How to fix Perl warning message when loading gdata package? - r

Question

I've updated Strawberry Perl 64-bit 5.30.2001 and the gdata package. Now, when loading library(gdata) I always get this warning messages which appear to be related to Perl.
suppressPackageStartupMessages(library(gdata))
# Warning messages:
# 1: In system(cmd, intern = intern, wait = wait | intern, show.output.on.console = wait, :
# running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
# 2: In system(cmd, intern = intern, wait = wait | intern, show.output.on.console = wait, :
# running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
However, read.xls, the function I need, seems to run well, except that the warning is repeated every time I use it.
read.xls("http://file-examples-com.github.io/uploads/2017/02/file_example_XLS_10.xls")
# trying URL 'http://file-examples-com.github.io/uploads/2017/02/file_example_XLS_10.xls'
# Content type 'application/vnd.ms-excel' length 8704 bytes
# downloaded 8704 bytes
# X0 First.Name Last.Name Gender Country Age Date Id
# 1 1 Dulce Abril Female United States 32 15/10/2017 1562
# 2 2 Mara Hashimoto Female Great Britain 25 16/08/2016 1582
# 3 3 Philip Gent Male France 36 21/05/2015 2587
# 4 4 Kathleen Hanner Female United States 25 15/10/2017 3549
# 5 5 Nereida Magwood Female United States 58 16/08/2016 2468
# 6 6 Gaston Brumm Male United States 24 21/05/2015 2554
# 7 7 Etta Hurn Female Great Britain 56 15/10/2017 3598
# 8 8 Earlean Melgar Female United States 27 16/08/2016 2456
# 9 9 Vincenza Weiland Female United States 40 21/05/2015 6548
# Warning messages:
# 1: In system(cmd, intern = intern, wait = wait | intern, show.output.on.console = wait, :
# running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
# 2: In system(cmd, intern = intern, wait = wait | intern, show.output.on.console = wait, :
# running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
I'm not sure how to deal with this warning because it says nothing to me, I could probably just ignore it and wrap a suppressWarnings() around it.
Nevertheless, does anybody know a way to fix this? I couldn't find anything by googling and don't know where to start and what's actually wrong.
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] gdata_2.18.0
loaded via a namespace (and not attached):
[1] compiler_4.0.2 tools_4.0.2 gtools_3.8.2

Answer 1

I had the same issue with a freshly installed version of R, gdata and Strawberry Perl. I finally found this answer to a different (but related) question. Adapting the suggestion there, I ran the following on an elevated command promt:
FTYPE perl=C:\Strawberry\perl\bin\perl.exe %1 %*
This solved the issue for me – however: I am not sure if setting the FTYPE like this might have any unwanted side effects. So be careful.
Update: The command above did suppress the warning "ftype perl' had status 2" for me, but gdata still had issues:
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.
gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.
However, installXLSXsupport() failed with an unspecific error message.
I then ran
Sys.which("perl")
perl
"C:\\rtools40\\usr\\bin\\perl.exe"
and realized that the Perl version from RTools takes precedence over my Strawberry Perl installation – and apparently gdata does not "like" that Perl version.
Therefore, I decided to give Strawberry Perl precedence over RTools by changing my .Renviron file (usethis::edit_r_environ()):
PATH="${RTOOLS40_HOME}\usr\bin;${PATH}" # old
PATH="${PATH};${RTOOLS40_HOME}\usr\bin" # new
Again, I'm not entirely sure what ramifications this might have, but it fixed gdata for me.
Maybe adjusting the PATH alone would also have done the trick (without the ftype stunt I made first), but I cannot test this anymore.
What I recommend:
Adjust the PATH first.
If gdata still complains about the ftype, set the ftype.