[Bug] Unable to install packages from Bioconductor
kpadm opened this issue · comments
Hello,
I am unable to install any package from Bioconductor using the format of the remotes argument given in the help section. For example, see below:
> jetpack::add("SummarizedExperiment", remotes="bioc::3.7/SummarizedExperiment, bioc::release/Biobase") svn: E175013: Unable to connect to a repository at URL 'https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_7/madman/Rpacks/SummarizedExperiment' svn: E175013: Access to 'https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_7/madman/Rpacks/SummarizedExperiment' forbidden Error: There was a problem retrieving the current SVN revision In addition: Warning message: In system2(svn_binary_path, paste("info --xml", url), stdout = TRUE) : running command ''/usr/bin/svn' info --xml --username readonly --password readonly https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_7/madman/Rpacks/SummarizedExperiment' had status 1 Error in unloadNamespace(pkgName) : namespace ‘httr’ is imported by ‘biomaRt’ so cannot be unloaded In addition: Warning message: ‘httr’ namespace cannot be unloaded: namespace ‘httr’ is imported by ‘biomaRt’ so cannot be unloaded Error in unloadNamespace(pkgName) : namespace ‘withr’ is imported by ‘pkgmaker’ so cannot be unloaded In addition: Warning message: ‘withr’ namespace cannot be unloaded: namespace ‘withr’ is imported by ‘pkgmaker’ so cannot be unloaded
Please help me figure out what I am doing wrong. Thanks.
Regards,
Karthik
Hey @kpadm, thanks for reporting 👍 It looks like that remote scheme only works with earlier versions of Bioconductor. You should be able to do:
jetpack::add("SummarizedExperiment", remotes="bioc::SummarizedExperiment")Unfortunately, it then fails to download the package source when snapshotting. I'm able to reproduce with Packrat, but haven't found a fix.
packrat::init()
source("https://bioconductor.org/biocLite.R")
packrat::extlib(c("withr", "devtools"))
devtools::install_bioc("Biobase")
packrat::snapshot()Installation should be fixed on master. Install the latest version with:
devtools::install_github("ankane/jetpack")And install packages with:
jetpack::add("SummarizedExperiment", remotes="bioc::SummarizedExperiment")However, looks like there are still issues when other collaborators try to do jetpack::install(), so going to leave this open until that is addressed.
It looks like downloads are failing due to an issue with the Bioconductor archive. I notified the Bioconductor team. If this is addressed, just need to merge a small change from the bioconductor branch and everything should work.
Thanks Andrew, I installed the latest version and am now able to install packages from Bioconductor.