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Question: Biostrings install error
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gravatar for owenchapman1
28 days ago by
owenchapman10 wrote:

Haven't seen other posts with useful solutions for similar errors, so making a new post.  Trying to install Biostrings using BiocManager, which breaks.  Looks like gcc is throwing a warning on a function called filexp_tell (no mention of it on google...), which eventually prevents loading of the package. Version information: Bioconductor version 3.8 (BiocManager 1.30.3), R 3.5.1 (2018-07-02). OS information: Ubuntu 16.040.5 LTS Xenial Xerus, embedded in Windows 10.

Logs below:

gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include"    -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c read_fasta_files.c -o read_fasta_files.o
read_fasta_files.c: In function ‘get_fasta_seqlengths’:
read_fasta_files.c:375:22: warning: implicit declaration of function ‘filexp_tell’ [-Wimplicit-function-declaration]
   offset0 = offset = filexp_tell(filexp);
                      ^
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include"    -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c read_fastq_files.c -o read_fastq_files.o
read_fastq_files.c: In function ‘get_fastq_seqlengths’:
read_fastq_files.c:359:22: warning: implicit declaration of function ‘filexp_tell’ [-Wimplicit-function-declaration]
   offset0 = offset = filexp_tell(filexp);
                      ^
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include"    -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c replaceAt.c -o replaceAt.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include"    -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c replace_letter_at.c -o replace_letter_at.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include"    -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c strutils.c -o strutils.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include"    -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c translate.c -o translate.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include"    -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include"    -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include"    -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c xscat.c -o xscat.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/Biostrings/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘twoWayAlphabetFrequencyByQuality’ with signature ‘"QualityScaledXStringSet"’: no definition for class “QualityScaledXStringSet”
Creating a new generic function for ‘strsplit’ in package ‘Biostrings’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘Biostrings’
Creating a new generic function for ‘offset’ in package ‘Biostrings’
** help
Warning: /tmp/Rtmpp7dVhj/R.INSTALL8897293b94b/Biostrings/man/translate.Rd:59: unexpected TEXT '(no.init.codon)', expecting '{'
Warning: /tmp/Rtmpp7dVhj/R.INSTALL8897293b94b/Biostrings/man/translate.Rd:67: unknown macro '\item'
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for ‘Biostrings’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/usr/local/lib/R/site-library/Biostrings/libs/Biostrings.so':
  /usr/local/lib/R/site-library/Biostrings/libs/Biostrings.so: undefined symbol: filexp_tell
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/Biostrings’

ADD COMMENTlink modified 28 days ago • written 28 days ago by owenchapman10
0
gravatar for owenchapman1
28 days ago by
owenchapman10 wrote:

filexp_tell is a new function in the latest (Sept 30 2018) version of XVector.  Somehow I had gotten v0.22.0 of XVector, without getting all of the actual updates (my /usr/local/lib/R/site_library/XVector/include/XVector_interface.h file did not have filexp_tell ), but because the version number was up-to-date R didn't recognize the need to redownload XVector. Uninstalling and reinstalling XVector got me the the actual version 0.22.0 and allowed me to successfully install Biostrings.

ADD COMMENTlink modified 28 days ago • written 28 days ago by owenchapman10

Hi,

Are you using BiocManager::install() as recommended to install and update packages? It will spare you version mismatch headaches like the above.

H.

ADD REPLYlink written 28 days ago by Hervé Pagès ♦♦ 13k
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