Question: updating bioconductor gives problem with coin
0
gravatar for vhertzb
21 months ago by
vhertzb0
vhertzb0 wrote:

I am attempting to update Bioconductor within my RStudio environment. When I do so, it gives the following warning message at the end:

 

  1. In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  2.   installation of package ‘coin’ had non-zero exit status

 

I am running coin v 1.1-3. 

 

I downloaded the new version of coin from RForge, attempted to install it from source and get the following:

 

  1. * installing *source* package ‘coin’ ...
  2. ** package ‘coin’ successfully unpacked and MD5 sums checked
  3. ** libs
  4. clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Classes.c -o Classes.o
  5. clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Helpers.c -o Helpers.o
  6. clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c LinearStatistic.c -o LinearStatistic.o
  7. clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c StreitbergRoehmel.c -o StreitbergRoehmel.o
  8. clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c coin-init.c -o coin-init.o
  9. clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c vandeWiel.c -o vandeWiel.o
  10. clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o coin.so Classes.o Helpers.o LinearStatistic.o StreitbergRoehmel.o coin-init.o vandeWiel.o -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
  11. ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
  12. ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
  13. ld: library not found for -lgfortran
  14. clang: error: linker command failed with exit code 1 (use -v to see invocation)
  15. make: *** [coin.so] Error 1
  16. ERROR: compilation failed for package ‘coin’
  17. * removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/coin’
  18. * restoring previous ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/coin’
  19. Warning in install.packages :
  20.   installation of package ‘/Users/vicki/Downloads/coin’ had non-zero exit status

 

Here is the sessionInfo:

 

  1. sessionInfo()
  2. R version 3.4.0 (2017-04-21)
  3. Platform: x86_64-apple-darwin15.6.0 (64-bit)
  4. Running under: macOS Sierra 10.12.5
  5.  
  6. Matrix products: default
  7. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
  8. LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
  9.  
  10. locale:
  11. [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
  12.  
  13. attached base packages:
  14. [1] stats     graphics  grDevices utils     datasets  methods   base    
  15.  
  16. other attached packages:
  17. [1] BiocInstaller_1.26.0
  18.  
  19. loaded via a namespace (and not attached):
  20. [1] compiler_3.4.0 tools_3.4.0  

 

What am I doing wrong? Please let me know if there is other information you need.

 

software error coin • 546 views
ADD COMMENTlink modified 21 months ago by Lucas Schiffer220 • written 21 months ago by vhertzb0
Answer: updating bioconductor gives problem with coin
0
gravatar for Mike Smith
21 months ago by
Mike Smith3.3k
EMBL Heidelberg / de.NBI
Mike Smith3.3k wrote:

It looks like you're missing the fortran libraries needed to compile this package.  I don't have a Mac to test this with, but I would download and install GFortran 6.1 from https://gcc.gnu.org/wiki/GFortranBinaries#MacOS 

A direct link to the version recommended for R-3.4.0 is http://coudert.name/software/gfortran-6.1-ElCapitan.dmg

ADD COMMENTlink written 21 months ago by Mike Smith3.3k

It might also be worth while to investigate why the source package is being installed; if it were binary (the default, I think) then there would be no need to compile it.

One common scenario is that the package is not available as a binary because it fails to pass R CMD build and check on mac. This seems to be the case for coin as evidenced by it's check report. The end result is that by installing from source, the user goes to great lengths to install a broken package.

But actually in this case the CRAN check report looks unusual -- I don't know how to contact the CRAN people about these issues.

ADD REPLYlink written 21 months ago by Martin Morgan ♦♦ 23k
Answer: updating bioconductor gives problem with coin
0
gravatar for Lucas Schiffer
21 months ago by
Boston University, Boston, MA
Lucas Schiffer220 wrote:

R has a number of dependencies that are sometimes difficult to satisfy on macOS. If possible, you might consider installing R using homebrew (https://brew.sh/) by first installing homebrew following the instructions on the site and then doing the following from terminal to install R.

brew update
brew upgrade
brew tap homebrew/science
brew install r

This will install R and all dependencies (e.g. GFortran), RStudio will be able to find and use them, and then you will be able to install coin using the standard procedure.

ADD COMMENTlink written 21 months ago by Lucas Schiffer220

The downside to a homebrew installation is that you will have to compile every package by source, though, which can be a pain ...

ADD REPLYlink written 21 months ago by Steve Lianoglou12k

I think the alternative is to follow the R-core recommendations.

https://r.research.att.com/man/R-admin.html#Installing-R-under-macOS
https://r.research.att.com/
https://r.research.att.com/tools/

at least for packages like coin that make use of C / C++ / fortran code but not other specialized libraries

ADD REPLYlink written 21 months ago by Martin Morgan ♦♦ 23k
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