Entering edit mode
On Wed, Jan 19, 2011 at 10:53 PM, Ðì¼Ó±ª <xujiabao@genomics.org.cn>
wrote:
> Dan Tenenbaum:
> Thank you for your reply.However the cluster with linux
system
> can not connect to the internet for the reason of security. So the
function
> below can't work anymore.
> source(" http://bioconductor.org/biocLite.R ")
> biocLite("ShortRead")
>
> Is there other way to solve the prolem?
>
Hi,
You need to create your own internal repository which you can access
from
your cluster, and install
the packages from there.
Our page on creating mirrors should help you:
http://bioconductor.org/about/mirrors/mirror-how-to/
Dan
>
> BEST!
>
> JiaBao Xu
>
>
> ·¢¼þÈË: "Dan Tenenbaum" <dtenenba@fhcrc.org>
> ÊÕ¼þÈË: "xujiabao" <xujiabao@genomics.org.cn>
> ³ËÍ: bioconductor@stat.math.ethz.ch
> ·¢ËÍʱ¼ä: ÐÇÆÚËÄ, 2011Äê 1 Ô 20ÈÕ ÉÏÎç 5:26:33
> Ö÷Ìâ: Re: [BioC] A question about ShortRead_1.8.2.tar.gz.
>
>
>
>
> On Tue, Jan 18, 2011 at 5:46 PM, xujiabao < xujiabao@genomics.org.cn
>
> wrote:
>
>
> Dear bioconductors£º
> 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]]
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
[[alternative HTML version deleted]]
