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Hi there, i cannot install package "microbiome" in R (ver 4.2.1),
when i input the code, it seems OK,
BiocManager::install("microbiome", force = TRUE)
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt)
Installing package(s) 'microbiome'
trying URL 'https://bioconductor.org/packages/3.15/bioc/bin/windows/contrib/4.2/microbiome_1.18.0.zip'
Content type 'application/zip' length 1044918 bytes (1020 KB)
downloaded 1020 KB
package ‘microbiome’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\work\AppData\Local\Temp\RtmpklUZ1g\downloaded_packages
but...
library(microbiome)
Loading required package: phyloseq
Error: package or namespace load failed for ‘phyloseq’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘GenomeInfoDbData’
Error: package ‘phyloseq’ could not be loaded
So, i tried to install "phyloseq",
BiocManager::install("phyloseq", force = TRUE)
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt)
Installing package(s) 'phyloseq'
trying URL 'https://bioconductor.org/packages/3.15/bioc/bin/windows/contrib/4.2/phyloseq_1.40.0.zip'
Content type 'application/zip' length 4630961 bytes (4.4 MB)
downloaded 4.4 MB
package ‘phyloseq’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\work\AppData\Local\Temp\RtmpklUZ1g\downloaded_packages
but...
library(phyloseq)
Error: package or namespace load failed for ‘phyloseq’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘GenomeInfoDbData’
then, i tried to install "GenomeInfoDbData", but...
BiocManager::install("GenomeInfoDbData", force = TRUE)
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt)
Installing package(s) 'GenomeInfoDbData'
installing the source package ‘GenomeInfoDbData’
trying URL 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/GenomeInfoDbData_1.2.8.tar.gz'
Content type 'application/x-gzip' length 11512907 bytes (11.0 MB)
downloaded 11.0 MB
The downloaded source packages are in
‘C:\Users\work\AppData\Local\Temp\RtmpklUZ1g\downloaded_packages’
Warning message:
In install.packages(...) :
installation of package ‘GenomeInfoDbData’ had non-zero exit status
i checked the library, there is no "GenomeInfoDbData" there,
remove.packages("GenomeInfoDbData", lib = "C:/Users/work/AppData/Local/R/win-library/4.2")
Error in remove.packages : there is no package called ‘GenomeInfoDbData’
remove.packages("GenomeInfoDbData", lib = "C:/Program Files/R/R-4.2.1/library")
Error in remove.packages : there is no package called ‘GenomeInfoDbData’
how can i resolve this error? Thank you !
Is there any additional output / ERROR when you try
Thank you for reply~
Hi @61191329 ,
Unfortunately, I am unable to reproduce the issue on Windows. Please provide additional information, namely
BiocManager::valid()
,.libPaths()
, andsessionInfo()
.sessionInfo()
Best,
Marcel