Back to the "Multiple platform build/check report" A  B  C  D  E  F [G] H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

Package 223/553HostnameOS / ArchBUILDCHECKBUILD BIN
GenomicFeatures 1.8.3
Bioconductor Package Maintainer
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/GenomicFeatures
Last Changed Rev: 68748 / Revision: 69725
Last Changed Date: 2012-08-23 15:57:10 -0700 (Thu, 23 Aug 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: GenomicFeatures
Version: 1.8.3
Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.8.3.tar.gz
StartedAt: 2012-09-24 01:06:58 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 01:14:44 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 466.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GenomicFeatures.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/GenomicFeatures.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 ‘GenomicFeatures/DESCRIPTION’ ... OK
* this is package ‘GenomicFeatures’ version ‘1.8.3’
* 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 ‘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 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 ... NOTE
.getBiomartDbVersion: no visible binding for global variable ‘mart’
.getMetaDataValue: no visible global function definition for ‘error’
.valid.FeatureDb: no visible global function definition for
  ‘.valid.metadata.table’
.validate.colnames: no visible global function definition for
  ‘.valid.colnames’
* checking Rd files ... OK
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'asBED,TranscriptDb-method':
  ‘TranscriptDb-class.Rd’ ‘as-format-methods.Rd’
Rd files with duplicated alias 'asGFF,TranscriptDb-method':
  ‘TranscriptDb-class.Rd’ ‘as-format-methods.Rd’
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘GenomicFeatures_unit_tests.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ calls not declared from:
  ‘DESeq’ ‘DEXSeq’ ‘Rsamtools’ ‘xtable’
* 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

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/GenomicFeatures.Rcheck/00check.log’
for details.

GenomicFeatures.Rcheck/00install.out:

* installing *source* package ‘GenomicFeatures’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘GenomicFeatures.Rnw’ 
   ‘spliceGraph.Rnw’ 
** testing if installed package can be loaded

* DONE (GenomicFeatures)

GenomicFeatures.Rcheck/GenomicFeatures-Ex.timings:

nameusersystemelapsed
DEFAULT_CIRC_SEQS000
TranscriptDb-class1.1440.0841.243
as-format-methods2.7560.0042.901
extractTranscriptsFromGenome 79.621 13.464100.606
features0.10.00.1
id2name0.0720.0080.081
makeFeatureDbFromUCSC 4.629 0.06416.635
makeTranscriptDb0.0760.0120.085
makeTranscriptDbFromBiomart 1.936 0.04019.420
makeTranscriptDbFromUCSC2.5360.0408.801
makeTxDbPackage0.5600.0080.578
saveFeatures0.0640.0040.073
spliceGraph0.0000.0000.002
transcripts0.5640.0040.569
transcriptsBy2.1640.0122.176
transcriptsByOverlaps0.3280.0000.330