[Bioc-devel] citation() error for BiocParallel and S4Vectors

[Morgan, Martin]

It is this commit

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r69509 | hornik | 2015-10-12 07:06:54 -0400 (Mon, 12 Oct 2015) | 1 line

Fixes for PR #16240 and PR #16550.
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which is failing when z$url == meta$URL[1] == NULL. I have bcc'd Kurt Hornik

Martin

________________________________________
From: Bioc-devel [bioc-devel-bounces at r-project.org] on behalf of Leonardo Collado Torres [lcollado at jhu.edu]
Sent: Tuesday, November 03, 2015 10:50 PM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] citation() error for BiocParallel and S4Vectors

Hi,

The daily build report showed a similar error in several of my
packages when building on Linux and Windows. I was able to reproduce
this error under R-devel on Windows and it pops up when using the
citation() function. In particular with BiocParallel and S4Vectors.

This error doesn't pop up in the build report for BiocParallel or
S4Vectors and I believe that's because they are not using the
citation() function in their vignettes. However, I would have guessed
that this error would affect the Bioc-devel landing pages but it
hasn't.

I haven't found any leads when looking at the DESCRIPTION files for
these packages (they don't have a inst/CITATION file). So my guess is
that this is really a bug in citation() for R-devel. If anyone has a
guess please let me know.

I didn't see a thread about this in R-devel (last 3 months) so I'll
likely re-post this there if needed.

Thanks,
Leo


> citation('BiocParallel')
Error in if (!length(z$url) && !is.na(url <- meta$URL[1L])) { :
  missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In citation("BiocParallel") :
  no date field in DESCRIPTION file of package ‘BiocParallel’
2: In is.na(url <- meta$URL[1L]) :
  is.na() applied to non-(list or vector) of type 'NULL'
> traceback()
1: citation("BiocParallel")

> citation('S4Vectors')
Error in if (!length(z$url) && !is.na(url <- meta$URL[1L])) { :
  missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In citation("S4Vectors") :
  no date field in DESCRIPTION file of package ‘S4Vectors’
2: In is.na(url <- meta$URL[1L]) :
  is.na() applied to non-(list or vector) of type 'NULL'
> traceback()
1: citation("S4Vectors")

> sessionInfo()
R Under development (unstable) (2015-11-02 r69589)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

> packageVersion('BiocParallel')
[1] ‘1.5.0’
> packageVersion('S4Vectors')
[1] ‘0.9.6’

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