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gfortran errors when building R recipes that are dependent on gcc #1424

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daler opened this issue Oct 3, 2016 · 14 comments
Closed

gfortran errors when building R recipes that are dependent on gcc #1424

daler opened this issue Oct 3, 2016 · 14 comments
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locked [bot] locked due to inactivity

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@daler
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daler commented Oct 3, 2016

When building some R packages, I'm getting errors related to gfortran. This happens on R packages ash, blockmodeling, robustbase, fields, spam, cghflasso, and others.

Here's how to reproduce:

docker run -it condaforge/linux-anvil /bin/bash -c \
"conda skeleton cran r-ash; conda build r-ash -c r"

Here's the full log:

Tip: install CacheControl (conda package) to cache the CRAN metadata
Fetching metadata from http://cran.r-project.org/
INFO:requests.packages.urllib3.connectionpool:Starting new HTTP connection (1): cran.r-project.org
Tip: install CacheControl (conda package) to cache the CRAN metadata
INFO:requests.packages.urllib3.connectionpool:Starting new HTTP connection (1): cran.r-project.org
Writing recipe for ash
Done
INFO:/opt/conda/lib/python3.5/site-packages/conda_build/config.py:--keep-old-work flag not specified.  Removing source and build files.

BUILD START: r-ash-1.0_15-r3.3.1_0
    (actual version deferred until further download or env creation)
updating index in: /opt/conda/pkgs
updating index in: /opt/conda/conda-bld/linux-64
updating index in: /opt/conda/conda-bld/noarch
Using Anaconda API: https://api.anaconda.org

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    bzip2-1.0.6                |                3          83 KB  defaults
    ca-certificates-2016.8.31  |                0         163 KB  conda-forge
    gmp-5.1.2                  |                2         594 KB  r
    gsl-1.16                   |                1         6.8 MB  r
    icu-54.1                   |                0        11.3 MB  defaults
    jpeg-9b                    |                0         918 KB  conda-forge
    libffi-3.2.1               |                2          47 KB  conda-forge
    libgcc-4.8.5               |                1         922 KB  r
    pcre-8.38                  |                1         631 KB  conda-forge
    pixman-0.32.6              |                0         3.7 MB  conda-forge
    tk-8.6.6                   |                3         3.1 MB  conda-forge
    glib-2.43.0                |                2         7.4 MB  r
    isl-0.12.2                 |                0         1.1 MB  r
    libpng-1.6.24              |                0         311 KB  conda-forge
    libtiff-4.0.6              |                6         507 KB  conda-forge
    libxml2-2.9.2              |                0         4.2 MB  defaults
    mpfr-3.1.2                 |                0         407 KB  r
    ncurses-5.9                |                8         836 KB  r
    cloog-0.18.0               |                0         617 KB  r
    freetype-2.5.5             |                1         2.5 MB  defaults
    mpc-1.0.1                  |                0          61 KB  r
    readline-6.3               |                1         787 KB  conda-forge
    fontconfig-2.11.1          |                6         405 KB  defaults
    gcc-4.8.5                  |                6        64.4 MB  defaults
    cairo-1.12.18              |                6         594 KB  defaults
    harfbuzz-0.9.35            |                6         1.1 MB  r
    pango-1.36.8               |                3         796 KB  r
    r-base-3.3.1               |                3        21.7 MB  r
    ------------------------------------------------------------
                                           Total:       135.9 MB

The following NEW packages will be INSTALLED:

    bzip2:           1.0.6-3     defaults   
    ca-certificates: 2016.8.31-0 conda-forge
    cairo:           1.12.18-6   defaults   
    cloog:           0.18.0-0    r          
    curl:            7.49.1-1    conda-forge
    fontconfig:      2.11.1-6    defaults   
    freetype:        2.5.5-1     defaults   
    gcc:             4.8.5-6     defaults   
    glib:            2.43.0-2    r          
    gmp:             5.1.2-2     r          
    gsl:             1.16-1      r          
    harfbuzz:        0.9.35-6    r          
    icu:             54.1-0      defaults   
    isl:             0.12.2-0    r          
    jpeg:            9b-0        conda-forge
    libffi:          3.2.1-2     conda-forge
    libgcc:          4.8.5-1     r          
    libpng:          1.6.24-0    conda-forge
    libtiff:         4.0.6-6     conda-forge
    libxml2:         2.9.2-0     defaults   
    mpc:             1.0.1-0     r          
    mpfr:            3.1.2-0     r          
    ncurses:         5.9-8       r          
    openssl:         1.0.2h-2    conda-forge
    pango:           1.36.8-3    r          
    pcre:            8.38-1      conda-forge
    pixman:          0.32.6-0    conda-forge
    r-base:          3.3.1-3     r          
    readline:        6.3-1       conda-forge
    tk:              8.6.6-3     conda-forge
    xz:              5.2.2-0     conda-forge
    zlib:            1.2.8-3     conda-forge

WARNING:/opt/conda/lib/python3.5/site-packages/conda_build/build.py:Build prefix failed with prefix length 255
WARNING:/opt/conda/lib/python3.5/site-packages/conda_build/build.py:Error was: 
WARNING:/opt/conda/lib/python3.5/site-packages/conda_build/build.py:ERROR: placeholder '/opt/conda/envs/_build_placehold_placehold_placehold_placehold_placehold_placeho' too short in: conda-forge::tk-8.6.6-3

WARNING:/opt/conda/lib/python3.5/site-packages/conda_build/build.py:One or more of your package dependencies needs to be rebuilt with a longer prefix length.
WARNING:/opt/conda/lib/python3.5/site-packages/conda_build/build.py:Falling back to legacy prefix length of 80 characters.
WARNING:/opt/conda/lib/python3.5/site-packages/conda_build/build.py:Your package will not install into prefixes > 80 characters.
updating index in: /opt/conda/pkgs
updating: tk-8.6.6-3.tar.bz2
updating: libtiff-4.0.6-6.tar.bz2
updating: mpc-1.0.1-0.tar.bz2
updating: cloog-0.18.0-0.tar.bz2
updating: ca-certificates-2016.8.31-0.tar.bz2
updating: libpng-1.6.24-0.tar.bz2
updating: libxml2-2.9.2-0.tar.bz2
updating: readline-6.3-1.tar.bz2
updating: cairo-1.12.18-6.tar.bz2
updating: r-base-3.3.1-3.tar.bz2
updating: glib-2.43.0-2.tar.bz2
updating: icu-54.1-0.tar.bz2
updating: freetype-2.5.5-1.tar.bz2
updating: bzip2-1.0.6-3.tar.bz2
updating: gsl-1.16-1.tar.bz2
updating: libgcc-4.8.5-1.tar.bz2
updating: jpeg-9b-0.tar.bz2
updating: pcre-8.38-1.tar.bz2
updating: gcc-4.8.5-6.tar.bz2
updating: fontconfig-2.11.1-6.tar.bz2
updating: mpfr-3.1.2-0.tar.bz2
updating: gmp-5.1.2-2.tar.bz2
updating: isl-0.12.2-0.tar.bz2
updating: harfbuzz-0.9.35-6.tar.bz2
updating: pango-1.36.8-3.tar.bz2
updating: ncurses-5.9-8.tar.bz2
updating: libffi-3.2.1-2.tar.bz2
updating: pixman-0.32.6-0.tar.bz2
updating index in: /opt/conda/conda-bld/linux-64
updating index in: /opt/conda/conda-bld/noarch

The following NEW packages will be INSTALLED:

