[BioC] A question about ShortRead_1.8.2.tar.gz.
Martin Morgan
mtmorgan at fhcrc.org
Fri Jan 21 04:10:17 CET 2011
On 01/20/2011 11:21 AM, Dan Tenenbaum wrote:
> On Wed, Jan 19, 2011 at 10:53 PM, Ðì¼Ó±ª <xujiabao at 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?
Dan's suggestion is probably good in the long run if you're trying to
install many packages on your server.
Your problem suggests you're trying to install ShortRead on an older
version of R; the solution is to install the correct version of
ShortRead for your R. You could figure this out by visiting
http://bioconductor.org/help/index.html
looking for the 'Previous Versions' box, following the appropriate link
your version of R, and clicking on 'Software' and then ShortRead. You
might need to manually make sure that the Dependencies listed on that
page are satisfied. Provide the output of
sessionInfo()
for more explicit and helpful diagnosis.
Martin
>>
>
>
> 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 at fhcrc.org>
>> ÊÕ¼þÈË: "xujiabao" <xujiabao at genomics.org.cn>
>> ³ËÍ: bioconductor at 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 at 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]]
>>
>>
>> _______________________________________________
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>>
>>
>
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