Unable to install RefPlus - R=4.3.1, BiocManager=3.18
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@dc9796bd
Last seen 12 months ago
United States

When I am running R version 4.2.2 and BiocManager 3.16, I can install the package "RefPlus" just fine:

> BiocManager::install("RefPlus", force = FALSE, ask = FALSE, update=FALSE, checkBuilt=FALSE);
> system.file(package="RefPlus")
[1] "/home/d/R/x86_64-pc-linux-gnu-library/4.2/RefPlus"

However, when I run R version 4.3.1 (2023-06-16) -- "Beagle Scouts" and BiocManager 3.18, Attempting to install RefPlus fails:

> BiocManager::install("RefPlus", update=FALSE)
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16)
Installing package(s) 'RefPlus'
Warning message:
package 'RefPlus' is not available for Bioconductor version '3.18'

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 

> system.file(package="RefPlus")
[1] ""

> sessionInfo( )
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 23.10

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0

locale:
[1] C

time zone: America/Los_Angeles
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.22 compiler_4.3.1      tools_4.3.1

For reference, all other Bioc and rcran packages install just fine. The only package I'm having trouble with is RefPlus on this specific version.

The two installs are not related. I'll try downgrading the OS, R, and BiocManager next. However, I would like for this not to be a blocker.

I see there is a 3.18 branch in RefPlus in the bioconductor repo, but I don't see RefPlus in the github bioconductor org. Did the package get missed when you made github your primary repository?
Install instal • 2.6k views
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shepherl 4.1k
@lshep
Last seen 16 hours ago
United States

RefPlus has not yet built on the Bioconductor builds system for linux for 3.18. See RefPlus Build Report . Once it builds and checks correctly it will be available.
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Hi Lori,

Does that make the Windows binary unavailable as well? In other words, when BiocManager checks for availability, does it look for the source package regardless?

> library(BiocManager)
Bioconductor version 3.18
  (BiocManager 1.30.22), R 4.3.1
  (2023-06-16 ucrt)
> install("RefPlus")
'getOption("repos")' replaces
Bioconductor standard repositories,
see 'help("repositories", package =
"BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.org
Bioconductor version 3.18
  (BiocManager 1.30.22), R 4.3.1
  (2023-06-16 ucrt)
Installing package(s) 'RefPlus'
Installation paths not writeable,
  unable to update packages
  path: C:/Program Files/R/R-4.3.1/library
  packages:
    foreign, KernSmooth, lattice,
    Matrix, mgcv, nlme, rpart,
    spatial, survival
Old packages: 'edgeR',
  'GenomicFeatures',
  'GenomicRanges', 'htmlTable',
  'knitr', 'poorman', 'RSQLite',
  'withr'
Update all/some/none? [a/s/n]: n
Warning message:
package 'RefPlus' is not available for Bioconductor version '3.18'

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 

> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices
[4] utils     datasets  methods  
[7] base     

other attached packages:
[1] BiocManager_1.30.22

loaded via a namespace (and not attached):
[1] compiler_4.3.1 tools_4.3.1
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I recall discussing this with Herve at somepoint. We both decided this was a bug, because clearly a usable version of the package is available on Windows, but when he reported it to R-core their view point was that a missing source tarball meant that the package was broken and should not be available. The issue was closed at that point. I'll try to dig up the issue he created.

Edit: Here is a discussion of this same phenomena for a different package at the time of the 3.17 release (https://community-bioc.slack.com/archives/CEQ04GKEC/p1686573089903459)

and here is Herve's bug report (https://bugs.r-project.org/show_bug.cgi?id=18554)

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Thanks Mike. That's what I figured.

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And as followup.

> install("RefPlus", type = "win.binary")
'getOption("repos")' replaces
Bioconductor standard repositories,
see 'help("repositories", package =
"BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.org
Bioconductor version 3.18
  (BiocManager 1.30.22), R 4.3.1
  (2023-06-16 ucrt)
Installing package(s) 'RefPlus'
also installing the dependency 'affyPLM'

trying URL 'https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.3/affyPLM_1.78.0.zip'
Content type 'application/zip' length 2882886 bytes (2.7 MB)
downloaded 2.7 MB

trying URL 'https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.3/RefPlus_1.72.0.zip'
Content type 'application/zip' length 733576 bytes (716 KB)
downloaded 716 KB

package 'affyPLM' successfully unpacked and MD5 sums checked
package 'RefPlus' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\jmacdon\AppData\Local\Temp\Rtmp4cbYpS\downloaded_packages

As documented

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shepherl 4.1k
@lshep
Last seen 16 hours ago
United States

The windows and mac binaries should be available. It looks like it is only failing on linux and there are build binaries as reported on the package landing page https://bioconductor.org/packages/3.18/bioc/html/RefPlus.html
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Mike Smith ★ 6.6k
@mike-smith
Last seen 8 hours ago
EMBL Heidelberg

The RefPlus package is currently failing to build on the Bioconductor build system (see https://bioconductor.org/checkResults/release/bioc-LATEST/RefPlus/nebbiolo2-checksrc.html).

Since we're only days after the release of Bioconductor 3.18 there has never been a successful build of the package, and this in turn means that the source tarball has not propagated to the Bioconductor repository. It looks like the build issue is related to one or more of its dependencies, and will probably be resolved over time, but for now the source package will remain unavailable.

However you can install directly from the git repository using the command below. This works for me.

remotes::install_git("https://git.bioconductor.org/packages/RefPlus")

`
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