On Sun, May 23, 2021 at 10:00 PM Dario Strbenac <dstr7...@uni.sydney.edu.au>
wrote:
> Good day,
>
> I apparently have a valid Bioconductor package library but
> VariantAnnotation won't install successfully.
>
> > valid()
> [1] TRUE
> > install("VariantAnnotation")
> Bioconductor version 3.13 (BiocManager 1.30.15), R 4.1.0 (2021-05-18)
> Installing package(s) 'VariantAnnotation'
> trying URL '
> https://bioconductor.org/packages/3.13/bioc/src/contrib/VariantAnnotation_1.38.0.tar.gz
> '
> Content type 'application/x-gzip' length 1726088 bytes (1.6 MB)
> ==================================================
> downloaded 1.6 MB
>
> NULL
>
The NULL here doesn't look good
I see
trying URL '
https://bioconductor.org/packages/3.13/bioc/src/contrib/VariantAnnotation_1.38.0.tar.gz
'
Content type 'application/x-gzip' length 1726088 bytes (1.6 MB)
==================================================
downloaded 1.6 MB
* installing *source* package ‘VariantAnnotation’ ...
** using staged installation
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include"
-DNDEBUG -D_FILE_OFFSET_BITS=64
-I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/S4Vectors/include'
-I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/IRanges/include'
-I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/XVector/include'
-I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Biostrings/include'
-I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rhtslib/include'
-I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c
Biostrings_stubs.c -o Biostrings_stubs.o
> * installing *source* package ‘VariantAnnotation’ ...
> ** using staged installation
> ** libs
> gcc -I"/verona/biostat/software/R-4.1.0/include" -DNDEBUG NULL
> -D_FILE_OFFSET_BITS=64
> -I'/dskh/biostat/software/R-4.1.0/library/S4Vectors/include'
> -I'/dskh/biostat/software/R-4.1.0/library/IRanges/include'
> -I'/dskh/biostat/software/R-4.1.0/library/XVector/include'
> -I'/dskh/biostat/software/R-4.1.0/library/Biostrings/include'
> -I'/dskh/biostat/software/R-4.1.0/library/Rhtslib/include'
> -I/usr/local/include -fpic -g -O2 -c Biostrings_stubs.c -o
> Biostrings_stubs.o
> gcc: error: NULL: No such file or directory
> make: *** [/verona/biostat/software/R-4.1.0/etc/Makeconf:168:
> Biostrings_stubs.o] Error 1
> ERROR: compilation failed for package ‘VariantAnnotation’
>
> > sessionInfo()
> R version 4.1.0 (2021-05-18)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Debian GNU/Linux 10 (buster)
> BLAS: /dskh/biostat/software/R-4.1.0/lib/libRblas.so
> LAPACK: /dskh/biostat/software/R-4.1.0/lib/libRlapack.so
>
> --------------------------------------
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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