class ...Args>
  2745. ^
  2746. 
  2747. ./boost/thread/detail/invoke.hpp:312:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2748. invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2749. ^
  2750. 
  2751. ./boost/thread/detail/invoke.hpp:312:97: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2752. invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2753. ^
  2754. 
  2755. ./boost/thread/detail/invoke.hpp:317:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2756. template <class Ret, class A, class A0, class ...Args>
  2757. ^
  2758. 
  2759. ./boost/thread/detail/invoke.hpp:324:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2760. invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2761. ^
  2762. 
  2763. ./boost/thread/detail/invoke.hpp:324:100: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2764. invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2765. ^
  2766. ./boost/thread/detail/invoke.hpp:329:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2767. template <class Ret, class A, class A0, class ...Args>
  2768. ^
  2769. ./boost/thread/detail/invoke.hpp:336:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2770. invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2771. ^
  2772. ./boost/thread/detail/invoke.hpp:336:106: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2773. invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2774. ^
  2775. 
  2776. ./boost/thread/detail/invoke.hpp:398:42: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2777. template <class Ret, class Fp, class ...Args>
  2778. ^
  2779. ./boost/thread/detail/invoke.hpp:405:68: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2780. invoke(BOOST_THREAD_RV_REF(Fp) f, BOOST_THREAD_RV_REF(Args) ...args)
  2781. ^
  2782. ./boost/thread/detail/invoke.hpp:409:32: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2783. template <class Ret, class ...Args>
  2784. ^
  2785. ./boost/thread/detail/invoke.hpp:411:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2786. invoke(Ret(*f)(Args... ), BOOST_THREAD_RV_REF(Args) ...args)
  2787. ^
  2788. ./boost/thread/detail/invoke.hpp:411:60: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2789. invoke(Ret(*f)(Args... ), BOOST_THREAD_RV_REF(Args) ...args)
  2790. ^
  2791. 
  2792. In file included from ./boost/thread/once.hpp:20:0,
  2793. from boost/thread/src/pthread/./once_atomic.cpp:9,
  2794. from boost/thread/src/pthread/once.cpp:8:
  2795. ./boost/thread/pthread/once_atomic.hpp:120:37: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2796. template<typename Function, class ...ArgTypes>
  2797. ^
  2798. 
  2799. ./boost/thread/pthread/once_atomic.hpp:121:108: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2800. inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args)
  2801. ^
  2802. 
  2803. 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
  2804. In file included from ./boost/chrono/duration.hpp:42:0,
  2805. from ./boost/chrono/time_point.hpp:33,
  2806. from ./boost/thread/lock_types.hpp:22,
  2807. from ./boost/thread/pthread/thread_data.hpp:12,
  2808. from ./boost/thread/thread_only.hpp:17,
  2809. from boost/thread/src/pthread/thread.cpp:11:
  2810. ./boost/type_traits/common_type.hpp:69:22: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2811. template<typename... T>
  2812. ^
  2813. 
  2814. ./boost/type_traits/common_type.hpp:149:46: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2815. template<typename T, typename U, typename... V>
  2816. ^
  2817. 
  2818. In file included from ./boost/thread/detail/thread.hpp:21:0,
  2819. from ./boost/thread/thread_only.hpp:22,
  2820. from boost/thread/src/pthread/thread.cpp:11:
  2821. ./boost/thread/detail/make_tuple_indices.hpp:35:26: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2822. template <std::size_t...> struct tuple_indices
  2823. ^
  2824. 
  2825. ./boost/thread/detail/make_tuple_indices.hpp:41:46: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2826. template <std::size_t Sp, std::size_t ...Indices, std::size_t Ep>
  2827. ^
  2828. ./boost/thread/detail/make_tuple_indices.hpp:47:46: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2829. template <std::size_t Ep, std::size_t ...Indices>
  2830. ^
  2831. 
  2832. In file included from ./boost/thread/detail/thread.hpp:22:0,
  2833. from ./boost/thread/thread_only.hpp:22,
  2834. from boost/thread/src/pthread/thread.cpp:11:
  2835. ./boost/thread/detail/invoke.hpp:242:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2836. template <class Ret, class A, class A0, class ...Args>
  2837. ^
  2838. 