    bzip2:           1.0.6-3     defaults   
    ca-certificates: 2016.8.31-0 conda-forge
    cairo:           1.12.18-6   defaults   
    cloog:           0.18.0-0    r          
    curl:            7.49.1-1    conda-forge
    fontconfig:      2.11.1-6    defaults   
    freetype:        2.5.5-1     defaults   
    gcc:             4.8.5-6     defaults   
    glib:            2.43.0-2    r          
    gmp:             5.1.2-2     r          
    gsl:             1.16-1      r          
    harfbuzz:        0.9.35-6    r          
    icu:             54.1-0      defaults   
    isl:             0.12.2-0    r          
    jpeg:            9b-0        conda-forge
    libffi:          3.2.1-2     conda-forge
    libgcc:          4.8.5-1     r          
    libpng:          1.6.24-0    conda-forge
    libtiff:         4.0.6-6     conda-forge
    libxml2:         2.9.2-0     defaults   
    mpc:             1.0.1-0     r          
    mpfr:            3.1.2-0     r          
    ncurses:         5.9-8       r          
    openssl:         1.0.2h-2    conda-forge
    pango:           1.36.8-3    r          
    pcre:            8.38-1      conda-forge
    pixman:          0.32.6-0    conda-forge
    r-base:          3.3.1-3     r          
    readline:        6.3-1       conda-forge
    tk:              8.6.6-3     conda-forge
    xz:              5.2.2-0     conda-forge
    zlib:            1.2.8-3     conda-forge

/opt/conda/conda-bld/r-ash_1475503163962/_b_env_placehold_placehold_placehold_pl/bin/.gcc-post-link.sh: line 10: lsb_release: command not found

WARNING: conda-build appears to be out of date. You have version 2.0.1 but the
latest version is 2.0.2. Run

conda update -n root conda-build

to get the latest version.


WARNING: conda-build appears to be out of date. You have version 2.0.1 but the
latest version is 2.0.2. Run

conda update -n root conda-build

to get the latest version.

Source cache directory is: /opt/conda/conda-bld/src_cache
Downloading source to cache: ash_1.0-15.tar.gz
Downloading http://cran.r-project.org/src/contrib/ash_1.0-15.tar.gz
Success
Extracting download
BUILD START (revised): r-ash-1.0_15-r3.3.1_0
Package: r-ash-1.0_15-r3.3.1_0
source tree in: /opt/conda/conda-bld/r-ash_1475503163962/work/ash
+ source /opt/conda/bin/activate /opt/conda/conda-bld/r-ash_1475503163962/_b_env_placehold_placehold_placehold_pl
+ mv DESCRIPTION DESCRIPTION.old
+ grep -v '^Priority: ' DESCRIPTION.old
+ /opt/conda/conda-bld/r-ash_1475503163962/_b_env_placehold_placehold_placehold_pl/bin/R CMD INSTALL --build .
* installing to library ‘/opt/conda/conda-bld/r-ash_1475503163962/_b_env_placehold_placehold_placehold_pl/lib/R/library’
* installing *source* package ‘ash’ ...
** package ‘ash’ successfully unpacked and MD5 sums checked
** libs
gfortran   -fpic  -I/opt/conda/conda-bld/r-ash_1475503163962/_b_env_placehold_placehold_placehold_pl/include -L/opt/conda/conda-bld/r-ash_1475503163962/_b_env_placehold_placehold_placehold_pl/lib  -c ash.f -o ash.o
f951: internal compiler error: Illegal instruction
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://gcc.gnu.org/bugs.html> for instructions.
make: *** [ash.o] Error 1
ERROR: compilation failed for package ‘ash’
* removing ‘/opt/conda/conda-bld/r-ash_1475503163962/_b_env_placehold_placehold_placehold_pl/lib/R/library/ash’
Command failed: /bin/bash -x -e /opt/conda/conda-bld/r-ash_1475503163962/work/ash/conda_build.sh

The information I've found makes me think it's an issue with how it was compiled, e.g.,
@daler daler mentioned this issue Oct 3, 2016
Closed
@bgruening
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Thanks @daler for bringing this up. I have also seen this a few times.

