[Bioc-devel] Problem installing Biostrings - development version
Hervé Pagès
hpages at fhcrc.org
Wed Apr 1 23:11:08 CEST 2009
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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