[Bioc-devel] Problem installing Biostrings - development version
Hervé Pagès
hpages at fhcrc.org
Thu Apr 2 00:11:40 CEST 2009
Hi Karl,
I fixed our build scripts and all the latest versions of the development
packages are now online (granted they passed 'R CMD check' on today's
builds -- see http://bioconductor.org/checkResults/2.4/bioc-LATEST/).
Please try again to install Biostrings with biocLite() (you should get
version 2.11.46) and let me know if you encounter any other issues.
Cheers,
H.
Hervé Pagès wrote:
> Hi Karl,
>
> This problem has been fixed in Biostrings >= 2.11.45 but thanks to your
> post I discovered that package updates have not been propagated to our
> public
> software repository for the last couple of days. I'm currently
> investigating
> this and will keep you informed. Thanks!
>
> H.
>
>
> Dykema, Karl wrote:
>> Hello All,
>>
>> I would like to use the latest version of ShortRead so I am attempting
>> to install development versions of R and Bioconductor. I downloaded
>> the development snapshot of R that was released yesterday, March 31,
>> and it compiled on my system without any problems. Then I tried to
>> install Biobase using biocLite() and it worked until it got to the
>> Biostrings package where it had an error. The package passes the most
>> recent build/check report, but the server (wilson1) is using a
>> snapshot of R from March 1. My first thought was to try using that
>> exact version of R but I was not able to locate it...
>>
>> I have recreated the error below along with my sessionInfo(). Thanks
>> in advance for any help you can offer!
>>
>>
>>
>> -------------------------------------------
>> Karl Dykema
>> Computational Biologist
>> Laboratory of Computational Biology
>> Van Andel Research Institute
>> 333 Bostwick Ave NE
>> Grand Rapids, MI 49503
>>
>>
>>
>>
>>
>>
>>> sessionInfo()
>> R version 2.9.0 alpha (2009-03-31 r48262) x86_64-unknown-linux-gnu
>>
>> locale:
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] Biobase_2.3.11
>>
>>
>>> source("http://bioconductor.org/biocLite.R")
>>> biocLite("Biostrings")
>> Running biocinstall version 2.4.6 with R version 2.9.0 (under
>> development) Your version of R requires version 2.4 of Bioconductor.
>> trying URL
>> 'http://bioconductor.org/packages/2.4/bioc/src/contrib/Biostrings_2.11.44.tar.gz'
>>
>> Content type 'application/x-gzip' length 1038622 bytes (1014 Kb)
>> opened URL ==================================================
>> downloaded 1014 Kb
>>
>> * Installing *source* package 'Biostrings' ...
>> ** libs
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> BAB_class.c -o BAB_class.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> Dups_utils.c -o Dups_utils.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> IRanges_stubs.c -o IRanges_stubs.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> MIndex_utils.c -o MIndex_utils.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> PreprocessedTB_class.c -o PreprocessedTB_class.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> R_init_Biostrings.c -o R_init_Biostrings.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> RoSeq_utils.c -o RoSeq_utils.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> SparseList_utils.c -o SparseList_utils.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> XStringSet_class.c -o XStringSet_class.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> XString_class.c -o XString_class.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> align_needwunsQS.c -o align_needwunsQS.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> align_pairwiseAlignment.c -o align_pairwiseAlignment.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> align_utils.c -o align_utils.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> char_frequency.c -o char_frequency.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> char_translate.c -o char_translate.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> copy_seq.c -o copy_seq.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> fasta_io.c -o fasta_io.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> find_palindromes.c -o find_palindromes.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> inject_code.c -o inject_code.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> match_BOC.c -o match_BOC.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> match_BOC2.c -o match_BOC2.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> match_PWM.c -o match_PWM.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> match_pattern.c -o match_pattern.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> match_pattern_at.c -o match_pattern_at.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> match_pattern_boyermoore.c -o match_pattern_boyermoore.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> match_pattern_indels.c -o match_pattern_indels.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> match_pattern_shiftor.c -o match_pattern_shiftor.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> match_pdict.c -o match_pdict.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> match_pdict_ACtree.c -o match_pdict_ACtree.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> match_pdict_ACtree2.c -o match_pdict_ACtree2.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> match_pdict_Twobit.c -o match_pdict_Twobit.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> match_reporting.c -o match_reporting.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> matchprobes.c -o matchprobes.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> pmatchPattern.c -o pmatchPattern.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> replace_letter_at.c -o replace_letter_at.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> strutils.c -o strutils.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> utils.c -o utils.o
>> gcc -std=gnu99 -I/home/karl/R-alpha/include -I/usr/local/include
>> -I"/mnt/disk3/karl/R-alpha/library/IRanges/include" -fpic -g -O2 -c
>> xscat.c -o xscat.o
>> gcc -std=gnu99 -shared -L/usr/local/lib64 -o Biostrings.so BAB_class.o
>> Dups_utils.o IRanges_stubs.o MIndex_utils.o PreprocessedTB_class.o
>> R_init_Biostrings.o RoSeq_utils.o SparseList_utils.o
>> XStringSet_class.o XString_class.o align_needwunsQS.o
>> align_pairwiseAlignment.o align_utils.o char_frequency.o
>> char_translate.o copy_seq.o fasta_io.o find_palindromes.o
>> inject_code.o match_BOC.o match_BOC2.o match_PWM.o match_pattern.o
>> match_pattern_at.o match_pattern_boyermoore.o match_pattern_indels.o
>> match_pattern_shiftor.o match_pdict.o match_pdict_ACtree.o
>> match_pdict_ACtree2.o match_pdict_Twobit.o match_reporting.o
>> matchprobes.o pmatchPattern.o replace_letter_at.o strutils.o utils.o
>> xscat.o
>> ** R
>> ** data
>> ** inst
>> ** preparing package for lazy loading
>>
>> Attaching package: 'IRanges'
>>
>>
>> The following object(s) are masked from package:base :
>>
>> cbind,
>> duplicated,
>> order,
>> pmax,
>> pmax.int,
>> pmin,
>> pmin.int,
>> rank,
>> rbind,
>> rep.int,
>> sapply,
>> sort,
>> table,
>> unique
>>
>> Warning in matchSignature(signature, fdef, where) :
>> in the method signature for function "XString" no definition for
>> class: "AsIs"
>> Warning in matchSignature(signature, fdef, where) :
>> in the method signature for function "XStringSet" no definition for
>> class: "AsIs"
>> Creating a new generic function for "setequal" in "Biostrings"
>> Warning in matchSignature(signature, fdef, where) :
>> in the method signature for function "BStringViews" no definition
>> for class: "file"
>> Creating a new generic function for "ls" in "Biostrings"
>> Creating a new generic function for "head" in "Biostrings"
>> Creating a new generic function for "tail" in "Biostrings"
>> Warning in matchSignature(signature, fdef, where) :
>> in the method signature for function "PDict" no definition for
>> class: "AsIs"
>> Error: no function to return from, jumping to top level Execution halted
>>
>> The downloaded packages are in
>> '/mnt/disk2/tmp/RtmpkjnnZ8/downloaded_packages'
>> Updating HTML index of packages in '.Library'
>> Warning message:
>> In install.packages(pkgs = pkgs, repos = repos, dependencies =
>> dependencies, :
>> installation of package 'Biostrings' had non-zero exit status
>> This email message, including any attachments, is for ...{{dropped:20}}
>
> _______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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