@mingwandroid
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Contributor

I cannot reproduce this problem:

(/root/r_3_3_1-x64-3.5) [root@localhost r-ash]# conda-build . -c r
BUILD START: r-ash-1.0_15-r3.3.1_0
    (actual version deferred until further download or env creation)
updating index in: /root/r_3_3_1-x64-3.5/conda-bld/linux-64
updating index in: /root/r_3_3_1-x64-3.5/conda-bld/noarch

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    gmp-5.1.2                  |                2         594 KB  r
    isl-0.12.2                 |                0         1.1 MB  r
    mpfr-3.1.2                 |                0         407 KB  r
    cloog-0.18.0               |                0         617 KB  r
    mpc-1.0.1                  |                0          61 KB  r
    gcc-4.8.5                  |                6        64.4 MB
    ------------------------------------------------------------
                                           Total:        67.1 MB

The following NEW packages will be INSTALLED:

    bzip2:      1.0.6-3    
    cairo:      1.12.18-6  
    cloog:      0.18.0-0  r
    curl:       7.49.0-1   
    fontconfig: 2.11.1-6   
    freetype:   2.5.5-1    
    gcc:        4.8.5-6    
    glib:       2.43.0-2  r
    gmp:        5.1.2-2   r
    gsl:        1.16-1    r
    harfbuzz:   0.9.35-6  r
    icu:        54.1-0     
    isl:        0.12.2-0  r
    jbig:       2.1-0      
    jpeg:       8d-2       
    libffi:     3.2.1-0    
    libgcc:     4.8.5-1   r
    libpng:     1.6.22-0   
    libtiff:    4.0.6-2    
    libxml2:    2.9.2-0    
    mpc:        1.0.1-0   r
    mpfr:       3.1.2-0   r
    ncurses:    5.9-8     r
    openssl:    1.0.2j-0   
    pango:      1.36.8-3  r
    pcre:       8.39-0     
    pixman:     0.32.6-0   
    r-base:     3.3.1-3   r
    readline:   6.2-2      
    tk:         8.5.18-0   
    xz:         5.2.2-0    
    zlib:       1.2.8-3    

updating index in: /root/r_3_3_1-x64-3.5/conda-bld/linux-64
updating index in: /root/r_3_3_1-x64-3.5/conda-bld/noarch

The following NEW packages will be INSTALLED:

    bzip2:      1.0.6-3    
    cairo:      1.12.18-6  
    cloog:      0.18.0-0  r
    curl:       7.49.0-1   
    fontconfig: 2.11.1-6   
    freetype:   2.5.5-1    
    gcc:        4.8.5-6    
    glib:       2.43.0-2  r
    gmp:        5.1.2-2   r
    gsl:        1.16-1    r
    harfbuzz:   0.9.35-6  r
    icu:        54.1-0     
    isl:        0.12.2-0  r
    jbig:       2.1-0      
    jpeg:       8d-2       
    libffi:     3.2.1-0    
    libgcc:     4.8.5-1   r
    libpng:     1.6.22-0   
    libtiff:    4.0.6-2    
    libxml2:    2.9.2-0    
    mpc:        1.0.1-0   r
    mpfr:       3.1.2-0   r
    ncurses:    5.9-8     r
    openssl:    1.0.2j-0   
    pango:      1.36.8-3  r
    pcre:       8.39-0     
    pixman:     0.32.6-0   
    r-base:     3.3.1-3   r
    readline:   6.2-2      
    tk:         8.5.18-0   
    xz:         5.2.2-0    
    zlib:       1.2.8-3    

gcc install OS matches gcc build OS: Skipping post-link portability fixes.

WARNING: conda-build appears to be out of date. You have version 0.0.0 but the
latest version is 2.0.3. Run

conda update -n root conda-build

to get the latest version.


WARNING: conda-build appears to be out of date. You have version 0.0.0 but the
latest version is 2.0.3. Run

conda update -n root conda-build

to get the latest version.

