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Package 222/553HostnameOS / ArchBUILDCHECKBUILD BIN
genomes 2.2.0
Chris Stubben
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/genomes
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ ERROR ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  ERROR  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  ERROR  OK 

Summary

Package: genomes
Version: 2.2.0
Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings genomes_2.2.0.tar.gz
StartedAt: 2012-09-24 01:06:41 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 01:07:55 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 74.8 seconds
RetCode: 1
Status:  ERROR 
CheckDir: genomes.Rcheck
Warnings: NA

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/genomes.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genomes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genomes’ version ‘2.2.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package ‘genomes’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... ERROR
Running examples in ‘genomes-Ex.R’ failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ncbiTaxonomy
> ### Title: NCBI taxonomy database
> ### Aliases: ncbiTaxonomy
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> ncbiTaxonomy(c("Bacillus anthracis", "Yersinia pestis"))
[1] "WARNING: please set your email using Sys.setenv(email='name@email.com')"
[1] "WARNING: please set your email using Sys.setenv(email='name@email.com')"
[1] "2 results found"
Error in names(x) <- c("id", "rank", "division", "name", "common", "taxid",  : 
  'names' attribute [14] must be the same length as the vector [12]
Calls: ncbiTaxonomy
Execution halted

genomes.Rcheck/00install.out:

* installing *source* package ‘genomes’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘genome-tables.Rnw’ 
** testing if installed package can be loaded

* DONE (genomes)

genomes.Rcheck/genomes-Ex.timings:

nameusersystemelapsed
complete0.0440.0000.046
doublingTime0.3280.0040.330
efetch0.0080.0161.560
einfo0.0720.0040.769
elink0.0680.0081.932
enaExperiment3.4040.0129.851
enaFiles0.0200.0000.752
enaProject0.1000.0000.792
enaSRA2.3120.0084.307
enaStudy2.5920.0126.073
enaSubmission0.0040.0000.341
enaTaxonomy0.0200.0001.459
esearch0.0160.0080.926
esummary0.1360.0001.619
genomes-lines0.2720.0040.274
genomes-plot0.2480.0000.246
genomes-print0.2120.0000.213
genomes-subset0.0880.0000.088
genomes-summary0.0240.0000.025
genomes-update0.0000.0040.003
genomes0.2320.0000.230
genus0.1520.0000.153
image20.2320.0000.230
lenvs0.0240.0000.025
leuks0.0360.0000.066
like0.1480.0000.151
lproks0.3600.0040.366
ncbiGenome0.1040.0002.534
ncbiNucleotide0.4520.0002.097
ncbiProject0.9480.0042.107
ncbiPubmed0.1680.0001.049
ncbiRelease0.0120.0001.100
ncbiSubmit0.1200.0002.349