Problem package MKmisc

Bourbaki · May 24, 2022, 7:11pm

Hi,
I've tried to install MKmisc, but I've an error :
" Warning in install.packages : dependency ‘limma’ is not available "
When I want to charge this package with library, I've this :
" Error: package or namespace load failed for ‘MKmisc’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘limma’ "

So, I've tried to install limma with :

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("limma")

But I've the same problem
" Warning message: In install.packages(...) : installation of package ‘limma’ had non-zero exit status "

Do you have any idea ?
Thanks

andresrcs · May 24, 2022, 8:00pm

Can you please post the complete console output you get when you try to install it? The excerpt you are showing only tell us that the installation process has failed but it doesn't give us any clue about the cause.

Bourbaki · May 24, 2022, 8:21pm

Sorry, here is the complete script :

First :

> install.packages("MKmisc")

Warning in install.packages :
  dependency ‘limma’ is not available
trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/MKmisc_1.8.tgz'
Content type 'application/x-gzip' length 765425 bytes (747 KB)
==================================================
downloaded 747 KB

The downloaded binary packages are in
	/var/folders/dy/jw2kwlwd54qgcg3hrwh5g1_c0000gn/T//RtmppGU2gK/downloaded_packages

Then with BiocManager and try to install lima :

> install.packages("BiocManager")

trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/BiocManager_1.30.18.tgz'
Content type 'application/x-gzip' length 357940 bytes (349 KB)
==================================================
downloaded 349 KB

The downloaded binary packages are in
	/var/folders/dy/jw2kwlwd54qgcg3hrwh5g1_c0000gn/T//Rtmp3PSuBw/downloaded_packages

> BiocManager::install("limma")

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories'
for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.0 (2022-04-22)
Installing package(s) 'limma'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Package which is only available in source form, and may need compilation of
  C/C++/Fortran: ‘limma’
Do you want to attempt to install these from sources? (Yes/no/cancel) 
installing the source package ‘limma’

trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/limma_3.52.1.tar.gz'
Content type 'application/x-gzip' length 1513589 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

* installing *source* package ‘limma’ ...
** using staged installation
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c normexp.c -o normexp.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c weighted_lowess.c -o weighted_lowess.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o limma.so init.o normexp.o weighted_lowess.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: framework not found CoreFoundation
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [limma.so] Error 1
ERROR: compilation failed for package ‘limma’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/limma’

The downloaded source packages are in
	‘/private/var/folders/dy/jw2kwlwd54qgcg3hrwh5g1_c0000gn/T/Rtmp3PSuBw/downloaded_packages’
Old packages: 'parameters'
Update all/some/none? [a/s/n]: 
a
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.15/bioc/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.15/data/annotation/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.15/data/experiment/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.15/workflows/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'https://bioconductor.org/packages/3.15/books/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'

  There is a binary version available but the source version is later:
           binary source needs_compilation
parameters 0.17.0 0.18.0             FALSE

installing the source package ‘parameters’

trying URL 'https://cran.rstudio.com/src/contrib/parameters_0.18.0.tar.gz'
Content type 'application/x-gzip' length 563905 bytes (550 KB)
==================================================
downloaded 550 KB

* installing *source* package ‘parameters’ ...
** package ‘parameters’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (parameters)

The downloaded source packages are in
	‘/private/var/folders/dy/jw2kwlwd54qgcg3hrwh5g1_c0000gn/T/Rtmp3PSuBw/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘limma’ had non-zero exit status

Thanks

system · June 14, 2022, 8:21pm

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