Error with package ‘pgirmess’

General
#1

Hello,

I'm trying to download the ‘pgirmess’ package but keep getting this error message

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/pgirmess_1.6.9.tgz'
Content type 'application/x-gzip' length 260113 bytes (254 KB)

When I go to the URL a .tgz file downloads, I open it and that's where I get lost. I'm not sure what to do next.

Thank you in advance

#2

Could you post the command you are using for installing the package and the whole error message you are getting?

#3

My process is a follows

install.packages('pgirmess')
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/pgirmess_1.6.9.tgz'
Content type 'application/x-gzip' length 260113 bytes (254 KB)
==================================================
downloaded 254 KB

The downloaded binary packages are in
/var/folders/0k/bn4j3rz148g0c5ddh2b0hvwc0000gn/T//RtmpXeoqF9/downloaded_packages

Then I try to install the library because I didn't realize there was an issue

library(pgirmess)
Error: package or namespace load failed for ‘pgirmess’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘expm’

I try installing 'expm'

install.packages('expm')

There is a binary version available but the source version is later:
binary source needs_compilation
expm 0.999-3 0.999-4 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel)

I say Yes

installing the source package ‘expm’

trying URL 'https://cran.rstudio.com/src/contrib/expm_0.999-4.tar.gz'
Content type 'application/x-gzip' length 137075 bytes (133 KB)

downloaded 133 KB

  • installing source package ‘expm’ ...
    ** package ‘expm’ successfully unpacked and MD5 sums checked
    ** libs
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c R_dgebal.c -o R_dgebal.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c expm-eigen.c -o expm-eigen.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c expm.c -o expm.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
    clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c logm-eigen.c -o logm-eigen.o
    gfortran -fPIC -g -O2 -c matexp.f -o matexp.o
    /var/folders/0k/bn4j3rz148g0c5ddh2b0hvwc0000gn/T//ccKQVrBO.s:1:9: error: unsupported directive '.stabs'
    .stabs "/private/var/folders/0k/bn4j3rz148g0c5ddh2b0hvwc0000gn/T/Rtmp1ZLpGs/R.INSTALL18205049abe5/expm/src/",100,0,7,Ltext0
    ^
    /var/folders/0k/bn4j3rz148g0c5ddh2b0hvwc0000gn/T//ccKQVrBO.s:2:9: error: unsupported directive '.stabs'
    .stabs "matexp.f",100,0,7,Ltext0
    ^
    /var/folders/0k/bn4j3rz148g0c5ddh2b0hvwc0000gn/T//ccKQVrBO.s:5:9: error: unsupported directive '.stabs'
    .stabs "gcc2_compiled.",60,0,0,0
    ^
    .
    .
    .
    .
    /var/folders/0k/bn4j3rz148g0c5ddh2b0hvwc0000gn/T//ccKQVrBO.s:1217:11: warning: section "__textcoal_nt" is deprecated
    .section __TEXT,__textcoal_nt,coalesced,pure_instructions
    ^ ~~~~~~~~~~~~~
    /var/folders/0k/bn4j3rz148g0c5ddh2b0hvwc0000gn/T//ccKQVrBO.s:1217:11: note: change section name to "__text"
    .section __TEXT,__textcoal_nt,coalesced,pure_instructions
    ^ ~~~~~~~~~~~~~
    make: *** [matexp.o] Error 1
    ERROR: compilation failed for package ‘expm’
  • removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/expm’
    Warning in install.packages :
    installation of package ‘expm’ had non-zero exit status

The downloaded source packages are in
‘/private/var/folders/0k/bn4j3rz148g0c5ddh2b0hvwc0000gn/T/RtmpXeoqF9/downloaded_packages’

#4

Apparently you have some problems with your gcc compiler, fixing this could be a little tricky and is very system specific, so if you don't need the latest version right now, you can just install the binary version with

install.packages("expm", type = "binary")
#5

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