Error in `dplyr::full_join() while using importRdata

[Harshangda Karan Puri]

Hi,

I have written the following code :

mySwitchList <- importRdata(
  isoformCountMatrix   = Txi_trans$counts,
  isoformRepExpression = Txi_trans$abundance,
  designMatrix         = targets,
  removeNonConvensionalChr = TRUE,
  addAnnotatedORFs=TRUE,
  ignoreAfterPeriod=TRUE,
  isoformExonAnnoation = "/mnt/panfs1/scratch/wsspaces/hkaranpuri-Alternative-Splicing-0/Salmon2/Mus_musculus.GRCm39.109.gtf",
  isoformNtFasta       = "/mnt/panfs1/scratch/wsspaces/hkaranpuri-Alternative-Splicing-0/Salmon2/Mus_musculus.GRCm39.cdna.all.fa",
  showProgress = TRUE)

but I am getting this error: 

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

Can anyone please tell me what is the problem in the code and how can I rectify it?

Thanks,

Harshangda

[Kristoffer Vitting-Seerup]

Thanks for reaching out :-) 

It is a dplyr update causing the problems. If you just install the newest version for GitHub this error has been fixed. Remember to restart R before running again (as it sometimes does not load the updated package if the package is already loaded)

[Harshangda Karan Puri]

Hi,

Thank you so much for your prompt answer. Do I also need to update to R4.3 and Bioconductor 3.17 to be able to work with this update? 

Also when I run the command for installing pfamAnalyzeR package it doesn't show that it is loading or installing anything. As soon as I run the code it shows the ">" in the next line which looks like the code is executed but when I check in my packages, I can't find the package.

Can you please help with this as well?

Thanks,

Harsha

[Harshangda Karan Puri]

Also,

I have downloaded R4.3 but the Bioconductor version 3.17 says that DESeq (which is required for IsoformSwitchAnalyzeR) is out out date. When I try to install it, it throws an error saying:

Old packages: 'DESeq2'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES'

Can you also help with this?

Regards,

Harsha

[Kristoffer Vitting-Seerup]

Ahh - you should not install from Bioconductor right now but from GitHub as described on the GitHub.

I'm still waiting for Bioconductor to approve the pfamAnalyzeR package and since IsoformSwitchAnalyzeR replies on it I cannot update Bioconductor yet.

[Harshangda Karan Puri]

So, I am using this command to install from GitHub: devtools::install_github("kvittingseerup/IsoformSwitchAnalyzeR", build_vignettes = TRUE)

But it gives me this error: 

── R CMD build ──────────────────────────────────────────────────────────────────
✔  checking for file ‘/private/var/folders/l7/fr0v54zj0b363prqzx5ylz540000gr/T/RtmpmQQLLT/remotes1554677fd8e5b/kvittingseerup-IsoformSwitchAnalyzeR-5db7290/DESCRIPTION’ ...
─  preparing ‘IsoformSwitchAnalyzeR’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  installing the package to build vignettes
         -----------------------------------
─  installing *source* package ‘IsoformSwitchAnalyzeR’ ...
   ** using staged installation
   ** libs
   using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
   using SDK: ‘MacOSX13.1.sdk’
   clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c utils.c -o utils.o
   clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o IsoformSwitchAnalyzeR.so utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
   ld: warning: -undefined dynamic_lookup may not work with chained fixups
   installing to /private/var/folders/l7/fr0v54zj0b363prqzx5ylz540000gr/T/RtmpwCPRpt/Rinst15da566f5052f/00LOCK-IsoformSwitchAnalyzeR/00new/IsoformSwitchAnalyzeR/libs
   ** R
   ** data
   ** inst
   ** byte-compile and prepare package for lazy loading
   Error: package or namespace load failed for ‘DESeq2’ in dyn.load(file, DLLpath = DLLpath, ...):
    unable to load shared object '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/DESeq2/libs/DESeq2.so':
     dlopen(/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/DESeq2/libs/DESeq2.so, 0x0006): tried: '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/DESeq2/libs/DESeq2.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/DESeq2/libs/DESeq2.so' (no such file), '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/DESeq2/libs/DESeq2.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64'))
   Execution halted
   ERROR: lazy loading failed for package ‘IsoformSwitchAnalyzeR’
─  removing ‘/private/var/folders/l7/fr0v54zj0b363prqzx5ylz540000gr/T/RtmpwCPRpt/Rinst15da566f5052f/IsoformSwitchAnalyzeR’
         -----------------------------------
   ERROR: package installation failed
Error: Failed to install 'IsoformSwitchAnalyzeR' from GitHub:
  ! System command 'R' failed

[Kristoffer Vitting-Seerup]

When I read it I notice this sentence:

"Error: package or namespace load failed for ‘DESeq2’ "

Looks like you do not have DESeq2 (and other requirements?) installed?

[Harshangda Karan Puri]

Hi,

Thanks! I needed to upgrade DESeq2. So this is resolved.

Harsha