Re: [Bioc-devel] VariantAnnotation Installation Compile Error
Hello, The problem stemed from an .Rprofile file which was setting .libPaths with the directory path to a library of packages for the previous version of R and starting R with the --vanilla option avoided the problem. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] VariantAnnotation Installation Compile Error
Good day, I also see NULL on R start-up. I installed R from source. $ R-4.1.0/bin/R R version 4.1.0 (2021-05-18) -- "Camp Pontanezen" ...... Type 'q()' to quit R. NULL > I noticed a couple of error messages at the end of the installation which I thought were harmless. I will reinstall R. The extracted directory and prefix directory were the same, which might be problematic. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] VariantAnnotation Installation Compile Error
On Sun, May 23, 2021 at 10:00 PM Dario Strbenac
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
>
--
The information in this e-mail is intended only for the ...{{dropped:18}}
___
Bioc-devel@r-project.org mailing list
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Re: [Bioc-devel] VariantAnnotation Installation Compile Error
Good day, No, the temporary directory has space remaining. I wonder what file it is referring to by "No such file or directory". I had an idea to reinstall Biostrings using force = TRUE, but it didn't help. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] VariantAnnotation Installation Compile Error
Thanks for the report. I just installed from source successfully with
> sessionInfo()
R version 4.1.0 Patched (2021-05-23 r80366)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS (fossa-melisa X20)
Matrix products: default
BLAS: /home/stvjc/R-4-1-dist/lib/R/lib/libRblas.so
LAPACK: /home/stvjc/R-4-1-dist/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] VariantAnnotation_1.38.0Rsamtools_2.8.0
[3] Biostrings_2.60.0 XVector_0.32.0
[5] SummarizedExperiment_1.22.0 Biobase_2.52.0
[7] GenomicRanges_1.44.0GenomeInfoDb_1.28.0
[9] IRanges_2.26.0 S4Vectors_0.30.0
[11] MatrixGenerics_1.4.0matrixStats_0.58.0
[13] BiocGenerics_0.38.0
It is good that BiocManager::valid() returns TRUE. Might you be out of temp
space?
On Sun, May 23, 2021 at 10:00 PM Dario Strbenac
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
> * 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
>
--
The information in this e-mail is intended only for the ...{{dropped:18}}
___
Bioc-devel@r-project.org mailing list
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[Bioc-devel] VariantAnnotation Installation Compile Error
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
* 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
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