[BioC] Problem when I install shortread

Wei Wu wuwei at ucalgary.ca
Wed Sep 21 01:26:05 CEST 2011


Hello, everyone,

I have installed R successfully. But when I install the ShortRead with 
the command:

     source("http://www.bioconductor.org/biocLite.R")
     biocLite("ShortRead")

I met the problem:

g++ -I/bigstor2/wei/lib64/R/include  -I/usr/local/include -I"/bigstor2/wei/lib64/R/library/IRanges/include" -I"/bigstor2/wei/lib64/R/library/Biostrings/include"  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -DHAVE_LIBZ=1 -fpic  -g -O2 -c readBfaToc.cc -o readBfaToc.o
/bin/sh: g++: command not found
make: *** [readBfaToc.o] Error 127
ERROR: compilation failed for package 'ShortRead'
* removing '/bigstor2/wei/lib64/R/library/ShortRead'
* restoring previous '/bigstor2/wei/lib64/R/library/ShortRead'

The downloaded packages are in
         '/tmp/RtmpbuyOyI/downloaded_packages'
Updating HTML index of packages in '.Library'
Making packages.html  ... done
Warning message:
In install.packages(pkgs = pkgs, repos = repos, ...) :
   installation of package 'ShortRead' had non-zero exit status

What should I do next?

Thanks

Wei Wu



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