VariantRecalibrator R-script fails if scales v1.3.0 is installed

[MikkelSchubert]

Bug Report

Affected tool(s) or class(es)

VariantRecalibrator

Affected version(s)

• Latest public release version [4.5.0.0]
• Latest master branch as of [date of test?]

Description

As of v1.3.0 the scales R package turns the use of deprecated values for the space parameter into a hard error, resulting in the VariantRecalibrator R-script terminating with the following message:

The space argument of pal_gradient_n() only supports be "Lab" as of scales 0.3.0.

This parameter is used repeatedly in the generated R-script via

scale_fill_gradient(high="green", low="red", space="rgb")

Steps to reproduce

$ R --version
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
$ rm -rf ~/R
$ R
> install.packages("ggplot2", repos="https://cloud.r-project.org/")
> packageVersion("scales")
[1] ‘1.3.0’
> quit()
$ gatk --version
The Genome Analysis Toolkit (GATK) v4.5.0.0
HTSJDK Version: 4.1.0
Picard Version: 3.1.1
$ gatk VariantRecalibrator  [arguments omitted for brevity]
org.broadinstitute.hellbender.utils.R.RScriptExecutorException: 
Rscript exited with 1
Command Line: Rscript -e tempLibDir = '/tmp/Rlib.9339186078473502558';source('/path/to/rscript.r');
Stdout: 
Stderr: Error:
! The `space` argument of `pal_gradient_n()` only supports be "Lab" as
  of scales 0.3.0.
Backtrace:
     ▆
  1. ├─base::source("/path/to/rscript.r")
  2. │ ├─base::withVisible(eval(ei, envir))
  3. │ └─base::eval(ei, envir)
  4. │   └─base::eval(ei, envir)
  5. └─ggplot2::scale_fill_gradient(high = "green", low = "red", space = "rgb")
  6.   ├─ggplot2::continuous_scale(...)
  7.   │ └─ggplot2::ggproto(...)
  8.   │   └─rlang::list2(...)
  9.   └─scales::seq_gradient_pal(low, high, space)
 10.     └─scales::pal_gradient_n(c(low, high), space = space)
 11.       └─lifecycle::deprecate_stop("0.3.0", "pal_gradient_n(space = 'only supports be \"Lab\"')")
 12.         └─lifecycle:::deprecate_stop0(msg)
 13.           └─rlang::cnd_signal(...)
Execution halted
$ R
> install.packages("remotes", repos="https://cloud.r-project.org/")
> library(remotes)
> install_version("scales", version="1.2.1", repos="https://cloud.r-project.org/")
> packageVersion("scales")
[1] ‘1.2.1’
> quit()
$ gatk VariantRecalibrator [arguments omitted for brevity]
$

Expected behavior

The output rscript file is used to generate a PDF.

Actual behavior

Generation of the PDF fails due to an deprecation in the scales library causing the Rscript command to abort.

[lbergelson]

Looks like we need to update our Rscripts... thanks for the report!

[wanqiangdehuoguo]

Hi, i face the same bug.

Could you tell me which version ggplot2 can be used or how many times you can fix this problem?

tahanks!

[gokalpcelik]

R version 3.6 and compatible ggplot2 is needed. Compatible versions are listed in the gatkcondaenv.yml

# core R dependencies; these should only be used for plotting and do not take precedence over core python dependencies!
- r-base=3.6.2
- r-data.table=1.12.8
- r-dplyr=0.8.5
- r-getopt=1.20.3
- r-ggplot2=3.3.0
- r-gplots=3.0.3
- r-gsalib=2.1
- r-optparse=1.6.4
- r-backports=1.1.10

[Lotteaveline]

Hi, I also face this problem:

Runtime.totalMemory()=8598323200`
org.broadinstitute.hellbender.utils.R.RScriptExecutorException: 
Rscript exited with 1
Command Line: Rscript -e tempLibDir = '/tmp/Rlib.3561179774649616878';source('/mnt/filename.snps.plots.R');
Stdout: 
Stderr: Error:
! The `space` argument of `pal_gradient_n()` only supports be "Lab" as
  of scales 0.3.0.
Backtrace:
     ▆
  1. ├─base::source("/mnt/filename.snps.plots.R")
  2. │ ├─base::withVisible(eval(ei, envir))
  3. │ └─base::eval(ei, envir)
  4. │   └─base::eval(ei, envir)
  5. └─ggplot2::scale_fill_gradient(high = "green", low = "red", space = "rgb")
  6.   ├─ggplot2::continuous_scale(...)
  7.   │ └─ggplot2::ggproto(...)
  8.   │   └─rlang::list2(...)
  9.   └─scales::pal_seq_gradient(low, high, space)
 10.     └─scales::pal_gradient_n(c(low, high), space = space)
 11.       └─lifecycle::deprecate_stop("0.3.0", "pal_gradient_n(space = 'only supports be \"Lab\"')")
 12.         └─lifecycle:::deprecate_stop0(msg)
 13.           └─rlang::cnd_signal(...)
Execution halted

My versions of R and packages are
R = 4.2.3
ggplot2 = 3.5.0

Did you already find a solution to this problem?

Thanks!

[gokalpcelik]

Hi @Lotteaveline
Recent versions of R and libraries are known to have issues therefore our suggestion is to stick with the versions recommended in the list above.

[Lotteaveline]

Okay thank you for the quick response!