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

This is in the devel version of Rsamtools. There was a changed in a package Rsamtools depends on (S4Vectors) that broke Rsamtools. Rsamtools has since been updated to correct this, and should be available again once the build completes at around noon today Seattle time.

Dear Martin Morgan,

Thanks for the clarification!

Cheers,

Maarten