vcfR2tidy error (Can't combine `..1$tt` <logical> and `..2$tt` <character>.)

[fpsom]

First of all, thanks @knausb for creating and maintaining this very useful package!

I was testing my existing scripts (after the recent update of R4.0.0 and dplyr), and I came across the following error:

library(vcfR)
data("vcfR_test")
vcfR_test

Output normal

***** Object of Class vcfR *****
3 samples
1 CHROMs
5 variants
Object size: 0 Mb
0 percent missing data
*****        *****         *****

Attempting to run vcfR2tidy

vcfR2tidy(vcfR_test)

Error

Error: Can't combine `..1$tt` <logical> and `..2$tt` <character>.
Run `rlang::last_error()` to see where the error occurred.

I assume that this is due to the recent update, but I cannot pinpoint where the particular error might be.

If there are any suggestions on how to move around actually calling vcfR2tidy, they would be very helpful (given also the fact that you probably have extremely limited time).

[knausb]

Hi @fpsom ,

Thank you for bringing this to my attention! And thank you for providing a mre. It sounds like you are aware of this, but there have been some major changes in the R universe lately. In April R 4.0.0 was released and in May dplyr 1.0.0 was released. I appear to have addressed this issue in my development version. If you'd like to try it you can use the following.

devtools::install_github(repo="knausb/vcfR")

I've been struggling with dependency issues associated with R 4.0.0. But I think I'm finally at a place where I can update the CRAN version. Hopefully this week.

Thanks! Brian

[fpsom]

Hi @knausb ! Thank you very much for the swift reply!

I've just checked with the dev version, and it works absolutely fine - including some additional vcfR function calls I had in the test.

Thanks again!

[skanwal]

Hi @knausb,

First, thanks for the great resource. I am hitting the same issue as originally posted by Fotis.

I am also not able to install the development version.

Downloading GitHub repo knausb/vcfR@master
✓  checking for file ‘/private/var/folders/_v/g24brqws13v3gtrvcz2j57ldbdw8jg/T/RtmpvIKCnE/remotese18e215e69a0/knausb-vcfR-5fb215b/DESCRIPTION’ ...
─  preparing ‘vcfR’:
✓  checking DESCRIPTION meta-information ...
─  cleaning src
─  running ‘cleanup’
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘vcfR_1.11.0.tar.gz’
   Warning: invalid uid value replaced by that for user 'nobody'
   Warning: invalid gid value replaced by that for user 'nobody'

* installing *source* package ‘vcfR’ ...
** using staged installation
./configure: line 4: checkbashisms: command not found
Error in system(cmd) : (converted from warning) error in running command
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/vcfR’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/vcfR’
Error: Failed to install 'vcfR' from GitHub:
  (converted from warning) installation of package ‘/var/folders/_v/g24brqws13v3gtrvcz2j57ldbdw8jg/T//RtmpvIKCnE/filee18e1df3560a/vcfR_1.11.0.tar.gz’ had non-zero exit status

I am trying to install it on MAC and my R version is 4.0.0.

Did you mange to update the CRAN version? The vcfR version I currently have is:

   *****       ***   vcfR   ***       *****
   This is vcfR 1.10.0 
     browseVignettes('vcfR') # Documentation
     citation('vcfR') # Citation
   *****       *****      *****       *****