[BioC] Difficulties updating Biostrings on Ubuntu

Erik Wright eswright at wisc.edu
Sun Aug 22 16:42:57 CEST 2010


Hi Benilton,

Yes, all I need to do was upgrade R.  Apparently the CRAN mirror I was using no longer exists, so apt-get updates were not occurring automatically and I never noticed.

Thanks,
Erik


On Aug 21, 2010, at 9:05 PM, Benilton Carvalho wrote:

> You should start by upgrading R.
> 
> Version 2.14.12 is the best you can get when running R-2.10.x... And
> "mix-and-match" is not recommended.
> 
> b
> 
> On 22 August 2010 02:45, Erik Wright <eswright at wisc.edu> wrote:
>> Hello,
>> 
>> I am attempting to upgrade the Biostrings package on a linux box running Ubuntu (10.04).
>> 
>> If I use:
>>> source("http://bioconductor.org/biocLite.R")
>>> biocLite("Biostrings")
>> Afterwards the computer still has the same (presumably outdated) version (2.14.12).
>> 
>> So I tried installing the development version from source with:
>> $ R CMD INSTALL './Biostrings_2.8.18.tar.gz'
>> and got the following error:
>> Error in isSingleNumber(length) : element 1 is empty;
>>   the part of the args list of 'is.numeric' being evaluated was:
>>   (x)
>> 
>> Then I tried install a release version from source using:
>> $ R CMD INSTALL './Biostrings_2.17.29.tar.gz'
>> and received a different error:
>> make: *** [MIndex_class.o] Error 1
>> ERROR: compilation failed for package ‘Biostrings’
>> 
>> What am I doing wrong?
>> 
>> Thanks,
>> Erik
>> 
>> 
>>> sessionInfo()
>> R version 2.10.1 (2009-12-14)
>> x86_64-pc-linux-gnu
>> 
>> locale:
>>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>> 
>> other attached packages:
>> [1] Biostrings_2.14.12 IRanges_1.4.16
>> 
>> loaded via a namespace (and not attached):
>> [1] Biobase_2.6.1
>> 
>> 
>> 
>> $ R CMD INSTALL './Biostrings_2.8.18.tar.gz'
>> * installing to library ‘/R/x86_64-pc-linux-gnu-library/2.10’
>> * installing *source* package ‘Biostrings’ ...
>> ** libs
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c ACtree_utils.c -o ACtree_utils.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c IRanges_class.c -o IRanges_class.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c IRanges_utils.c -o IRanges_utils.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c MIndex_utils.c -o MIndex_utils.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c R_init_Biostrings.c -o R_init_Biostrings.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c SparseList_utils.c -o SparseList_utils.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c XInteger.c -o XInteger.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c XRaw_class.c -o XRaw_class.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c XRaw_utils.c -o XRaw_utils.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c XStringSet_class.c -o XStringSet_class.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c XString_class.c -o XString_class.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c align_needwunsQS.c -o align_needwunsQS.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c bufutils.c -o bufutils.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c char_frequency.c -o char_frequency.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c char_translate.c -o char_translate.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c copy_seq.c -o copy_seq.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c find_palindromes.c -o find_palindromes.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c inject_code.c -o inject_code.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c match_BOC.c -o match_BOC.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c match_BOC2.c -o match_BOC2.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c match_PWM.c -o match_PWM.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c match_TBdna.c -o match_TBdna.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c match_pattern.c -o match_pattern.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c match_pattern_shiftor.c -o match_pattern_shiftor.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c match_reporting.c -o match_reporting.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c match_utils.c -o match_utils.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c pmatchPattern.c -o pmatchPattern.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c replace_locs.c -o replace_locs.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c seqs_to_seqs.c -o seqs_to_seqs.o
>> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c utils.c -o utils.o
>> gcc -std=gnu99 -shared -o Biostrings.so ACtree_utils.o IRanges_class.o IRanges_utils.o MIndex_utils.o R_init_Biostrings.o SparseList_utils.o XInteger.o XRaw_class.o XRaw_utils.o XStringSet_class.o XString_class.o align_needwunsQS.o align_pairwiseAlignment.o bufutils.o char_frequency.o char_translate.o copy_seq.o find_palindromes.o inject_code.o match_BOC.o match_BOC2.o match_PWM.o match_TBdna.o match_pattern.o match_pattern_boyermoore.o match_pattern_shiftor.o match_reporting.o match_utils.o pmatchPattern.o replace_locs.o seqs_to_seqs.o utils.o -L/usr/lib64/R/lib -lR
>> ** R
>> ** data
>> ** inst
>> ** preparing package for lazy loading
>> Creating a new generic function for "start" in "Biostrings"
>> Creating a new generic function for "end" in "Biostrings"
>> Creating a new generic function for "as.data.frame" in "Biostrings"
>> Creating a new generic function for "update" in "Biostrings"
>> Creating a new generic function for "duplicated" in "Biostrings"
>> Creating a new generic function for "as.matrix" in "Biostrings"
>> Creating a new generic function for "append" in "Biostrings"
>> Creating a new generic function for "ls" in "Biostrings"
>> Creating a new generic function for "as.list" in "Biostrings"
>> Creating a new generic function for "toString" in "Biostrings"
>> Error in isSingleNumber(length) : element 1 is empty;
>>   the part of the args list of 'is.numeric' being evaluated was:
>>   (x)
>> Error : unable to load R code in package 'Biostrings'
>> ERROR: lazy loading failed for package ‘Biostrings’
>> * removing ‘/R/x86_64-pc-linux-gnu-library/2.10/Biostrings’
>> * restoring previous ‘/R/x86_64-pc-linux-gnu-library/2.10/Biostrings’
>> 
>> 
>> 
>> $ R CMD INSTALL './Biostrings_2.17.29.tar.gz'
>> * installing to library ‘/R/x86_64-pc-linux-gnu-library/2.10’
>> * installing *source* package ‘Biostrings’ ...
>> ** libs
>> gcc -std=gnu99 -I/usr/share/R/include   -I"/R/x86_64-pc-linux-gnu-library/2.10/IRanges/include"   -fpic  -g -O2 -c BAB_class.c -o BAB_class.o
>> gcc -std=gnu99 -I/usr/share/R/include   -I"/R/x86_64-pc-linux-gnu-library/2.10/IRanges/include"   -fpic  -g -O2 -c BitMatrix.c -o BitMatrix.o
>> gcc -std=gnu99 -I/usr/share/R/include   -I"/R/x86_64-pc-linux-gnu-library/2.10/IRanges/include"   -fpic  -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
>> gcc -std=gnu99 -I/usr/share/R/include   -I"/R/x86_64-pc-linux-gnu-library/2.10/IRanges/include"   -fpic  -g -O2 -c MIndex_class.c -o MIndex_class.o
>> MIndex_class.c: In function ‘ByPos_MIndex_combine’:
>> MIndex_class.c:261: error: too many arguments to function ‘IntAE_qsort’
>> MIndex_class.c:263: warning: implicit declaration of function ‘new_INTEGER_from_IntAE’
>> MIndex_class.c:263: warning: assignment makes pointer from integer without a cast
>> make: *** [MIndex_class.o] Error 1
>> ERROR: compilation failed for package ‘Biostrings’
>> * removing ‘/R/x86_64-pc-linux-gnu-library/2.10/Biostrings’
>> * restoring previous ‘/R/x86_64-pc-linux-gnu-library/2.10/Biostrings’
>> 
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