On Tue, Jan 18, 2011 at 5:46 PM, xujiabao <xujiabao@genomics.org.cn> wrote:

> Dear bioconductors：
>            Yesterday I installed the package ShortRead_1.8.2.tar.gz via the
> command ," R CMD INSTALL ./pkg2/ShortRead_1.8.2.tar.gz  -l ./library/
> ".However ,the error happened with the message in  the attachment.The error
> message is below:
>
>
> * installing *source* package 'ShortRead' ...
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking how to run the C preprocessor... gcc -E
> checking for grep that handles long lines and -e... /bin/grep
> checking for egrep... /bin/grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking size of unsigned long... 8
> checking for gzeof in -lz... yes
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include
>  -I/usr/local/include
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include"
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include"
> -fpic  -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o
> gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include
>  -I/usr/local/include
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include"
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include"
> -fpic  -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
> gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include
>  -I/usr/local/include
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include"
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include"
> -fpic  -g -O2 -c R_init_ShortRead.c -o R_init_ShortRead.o
> gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include
>  -I/usr/local/include
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include"
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include"
> -fpic  -g -O2 -c alphabet.c -o alphabet.o
> gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include
>  -I/usr/local/include
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include"
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include"
> -fpic  -g -O2 -c io.c -o io.o
> gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include
>  -I/usr/local/include
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include"
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include"
> -fpic  -g -O2 -c io_bowtie.c -o io_bowtie.o
> gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include
>  -I/usr/local/include
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include"
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include"
> -fpic  -g -O2 -c io_soap.c -o io_soap.o
> gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include
>  -I/usr/local/include
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include"
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include"
> -fpic  -g -O2 -c pileup.c -o pileup.o
> g++ -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include  -I/usr/local/include
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include"
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/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
> g++ -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include  -I/usr/local/include
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include"
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/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
> read_maq_map.cc -o read_maq_map.o
> gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include
>  -I/usr/local/include
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include"
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include"
> -fpic  -g -O2 -c sampler.c -o sampler.o
> gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include
>  -I/usr/local/include
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include"
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include"
> -fpic  -g -O2 -c util.c -o util.o
> gcc -std=gnu99 -I/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/include
>  -I/usr/local/include
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/IRanges/include"
> -I"/ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/Biostrings/include"
> -fpic  -g -O2 -c xsnap.c -o xsnap.o
> g++ -shared -L/usr/local/lib64 -o ShortRead.so Biostrings_stubs.o
> IRanges_stubs.o R_init_ShortRead.o alphabet.o io.o io_bowtie.o io_soap.o
> pileup.o readBfaToc.o read_maq_map.o sampler.o util.o xsnap.o -lz
> installing to
> /ifs1/DGE_SR/xujiabao/bin/R/bin/lib64/R/library/ShortRead/libs
> ** R
> ** inst
> ** preparing package for lazy loading
>
> Attaching package: 'IRanges'
>
> The following object(s) are masked from 'package:base':
>
>    Map, cbind, eval, mapply, order, paste, pmax, pmax.int, pmin,
>    pmin.int, rbind, rep.int, table
>
> Error in eval(expr, envir, enclos) :
>  could not find function "setRefClass"
> Error : unable to load R code in package 'ShortRead'
> ERROR: lazy loading failed for package 'ShortRead'
> * removing 'home/xjb/R/bin/lib64/R/library/ShortRead'
>
>
> Can you help me to solve the problem? Thanks. Hope for your reply.
>
>

Hello JiaBao,

The recommended way to install a package is from within R using the
biocLite() function. This takes care of installing the appropriate package
for your version of R. Try this:

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

If you still have problems, please post the output of those commands, plus
the output of sessionInfo().

Thanks,
Dan


      BEST!
>
>     JiaBao Xu
>        [[alternative HTML version deleted]]
>
>
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