Question: Bioc 3.3 Windows 10 eiR package fails to install
0
gravatar for rjrich
3.5 years ago by
rjrich0
rjrich0 wrote:

Windows 10 64 bit, R 3.3, Bioconductor 3.3, CygWin64 2.5.1, Rtools 3.3, MikTex 2.9.5972, Strawberry Perl, 5.24.0.1 (64 bit), devtools 1.11.1., Rstudio 0.99.902.

Unable to install eiR package. Code:

Bioconductor version 3.3 (BiocInstaller 1.22.2), ?biocLite for help
> biocLite("eiR")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.2), R 3.3.0 (2016-05-03).
Installing package(s) ‘eiR’
Package which is only available in source form, and may need
  compilation of C/C++/Fortran: ‘eiR’
Do you want to attempt to install these from sources?
y/n: y
installing the source package ‘eiR’

trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/eiR_1.12.2.tar.gz'
Content type 'application/x-gzip' length 310617 bytes (303 KB)
downloaded 303 KB

* installing *source* package 'eiR' ...
** libs

*** arch - i386
Warning: running command 'make -f "Makevars.win" -f "C:/PROGRA~1/R/R-33~1.0/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-33~1.0/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="eiR.dll" OBJECTS="apost.o char_bit_cnt.o embedCoords.o eucsearch.o format.o mplsh-model.o mplsh.o profiling.o r_wrap.o recordfile.o routines.o scan.o search_r.o solver.o"' had status 123
ERROR: compilation failed for package 'eiR'
* removing 'C:/Users/rjrich/Documents/R/win-library/3.3/eiR'

The downloaded source packages are in
    ‘C:\Users\rjrich\AppData\Local\Temp\RtmpGua9D1\downloaded_packages’
Old packages: 'nlme', 'survival'
Update all/some/none? [a/s/n]: 
a
Warning in install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  'lib = "C:/Program Files/R/R-3.3.0/library"' is not writable
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/nlme_3.1-128.zip'
Content type 'application/zip' length 2145355 bytes (2.0 MB)
downloaded 2.0 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/survival_2.39-4.zip'
Content type 'application/zip' length 4820930 bytes (4.6 MB)
downloaded 4.6 MB

package ‘nlme’ successfully unpacked and MD5 sums checked
package ‘survival’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\rjrich\AppData\Local\Temp\RtmpGua9D1\downloaded_packages
Warning messages:
1: running command '"C:/PROGRA~1/R/R-33~1.0/bin/x64/R" CMD INSTALL -l "C:\Users\rjrich\Documents\R\win-library\3.3" C:\Users\rjrich\AppData\Local\Temp\RtmpGua9D1/downloaded_packages/eiR_1.12.2.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘eiR’ had non-zero exit status

Sessioninfo() output:

R version 3.3.0 (2016-05-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.22.2

loaded via a namespace (and not attached):
[1] rsconnect_0.4.3 tools_3.3.0    

=====

The eiR package installed just fine in Linux (Linux Mint 17.3 64 bit Xfce).

Thank you for any assistance you might be able to provide.

=====

 

ADD COMMENTlink modified 3.5 years ago by khoran0 • written 3.5 years ago by rjrich0
1

eiR is not supported on windows. That's why there is no binary version, and why it's not surprising that you can't get it to build from source. Not sure/don't remember why this is, maybe the eiR maintainer will chime in and let us know.

 

ADD REPLYlink written 3.5 years ago by Dan Tenenbaum8.2k

Thank you for your quick and helpful response! I should have realized that eiR was not supported on Windows, but your comment has saved me from a great deal of further frustration. When I wish to run eiR, I will do it in linux, where it installs with no apparent issues. 

ADD REPLYlink written 3.5 years ago by rjrich0
Answer: Bioc 3.3 Windows 10 eiR package fails to install
0
gravatar for khoran
3.5 years ago by
khoran0
khoran0 wrote:

I am the maintainer for eiR. As Dan mentioned, eiR currently relies on some code that will not compile on windows so it is not supported there. I am working on a new version of eiR that will replace this library and then hopefully it will then be supported on windows. This will be at least a few months out though. 

Kevin

ADD COMMENTlink written 3.5 years ago by khoran0
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