Hi I have been trying to install SeqArray however I have been having the same problem with the ‘GenomeInfoDbData’. Somebody could help me please, I already restart R, I have the last version, but I really dont understand what is happening. bellow the code and the error:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SeqArray")
library(SeqArray)
BiocManager::install("SeqArray", force = TRUE)
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.17), R 4.1.3 (2022-03-10)
Installing package(s) 'SeqArray'
trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/windows/contrib/4.1/SeqArray_1.34.0.zip'
Content type 'application/zip' length 3934742 bytes (3.8 MB)
downloaded 3.8 MB
package ‘SeqArray’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\User\AppData\Local\Temp\Rtmp46IWLK\downloaded_packages
> library(SeqArray)
Error: package or namespace load failed for ‘SeqArray’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘GenomeInfoDbData’
You seem to have a broken installation: The SeqArray package depends indirectly on GenomeInfoDbData (i.e. it depends on GenomeInfoDb which itself depends on GenomeInfoDbData) but it looks like you don't have that package so SeqArray cannot be loaded.
It's not clear how you would end up in such situation. The fact that at some point you managed to install GenomeInfoDb without installing GenomeInfoDbData suggests that maybe you didn't use BiocManager::install() to install it? As a reminder, you should _always_ use BiocManager::install() to install Bioconductor packages.
Try to install GenomeInfoDbData with BiocManager::install(GenomeInfoDbData) and see if that solves the problem. Note that you could have other missing dependencies.
> BiocManager::install("GenomeInfoDbData")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.17), R 4.1.3 (2022-03-10)
Installing package(s) 'GenomeInfoDbData'
package ‘GenomeInfoDbData’ is available as a source package but not as a binary
Old packages: 'cluster', 'MASS', 'Matrix', 'mgcv', 'nlme'
Update all/some/none? [a/s/n]:
a
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/cluster_2.1.3.zip'
Content type 'application/zip' length 620624 bytes (606 KB)
downloaded 606 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/MASS_7.3-57.zip'
Content type 'application/zip' length 1190704 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/Matrix_1.4-1.zip'
Content type 'application/zip' length 5501752 bytes (5.2 MB)
downloaded 5.2 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/mgcv_1.8-40.zip'
Content type 'application/zip' length 3379380 bytes (3.2 MB)
downloaded 3.2 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/nlme_3.1-157.zip'
Content type 'application/zip' length 2385029 bytes (2.3 MB)
downloaded 2.3 MB
package ‘cluster’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘cluster’
Warning: restored ‘cluster’
package ‘MASS’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘MASS’
Warning: restored ‘MASS’
package ‘Matrix’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘Matrix’
Warning: restored ‘Matrix’
package ‘mgcv’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘mgcv’
Warning: restored ‘mgcv’
package ‘nlme’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘nlme’
Warning: restored ‘nlme’
The downloaded binary packages are in
C:\Users\User\AppData\Local\Temp\RtmpGexEGV\downloaded_packages
Warning message:
package ‘GenomeInfoDbData’ is not available as a binary package for Bioconductor version '3.14'
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages `
