Infinite install of BiocManager about capsule

[nickbien]

You are correct! Just ignored the reload and it works. Also the svg is now working as expected! Thank you!

[NElnour]

Hey I'm not seeing these messages. Did you pull from main/master? If so, could you share the command to replicate this issue?

[nickbien]

Hi thanks for your effort on this.

Yes i did pull the latest commit using: git pull

Here is the log.

commit 9a29b4e730a8612d17e80cf4426be6e22399eb53 (HEAD -> master, origin/master, origin/HEAD)
Merge: 8088110 5beaeb7
Author: Nada Elnour <[email protected]>
Date:   Thu May 5 03:19:10 2022 -0400

    Merge pull request #3 from NElnour/issue-2

    Issue 2

[NElnour]

That's very strange. I just pulled and here's the results of source for me:
`source("./inst/scripts/scriptTemplate.R")
Error in install.packages : Updating loaded packages

Restarting R session...

install.packages("BiocManager")
Installing package into ‘/home/nada/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/BiocManager_1.30.17.tar.gz'
Content type 'application/x-gzip' length 287948 bytes (281 KB)

downloaded 281 KB

• installing source package ‘BiocManager’ ...
  ** package ‘BiocManager’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** installing vignettes
  ** testing if installed package can be loaded from temporary location
  ** testing if installed package can be loaded from final location
  ** testing if installed package keeps a record of temporary installation path
• DONE (BiocManager)

The downloaded source packages are in
‘/tmp/Rtmpwb9S6g/downloaded_packages’`

can you run sessionInfo() and paste the results here?

[nickbien]

Here it is. Im still very new to this so please bear with me. I might need something from rstudio to refresh packages?

R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.2.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.52.0      BiocManager_1.30.17 stringr_1.4.0       tibble_3.1.7       

loaded via a namespace (and not attached):
 [1] KEGGREST_1.36.0        progress_1.2.2         tidyselect_1.1.2       purrr_0.3.4           
 [5] vctrs_0.4.1            generics_0.1.2         stats4_4.2.0           BiocFileCache_2.4.0   
 [9] utf8_1.2.2             blob_1.2.3             XML_3.99-0.9           rlang_1.0.2           
[13] pillar_1.7.0           glue_1.6.2             DBI_1.1.2              rappdirs_0.3.3        
[17] BiocGenerics_0.42.0    bit64_4.0.5            dbplyr_2.1.1           GenomeInfoDbData_1.2.8
[21] lifecycle_1.0.1        zlibbioc_1.42.0        Biostrings_2.64.0      memoise_2.0.1         
[25] Biobase_2.56.0         IRanges_2.30.0         fastmap_1.1.0          GenomeInfoDb_1.32.1   
[29] curl_4.3.2             AnnotationDbi_1.58.0   fansi_1.0.3            Rcpp_1.0.8.3          
[33] filelock_1.0.2         cachem_1.0.6           S4Vectors_0.34.0       XVector_0.36.0        
[37] bit_4.0.4              hms_1.1.1              png_0.1-7              digest_0.6.29         
[41] stringi_1.7.6          dplyr_1.0.9            cli_3.3.0              tools_4.2.0           
[45] bitops_1.0-7           magrittr_2.0.3         RCurl_1.98-1.6         RSQLite_2.2.13        
[49] crayon_1.5.1           pkgconfig_2.0.3        ellipsis_0.3.2         xml2_1.3.3            
[53] prettyunits_1.1.1      assertthat_0.2.1       httr_1.4.3             R6_2.5.1              
[57] compiler_4.2.0

[NElnour]

Doesn't seem like there's a circular callback to BiocManager anywhere else and the dependency versions are up-to-date. Can you try applying the latest patch first before sourcing without reload?

From the original log, BiocManager eventually exited suggesting it wasn't infinite after all. It could be that you invoked source several times as well.