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conda skeleton cran: "CMD: command not found" #2603

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nick-youngblut opened this issue Dec 26, 2017 · 10 comments · Fixed by #2614
Closed

conda skeleton cran: "CMD: command not found" #2603

nick-youngblut opened this issue Dec 26, 2017 · 10 comments · Fixed by #2614
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@nick-youngblut
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I'm trying to create conda packages for some R packages hosted on CRAN. I'm using conda skeleton cran, which worked for the PACo R package:

conda skeleton cran paco
conda-build r-paco/
anaconda upload ...

However, I'm getting an error when trying to do the same for the PMA R package:

conda skeleton cran pma
# change "r-impute" to "bioconductor-impute" in the meta.yaml file
conda-build r-pma/

This generates the following output:

$ conda build r-pma
Adding in variants from internal_defaults
INFO:conda_build.variants:Adding in variants from internal_defaults
Attempting to finalize metadata for r-pma
INFO:conda_build.metadata:Attempting to finalize metadata for r-pma
BUILD START: ['r-pma-1.0.9-r341h6bb024c_0.tar.bz2']

The following NEW packages will be INSTALLED:

    binutils_impl_linux-64: 2.28.1-h04c84fa_2
    binutils_linux-64:      7.2.0-19
    bioconductor-impute:    1.52.0-r3.4.1_0   bioconda
    bzip2:                  1.0.6-1           conda-forge
    ca-certificates:        2017.11.5-0       conda-forge
    cairo:                  1.14.10-0         conda-forge
    curl:                   7.55.1-0          conda-forge
    fontconfig:             2.12.6-0          conda-forge
    freetype:               2.8.1-0           conda-forge
    gcc_impl_linux-64:      7.2.0-hc5ce805_2
    gcc_linux-64:           7.2.0-19
    gettext:                0.19.7-1          conda-forge
    glib:                   2.55.0-0          conda-forge
    graphite2:              1.3.10-0          conda-forge
    gsl:                    2.1-2             conda-forge
    gxx_impl_linux-64:      7.2.0-hd3faf3d_2
    gxx_linux-64:           7.2.0-19
    harfbuzz:               1.7.1-0           conda-forge
    icu:                    58.2-0            conda-forge
    jpeg:                   9b-2              conda-forge
    krb5:                   1.14.2-0          conda-forge
    libffi:                 3.2.1-3           conda-forge
    libgcc:                 7.2.0-h69d50b8_2
    libgcc-ng:              7.2.0-h7cc24e2_2
    libiconv:               1.15-0            conda-forge
    libpng:                 1.6.34-0          conda-forge
    libssh2:                1.8.0-2           conda-forge
    libstdcxx-ng:           7.2.0-h7a57d05_2
    libtiff:                4.0.9-0           conda-forge
    libxml2:                2.9.5-2           conda-forge
    make:                   4.2.1-0           conda-forge
    ncurses:                5.9-10            conda-forge
    openssl:                1.0.2n-0          conda-forge
    pango:                  1.40.14-0         conda-forge
    pcre:                   8.39-0            conda-forge
    pixman:                 0.34.0-1          conda-forge
    r-base:                 3.4.1-3           conda-forge
    r-plyr:                 1.8.4-r3.4.1_0    conda-forge
    r-rcpp:                 0.12.13-r3.4.1_0  conda-forge
    readline:               7.0-0             conda-forge
    tk:                     8.6.7-0           conda-forge
    xz:                     5.2.3-0           conda-forge
    zlib:                   1.2.11-0          conda-forge

