[BioC] Difficulties updating Biostrings on Ubuntu
Benilton Carvalho
beniltoncarvalho at gmail.com
Sun Aug 22 04:05:00 CEST 2010
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 Afterwards the computer still has the same (presumably outdated) version (2.14.12).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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