Issue Installing Biostrings Package: gcc Compilation Errors
0
0
Entering edit mode
semra • 0
@848d33f7
Last seen 16 days ago
Türkiye

I am encountering an issue while trying to install the Biostrings package from Bioconductor on my Ubuntu 20.04.6 LTS system with R version 4.4.1. The installation process fails with several gcc compilation errors.


BiocManager::install("Biostrings")
----------------------------------

'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.19 (BiocManager 1.30.25), R 4.4.1 (2024-06-14)
Installing package(s) 'Biostrings'
URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/Biostrings_2.72.1.tar.gz' attempting to download
Content type 'application/x-gzip' length 12408794 bytes (11.8 MB)
==================================================
downloaded 11.8 MB

* installing *source* package 'Biostrings' ...
** using staged installation
** libs
using C compiler: 'gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0'
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/semra/R/x86_64-pc-linux-gnu-library/4.4/S4Vectors/include' -I'/home/semra/R/x86_64-pc-linux-gnu-library/4.4/IRanges/include' -I'/home/semra/R/x86_64-pc-linux-gnu-library/4.4/XVector/include'     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-ZyAkbF/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c BAB_class.c -o BAB_class.o
...
gcc -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 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 /home/semra/R/x86_64-pc-linux-gnu-library/4.4/00LOCK-Biostrings/00new/Biostrings/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error in buildLookupTable(letter_byte_vals, codes) : 
  'vals' must be a vector of the length of 'keys'
Error: unable to load R code in package 'Biostrings'
Installation halted
ERROR: lazy loading failed for package 'Biostrings'
* removing '/home/semra/R/x86_64-pc-linux-gnu-library/4.4/Biostrings'

The downloaded source packages are in
    '/tmp/Rtmpe5NvMm/downloaded_packages'
Warning messages:
In install.packages(...) :
  installation of package 'Biostrings' had non-zero exit status
> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=tr_TR.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=tr_TR.UTF-8        LC_COLLATE=tr_TR.UTF-8    
 [5] LC_MONETARY=tr_TR.UTF-8    LC_MESSAGES=tr_TR.UTF-8   
 [7] LC_PAPER=tr_TR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=tr_TR.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Istanbul
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.25 compiler_4.4.1      tools_4.4.1        
[4] curl_5.2.2          remotes_2.5.0
Biostrings packageinstallation • 343 views
ADD COMMENT
0
Entering edit mode

The error here is in Biostrings on this line:

Error in buildLookupTable(letter_byte_vals, codes) : 
  'vals' must be a vector of the length of 'keys'

This is normally called on setup when Biostrings builds lookup tables for XString objects.

However, I'm not sure what's causing this error, and it doesn't seem to be reproducible on Ubuntu 22.04 LTS (build report). I'm also not able to reproduce this error on an arm Mac.

My suspicion is that it has something to do with language encoding...but I'm also not able to reproduce it by changing my locale to Turkish UTF-8 encoding. I'm working on building a docker image with Ubuntu 20.04 to check that as well, but I'm doubtful it will be any different.

The installation process fails with several gcc compilation errors.

None of your post shows any gcc compilation errors, are there additional error messages you're not showing?

I also saw in your reddit post that you were going to try reinstalling from scratch, did you try that yet?

Edit: If you haven't fixed it yet, could you also provide the output of the following lines? I'm hoping this will show any potential differences in locale-specific encoding.

letters
as.integer(charToRaw(paste(letters, collapse="")))
as.integer(charToRaw(paste(c("*", "-", "+", "."), collapse="")))
ADD REPLY

Login before adding your answer.

Traffic: 906 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6