Source cache directory is: /ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/src_cache
Found source in cache: PMA_1.0.9_787641323e.tar.gz
Extracting download
source tree in: /ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/work
INFO: activate-binutils_linux-64.sh made the following environmental changes:
+ADDR2LINE=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-addr2line
+AR=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-ar
+AS=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-as
+CXXFILT=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++filt
+ELFEDIT=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-elfedit
+GPROF=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-gprof
+HOST=x86_64-conda_cos6-linux-gnu
+LD=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-ld
+LD_GOLD=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-ld.gold
+NM=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-nm
+OBJCOPY=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-objcopy
+OBJDUMP=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-objdump
+RANLIB=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-ranlib
+READELF=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-readelf
+SIZE=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-size
+STRINGS=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-strings
+STRIP=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-strip
INFO: activate-gcc_linux-64.sh made the following environmental changes:
+CC=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc
+CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
+CPP=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-cpp
+CPPFLAGS=-D_FORTIFY_SOURCE=2 -O2
+DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments -I/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
+GCC_AR=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc-ar
+GCC=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc
+GCC_NM=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc-nm
+GCC_RANLIB=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc-ranlib
+LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,-rpath,/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib -L/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib
+_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
INFO: activate-gxx_linux-64.sh made the following environmental changes:
+CXX=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++
+CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
+DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments -I/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
+GXX=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/_build_env/bin/x86_64-conda_cos6-linux-gnu-g++
/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/work/conda_build.sh: line 64: CMD: command not found
Traceback (most recent call last):
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/bin/conda-build", line 11, in <module>
    sys.exit(main())
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 393, in main
    execute(sys.argv[1:])
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 384, in execute
    verify=args.verify)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/api.py", line 186, in build
    need_source_download=need_source_download, config=config, variants=variants)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/build.py", line 1885, in build_tree
    notest=notest,
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/build.py", line 1194, in build
    utils.check_call_env(cmd, env=env, cwd=src_dir)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/utils.py", line 677, in check_call_env
    return _func_defaulting_env_to_os_environ(subprocess.check_call, *popenargs, **kwargs)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/utils.py", line 673, in _func_defaulting_env_to_os_environ
    return func(_args, **kwargs)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/subprocess.py", line 291, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/bin/bash', '-e', '/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/work/conda_build.sh']' returned non-zero exit status 127.

I don't see why I'm getting the error: /ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/work/conda_build.sh: line 64: CMD: command not found

My conda environment is:

asn1crypto                0.22.0           py36h265ca7c_1
beautifulsoup4            4.6.0                    py36_0    conda-forge
bzip2                     1.0.6                         1    conda-forge
ca-certificates           2017.08.26           h1d4fec5_0
cairo                     1.14.10                       0    conda-forge
certifi                   2017.7.27.1      py36h8b7b77e_0
cffi                      1.10.0           py36had8d393_1
chardet                   3.0.4            py36h0f667ec_1
conda                     4.3.29                   py36_0    conda-forge
conda-build               3.2.0                    py36_0
conda-env                 2.6.0                         0    conda-forge
conda-verify              2.0.0                    py36_0    conda-forge
cryptography              2.0.3            py36ha225213_1
curl                      7.55.1                        0    conda-forge
filelock                  2.0.6                    py36_0    conda-forge
fontconfig                2.12.6                        0    conda-forge
freetype                  2.8.1                         0    conda-forge
gettext                   0.19.7                        1    conda-forge
glib                      2.55.0                        0    conda-forge
glob2                     0.4.1                    py36_0    bioconda
graphite2                 1.3.10                        0    conda-forge
gsl                       2.1                           2    conda-forge
harfbuzz                  1.7.1                         0    conda-forge
icu                       58.2                          0    conda-forge
idna                      2.6              py36h82fb2a8_1
jinja2                    2.9.6                    py36_0    conda-forge
jpeg                      9b                            2    conda-forge
krb5                      1.14.2                        0    conda-forge
libedit                   3.1.20170329                  0    conda-forge
libffi                    3.2.1                h4deb6c0_3
libgcc                    7.2.0                h69d50b8_2
libgcc-ng                 7.2.0                h7cc24e2_2
libiconv                  1.15                          0    conda-forge
libpng                    1.6.34                        0    conda-forge
libssh2                   1.8.0                         2    conda-forge
libstdcxx-ng              7.2.0                h7a57d05_2
libtiff                   4.0.9                         0    conda-forge
libxml2                   2.9.5                         2    conda-forge
markupsafe                1.0                      py36_0    conda-forge
ncurses                   5.9                          10    conda-forge
openssl                   1.0.2l               h077ae2c_5
pango                     1.40.14                       0    conda-forge
patchelf                  0.9                           2    conda-forge
pcre                      8.39                          0    conda-forge
pip                       9.0.1            py36h8ec8b28_3
pixman                    0.34.0                        1    conda-forge
pkginfo                   1.4.1                    py36_0    conda-forge
pycosat                   0.6.2            py36h1a0ea17_1
pycparser                 2.18             py36hf9f622e_1
pycrypto                  2.6.1                    py36_1    conda-forge
pyopenssl                 17.2.0           py36h5cc804b_0
pysocks                   1.6.7            py36hd97a5b1_1
python                    3.6.4                         0    conda-forge
pyyaml                    3.12                     py36_1    conda-forge
r-base                    3.4.1                         3    conda-forge
readline                  7.0                           0    conda-forge
requests                  2.18.4           py36he2e5f8d_1
ruamel_yaml               0.11.14          py36ha2fb22d_2
setuptools                36.5.0           py36he42e2e1_0
six                       1.10.0           py36hcac75e4_1
sqlite                    3.20.1               h6d8b0f3_1
tk                        8.6.7                h5979e9b_1
urllib3                   1.22             py36hbe7ace6_0
wheel                     0.29.0           py36he7f4e38_1
xz                        5.2.3                h2bcbf08_1
yaml                      0.1.7                h96e3832_1
zlib                      1.2.11               hfbfcf68_1
@msarahan
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msarahan commented Jan 2, 2018

