Question

ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS

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semra • 0

@848d33f7

Last seen 6 weeks ago

Türkiye

Hello,

I am encountering errors while trying to install the clusterProfiler package on Ubuntu 20.04.6 LTS with R 4.4.1 and Bioconductor 3.19. The installation fails with the following error messages:

 r

BiocManager::install("clusterProfiler")
Output:

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
Error: lazy loading failed for package Biostrings
Error: unable to load R code in package R.oo
Error: lazy loading failed for package R.oo
Error: unable to load R code in package yulab.utils
I have tried updating Bioconductor and reinstalling dependencies individually, but the issue persists.

Here is my session info:

> r
Kodu kopyala
sessionInfo()
Output:
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

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] pak_0.8.0

Any help or guidance would be greatly appreciated!

Thank you.

Bioconductor clusterProfiler • 561 views

ADD COMMENT • link updated 6 weeks ago by Lluís Revilla Sancho ▴ 760 • written 8 weeks ago by semra • 0

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What is the output from

install("Biostrings, force = TRUE)
library(Biostrings)

ADD REPLY • link 8 weeks ago James W. MacDonald 67k

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install(Biostrings, force = TRUE) Error in install(Biostrings, force = TRUE) : install fonksiyonu bulunamadı

library(Biostrings) Error in library(Biostrings) : there is no package called Biostrings

ADD REPLY • link 8 weeks ago semra • 0

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If you ever see the error fonksiyonu bulunamadı, that means you haven't loaded the package containing that function yet. I didn't think I needed to tell you to load BiocManager prior to using it to install a package, but you do need to load that package first. So do that, and then try to force the installation of Biostrings.

ADD REPLY • link 8 weeks ago James W. MacDonald 67k

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>BiocManager::install(version = "3.19", lib = "~/R/x86_64-pc-linux-gnu-library/4.4")
'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)
> library(BiocManager)
> BiocManager::install("clusterProfiler", lib = "~/R/x86_64-pc-linux-gnu-library/4.4")

'getOption("repos")' replaces Bioconductor standard repositories.
Replacement repositories:
    CRAN: https://cloud.r-project.org

** 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'
Execution halted
ERROR: lazy loading failed for package 'Biostrings'
* removing '~/R/x86_64-pc-linux-gnu-library/4.4/Biostrings'

... (similar errors for other dependencies like 'R.oo', 'yulab.utils', etc.) ...

ERROR: dependencies 'AnnotationDbi', 'DOSE', 'enrichplot', 'GO.db', 'GOSemSim', 'yulab.utils' are not available for package 'clusterProfiler'
* removing '~/R/x86_64-pc-linux-gnu-library/4.4/clusterProfiler'

The downloaded source packages are in '/tmp/RtmpQoyAZ0/downloaded_packages'

18 errors occurred.

Also when ı attempt

>BiocManager::install(Biostrings, force = TRUE)

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
Hata: unable to load R code in package Biostrings
Çalıştırma durduruldu
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/RtmpQoyAZ0/downloaded_packages
Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    boot, codetools, foreign, lattice, Matrix, nlme
Uyarı mesajları:
In install.packages(...) :
  installation of package Biostrings had non-zero exit status
> library(Biostrings)

Error in library(Biostrings) : there is no package called Biostrings

ADD REPLY • link updated 8 weeks ago by James W. MacDonald 67k • written 8 weeks ago by semra • 0

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I would recommend to update the recommended packages (boot, codetools, foreign, lattice, Matrix, nlme) and try again. But this is a bit weird. Do you have several libraries or permission problems on that computer?

ADD REPLY • link 6 weeks ago Lluís Revilla Sancho ▴ 760