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BioC 2.12: CHECK report for GenomicFeatures on petty

This page was generated on 2013-10-09 09:39:48 -0700 (Wed, 09 Oct 2013).

Package 270/671HostnameOS / ArchBUILDCHECKBUILD BIN
GenomicFeatures 1.12.4
Bioconductor Package Maintainer
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/GenomicFeatures
Last Changed Rev: 80690 / Revision: 81334
Last Changed Date: 2013-09-23 16:53:10 -0700 (Mon, 23 Sep 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 

Summary

Package: GenomicFeatures
Version: 1.12.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicFeatures_1.12.4.tar.gz
StartedAt: 2013-10-08 22:32:34 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 22:45:33 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 779.0 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 3.0.1 (2013-05-16)
* 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 '1.12.4'
* 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 ... [32s/33s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [213s/315s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
extractTranscriptsFromGenome 134.205 19.720 155.608
makeFeatureDbFromUCSC         12.389  0.451  71.932
makeTranscriptDbFromUCSC       7.141  0.161  31.547
makeTranscriptDbFromBiomart    3.091  0.156  19.393
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'GenomicFeatures_unit_tests.R' [132s/147s]
 [132s/148s] 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_SEQS0.0060.0040.009
FeatureDb-class0.0790.0080.087
TranscriptDb-class1.2880.1581.582
as-format-methods3.1610.0293.196
extractTranscriptsFromGenome134.205 19.720155.608
features0.1360.0080.145
getPromoterSeq-methods3.8970.6504.648
id2name0.1250.0130.138
makeFeatureDbFromUCSC12.389 0.45171.932
makeTranscriptDb0.1920.0200.212
makeTranscriptDbFromBiomart 3.091 0.15619.393
makeTranscriptDbFromGFF3.3580.1123.510
makeTranscriptDbFromUCSC 7.141 0.16131.547
makeTxDbPackage0.7770.0330.849
saveFeatures0.0030.0070.010
select-methods0.4160.0350.452
transcripts1.1400.0251.166
transcriptsBy3.1880.0233.221
transcriptsByOverlaps0.4340.0100.444