Issues with installation status of R package rtracklayer
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svlachavas ▴ 780
@svlachavas-7225
Last seen 6 weeks ago
Germany/Heidelberg/German Cancer Resear…

Dear BioC community, I would like initially to wish everyone a happy new year with less masks, more hugs and happy coding !! based on the update of the latest version of R, along with Rstudio I re-installed various core packages, along with the R package rtracklayer, as illustrated below:


BiocManager::install("rtracklayer")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'rtracklayer'

  There is a binary version available but the source version is later:
            binary source needs_compilation
rtracklayer 1.49.5 1.50.0              TRUE

  Binaries will be installed
trying URL 'https://bioconductor.org/packages/3.12/bioc/bin/windows/contrib/4.0/rtracklayer_1.49.5.zip'
Content type 'application/zip' length 2929936 bytes (2.8 MB)
downloaded 2.8 MB

package ‘rtracklayer’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\admin\AppData\Local\Temp\RtmpaGmyKA\downloaded_packages
Old packages: 'rtracklayer'
Update all/some/none? [a/s/n]: 
a

  There is a binary version available but the source version is later:
            binary source needs_compilation
rtracklayer 1.49.5 1.50.0              TRUE

  Binaries will be installed
trying URL 'https://bioconductor.org/packages/3.12/bioc/bin/windows/contrib/4.0/rtracklayer_1.49.5.zip'
Content type 'application/zip' length 2929936 bytes (2.8 MB)
downloaded 2.8 MB

package ‘rtracklayer’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\admin\AppData\Local\Temp\RtmpaGmyKA\downloaded_packages
> BiocManager::valid()

* sessionInfo()

R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

loaded via a namespace (and not attached):
 [1] compiler_4.0.3      BiocManager_1.30.10 prettyunits_1.1.1   remotes_2.2.0      
 [5] tools_4.0.3         testthat_3.0.1      digest_0.6.27       pkgbuild_1.2.0     
 [9] pkgload_1.1.0       memoise_1.1.0       evaluate_0.14       lifecycle_0.2.0    
[13] rlang_0.4.10        cli_2.2.0           rstudioapi_0.13     yaml_2.2.1         
[17] parallel_4.0.3      xfun_0.19           knitr_1.30          withr_2.3.0        
[21] desc_1.2.0          fs_1.5.0            S4Vectors_0.28.1    devtools_2.3.2     
[25] stats4_4.0.3        rprojroot_2.0.2     glue_1.4.2          R6_2.5.0           
[29] processx_3.4.5      fansi_0.4.1         rmarkdown_2.6       sessioninfo_1.1.1  
[33] callr_3.5.1         purrr_0.3.4         magrittr_2.0.1      htmltools_0.5.0    
[37] ps_1.5.0            ellipsis_0.3.1      usethis_2.0.0       BiocGenerics_0.36.0
[41] assertthat_0.2.1    tinytex_0.28        crayon_1.3.4       

Bioconductor version '3.12'

  * 1 packages out-of-date
  * 0 packages too new

create a valid installation with

  BiocManager::install("rtracklayer", update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message:
1 packages out-of-date; 0 packages too new 
> BiocManager::valid()$out_of_date
            Package       LibPath                              Installed Built  
rtracklayer "rtracklayer" "C:/Program Files/R/R-4.0.3/library" "1.49.5"  "4.0.2"
            ReposVer Repository                                               
rtracklayer "1.50.0" "https://bioconductor.org/packages/3.12/bioc/src/contrib"


sessionInfo( )

As you can see from above, despite the update, it seems that continuously the rtracklayer R package seems out of date-is there any way to fix this, or illustrates some other problem with my current session or packages ? (I also tried manually to remove and re-install, but the same "behavior" appears..)

Best,

Efstathios

rtracklayer Bioconductor • 408 views
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0
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I think this message

There is a binary version available but the source version is later:
            binary source needs_compilation

Means that the binary is currently behind the source version of the package. From the rest of the output, it seems you choose to use the binary since it says "Binaries will be installed" . If you choose to install the binary, you will still have the "out-of-date" package. You could either choose to install the source version of the package which involves compilation or you could wait until the binary package is updated (which is recommended). Generally if the binary isn't available for the package, there was an issue building or checking the package for that given platform and more than likely needs a fix from the maintainer.

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3
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@martin-morgan-1513
Last seen 9 weeks ago
United States

It looks like the '1.50.0' version of rtacklayer fails to build on Windows https://bioconductor.org/checkResults/release/bioc-LATEST/rtracklayer/ , and you're getting the most recent version available. Unless you are having trouble with the version that is installed, I suggest waiting until the package has been fixed 'upstream', and the updated version (probably 1.50.1) becomes available. I opened an issue on the maintainer's github repository https://github.com/lawremi/rtracklayer/issues/38

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Entering edit mode

Dear Martin,

thank you for your feedback, support and suggestions, and please excuse me for the late reply !! Indeed, with the current version installed, I'm facing some "weird" issues while the rtracklayer current version is also used for the download of MultiAssayExperiment cancer data, and especially hg19 mutational data from Broad Firehose. Thus, I will probably wait until any further updates and fixes-

Efstathios

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