Not latest package version through 'BiocManager::install()'
2
0
Entering edit mode
@wanglingjue-22347
Last seen 9 weeks ago
United States

Hi everyone,

I recently want to update the R packages 'xcms' and 'MSnbase' through following BiocManager command.

BiocManager::install("xcms")
BiocManager::install("MSnbase")


I noticed the version I installed through this command is not the latest release version of these two packages. I am not sure if this is the developers issue or the install() function does not refer to the latest version. For now, I just manually download the tgz file to install the latest version.

Thanks, Lingjue

Thanks for the critic and answers. I fixed the issue by updating R version (3.5.3 -> 3.6.1) for latest Bioconductor 3.10. I did not notice the R packages in bioconductor is batched under different bioconductor version.

FYI, here is the original sessionInfo():

> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] xcms_3.4.4          MSnbase_2.8.3       ProtGenerics_1.14.0 S4Vectors_0.20.1
[5] mzR_2.16.2          Rcpp_1.0.3          BiocParallel_1.16.6 Biobase_2.42.0
[9] BiocGenerics_0.28.0

loaded via a namespace (and not attached):
[1] tidyselect_0.2.5       purrr_0.3.3            splines_3.5.3          lattice_0.20-38
[5] colorspace_1.4-1       vsn_3.50.0             XML_3.98-1.20          survival_3.1-7
[9] rlang_0.4.1            pillar_1.4.2           glue_1.3.1             affy_1.60.0
[13] RColorBrewer_1.1-2     affyio_1.52.0          foreach_1.4.7          plyr_1.8.4
[17] mzID_1.20.1            robustbase_0.93-5      zlibbioc_1.28.0        munsell_0.5.0
[21] pcaMethods_1.74.0      gtable_0.3.0           codetools_0.2-16       IRanges_2.16.0
[25] doParallel_1.0.15      MassSpecWavelet_1.48.1 preprocessCore_1.44.0  DEoptimR_1.0-8
[29] scales_1.0.0           BiocManager_1.30.9     limma_3.38.3           RANN_2.6.1
[33] impute_1.56.0          ggplot2_3.2.1          digest_0.6.22          dplyr_0.8.3
[37] ncdf4_1.17             grid_3.5.3             tools_3.5.3            magrittr_1.5
[41] lazyeval_0.2.2         tibble_2.1.3           crayon_1.3.4           pkgconfig_2.0.3
[45] MASS_7.3-51.4          Matrix_1.2-17          assertthat_0.2.1       rstudioapi_0.10
[49] iterators_1.0.12       R6_2.4.1               MALDIquant_1.19.3      multtest_2.38.0
[53] compiler_3.5.3

debug BiocManager R pacakge R mass spectrometry • 816 views
0
Entering edit mode
@james-w-macdonald-5106
Last seen 1 hour ago
United States

You don't show the results of sessionInfo so it's not possible to help you. Assuming you have an older version of R, you need to update. Do note that we don't provide help for those who download things and install separately. Each release is intended to work, but there are no guarantees that you can get things to work if you mix and match like that, and therefore the onus is on you to make sure you are doing the right thing (which by definition you aren't, hence the lack of support).

0
Entering edit mode

Thank you for the comment. I have fixed it.

0
Entering edit mode
shepherl 3.3k
@lshep
Last seen 5 hours ago
United States

What version of R are you running? R3.6.1?
And what version is BicoManager using?

sessionInfo()
BiocManager::version()


If it still using "3.9" , You may have to update the version BiocManager uses since the new release 3.10 uses the same version of R as 3.9.

Please use the following to update the Bioconductor version and related packages.

BiocManager::install(version="3.10")
BioManager::install()


Info can also be found at Bioconductor Install Page

Normally there is a message that indicates there is a newer version to use. This is broken in the current BiocManager version but is in the process of getting corrected.

0
Entering edit mode

And as James mentioned - This assumes you have the latest compatible version of R installed as well. If you don't have the latest version of R you would need to update in order to get the latest packages through BiocManager::install

0
Entering edit mode

Thanks, this is very useful! I did not notice the latest bioconductor version (3.10) is not compatible with R <3.6. I have fixed it.