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 247/609HostnameOS / ArchBUILDCHECKBUILD BIN
GenomicFeatures 1.10.2
Bioconductor Package Maintainer
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/GenomicFeatures
Last Changed Rev: 73739 / Revision: 74773
Last Changed Date: 2013-02-25 13:12:15 -0800 (Mon, 25 Feb 2013)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: GenomicFeatures
Version: 1.10.2
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicFeatures_1.10.2.tar.gz
StartedAt: 2013-03-24 23:42:16 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 23:51:21 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 544.9 seconds
RetCode: 0
Status:  OK 
CheckDir: GenomicFeatures.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/GenomicFeatures.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GenomicFeatures/DESCRIPTION' ... OK
* this is package 'GenomicFeatures' version '1.10.2'
* 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 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 ... OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
extractTranscriptsFromGenome 107.668 25.256 140.814
makeFeatureDbFromUCSC          5.887  0.318  20.163
makeTranscriptDbFromUCSC       3.039  0.112   9.322
makeTranscriptDbFromBiomart    1.854  0.163  27.442
* 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-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' 
** testing if installed package can be loaded

* DONE (GenomicFeatures)

GenomicFeatures.Rcheck/GenomicFeatures-Ex.timings:

nameusersystemelapsed
DEFAULT_CIRC_SEQS000
FeatureDb-class0.0390.0050.045
TranscriptDb-class1.0650.3071.544
as-format-methods1.9980.0202.027
extractTranscriptsFromGenome107.668 25.256140.814
features0.0770.0040.082
getPromoterSeq-methods2.9480.6553.952
id2name0.0730.0070.081
makeFeatureDbFromUCSC 5.887 0.31820.163
makeTranscriptDb0.1230.0130.137
makeTranscriptDbFromBiomart 1.854 0.16327.442
makeTranscriptDbFromGFF3.7130.1523.972
makeTranscriptDbFromUCSC3.0390.1129.322
makeTxDbPackage0.5510.0310.624
saveFeatures0.0000.0000.001
select-methods0.2520.0090.268
transcripts0.6920.0110.715
transcriptsBy2.1230.0152.150
transcriptsByOverlaps0.3020.0050.309