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

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