From hpages at fredhutch.org  Sat Apr 18 03:05:06 2015
From: hpages at fredhutch.org (=?UTF-8?B?SGVydsOpIFBhZ8Oocw==?=)
Date: Fri, 17 Apr 2015 18:05:06 -0700
Subject: [Rd] truncated warning messages
Message-ID: <5531ADC2.8000804@fredhutch.org>

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



[Rd] truncated warning messages
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