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Question: Can't install package because of sp package
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gravatar for MarcinKosiński
2.1 years ago by
Poland
MarcinKosiński0 wrote:

I am trying to install RTCGA.mutations package from bioconductor but there appears an error because of `sp` package has different binary and source sotware versions. I've tried many methods to install that package. Does anyone know how to fix this problem?

 

> biocLite("RTCGA.mutations")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.5), R version 3.2.2.
Installing package(s) ‘RTCGA.mutations’
Old packages: 'sp'
Update all/some/none? [a/s/n]: 
a

  There is a binary version available but the source version is later:
   binary source needs_compilation
sp  1.2-0  1.2-1              TRUE

Do you want to install from sources the package which needs compilation?
y/n: y
installing the source package ‘sp’

trying URL 'http://cran.rstudio.com/src/contrib/sp_1.2-1.tar.gz'
Content type 'application/x-gzip' length 1227402 bytes (1.2 MB)
downloaded 1.2 MB

* installing *source* package 'sp' ...
** package 'sp' successfully unpacked and MD5 sums checked
** libs
cygwin warning:
  MS-DOS style path detected: D:/R-32~1.2/etc/x64/Makeconf
  Preferred POSIX equivalent is: /cygdrive/d/R-32~1.2/etc/x64/Makeconf
  CYGWIN environment variable option "nodosfilewarning" turns off this warning.
  Consult the user's guide for more details about POSIX paths:
    http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
gcc -m64 -I"D:/R-32~1.2/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Rcentroid.c -o Rcentroid.o
gcc: not found
make: *** [Rcentroid.o] Error 127
Warning: running command 'make -f "D:/R-32~1.2/etc/x64/Makeconf" -f "D:/R-32~1.2/share/make/winshlib.mk" SHLIB="sp.dll" WIN=64 TCLBIN=64 OBJECTS="Rcentroid.o gcdist.o init.o pip.o pip2.o sp_xports.o surfaceArea.o zerodist.o"' had status 2
ERROR: compilation failed for package 'sp'
* removing 'C:/Users/Marcin/Documents/R/win-library/3.2/sp'
* restoring previous 'C:/Users/Marcin/Documents/R/win-library/3.2/sp'

The downloaded source packages are in
    ‘C:\Users\Marcin\AppData\Local\Temp\RtmpoRaUZq\downloaded_packages’
Warning messages:
1: package ‘RTCGA.mutations’ is not available (for R version 3.2.2) 
2: running command '"D:/R-32~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\Marcin\Documents\R\win-library\3.2" C:\Users\Marcin\AppData\Local\Temp\RtmpoRaUZq/downloaded_packages/sp_1.2-1.tar.gz' had status 1 
3: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘sp’ had non-zero exit status
> install.packages('sp')
Installing package into ‘C:/Users/Marcin/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)

  There is a binary version available but the source version is later:
   binary source needs_compilation
sp  1.2-0  1.2-1              TRUE

Do you want to install from sources the package which needs compilation?
y/n: n
trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.2/sp_1.2-0.zip'
Content type 'application/zip' length 1562134 bytes (1.5 MB)
downloaded 1.5 MB

package ‘sp’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Marcin\AppData\Local\Temp\RtmpoRaUZq\downloaded_packages
> biocLite("RTCGA.mutations")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.5), R version 3.2.2.
Installing package(s) ‘RTCGA.mutations’
Old packages: 'sp'
Update all/some/none? [a/s/n]: 
n
Warning message:
package ‘RTCGA.mutations’ is not available (for R version 3.2.2) 
> biocLite("RTCGA.mutations")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.5), R version 3.2.2.
Installing package(s) ‘RTCGA.mutations’
Old packages: 'sp'
Update all/some/none? [a/s/n]: 
a

  There is a binary version available but the source version is later:
   binary source needs_compilation
sp  1.2-0  1.2-1              TRUE

Do you want to install from sources the package which needs compilation?
y/n: n
trying URL 'http://cran.rstudio.com/bin/windows/contrib/3.2/sp_1.2-0.zip'
Content type 'application/zip' length 1562134 bytes (1.5 MB)
downloaded 1.5 MB

package ‘sp’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Marcin\AppData\Local\Temp\RtmpoRaUZq\downloaded_packages
Warning message:
package ‘RTCGA.mutations’ is not available (for R version 3.2.2) 

ADD COMMENTlink written 2.1 years ago by MarcinKosiński0

You need to install bioconductor 3.2 as follows:

library(BiocInstaller)
biocLite("BiocUpgrade")

Your package does not exist for earlier versions of Bioconductor.

Also, the machine you are on does not have compilation tools, so you should always answer 'n' when asked if you want to install the source version of a package.

ADD REPLYlink written 2.1 years ago by Dan Tenenbaum ♦♦ 8.2k
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