[Bioc-devel] VariantAnnotation Installation Compile Error

[Vincent Carey]

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-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_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] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] VariantAnnotation_1.38.0    Rsamtools_2.8.0
 [3] Biostrings_2.60.0           XVector_0.32.0
 [5] SummarizedExperiment_1.22.0 Biobase_2.52.0
 [7] GenomicRanges_1.44.0        GenomeInfoDb_1.28.0
 [9] IRanges_2.26.0              S4Vectors_0.30.0
[11] MatrixGenerics_1.4.0        matrixStats_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 <dstr7320 using 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
> * 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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> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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