Question

Bioconductor unable to update 'curl'

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kagodwi2 • 0

@bf3e612e

Last seen 2 days ago

United States

Hello!

I am having issues with updating package 'curl.' Specifically, when performing BiocManager::valid(), I obtain the standard advice to run the command:

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

Doing so performs the update routine as expected. However, when performing BiocManager::valid() again, I obtain the same result of BiocManager informing me that 'curl' is out of date and should be updated to create a valid installation.

Running BiocManager::install("curl"), followed by BiocManager::valid() leads to the same outcome.

What exactly does 'curl' do, and is there a way that I can update this package to ensure Bioconductor is up to date?

Many Thanks!

> sessionInfo()
R version 4.4.3 (2025-02-28 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8 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 utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.25 compiler_4.4.3      tools_4.4.3         rstudioapi_0.17.1

curl HELP • 222 views

ADD COMMENT • link 2 days ago kagodwi2 • 0

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what is the result of .libPaths() It could be that curl was installed with an admin account or in a different location that would need to be specified for the update to complete.

ADD REPLY • link 2 days ago shepherl 4.1k

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Thank you for the advice. As requested:

[1] "C:/Users/kenda/AppData/Local/R/win-library/4.4"
[2] "C:/Program Files/R/R-4.4.3/library"

In the past, I have been experiencing issues with "paths not writeable" or "permission denied." For instance, in updating the package "Jpeg" today, I had to manually go into my R library to delete the old version and reinstall the package. I am not sure why I am encountering these permission issues since I have given the necessary permissions to R and RStudio, and this is a personal computer used only by myself. I wouldn't be surprised if this is why I am seeing issues with 'curl' as well, but it is unclear to me how I can resolve this issue with permissions, since even running RStudio as an administrator will occasionally give me "permission denied" errors.

ADD REPLY • link 2 days ago kagodwi2 • 0

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Not sure how to completely clear the issues but it might be useful to see which location curl is in find.package("curl") and if necessary add the correct lib path to BiocManager i.e something like install("curl", lib=.libPaths()[2]) . Or if necessary remove it from one location and reinstall in the other libPath

ADD REPLY • link 2 days ago shepherl 4.1k

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Thank you! This seems to narrow down the issue, at least.

I successfully installed "curl" into both paths, but received the same issue of "package is out of date." I then removed "curl" entirely from both paths, confirmed that, with no "curl" package, BiocManager::valid() is TRUE, and reinstalled "curl" as follows:

BiocManager::install("curl")

This worked with no errors, but it told me the package needed to be updated. Specifically:

There is a binary version available but the source version is later:
     binary source needs_compilation
curl  6.2.1  6.2.2              TRUE

  Binaries will be installed

Again, no errors, but when the operation was completed successfully:

> BiocManager::valid()
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/

* sessionInfo()

R version 4.4.3 (2025-02-28 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)

Matrix products: default


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

time zone: America/New_York
tzcode source: internal

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

other attached packages:
 [1] ShortRead_1.64.0            GenomicAlignments_1.42.0    SummarizedExperiment_1.36.0
 [4] Biobase_2.66.0              MatrixGenerics_1.18.1       matrixStats_1.5.0          
 [7] Rsamtools_2.22.0            GenomicRanges_1.58.0        Biostrings_2.74.1          
[10] GenomeInfoDb_1.42.3         XVector_0.46.0              IRanges_2.40.1             
[13] S4Vectors_0.44.0            BiocParallel_1.40.0         BiocGenerics_0.52.0        
[16] dada2_1.34.0                Rcpp_1.0.14                

loaded via a namespace (and not attached):
 [1] generics_0.1.3          SparseArray_1.6.2       bitops_1.0-9           
 [4] stringi_1.8.4           jpeg_0.1-11             lattice_0.22-6         
 [7] magrittr_2.0.3          RColorBrewer_1.1-3      grid_4.4.3             
[10] plyr_1.8.9              jsonlite_1.9.1          Matrix_1.7-3           
[13] BiocManager_1.30.25     httr_1.4.7              UCSC.utils_1.2.0       
[16] scales_1.3.0            codetools_0.2-20        abind_1.4-8            
[19] cli_3.6.4               rlang_1.1.5             crayon_1.5.3           
[22] munsell_0.5.1           DelayedArray_0.32.0     S4Arrays_1.6.0         
[25] tools_4.4.3             parallel_4.4.3          reshape2_1.4.4         
[28] deldir_2.0-4            dplyr_1.1.4             interp_1.1-6           
[31] colorspace_2.1-1        ggplot2_3.5.1           GenomeInfoDbData_1.2.13
[34] hwriter_1.3.2.1         png_0.1-8               vctrs_0.6.5            
[37] R6_2.6.1                lifecycle_1.0.4         stringr_1.5.1          
[40] pwalign_1.2.0           zlibbioc_1.52.0         pkgconfig_2.0.3        
[43] RcppParallel_5.1.10     pillar_1.10.1           gtable_0.3.6           
[46] glue_1.8.0              tibble_3.2.1            tidyselect_1.2.1       
[49] latticeExtra_0.6-30     rstudioapi_0.17.1       compiler_4.4.3         

Bioconductor version '3.20'

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

create a valid installation with

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

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

I'm back to where I started.

ADD REPLY • link 2 days ago kagodwi2 • 0

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UPDATE:

I was able to get curl to work! It seems that because the new version was literally JUST released, there is something "funky" going on with the binaries on Windows. By using:

install.packages("curl", repos = "https://jeroen.r-universe.dev")

the package installed perfectly. The true test:

> BiocManager::valid()
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
[1] TRUE

I can rest easy tonight. Thanks for all of the help! It is VERY much appreciated.

ADD REPLY • link 2 days ago kagodwi2 • 0