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
>
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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.
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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.
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.