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Hard-coded path to sed causes package installation failure #92

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jamesabbott opened this issue Jul 11, 2019 · 1 comment · Fixed by #93
Closed

Hard-coded path to sed causes package installation failure #92

jamesabbott opened this issue Jul 11, 2019 · 1 comment · Fixed by #93

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@jamesabbott
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Issue: Installing RcppParallel in r-base=3.6.1 fails due to hard-coded path in R. No r-cppparallel package is available yet for R 3.6.1

* installing *source* package ‘RcppParallel’ ...
** package ‘RcppParallel’ successfully unpacked and MD5 sums checked
** using staged installation
/cluster/gjb_lab/jabbott/miniconda3/envs/dada2-1.12/lib/R/bin/R: line 211: /home/conda/feedstock_root/build_artifacts/r-base_1562703117796/_build_env/bin/sed: No such file or directory
/cluster/gjb_lab/jabbott/miniconda3/envs/dada2-1.12/lib/R/bin/R: line 211: /home/conda/feedstock_root/build_artifacts/r-base_1562703117796/_build_env/bin/sed: No such file or directory
Fatal error: cannot open file '': No such file or directory
ERROR: configuration failed for package ‘RcppParallel’
* removing ‘/cluster/gjb_lab/jabbott/miniconda3/envs/dada2-1.12/lib/R/library/RcppParall

Modifying R to point to a real sed version resolves the issue:

sed -i 's|^SED=.*|SED=/bin/sed|' $(which R)
sed -i 's|^SED=.*|SED=/bin/sed|'  $(dirname $(which R))/../lib/R/bin/R

(dada2-1.12) ningal:~ $ R

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-conda_cos6-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages('RcppParallel')
......[snip].....
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RcppParallel)

Environment (conda list): 
# packages in environment at /cluster/gjb_lab/jabbott/miniconda3/envs/dada2-1.12:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main
_r-mutex                  1.0.1               anacondar_1    conda-forge
binutils_impl_linux-64    2.31.1               h6176602_1
binutils_linux-64         2.31.1               h6176602_7
bwidget                   1.9.11                        1
bzip2                     1.0.6             h14c3975_1002    conda-forge
ca-certificates           2019.6.16            hecc5488_0    conda-forge
cairo                     1.16.0            h18b612c_1001    conda-forge
curl                      7.64.1               hf8cf82a_0    conda-forge
fontconfig                2.13.1            he4413a7_1000    conda-forge
freetype                  2.10.0               he983fc9_0    conda-forge
gcc_impl_linux-64         7.3.0                habb00fd_1    conda-forge
gcc_linux-64              7.3.0                h553295d_7    conda-forge
gettext                   0.19.8.1          hc5be6a0_1002    conda-forge
gfortran_impl_linux-64    7.3.0                hdf63c60_1
gfortran_linux-64         7.3.0                h553295d_7
glib                      2.58.3            h6f030ca_1001    conda-forge
graphite2                 1.3.13            hf484d3e_1000    conda-forge
gsl                       2.5                  h294904e_0    conda-forge
gxx_impl_linux-64         7.3.0                hdf63c60_1    conda-forge
gxx_linux-64              7.3.0                h553295d_7    conda-forge
harfbuzz                  2.4.0                h37c48d4_1    conda-forge
icu                       58.2              hf484d3e_1000    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
krb5                      1.16.3            h05b26f9_1001    conda-forge
libblas                   3.8.0               10_openblas    conda-forge
libcblas                  3.8.0               10_openblas    conda-forge
libcurl                   7.64.1               hda55be3_0    conda-forge
libedit                   3.1.20170329      hf8c457e_1001    conda-forge
libffi                    3.2.1             he1b5a44_1006    conda-forge
libgcc-ng                 9.1.0                hdf63c60_0
libgfortran-ng            7.3.0                hdf63c60_0
libiconv                  1.15              h516909a_1005    conda-forge
liblapack                 3.8.0               10_openblas    conda-forge
libopenblas               0.3.6                h6e990d7_4    conda-forge
libpng                    1.6.37               hed695b0_0    conda-forge
libssh2                   1.8.2                h22169c7_2    conda-forge
libstdcxx-ng              9.1.0                hdf63c60_0
libtiff                   4.0.10            h57b8799_1003    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.9                h13577e0_1    conda-forge
lz4-c                     1.8.3             he1b5a44_1001    conda-forge
make                      4.2.1             h14c3975_2004    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
openblas                  0.3.6                h6e990d7_4    conda-forge
openssl                   1.1.1c               h516909a_0    conda-forge
pango                     1.40.14           he7ab937_1005    conda-forge
pcre                      8.41              hf484d3e_1003    conda-forge
pixman                    0.38.0            h516909a_1003    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
r-base                    3.6.1                h8900bf8_1    conda-forge
readline                  8.0                  hf8c457e_0    conda-forge
tk                        8.6.9             hed695b0_1002    conda-forge
tktable                   2.10                 h14c3975_0
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.9             h516909a_1004    conda-forge
xorg-libsm                1.2.3             h84519dc_1000    conda-forge
xorg-libx11               1.6.7             h14c3975_1000    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxrender           0.9.10            h516909a_1002    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
zlib                      1.2.11            h14c3975_1004    conda-forge
zstd                      1.4.0                h3b9ef0a_0    conda-forge

Details about conda and system ( conda info ): 
     active environment : dada2-1.12
    active env location : /cluster/gjb_lab/jabbott/miniconda3/envs/dada2-1.12
            shell level : 2
       user config file : /homes/jabbott/.condarc
 populated config files : /homes/jabbott/.condarc
          conda version : 4.7.5
    conda-build version : 3.18.7
         python version : 3.7.3.final.0
       virtual packages :
       base environment : /cluster/gjb_lab/jabbott/miniconda3  (writable)
           channel URLs : https://dag.compbio.dundee.ac.uk/conda_dev/linux-64
                          https://dag.compbio.dundee.ac.uk/conda_dev/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /cluster/gjb_lab/jabbott/miniconda3/pkgs
                          /homes/jabbott/.conda/pkgs
       envs directories : /cluster/gjb_lab/jabbott/miniconda3/envs
                          /homes/jabbott/.conda/envs
               platform : linux-64
             user-agent : conda/4.7.5 requests/2.22.0 CPython/3.7.3 Linux/2.6.32-754.el6.x86_64 centos/6.10 glibc/2.12
                UID:GID : 14463:8000
             netrc file : None
           offline mode : False
@isuruf
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isuruf commented Jul 11, 2019

@jamesabbott, can you send a PR? You need to fix it like

r-base-feedstock/recipe/build.sh

Line 118 in e1740a0

sed -i.bak 's/SED=.*/SED=${SED-sed}/g' ${PREFIX}/lib/R/etc/Renviron

@isuruf isuruf mentioned this issue Jul 11, 2019
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Add sed as a dependency isuruf/r-base-feedstock
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@isuruf @jamesabbott