Source cache directory is: /root/r_3_3_1-x64-3.5/conda-bld/src_cache
Downloading source to cache: ash_1.0-15.tar.gz
Downloading http://cran.r-project.org/src/contrib/ash_1.0-15.tar.gz
Success
Extracting download
BUILD START (revised): r-ash-1.0_15-r3.3.1_0
Package: r-ash-1.0_15-r3.3.1_0
source tree in: /root/r_3_3_1-x64-3.5/conda-bld/r-ash_1475530308383/work/ash
+ source /root/r_3_3_1-x64-3.5/bin/activate /root/r_3_3_1-x64-3.5/conda-bld/r-ash_1475530308383/_b_env_placehold_placehold_p
+ mv DESCRIPTION DESCRIPTION.old
+ grep -v '^Priority: ' DESCRIPTION.old
+ /root/r_3_3_1-x64-3.5/conda-bld/r-ash_1475530308383/_b_env_placehold_placehold_p/bin/R CMD INSTALL --build .
* installing to library ‘/root/r_3_3_1-x64-3.5/conda-bld/r-ash_1475530308383/_b_env_placehold_placehold_p/lib/R/library’
* installing *source* package ‘ash’ ...
** package ‘ash’ successfully unpacked and MD5 sums checked
** libs
gfortran   -fpic  -I/root/r_3_3_1-x64-3.5/conda-bld/r-ash_1475530308383/_b_env_placehold_placehold_p/include -L/root/r_3_3_1-x64-3.5/conda-bld/r-ash_1475530308383/_b_env_placehold_placehold_p/lib  -c ash.f -o ash.o
gfortran   -fpic  -I/root/r_3_3_1-x64-3.5/conda-bld/r-ash_1475530308383/_b_env_placehold_placehold_p/include -L/root/r_3_3_1-x64-3.5/conda-bld/r-ash_1475530308383/_b_env_placehold_placehold_p/lib  -c sort.f -o sort.o
gcc -std=gnu99 -shared -L/root/r_3_3_1-x64-3.5/conda-bld/r-ash_1475530308383/_b_env_placehold_placehold_p/lib/R/lib -L/root/r_3_3_1-x64-3.5/conda-bld/r-ash_1475530308383/_b_env_placehold_placehold_p/lib -lgfortran -o ash.so ash.o sort.o -lgfortran -lm -lquadmath -L/root/r_3_3_1-x64-3.5/conda-bld/r-ash_1475530308383/_b_env_placehold_placehold_p/lib/R/lib -lR
installing to /root/r_3_3_1-x64-3.5/conda-bld/r-ash_1475530308383/_b_env_placehold_placehold_p/lib/R/library/ash/libs

Can you try without any conda-forge packages to see if that builds successfully?

@daler
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Contributor Author

daler commented Oct 4, 2016

Still no luck:

docker run -it condaforge/linux-anvil /bin/bash -c "\
conda config --remove channels conda-forge;
conda config --get;
conda skeleton cran r-ash;
conda build r-ash -c r"
--add channels 'defaults'   # lowest priority
--set show_channel_urls True
Tip: install CacheControl (conda package) to cache the CRAN metadata
Fetching metadata from http://cran.r-project.org/
INFO:requests.packages.urllib3.connectionpool:Starting new HTTP connection (1): cran.r-project.org
Tip: install CacheControl (conda package) to cache the CRAN metadata
INFO:requests.packages.urllib3.connectionpool:Starting new HTTP connection (1): cran.r-project.org
Writing recipe for ash
Done
INFO:/opt/conda/lib/python3.5/site-packages/conda_build/config.py:--keep-old-work flag not specified.  Removing source and build files.

BUILD START: r-ash-1.0_15-r3.3.1_0
    (actual version deferred until further download or env creation)
updating index in: /opt/conda/pkgs
updating index in: /opt/conda/conda-bld/linux-64
updating index in: /opt/conda/conda-bld/noarch
Using Anaconda API: https://api.anaconda.org

