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Package 189/462HostnameOS / ArchBUILDCHECKBUILD BIN
GenomicFeatures 1.5.5
Biocore Team c/o BioC user list
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicFeatures
Last Changed Rev: 55286 / Revision: 55359
Last Changed Date: 2011-05-05 17:00:33 -0700 (Thu, 05 May 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: GenomicFeatures
Version: 1.5.5
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.5.5.tar.gz
StartedAt: 2011-05-09 12:36:38 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 12:42:56 -0700 (Mon, 09 May 2011)
EllapsedTime: 377.9 seconds
RetCode: 0
Status:  OK 
CheckDir: GenomicFeatures.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/GenomicFeatures.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK
* this is package ‘GenomicFeatures’ version ‘1.5.5’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘GenomicFeatures’ 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... NOTE
.getMetaDataValue: no visible global function definition for ‘error’
* 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 ... NOTE
‘library’ or ‘require’ call not declared from: ‘BSgenome.Celegans.UCSC.ce2’
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘GenomicFeatures_unit_tests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

GenomicFeatures.Rcheck/00install.out:

* installing *source* package ‘GenomicFeatures’ ...
** R
** inst
** preparing package for lazy loading

Attaching package: ‘IRanges’

The following object(s) are masked from ‘package:base’:

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘GenomicFeatures.Rnw’ 
   ‘examples.Rnw’ 
** testing if installed package can be loaded

* DONE (GenomicFeatures)

GenomicFeatures.Rcheck/GenomicFeatures-Ex.timings:

nameusersystemelapsed
DEFAULT_CIRC_SEQS000
TranscriptDb-class0.9320.0560.993
extractTranscriptsFromGenome55.21610.19266.607
features0.1240.0080.132
id2name0.1480.0000.148
makeFeatureDbFromUCSC 5.152 0.15648.916
makeTranscriptDb0.1760.0080.193
makeTranscriptDbFromBiomart 1.444 0.03618.778
makeTranscriptDbFromUCSC 2.524 0.04016.646
makeTxDbPackage0.0040.0000.003
saveFeatures0.0960.0000.102
transcripts0.4120.0000.412
transcriptsBy1.4800.0001.479
transcriptsByOverlaps0.6400.0440.688