Entering edit mode
Hi,
I'm trying to install the devel version of graph on the devel version of R. This fails with the error:
Error: object ‘CRAN.packages’ is not exported by 'namespace:utils'
What have I broken?
The full output of my session is below. I'm working on Debian Linux.
Best,
Tyler
R Under development (unstable) (2020-04-14 r78226) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
> BiocManager::install(version='devel')
Bioconductor version 3.11 (BiocManager 1.30.10), R Under development (unstable)
(2020-04-14 r78226)
> BiocManager::install("graph")
Bioconductor version 3.11 (BiocManager 1.30.10), R Under development (unstable)
(2020-04-14 r78226)
Installing package(s) 'graph'
trying URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/graph_1.65.2.tar.gz'
Content type 'application/x-gzip' length 957701 bytes (935 KB)
==================================================
downloaded 935 KB
* installing *source* package ‘graph’ ...
** using staged installation
** libs
gcc -I"/home/tws/hacking/r-devel/build/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c graph.c -o graph.o
gcc -shared -L/usr/local/lib -o graph.so graph.o
mv graph.so BioC_graph.so
installing to /home/tws/hacking/r-devel/build/library/00LOCK-graph/00new/graph/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘CRAN.packages’ is not exported by 'namespace:utils'
Execution halted
ERROR: lazy loading failed for package ‘graph’
* removing ‘/home/tws/hacking/r-devel/build/library/graph’
The downloaded source packages are in
‘/tmp/RtmpdZDWUC/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(...) :
installation of package ‘graph’ had non-zero exit status
>
> sessionInfo()
R Under development (unstable) (2020-04-14 r78226)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux bullseye/sid
Matrix products: default
BLAS: /home/tws/hacking/r-devel/build/lib/libRblas.so
LAPACK: /home/tws/hacking/r-devel/build/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_4.1.0 tools_4.1.0
>
Are you referring to the branch of R, or of Bioconductor? I am using R built from svn source, https://svn.r-project.org/R/trunk , as that was what I understood I should be doing to check a package for the April release. Is that incorrect, or do you mean I should change that for the October release?
You should be building R from
The R-4-0-branch was created at the start of the release cycle on 2020-03-24. The reason to use the R-4-0-branch is because the packages in the current Bioconductor 'devel' branch will become available to users who will be using R-4.0.0, not R-devel. Even after the spring release, Bioconductor 'devel' will still build on the R-4-0-branch, because in Fall Bioconductor 'devel' will become available to users who will still be using R built from the R-4-0-branch.
Immediately after the fall release, Bioconductor will switch it's 'devel' branch back to using R-devel, in preparation for the same dance next spring...
The support site is really meant for end-user support; better places for these questions / discussions are the bioc-devel mailing list and community slack