when you see errors like this, you need to look at the file that the error mentions:

/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514279826347/work/conda_build.sh

It shows:

# R refuses to build packages that mark themselves as Priority: Recommended
mv DESCRIPTION DESCRIPTION.old
grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
$R CMD INSTALL --build .

So the problem is that the R environment variable is not getting defined properly. That's a conda-build bug, and we'll look into it.

@mingwandroid mingwandroid mentioned this issue Jan 2, 2018
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@msarahan
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msarahan commented Jan 2, 2018

@mingwandroid fixed the cran skeleton generator at #2614. The problem was that the old generator wasn't correctly distinguishing between host and build dependencies. You'll need to regenerate or adapt any recipes you already have. I'll be tagging a new conda-build release later today.

@nick-youngblut
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Thanks for the clarification! I updated conda-build to v3.2.1, and tried again and am still getting what seems to be the same error:

$ conda skeleton cran pma
# change "r-impute" to "bioconductor-impute" in the meta.yaml file
$ conda-build r-pma/
Adding in variants from internal_defaults
INFO:conda_build.variants:Adding in variants from internal_defaults
Attempting to finalize metadata for r-pma
INFO:conda_build.metadata:Attempting to finalize metadata for r-pma
Solving environment: done
Solving environment: done
Solving environment: done
BUILD START: ['r-pma-1.0.9-r341hf484d3e_0.tar.bz2']
Solving environment: done

## Package Plan ##

  environment location: /ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_


The following NEW packages will be INSTALLED:

    bioconductor-impute: 1.52.0-r3.4.1_0  bioconda
    bzip2:               1.0.6-1          conda-forge
    ca-certificates:     2017.11.5-0      conda-forge
    cairo:               1.14.10-0        conda-forge
    curl:                7.55.1-0         conda-forge
    fontconfig:          2.12.6-0         conda-forge
    freetype:            2.8.1-0          conda-forge
    gettext:             0.19.7-1         conda-forge
    glib:                2.55.0-0         conda-forge
    graphite2:           1.3.10-0         conda-forge
    gsl:                 2.1-2            conda-forge
    harfbuzz:            1.7.1-0          conda-forge
    icu:                 58.2-0           conda-forge
    jpeg:                9b-2             conda-forge
    krb5:                1.14.2-0         conda-forge
    libffi:              3.2.1-3          conda-forge
    libgcc:              7.2.0-h69d50b8_2
    libgcc-ng:           7.2.0-h7cc24e2_2
    libiconv:            1.15-0           conda-forge
    libpng:              1.6.34-0         conda-forge
    libssh2:             1.8.0-2          conda-forge
    libstdcxx-ng:        7.2.0-h7a57d05_2
    libtiff:             4.0.9-0          conda-forge
    libxml2:             2.9.5-2          conda-forge
    ncurses:             5.9-10           conda-forge
    openssl:             1.0.2n-0         conda-forge
    pango:               1.40.14-0        conda-forge
    pcre:                8.39-0           conda-forge
    pixman:              0.34.0-1         conda-forge
    r-base:              3.4.1-3          conda-forge
    r-plyr:              1.8.4-r3.4.1_0   conda-forge
    r-rcpp:              0.12.13-r3.4.1_0 conda-forge
    readline:            7.0-0            conda-forge
    tk:                  8.6.7-0          conda-forge
    xz:                  5.2.3-0          conda-forge
    zlib:                1.2.11-0         conda-forge

