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BioC 2.13: CHECK report for GenomicFeatures on zin1

This page was generated on 2014-04-05 09:47:47 -0700 (Sat, 05 Apr 2014).

Package 299/750HostnameOS / ArchBUILDCHECKBUILD BIN
GenomicFeatures 1.14.5
Bioconductor Package Maintainer
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/GenomicFeatures
Last Changed Rev: 87404 / Revision: 88450
Last Changed Date: 2014-03-13 10:55:47 -0700 (Thu, 13 Mar 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: GenomicFeatures
Version: 1.14.5
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings GenomicFeatures_1.14.5.tar.gz
StartedAt: 2014-04-05 01:25:45 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:34:29 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 524.4 seconds
RetCode: 0
Status:  OK 
CheckDir: GenomicFeatures.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/GenomicFeatures.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.14.5’
* 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 ... [17s/17s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocGenerics’ ‘IRanges’ ‘GenomicRanges’ ‘rtracklayer’ ‘biomaRt’ ‘Biostrings’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
‘:::’ calls which should be ‘::’:
  ‘DBI:::dbGetQuery’ ‘DBI:::dbListFields’ ‘DBI:::dbListTables’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ‘:::’ calls:
  ‘Biostrings:::getDNAComplementLookup’ ‘biomaRt:::martBM’
  ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  ‘rtracklayer:::ucscTableOutputs’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.keys’ ‘.reverseColAbbreviations’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘GenomicFeatures.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [120s/252s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
extractTranscriptsFromGenome 81.381  5.400  87.634
makeFeatureDbFromUCSC         6.217  0.068  81.037
makeTranscriptDbFromUCSC      4.224  0.008  44.385
makeTranscriptDbFromBiomart   1.464  0.036  17.072
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘GenomicFeatures_unit_tests.R’ [97s/110s]
 [97s/111s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.13-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_SEQS0.2160.0000.218
FeatureDb-class0.040.000.04
TranscriptDb-class0.7560.0600.817
as-format-methods1.7640.0001.766
extractTranscriptsFromGenome81.381 5.40087.634
features0.0800.0000.082
getPromoterSeq-methods2.2120.1282.392
id2name0.0600.0040.063
makeFeatureDbFromUCSC 6.217 0.06881.037
makeTranscriptDb0.0840.0000.085
makeTranscriptDbFromBiomart 1.464 0.03617.072
makeTranscriptDbFromGFF1.4920.0081.538
makeTranscriptDbFromUCSC 4.224 0.00844.385
makeTxDbPackage0.3440.0080.361
nearest-methods1.1160.0121.128
saveFeatures0.0000.0000.001
select-methods0.2120.0040.216
transcripts2.7370.0202.809
transcriptsBy1.9400.0361.989
transcriptsByOverlaps0.3000.0000.303