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    bzip2-1.0.6                |                3          83 KB  defaults
    gmp-5.1.2                  |                2         594 KB  r
    gsl-1.16                   |                1         6.8 MB  r
    icu-54.1                   |                0        11.3 MB  defaults
    jbig-2.1                   |                0          29 KB  defaults
    jpeg-8d                    |                2         806 KB  defaults
    libffi-3.2.1               |                0          36 KB  defaults
    libgcc-4.8.5               |                1         922 KB  r
    openssl-1.0.2j             |                0         3.2 MB  defaults
    pixman-0.32.6              |                0         2.4 MB  defaults
    readline-6.2               |                2         606 KB  defaults
    tk-8.5.18                  |                0         1.9 MB  defaults
    xz-5.2.2                   |                0         644 KB  defaults
    zlib-1.2.8                 |                3         101 KB  defaults
    curl-7.49.0                |                1         543 KB  defaults
    glib-2.43.0                |                2         7.4 MB  r
    isl-0.12.2                 |                0         1.1 MB  r
    libpng-1.6.22              |                0         214 KB  defaults
    libtiff-4.0.6              |                2         1.5 MB  defaults
    libxml2-2.9.2              |                0         4.2 MB  defaults
    mpfr-3.1.2                 |                0         407 KB  r
    ncurses-5.9                |                8         836 KB  r
    pcre-8.39                  |                0         553 KB  defaults
    cloog-0.18.0               |                0         617 KB  r
    freetype-2.5.5             |                1         2.5 MB  defaults
    mpc-1.0.1                  |                0          61 KB  r
    fontconfig-2.11.1          |                6         405 KB  defaults
    gcc-4.8.5                  |                6        64.4 MB  defaults
    cairo-1.12.18              |                6         594 KB  defaults
    harfbuzz-0.9.35            |                6         1.1 MB  r
    pango-1.36.8               |                3         796 KB  r
    r-base-3.3.1               |                3        21.7 MB  r
    ------------------------------------------------------------
                                           Total:       138.2 MB

The following NEW packages will be INSTALLED:

    bzip2:      1.0.6-3   defaults
    cairo:      1.12.18-6 defaults
    cloog:      0.18.0-0  r       
    curl:       7.49.0-1  defaults
    fontconfig: 2.11.1-6  defaults
    freetype:   2.5.5-1   defaults
    gcc:        4.8.5-6   defaults
    glib:       2.43.0-2  r       
    gmp:        5.1.2-2   r       
    gsl:        1.16-1    r       
    harfbuzz:   0.9.35-6  r       
    icu:        54.1-0    defaults
    isl:        0.12.2-0  r       
    jbig:       2.1-0     defaults
    jpeg:       8d-2      defaults
    libffi:     3.2.1-0   defaults
    libgcc:     4.8.5-1   r       
    libpng:     1.6.22-0  defaults
    libtiff:    4.0.6-2   defaults
    libxml2:    2.9.2-0   defaults
    mpc:        1.0.1-0   r       
    mpfr:       3.1.2-0   r       
    ncurses:    5.9-8     r       
    openssl:    1.0.2j-0  defaults
    pango:      1.36.8-3  r       
    pcre:       8.39-0    defaults
    pixman:     0.32.6-0  defaults
    r-base:     3.3.1-3   r       
    readline:   6.2-2     defaults
    tk:         8.5.18-0  defaults
    xz:         5.2.2-0   defaults
    zlib:       1.2.8-3   defaults

WARNING:/opt/conda/lib/python3.5/site-packages/conda_build/build.py:Build prefix failed with prefix length 255
WARNING:/opt/conda/lib/python3.5/site-packages/conda_build/build.py:Error was: 
WARNING:/opt/conda/lib/python3.5/site-packages/conda_build/build.py:ERROR: placeholder '/root/miniconda3/envs/_build_placehold_placehold_placehold_placehold_placehold_p' too short in: r::glib-2.43.0-2

