Fail BiocManager::install(version='3.12')
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2
Entering edit mode
liqidong52 ▴ 20
@5c42e4aa
Last seen 2.0 years ago
Hong Kong

I don't have sudo, my R version is 4.0.2, I can not use BiocManager::install, because it notices me the version is not compatible. However, I can not degrade the Bioconductor version. Here is the problem capture:

>BiocManager::install()
Error: Bioconductor version '3.14' requires R version '4.1'; use
  `BiocManager::install(version = '3.12')` with R version 4.0; see
  https://bioconductor.org/install

>BiocManager::install(version = '3.12')
Downgrade 185 packages to Bioconductor version '3.12'? [y/n]:y
# download and install 185 packages

The downloaded source packages are in
        ‘/tmp/Rtmp7zU440/downloaded_packages’
Warning messages:
1: package(s) not installed when version(s) same as current; use `force = TRUE` to
  re-install: 'BiocVersion'
2: package(s) not installed when version(s) same as current; use `force = TRUE` to
  re-install: 'annotate' [... truncated]
3: In .inet_warning(msg) :
  installation of package ‘clusterProfiler’ had non-zero exit status

>BiocManager::install()
Error: Bioconductor version '3.14' requires R version '4.1'; use
  `BiocManager::install(version = '3.12')` with R version 4.0; see
  https://bioconductor.org/install

>BiocManager::install(version = '3.12')
Downgrade 185 packages to Bioconductor version '3.12'? [y/n]:n
Error: Bioconductor version not changed by 'install()'

sessionInfo( )
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 19.3

Matrix products: default
BLAS:   /home/a/a_local/lib/R/lib/libRblas.so
LAPACK: /home/a/a_local/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_HK.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_HK.UTF-8        LC_COLLATE=en_HK.UTF-8
 [5] LC_MONETARY=en_HK.UTF-8    LC_MESSAGES=en_HK.UTF-8
 [7] LC_PAPER=en_HK.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_HK.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] BiocManager_1.30.16

loaded via a namespace (and not attached):
[1] compiler_4.0.2 tools_4.0.2

Downgrade packages take me half an hour each time but do nothing, and I have been unable to use BiocManager::install(), may I know what I should do? Thanks in advance.

BioManager • 2.2k views
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0
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@james-w-macdonald-5106
Last seen 20 hours ago
United States

This part:

>BiocManager::install(version = '3.12')
Downgrade 185 packages to Bioconductor version '3.12'? [y/n]:y
# download and install 185 packages

The downloaded source packages are in
        ‘/tmp/Rtmp7zU440/downloaded_packages’
Warning messages:
1: package(s) not installed when version(s) same as current; use `force = TRUE` to
  re-install: 'BiocVersion'
2: package(s) not installed when version(s) same as current; use `force = TRUE` to
  re-install: 'annotate' [... truncated]
3: In .inet_warning(msg) :
  installation of package ‘clusterProfiler’ had non-zero exit status

indicates that all but BiocVersion, annotate, and clusterProfiler were installed. For the latter two, that was because you already have the 3.12 versions of those packages. So the only package that wasn't installed, and which might be problematic is clusterProfiler, but without showing that part of the installation it's impossible for anybody to say what the problem was.

You got another hint here:

>BiocManager::install(version = '3.12')
Downgrade 185 packages to Bioconductor version '3.12'? [y/n]:n
Error: Bioconductor version not changed by 'install()'

Which tells you the version wasn't changed. Perhaps the error message could also include that it wasn't changed because you already have that version of Bioconductor.

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0
Entering edit mode
Jiaxin • 0
@9e94487b
Last seen 6 weeks ago
United States

Add force=T when downgrade Bioconductor. BiocManager::install("BiocVersion", version = "3.12", force=T) Or packages like 'BiocVersion' won't be updated since a newer version than 3.12 has already been installed.

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0
Entering edit mode

You should use a new directory via e.g. libPaths() and not forcefully overwrite dozens of existing packages, imo.

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