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Solving environment: done
Solving environment: done

## Package Plan ##

  environment location: /ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env


The following NEW packages will be INSTALLED:

    binutils_impl_linux-64: 2.28.1-h04c84fa_2
    binutils_linux-64:      7.2.0-25
    gcc_impl_linux-64:      7.2.0-hc5ce805_2
    gcc_linux-64:           7.2.0-25
    gxx_impl_linux-64:      7.2.0-hd3faf3d_2
    gxx_linux-64:           7.2.0-25
    libstdcxx-ng:           7.2.0-h7a57d05_2
    make:                   4.2.1-0           conda-forge

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Source cache directory is: /ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/src_cache
Found source in cache: PMA_1.0.9_787641323e.tar.gz
Extracting download
source tree in: /ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/work
INFO: activate-binutils_linux-64.sh made the following environmental changes:
+ADDR2LINE=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-addr2line
+AR=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-ar
+AS=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-as
+CXXFILT=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++filt
+ELFEDIT=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-elfedit
+GPROF=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-gprof
+HOST=x86_64-conda_cos6-linux-gnu
+LD=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-ld
+LD_GOLD=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-ld.gold
+NM=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-nm
+OBJCOPY=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-objcopy
+OBJDUMP=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-objdump
+RANLIB=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-ranlib
+READELF=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-readelf
+SIZE=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-size
+STRINGS=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-strings
+STRIP=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-strip
INFO: activate-gcc_linux-64.sh made the following environmental changes:
+CC=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc
+CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
+CPP=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-cpp
+CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2
+DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -I/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
+DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og
+GCC_AR=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc-ar
+GCC=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc
+GCC_NM=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc-nm
+GCC_RANLIB=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-gcc-ranlib
+LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,-rpath,/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib -L/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib
+_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
INFO: activate-gxx_linux-64.sh made the following environmental changes:
+CXX=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++
+CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
+DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -I/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
+GXX=/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/_build_env/bin/x86_64-conda_cos6-linux-gnu-g++
Failed to import the site module
Traceback (most recent call last):
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site.py", line 544, in <module>
    main()
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site.py", line 530, in main
    known_paths = addusersitepackages(known_paths)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site.py", line 282, in addusersitepackages
    user_site = getusersitepackages()
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site.py", line 258, in getusersitepackages
    user_base = getuserbase() # this will also set USER_BASE
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site.py", line 248, in getuserbase
    USER_BASE = get_config_var('userbase')
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/sysconfig.py", line 601, in get_config_var
    return get_config_vars().get(name)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/sysconfig.py", line 550, in get_config_vars
    _init_posix(_CONFIG_VARS)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/sysconfig.py", line 421, in _init_posix
    _temp = __import__(name, globals(), locals(), ['build_time_vars'], 0)
ModuleNotFoundError: No module named '_sysconfigdata_x86_64_conda_cos6_linux_gnu'
Traceback (most recent call last):
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/bin/conda-build", line 11, in <module>
    sys.exit(main())
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 393, in main
    execute(sys.argv[1:])
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 384, in execute
    verify=args.verify)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/api.py", line 186, in build
    need_source_download=need_source_download, config=config, variants=variants)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/build.py", line 1909, in build_tree
    notest=notest,
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/build.py", line 1211, in build
    utils.check_call_env(cmd, env=env, cwd=src_dir)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/utils.py", line 677, in check_call_env
    return _func_defaulting_env_to_os_environ(subprocess.check_call, *popenargs, **kwargs)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/utils.py", line 673, in _func_defaulting_env_to_os_environ
    return func(_args, **kwargs)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/subprocess.py", line 291, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/bin/bash', '-e', '/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514970634188/work/conda_build.sh']' returned non-zero exit status 1.

Is there something that I'm doing wrong?

@mingwandroid
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This is a different error. In your root/base env please run conda update python

@nick-youngblut
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Thanks for the quick feedback! I tried updating python:

$ conda update python
Solving environment: done

## Package Plan ##

  environment location: /ebio/abt3_projects/software/dev/miniconda3_dev

  added / updated specs:
    - python


The following packages will be UPDATED:

    ca-certificates: 2017.08.26-h1d4fec5_0      --> 2017.11.5-0      conda-forge
    certifi:         2017.7.27.1-py36h8b7b77e_0 --> 2017.11.5-py36_0 conda-forge
    openssl:         1.0.2l-h077ae2c_5          --> 1.0.2n-0         conda-forge

Proceed ([y]/n)?

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Then, I re-did the entire process as listed above and am getting what appears to be the same error:

Failed to import the site module
Traceback (most recent call last):
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site.py", line 544, in <module>
    main()
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site.py", line 530, in main
    known_paths = addusersitepackages(known_paths)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site.py", line 282, in addusersitepackages
    user_site = getusersitepackages()
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site.py", line 258, in getusersitepackages
    user_base = getuserbase() # this will also set USER_BASE
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site.py", line 248, in getuserbase
    USER_BASE = get_config_var('userbase')
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/sysconfig.py", line 601, in get_config_var
    return get_config_vars().get(name)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/sysconfig.py", line 550, in get_config_vars
    _init_posix(_CONFIG_VARS)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/sysconfig.py", line 421, in _init_posix
    _temp = __import__(name, globals(), locals(), ['build_time_vars'], 0)
ModuleNotFoundError: No module named '_sysconfigdata_x86_64_conda_cos6_linux_gnu'
Traceback (most recent call last):
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/bin/conda-build", line 11, in <module>
    sys.exit(main())
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 393, in main
    execute(sys.argv[1:])
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 384, in execute
    verify=args.verify)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/api.py", line 186, in build
    need_source_download=need_source_download, config=config, variants=variants)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/build.py", line 1909, in build_tree
    notest=notest,
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/build.py", line 1211, in build
    utils.check_call_env(cmd, env=env, cwd=src_dir)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/utils.py", line 677, in check_call_env
    return _func_defaulting_env_to_os_environ(subprocess.check_call, *popenargs, **kwargs)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/site-packages/conda_build/utils.py", line 673, in _func_defaulting_env_to_os_environ
    return func(_args, **kwargs)
  File "/ebio/abt3_projects/software/dev/miniconda3_dev/lib/python3.6/subprocess.py", line 291, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/bin/bash', '-e', '/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/r-pma_1514972134025/work/conda_build.sh']' returned non-zero exit status 1.

@nick-youngblut
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I used conda update -c anaconda python and now the package is building without errors. Thanks for the help!

@mingwandroid
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mingwandroid commented Jan 3, 2018 •
edited
Loading

You have our compilers installed in your base env I think? This can only work if you also have a python that supports them.

You have two choices to get that, reinstall the latest miniconda (4.3.31) with -f over the top or unset _,PYTHON_SYSCONFIGDATA_NAME then update python from defaults.

Note, conda-forge Python does not support our compilers yet so you cannot have both that and our compilers installed in your base env. Ours is much faster and better anyway.

@mingwandroid
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Great. You are now building r packages with our new compilers. This "could" cause some issues for you as your r interpreter will not have been built using them and so will load your system libgcc or the one from the GCC 4.8.5 package and which libstdc++ gets loaded will depend on package load order.

You may need to modify conda skeleton cran to prevent this. We'll see.

@nick-youngblut
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Besides the pma package, I'd like to create a conda package for the microbiome R package, which is on bioconductor but not available on CRAN. Is there any way to use conda skeleton for this? I can't find any documentation on using conda skeleton for bioconductor packages.

The microbiome package has been available on bioconductor since Nov 2017, but it's still not available on any anaconda channels. It would be great to have this package available on conda.

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Hi there, thank you for your contribution!

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Please open a new issue if needed.

Thanks!

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Skeleton fixes mingwandroid/conda-build
3 participants
@msarahan @mingwandroid @nick-youngblut