  2839. ./boost/thread/detail/invoke.hpp:249:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2840. invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2841. ^
  2842. ./boost/thread/detail/invoke.hpp:249:91: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2843. invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2844. ^
  2845. 
  2846. ./boost/thread/detail/invoke.hpp:254:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2847. template <class Ret, class A, class A0, class ...Args>
  2848. ^
  2849. ./boost/thread/detail/invoke.hpp:261:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2850. invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2851. ^
  2852. ./boost/thread/detail/invoke.hpp:261:97: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2853. invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2854. ^
  2855. ./boost/thread/detail/invoke.hpp:266:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2856. template <class Ret, class A, class A0, class ...Args>
  2857. ^
  2858. ./boost/thread/detail/invoke.hpp:273:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2859. invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2860. ^
  2861. ./boost/thread/detail/invoke.hpp:273:100: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2862. invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2863. ^
  2864. 
  2865. ./boost/thread/detail/invoke.hpp:278:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2866. template <class Ret, class A, class A0, class ...Args>
  2867. ^
  2868. ./boost/thread/detail/invoke.hpp:285:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2869. invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2870. ^
  2871. ./boost/thread/detail/invoke.hpp:285:106: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2872. invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2873. ^
  2874. ./boost/thread/detail/invoke.hpp:293:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2875. template <class Ret, class A, class A0, class ...Args>
  2876. ^
  2877. ./boost/thread/detail/invoke.hpp:300:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2878. invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2879. ^
  2880. ./boost/thread/detail/invoke.hpp:300:91: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2881. invoke(Ret (A::*f)(Args...), BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2882. ^
  2883. 
  2884. ./boost/thread/detail/invoke.hpp:305:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2885. template <class Ret, class A, class A0, class ...Args>
  2886. ^
  2887. ./boost/thread/detail/invoke.hpp:312:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2888. invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2889. ^
  2890. ./boost/thread/detail/invoke.hpp:312:97: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2891. invoke(Ret (A::*f)(Args...) const, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2892. ^
  2893. ./boost/thread/detail/invoke.hpp:317:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2894. template <class Ret, class A, class A0, class ...Args>
  2895. ^
  2896. ./boost/thread/detail/invoke.hpp:324:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2897. invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2898. ^
  2899. ./boost/thread/detail/invoke.hpp:324:100: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2900. invoke(Ret (A::*f)(Args...) volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2901. ^
  2902. 
  2903. ./boost/thread/detail/invoke.hpp:329:51: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2904. template <class Ret, class A, class A0, class ...Args>
  2905. ^
  2906. ./boost/thread/detail/invoke.hpp:336:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2907. invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2908. ^
  2909. ./boost/thread/detail/invoke.hpp:336:106: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2910. invoke(Ret (A::*f)(Args...) const volatile, BOOST_THREAD_RV_REF(A0) a0, BOOST_THREAD_RV_REF(Args) ...args)
  2911. ^
  2912. ./boost/thread/detail/invoke.hpp:398:42: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2913. template <class Ret, class Fp, class ...Args>
  2914. ^
  2915. ./boost/thread/detail/invoke.hpp:405:68: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2916. invoke(BOOST_THREAD_RV_REF(Fp) f, BOOST_THREAD_RV_REF(Args) ...args)
  2917. ^
  2918. ./boost/thread/detail/invoke.hpp:409:32: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2919. template <class Ret, class ...Args>
  2920. ^
  2921. ./boost/thread/detail/invoke.hpp:411:24: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2922. invoke(Ret(*f)(Args... ), BOOST_THREAD_RV_REF(Args) ...args)
  2923. ^
  2924. ./boost/thread/detail/invoke.hpp:411:60: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2925. invoke(Ret(*f)(Args... ), BOOST_THREAD_RV_REF(Args) ...args)
  2926. ^
  2927. 
  2928. In file included from ./boost/thread/once.hpp:20:0,
  2929. from boost/thread/src/pthread/thread.cpp:17:
  2930. ./boost/thread/pthread/once_atomic.hpp:120:37: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2931. template<typename Function, class ...ArgTypes>
  2932. ^
  2933. 
