[Bioc-devel] VariantAnnotation Installation Compile Error

[Dario Strbenac]

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

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Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia