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Dear all,
I have a fresh installed R-devel (R-3.2.0) and got the following error when installing Rsamtools using BiocLite from BiocInstaller:
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG -I/usr/local/include -I"/usr/local/lib/R/library/S4Vectors/include" -I"/usr/local/lib/R/library/IRanges/include" -I"/usr/local/lib/R/library/XVector/include" -I"/usr/local/lib/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c fafile.c -o fafile.o fafile.c: In function ‘translate’: fafile.c:122:29: error: ‘Chars_holder’ has no member named ‘seq’ fafile.c:125:39: error: ‘Chars_holder’ has no member named ‘seq’ fafile.c: In function ‘scan_fa’: fafile.c:167:59: error: ‘Chars_holder’ has no member named ‘seq’ make: *** [fafile.o] Error 1 ERROR: compilation failed for package ‘Rsamtools’
Does anyone encountered this error before or knows how to resolve this issue?
Kind regards,
Maarten
sessionInfo() R Under development (unstable) (2014-11-25 r67060) Platform: x86_64-unknown-linux-gnu (64-bit) 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] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.17.1 loaded via a namespace (and not attached): [1] tools_3.2.0