WARNING:/opt/conda/lib/python3.5/site-packages/conda_build/build.py:One or more of your package dependencies needs to be rebuilt with a longer prefix length.
WARNING:/opt/conda/lib/python3.5/site-packages/conda_build/build.py:Falling back to legacy prefix length of 80 characters.
WARNING:/opt/conda/lib/python3.5/site-packages/conda_build/build.py:Your package will not install into prefixes > 80 characters.
updating index in: /opt/conda/pkgs
updating: libxml2-2.9.2-0.tar.bz2
updating: gmp-5.1.2-2.tar.bz2
updating: ncurses-5.9-8.tar.bz2
updating: libgcc-4.8.5-1.tar.bz2
updating: libtiff-4.0.6-2.tar.bz2
updating: cairo-1.12.18-6.tar.bz2
updating: gsl-1.16-1.tar.bz2
updating: mpc-1.0.1-0.tar.bz2
updating: jpeg-8d-2.tar.bz2
updating: readline-6.2-2.tar.bz2
updating: pcre-8.39-0.tar.bz2
updating: glib-2.43.0-2.tar.bz2
updating: jbig-2.1-0.tar.bz2
updating: curl-7.49.0-1.tar.bz2
updating: pango-1.36.8-3.tar.bz2
updating: zlib-1.2.8-3.tar.bz2
updating: freetype-2.5.5-1.tar.bz2
updating: openssl-1.0.2j-0.tar.bz2
updating: mpfr-3.1.2-0.tar.bz2
updating: cloog-0.18.0-0.tar.bz2
updating: libpng-1.6.22-0.tar.bz2
updating: icu-54.1-0.tar.bz2
updating: isl-0.12.2-0.tar.bz2
updating: fontconfig-2.11.1-6.tar.bz2
updating: r-base-3.3.1-3.tar.bz2
updating: gcc-4.8.5-6.tar.bz2
updating: tk-8.5.18-0.tar.bz2
updating: xz-5.2.2-0.tar.bz2
updating: libffi-3.2.1-0.tar.bz2
updating: bzip2-1.0.6-3.tar.bz2
updating: harfbuzz-0.9.35-6.tar.bz2
updating: pixman-0.32.6-0.tar.bz2
updating index in: /opt/conda/conda-bld/linux-64
updating index in: /opt/conda/conda-bld/noarch

The following NEW packages will be INSTALLED:

    bzip2:      1.0.6-3   defaults
    cairo:      1.12.18-6 defaults
    cloog:      0.18.0-0  r       
    curl:       7.49.0-1  defaults
    fontconfig: 2.11.1-6  defaults
    freetype:   2.5.5-1   defaults
    gcc:        4.8.5-6   defaults
    glib:       2.43.0-2  r       
    gmp:        5.1.2-2   r       
    gsl:        1.16-1    r       
    harfbuzz:   0.9.35-6  r       
    icu:        54.1-0    defaults
    isl:        0.12.2-0  r       
    jbig:       2.1-0     defaults
    jpeg:       8d-2      defaults
    libffi:     3.2.1-0   defaults
    libgcc:     4.8.5-1   r       
    libpng:     1.6.22-0  defaults
    libtiff:    4.0.6-2   defaults
    libxml2:    2.9.2-0   defaults
    mpc:        1.0.1-0   r       
    mpfr:       3.1.2-0   r       
    ncurses:    5.9-8     r       
    openssl:    1.0.2j-0  defaults
    pango:      1.36.8-3  r       
    pcre:       8.39-0    defaults
    pixman:     0.32.6-0  defaults
    r-base:     3.3.1-3   r       
    readline:   6.2-2     defaults
    tk:         8.5.18-0  defaults
    xz:         5.2.2-0   defaults
    zlib:       1.2.8-3   defaults

/opt/conda/conda-bld/r-ash_1475589857768/_b_env_placehold_placehold_placehold_pl/bin/.gcc-post-link.sh: line 10: lsb_release: command not found

WARNING: conda-build appears to be out of date. You have version 2.0.1 but the
latest version is 2.0.3. Run

conda update -n root conda-build

to get the latest version.


WARNING: conda-build appears to be out of date. You have version 2.0.1 but the
latest version is 2.0.3. Run

conda update -n root conda-build

to get the latest version.

