Question: WGCNA-unable to install GO.db package
2
gravatar for 852108577
6 months ago by
85210857720
85210857720 wrote:

I have been trying to work on a WGCNA analysis project. However, am stuck at this GO.db situation. It seems that this package is very important for the process. Thus, I'm desperately asking for help on this issue. Can anyone let me know that the issue might be, please?

situation: I was using R3.5 at the beginning, then the WGCNA needs support of an R 3.6. So, I updated R 3.5 to R 3.6. Then the GO.db problem came. The problem is, I need to do WGCNA, which needs R3.6, and I need GO.db to get WGCNA work. The latter process needs R3.5..I'm kinda out of moves.

All coding and analysis and all are done using Rstudio.

I'm unable to attach a snapshot, so I pasted the codes and error info here:

library(WGCNA)
Error: package or namespace load failed for ‘WGCNA’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 不存在叫‘GO.db’这个名字的程辑包
> if (!requireNamespace("BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
> BiocManager::install("GO.db", version = "3.8")
Error: Bioconductor version '3.8' requires R version '3.5'; see https://bioconductor.org/install
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help
> biocLite("GO.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.6.0 (2019-04-26).
Installing package(s) ‘GO.db’
also installing the dependencies ‘Biobase’, ‘IRanges’, ‘S4Vectors’, ‘AnnotationDbi’

Warning: unable to access index for repository https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.6:
  cannot open URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.6/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.7/data/annotation/bin/windows/contrib/3.6:
  cannot open URL 'https://bioconductor.org/packages/3.7/data/annotation/bin/windows/contrib/3.6/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.7/data/experiment/bin/windows/contrib/3.6:
  cannot open URL 'https://bioconductor.org/packages/3.7/data/experiment/bin/windows/contrib/3.6/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.7/workflows/bin/windows/contrib/3.6:
  cannot open URL 'https://bioconductor.org/packages/3.7/workflows/bin/windows/contrib/3.6/PACKAGES'
Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘Biobase’ ‘IRanges’ ‘S4Vectors’
  These will not be installed
installing the source packages ‘AnnotationDbi’, ‘GO.db’

trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/AnnotationDbi_1.42.1.tar.gz'
Content type 'application/x-gzip' length 4337155 bytes (4.1 MB)
downloaded 4.1 MB

trying URL 'https://bioconductor.org/packages/3.7/data/annotation/src/contrib/GO.db_3.6.0.tar.gz'
Content type 'application/x-gzip' length 31763273 bytes (30.3 MB)
downloaded 30.3 MB

ERROR: dependencies 'Biobase', 'IRanges', 'S4Vectors' are not available for package 'AnnotationDbi'
* removing 'C:/Users/Gege/Documents/R/win-library/3.6/AnnotationDbi'
ERROR: dependency 'AnnotationDbi' is not available for package 'GO.db'
* removing 'C:/Users/Gege/Documents/R/win-library/3.6/GO.db'

The downloaded source packages are in
    ‘C:\Users\Gege\AppData\Local\Temp\Rtmp6njHc1\downloaded_packages’
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘AnnotationDbi’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GO.db’ had non-zero exit status
go cancer • 856 views
ADD COMMENTlink modified 6 months ago by Martin Morgan ♦♦ 24k • written 6 months ago by 85210857720
Answer: WGCNA-unable to install GO.db package
1
gravatar for Martin Morgan
6 months ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

You're using R-3.6.0, but trying to install Bioconductor version 3.8. Try using BiocManager::install("Biobase"). If that works, then try BiocManager::install("GO.db").

If you have success, make sure your installation is valid with BiocManager::valid().

ADD COMMENTlink written 6 months ago by Martin Morgan ♦♦ 24k
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