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: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.10.2.tar.gz
StartedAt: 2013-03-25 01:28:49 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:37:39 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 530.1 seconds
RetCode: 0
Status:  OK 
CheckDir: GenomicFeatures.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/GenomicFeatures.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.10.2’
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
extractTranscriptsFromGenome 80.645 14.336 105.352
makeFeatureDbFromUCSC         5.460  0.120  25.082
makeTranscriptDbFromUCSC      2.788  0.044   9.724
makeTranscriptDbFromBiomart   2.080  0.032  20.905
* 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
  ‘/loc/home/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_SEQS0.0000.0000.001
FeatureDb-class0.0440.0000.057
TranscriptDb-class1.1160.0841.255
as-format-methods2.1680.0162.292
extractTranscriptsFromGenome 80.645 14.336105.352
features0.0800.0040.107
getPromoterSeq-methods2.1450.4562.898
id2name0.0720.0000.091
makeFeatureDbFromUCSC 5.460 0.12025.082
makeTranscriptDb0.1160.0080.126
makeTranscriptDbFromBiomart 2.080 0.03220.905
makeTranscriptDbFromGFF4.0240.0084.380
makeTranscriptDbFromUCSC2.7880.0449.724
makeTxDbPackage0.4810.0120.749
saveFeatures0.0000.0000.001
select-methods0.2720.0000.318
transcripts0.7240.0120.750
transcriptsBy2.1360.0162.284
transcriptsByOverlaps0.3080.0000.313