[Bioc-devel] Problem installing Biostrings - development version

[Dykema, Karl]

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
>
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