Source cache directory is: /opt/conda/conda-bld/src_cache
Downloading source to cache: ash_1.0-15.tar.gz
Downloading http://cran.r-project.org/src/contrib/ash_1.0-15.tar.gz
Success
Extracting download
BUILD START (revised): r-ash-1.0_15-r3.3.1_0
Package: r-ash-1.0_15-r3.3.1_0
source tree in: /opt/conda/conda-bld/r-ash_1475589857768/work/ash
+ source /opt/conda/bin/activate /opt/conda/conda-bld/r-ash_1475589857768/_b_env_placehold_placehold_placehold_pl
+ mv DESCRIPTION DESCRIPTION.old
+ grep -v '^Priority: ' DESCRIPTION.old
+ /opt/conda/conda-bld/r-ash_1475589857768/_b_env_placehold_placehold_placehold_pl/bin/R CMD INSTALL --build .
* installing to library ‘/opt/conda/conda-bld/r-ash_1475589857768/_b_env_placehold_placehold_placehold_pl/lib/R/library’
* installing *source* package ‘ash’ ...
** package ‘ash’ successfully unpacked and MD5 sums checked
** libs
gfortran   -fpic  -I/opt/conda/conda-bld/r-ash_1475589857768/_b_env_placehold_placehold_placehold_pl/include -L/opt/conda/conda-bld/r-ash_1475589857768/_b_env_placehold_placehold_placehold_pl/lib  -c ash.f -o ash.o
f951: internal compiler error: Illegal instruction
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://gcc.gnu.org/bugs.html> for instructions.
make: *** [ash.o] Error 1
ERROR: compilation failed for package ‘ash’
* removing ‘/opt/conda/conda-bld/r-ash_1475589857768/_b_env_placehold_placehold_placehold_pl/lib/R/library/ash’
Command failed: /bin/bash -x -e /opt/conda/conda-bld/r-ash_1475589857768/work/ash/conda_build.sh

@mingwandroid
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What CPU are you running?

@daler
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daler commented Oct 4, 2016 

cat /proc/cpuinfo
processor   : 0
vendor_id   : GenuineIntel
cpu family  : 6
model       : 23
model name  : Intel(R) Xeon(R) CPU           X5482  @ 3.20GHz
stepping    : 10
microcode   : 0xa07
cpu MHz     : 3192.351
cache size  : 6144 KB
physical id : 0
siblings    : 4
core id     : 0
cpu cores   : 4
apicid      : 0
initial apicid  : 0
fpu     : yes
fpu_exception   : yes
cpuid level : 13
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc arch_perfmon pebs bts rep_good nopl aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm dca sse4_1 xsave lahf_lm dtherm tpr_shadow vnmi flexpriority
bogomips    : 6384.70
clflush size    : 64
cache_alignment : 64
address sizes   : 38 bits physical, 48 bits virtual
power management:

...

@daler
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daler commented Oct 6, 2016

@mingwandroid Any ideas? Or suggestions for what I could try?

@mingwandroid
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I'm going to rebuild GCC soon for the new longer prefix. I've recently seen that on OS X, the old GCC isn't being used at all due to it being in the short version of the prefix folder while the long version is the one on PATH. Hopefully that is your problem too, i.e. it's using the system gfortran.

@daler
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daler commented Oct 6, 2016

Thanks, that would be great if it solved the problem, but I'm skeptical in this case because there's no gfortran on the system:

docker run condaforge/linux-anvil /bin/bash -c "which gfortran"
which: no gfortran in (/opt/conda/bin:/opt/rh/devtoolset-2/root/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/root/bin)

while the error when building the recipe is:

f951: internal compiler error: Illegal instruction

@daler
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daler commented Oct 28, 2016

@mingwandroid any updates on this? Are you able to reproduce with condaforge/linux-anvil?
This issue holding up many R and Bioconductor packages. Thanks.

@mingwandroid
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mingwandroid commented Oct 28, 2016 •
edited
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I cannot reproduce this so I cannot fix it. I'd suggest not using docker and seeing if that makes the problem go away.

@daler
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daler commented Oct 28, 2016

OK, thanks. I have the problem both with and without docker, so I'll look into CPU architecture issues.

@daler
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daler commented Oct 28, 2016

Turns out I can build on travis-ci's architecture but not on my local machine. I had no idea Xeon X5482 was considered too old for fortran! Sorry for the noise.

@daler daler closed this as completed Oct 28, 2016
@mingwandroid
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Well it's not really noise, more like useful information.

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Hi there, thank you for your contribution!

This issue has been automatically locked because it has not had recent activity after being closed.

Please open a new issue if needed.

Thanks!

@github-actions github-actions bot added the locked [bot] locked due to inactivity label Apr 19, 2022
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@daler @bgruening @mingwandroid