R devel - Apr 2015 - truncated warning messages

Hi,

I was installing hundreds of packages on a machine with a single call to
install.packages() and after a long time the call to install.packages()
finally returned with the following warnings and errors:

Warning messages:
1: packages ?hgu133aprobe?, ?hgu95av2.db?, ?BSgenome.Celegans.UCSC.ce2?, 
?BSgenome.Mmusculus.UCSC.mm10?, 
?BSgenome.Dmelanogaster.UCSC.dm3.masked?, 
?BSgenome.Hsapiens.UCSC.hg18.masked?, 
?BSgenome.Hsapiens.UCSC.hg19.masked?, 
?BSgenome.Mmusculus.UCSC.mm9.masked?, 
?BSgenome.Scerevisiae.UCSC.sacCer2?, ?BSgenome.Hsapiens.NCBI.GRCh38?, 
?BSgenome.Rnorvegicus.UCSC.rn5?, ?drosophila2probe?, ?hgu95av2probe?, 
?hgu95av2cdf?, ?SNPlocs.Hsapiens.dbSNP.20100427?, 
?SNPlocs.Hsapiens.dbSNP.20101109?, ?SNPlocs.Hsapiens.dbSNP.20110815?, 
?SNPlocs.Hsapiens.dbSNP141.GRCh38?, 
?XtraSNPlocs.Hsapiens.dbSNP141.GRCh38?, ?org.Sc.sgd.db?, ?org.Mm.eg.db?, 
?org.At.tair.db?, ?hom.Hs.inp.db?, ?GO.db?, 
?TxDb.Hsapiens.UCSC.hg18.knownGene?, 
?TxDb.Hsapiens.UCSC.hg19.knownGene?, 
?TxDb.Hsapiens.UCSC.hg38.knownGene?, 
?TxDb.Mmusculus.UCSC.mm9.knownGene?, 
?TxDb.Mmusculus.UCSC.mm10.knownGene?, ?TxDb.Dmelanogaster.UCSC. [... 
truncated]
2: In install.packages(pkgs = doing, lib = lib, ...) :
   installation of package ?humanStemCell? had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
   installation of package ?AnnotationForge? had non-zero exit status

As you can see the warning message is truncated so I can't see what
happened to these packages. What about having a message like

   package(s) not available: pkg1, pkg2, pkg3, etc...

so when it's truncated we don't loose the important part of the story?

I guess the same kind of change could be made to the other warning
messages, and, more generally, to any warning/error message obtained
by injecting an arbitrary (and potentially long) list of strings.

Thanks,
H.

-- 
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

On Fri, Apr 17, 2015 at 6:05 PM, Herv? Pag?s <hpages at fredhutch.org>
wrote:
> As you can see the warning message is truncated so I can't see what
> happened to these packages.

In this case you could also increase options("warning.length")

	[[alternative HTML version deleted]]

On 04/17/2015 08:25 PM, Jeroen Ooms wrote:
>
> On Fri, Apr 17, 2015 at 6:05 PM, Herv? Pag?s <hpages at fredhutch.org
> <mailto:hpages at fredhutch.org>> wrote:
>
>     As you can see the warning message is truncated so I can't see what
>     happened to these packages.
>
>
> In this case you could also increase options("warning.length")
>
and re-run my install.packages() command (which took about 30 minutes
to run) with the hope that this time I'll be able to see the entire
message? Even setting warning.length to the max (8170 on my machine),
might not be enough. Note that the workaround I used was to re-run
the command on only 1 of the packages listed in the warning message.
That does work and is quick!

Kind of a secondary point to me previous post is that displaying a
listing of thousand of things is not that useful, especially when you
cannot even copy/paste it to re-use at the command line (because of
the fancy quotes). But that's another story...

Cheers,
H.