ERROR happens when install "DSS" package
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@dadbfbf7
Last seen 14 days ago
United States

I don't know why it shows "Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘DSS’" when installing the "DSS" package.

I also try to use "BiocManager::install("DSS",type="source")" but still failed.

> BiocManager::install("DSS")

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

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

Bioconductor version 3.16 (BiocManager 1.30.17), R 4.2.0 (2022-04-22 ucrt)
Installing package(s) 'DSS'
Warning: 无法在貯藏處https://bioconductor.org/packages/3.16/data/annotation/bin/windows/contrib/4.2中读写索引:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/bin/windows/contrib/4.2/PACKAGES'
Package which is only available in source form, and may need compilation of
  C/C++/Fortran: ‘DSS’
  These will not be installed
Installation paths not writeable, unable to update packages
  path: C:/Program Files/R/R-4.2.0/library
  packages:
    MASS

sessionInfo( )
methylationArrayAnalysis ChAMP DMP DSS • 210 views
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This happened for windows. DSS has some compilation error for windows so windows binary package is not available on bioc. You can install from source, but you need to have proper compilers to compile the C code. For that, you need to install RTools: https://cran.r-project.org/bin/windows/Rtools/. Please try to install RTools and try to install again.

Sorry for the inconvenience. I’m trying to fix the error on Windows.

Hao

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Thanks for answering! Now the problem is solved when I update the RTools~~Thx

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@james-w-macdonald-5106
Last seen 2 days ago
United States

There's two parts to the answer.

  1. DSS is failing to build on the Windows builder because the vignette wants to run on multiple cores and it's not working. Because of that there is no binary package, so your only recourse is to build from source (until the problem is fixed on the builder or package, whichever is at fault).
  2. To install source packages that contain C/C++/Fortran code on Windows, you need RTools to be installed. In which case it goes like this:
> install("DSS", type = "source")
Bioconductor version 3.15 (BiocManager 1.30.17), R 4.2.0 (2022-04-22 ucrt)
Installing package(s) 'DSS'
trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/DSS_2.44.0.tar.gz'
Content type 'application/x-gzip' length 2112560 bytes (2.0 MB)
downloaded 2.0 MB

* installing *source* package 'DSS' ...
** using staged installation
** libs
gcc  -I"c:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c compute_var_smooth.c -o compute_var_smooth.o
gcc  -I"c:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c filter.c -o filter.o
gcc  -I"c:/PROGRA~1/R/R-42~1.0/include" -DNDEBUG     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c nitem.c -o nitem.o
gcc -shared -s -static-libgcc -o DSS.dll tmp.def compute_var_smooth.o filter.o nitem.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -Lc:/PROGRA~1/R/R-42~1.0/bin/x64 -lR
installing to C:/Users/jmacdon/AppData/Local/R/win-library/4.2/00LOCK-DSS/00new/DSS/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'matrixStats::rowMedians' by 'Biobase::rowMedians' when loading 'DSS'
Warning: replacing previous import 'matrixStats::anyMissing' by 'Biobase::anyMissing' when loading 'DSS'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'matrixStats::rowMedians' by 'Biobase::rowMedians' when loading 'DSS'
Warning: replacing previous import 'matrixStats::anyMissing' by 'Biobase::anyMissing' when loading 'DSS'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'matrixStats::rowMedians' by 'Biobase::rowMedians' when loading 'DSS'
Warning: replacing previous import 'matrixStats::anyMissing' by 'Biobase::anyMissing' when loading 'DSS'
** testing if installed package keeps a record of temporary installation path
* DONE (DSS)
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It's very kind of you!! I found that the problem was that I didn't update my RTools. Now it's solved. Thank you!

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