Entering edit mode
4 weeks ago
iamsmor
•
0
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. Has anyone encountered this and help me ?
>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
Pathway analysis for mouse gene sets ; Automated my docking results by using script ; Downloaded pdb's on rcsb.org ; autodockvina ; autodock vina on mac ; molecular docking for a ligand to multi protein ; pymol for superimpose by python script ; etc... etc...
thank you mostly ı am using upvote if its helpful, but ı wasnot awere of accept button. I will pay attention