package ‘pfamAnalyzeR’ is not available for Bioconductor version '3.16'

[ShannonTown]

Hi, I'm using bioconductor version 3.16 with R 4.2, is there a way to install pfamAnalyzerR without having to update to R 4.4 and bioconductor 3.19?

-- this is to install IsoformSwitchAnalyzeR from github, because the version acquired by BiocManager::install("IsoformSwitchAnalyzeR") gives an error:

> aSwitchList <- importRdata(
+     isoformCountMatrix   = salmonQuant$counts,
+     isoformRepExpression = salmonQuant$abundance,
+     designMatrix         = myDesign,
+     isoformExonAnnoation = "../supportive/Drosophila_melanogaster.BDGP6.46.112.gtf",
+     isoformNtFasta       = "../supportive/Drosophila_melanogaster.BDGP6.46.112.transcripts.fa",
+     fixStringTieAnnotationProblem = TRUE,
+     showProgress = FALSE
+ )
Step 1 of 7: Checking data...
Step 2 of 7: Obtaining annotation...
    importing GTF (this may take a while)...
Error in `dplyr::full_join()`:
! `...` must be empty.
✖ Problematic argument:
• all = TRUE
Backtrace:
 1. IsoformSwitchAnalyzeR::importRdata(...)
 4. IsoformSwitchAnalyzeR::importGTF(...)
 6. dplyr:::full_join.data.frame(...)
> library(IsoformSwitchAnalyzeR)
> packageVersion('IsoformSwitchAnalyzeR')
[1] '1.20.0'

[kvittingseerup]

Could you try installing from GitHub 😊

tirs. 30. jul. 2024 kl. 04.16 skrev ShannonTown @.***>:

Hi, I'm using bioconductor version 3.16 with R 4.2, is there a way to install pfamAnalyzerR without having to update to R 4.4 and bioconductor 3.19?

-- this is to install IsoformSwitchAnalyzeR from github, because the version acquired by BiocManager::install("IsoformSwitchAnalyzeR") gives an error:

aSwitchList <- importRdata(

• isoformCountMatrix = salmonQuant$counts,
• isoformRepExpression = salmonQuant$abundance,
• designMatrix = myDesign,
• isoformExonAnnoation = "../supportive/Drosophila_melanogaster.BDGP6.46.112.gtf",
• isoformNtFasta = "../supportive/Drosophila_melanogaster.BDGP6.46.112.transcripts.fa",
• fixStringTieAnnotationProblem = TRUE,
• showProgress = FALSE
• ) Step 1 of 7: Checking data... Step 2 of 7: Obtaining annotation... importing GTF (this may take a while)... Error in dplyr::full_join(): ! ... must be empty. ✖ Problematic argument: • all = TRUE Backtrace:
  1. IsoformSwitchAnalyzeR::importRdata(...)
  2. IsoformSwitchAnalyzeR::importGTF(...)
  3. dplyr:::full_join.data.frame(...) library(IsoformSwitchAnalyzeR) packageVersion('IsoformSwitchAnalyzeR') [1] '1.20.0'

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[ShannonTown]

Oh, how did I miss this 😂

After installing pfamAnalyzeR and manually installing a couple other packages, I got the following error when installing IsoformSwitchAnalyzeR:

> devtools::install_github("kvittingseerup/IsoformSwitchAnalyzeR", build_vignettes = TRUE)

Downloading GitHub repo kvittingseerup/IsoformSwitchAnalyzeR@HEAD
── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/tmp/RtmpQi8zLk/remotes2b5c467205fd/kvittingseerup-IsoformSwitchAnalyzeR-f6cd48a/DESCRIPTION’ (706ms)
─  preparing ‘IsoformSwitchAnalyzeR’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  installing the package to build vignettes
E  creating vignettes (2m 27.5s)
   --- re-building ‘IsoformSwitchAnalyzeR.Rmd’ using rmarkdown

   Quitting from lines 1156-1160 [unnamed-chunk-37] (IsoformSwitchAnalyzeR.Rmd)
   Error: processing vignette 'IsoformSwitchAnalyzeR.Rmd' failed with diagnostics:
   Failed to collect lazy table.
   Caused by error in `db_collect()`:
   ! Arguments in `...` must be used.
   ✖ Problematic argument:
   • ..1 = Inf
   ℹ Did you misspell an argument name?
   --- failed re-building ‘IsoformSwitchAnalyzeR.Rmd’

   SUMMARY: processing the following file failed:
     ‘IsoformSwitchAnalyzeR.Rmd’

   Error: Vignette re-building failed.
   Execution halted
Error: Failed to install 'IsoformSwitchAnalyzeR' from GitHub:
  ! System command 'R' failed