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Package 270/671HostnameOS / ArchBUILDCHECKBUILD BIN
GenomicFeatures 1.12.1
Bioconductor Package Maintainer
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/GenomicFeatures
Last Changed Rev: 76039 / Revision: 76155
Last Changed Date: 2013-04-25 14:36:56 -0700 (Thu, 25 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: GenomicFeatures
Version: 1.12.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicFeatures_1.12.1.tar.gz
StartedAt: 2013-05-01 05:57:51 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 06:11:17 -0700 (Wed, 01 May 2013)
EllapsedTime: 806.6 seconds
RetCode: 0
Status:  OK 
CheckDir: GenomicFeatures.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GenomicFeatures.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GenomicFeatures/DESCRIPTION' ... OK
* this is package 'GenomicFeatures' version '1.12.1'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'GenomicFeatures' can be installed ... [28s/29s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
.setseqnameStyle: no visible binding for global variable 'txdb'
* 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 installed files from 'inst/doc' ... OK
* checking examples ... [199s/295s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
extractTranscriptsFromGenome 125.986 21.686 153.922
makeFeatureDbFromUCSC         10.030  0.500  57.607
makeTranscriptDbFromUCSC       5.683  0.182  25.379
getPromoterSeq-methods         3.932  0.771   6.177
makeTranscriptDbFromBiomart    2.498  0.184  21.328
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'GenomicFeatures_unit_tests.R' [133s/228s]
 [134s/228s] 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-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
** testing if installed package can be loaded
* DONE (GenomicFeatures)

GenomicFeatures.Rcheck/GenomicFeatures-Ex.timings:

nameusersystemelapsed
DEFAULT_CIRC_SEQS0.0090.0050.014
FeatureDb-class0.0570.0080.065
TranscriptDb-class1.0570.2564.041
as-format-methods2.8450.0472.953
extractTranscriptsFromGenome125.986 21.686153.922
features0.1070.0090.140
getPromoterSeq-methods3.9320.7716.177
id2name0.0870.0150.134
makeFeatureDbFromUCSC10.030 0.50057.607
makeTranscriptDb0.1600.0250.185
makeTranscriptDbFromBiomart 2.498 0.18421.328
makeTranscriptDbFromGFF2.8410.1293.057
makeTranscriptDbFromUCSC 5.683 0.18225.379
makeTxDbPackage0.6100.0360.698
saveFeatures0.0030.0050.010
select-methods0.3360.0340.379
transcripts0.9250.0370.985
transcriptsBy2.6160.0302.679
transcriptsByOverlaps0.3390.0110.354