  2934. ./boost/thread/pthread/once_atomic.hpp:121:108: warning: variadic templates only available with -std=c++11 or -std=gnu++11
  2935. inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args)
  2936. ^
  2937. 
  2938. boost/thread/src/pthread/thread.cpp: In function ‘boost::detail::thread_data_base* boost::detail::get_current_thread_data()’:
  2939. boost/thread/src/pthread/thread.cpp:140:88: error: no matching function for call to ‘call_once(boost::once_flag&, void (&)())’
  2940. boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key);
  2941. ^
  2942. In file included from ./boost/thread/once.hpp:20:0,
  2943. from boost/thread/src/pthread/thread.cpp:17:
  2944. ./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>...)
  2945. inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args)
  2946. ^
  2947. 
  2948. ./boost/thread/pthread/once_atomic.hpp:121:15: note: template argument deduction/substitution failed:
  2949. boost/thread/src/pthread/thread.cpp:140:88: note: mismatched types ‘boost::detail::thread_move_t<T>’ and ‘void (*)()’
  2950. boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key);
  2951. ^
  2952. In file included from boost/thread/src/pthread/thread.cpp:17:0:
  2953. ./boost/thread/once.hpp:35:13: note: candidate: template<class Function> void boost::call_once(Function, boost::once_flag&)
  2954. inline void call_once(Function func,once_flag& flag)
  2955. ^
  2956. ./boost/thread/once.hpp:35:13: note: template argument deduction/substitution failed:
  2957. 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&’
  2958. boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key);
  2959. ^
  2960. 
  2961. boost/thread/src/pthread/thread.cpp: In function ‘void boost::detail::set_current_thread_data(boost::detail::thread_data_base*)’:
  2962. boost/thread/src/pthread/thread.cpp:146:88: error: no matching function for call to ‘call_once(boost::once_flag&, void (&)())’
  2963. boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key);
  2964. ^
  2965. In file included from ./boost/thread/once.hpp:20:0,
  2966. from boost/thread/src/pthread/thread.cpp:17:
  2967. ./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>...)
  2968. inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args)
  2969. ^
  2970. ./boost/thread/pthread/once_atomic.hpp:121:15: note: template argument deduction/substitution failed:
  2971. boost/thread/src/pthread/thread.cpp:146:88: note: mismatched types ‘boost::detail::thread_move_t<T>’ and ‘void (*)()’
  2972. boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key);
  2973. ^
  2974. In file included from boost/thread/src/pthread/thread.cpp:17:0:
  2975. ./boost/thread/once.hpp:35:13: note: candidate: template<class Function> void boost::call_once(Function, boost::once_flag&)
  2976. inline void call_once(Function func,once_flag& flag)
  2977. ^
  2978. ./boost/thread/once.hpp:35:13: note: template argument deduction/substitution failed:
  2979. 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&’
  2980. boost::call_once(current_thread_tls_init_flag,create_current_thread_tls_key);
  2981. ^
  2982. 
  2983. /usr/lib/R/etc/Makeconf:143: recipe for target 'boost/thread/src/pthread/thread.o' failed
  2984. make: *** [boost/thread/src/pthread/thread.o] Error 1
  2985. 
  2986. ERROR: compilation failed for package ‘mzR’
  2987. 
  2988. * removing ‘/usr/local/lib/R/site-library/mzR’
  2989. 
  2990. The downloaded source packages are in
  2991. ‘/tmp/RtmppcQqr5/downloaded_packages’
  2992. Warning message:
  2993. 
  2994. In install.packages(pkgs = doing, lib = lib, ...) :
  2995. 
  2996. installation of package ‘mzR’ had non-zero exit status
  2997. 
  2998. ---> 10aae02c3a0b
  2999. Successfully built 10aae02c3a0b
  3000. 10aae02c3a0b Image successfully pushed
  3001. 34010b913c12 Image successfully pushed
  3002. 47acfcf714e1 Image successfully pushed
  3003. 5cd07b70e123 Image successfully pushed
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