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BioC 2.14: CHECK report for annotate on zin2

This page was generated on 2014-10-08 08:47:29 -0700 (Wed, 08 Oct 2014).

Package 38/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotate 1.42.1
Bioconductor Package Maintainer
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/annotate
Last Changed Rev: 92532 / Revision: 95116
Last Changed Date: 2014-07-15 17:27:15 -0700 (Tue, 15 Jul 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  ERROR  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: annotate
Version: 1.42.1
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.42.1.tar.gz
StartedAt: 2014-10-07 21:42:13 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 21:53:35 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 681.6 seconds
RetCode: 0
Status:  OK 
CheckDir: annotate.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings annotate_1.42.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/annotate.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.42.1’
* 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 ‘annotate’ can be installed ... [9s/9s] 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:
  ‘AnnotationDbi’ ‘Biobase’ ‘XML’
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
Unexported object imported by a ':::' call: ‘AnnotationDbi:::makeFlatBimapUsingSelect’
  See the note in ?`:::` about the use of this operator.
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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [49s/579s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
chrCats        19.554  0.008  19.634
probesByLL      7.093  0.164   7.329
PWAmat          5.300  0.048   5.362
blastSequences  1.004  0.028 472.423
genbank         0.148  0.000  50.861
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘annotate_unit_tests.R’ [8s/8s]
 [8s/8s] 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 2 notes.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/annotate.Rcheck/00check.log’
for details.

annotate.Rcheck/00install.out:

* installing *source* package ‘annotate’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (annotate)

annotate.Rcheck/annotate-Ex.timings:

nameusersystemelapsed
ACCNUMStats2.0240.0242.061
GO2heatmap0.1480.0200.171
GOmnplot0.1920.0040.194
HTMLPage-class0.0000.0000.001
LL2homology000
PMIDAmat0.1360.0000.182
PWAmat5.3000.0485.362
UniGeneQuery0.0040.0000.003
accessionToUID0.1760.0042.156
annPkgName0.0000.0000.001
aqListGOIDs0.3960.0120.409
blastSequences 1.004 0.028472.423
buildChromLocation1.1000.0161.118
buildPubMedAbst0.0520.0000.520
chrCats19.554 0.00819.634
chromLocation-class1.0880.0001.088
compatibleVersions0.0680.0000.071
dropECode0.0760.0040.079
entrezGeneByID0.0040.0000.002
entrezGeneQuery0.0000.0000.001
filterGOByOntology0.0720.0000.073
findNeighbors0.0360.0000.050
genbank 0.148 0.00050.861
getAnnMap0.0720.0120.148
getEvidence0.0800.0000.081
getGOTerm0.2200.0080.229
getOntology0.0640.0080.070
getPMInfo0.6880.0001.170
getSYMBOL0.1600.0160.176
getSeq4Acc0.0000.0000.198
hasGOannote0.0440.0040.051
hgByChroms0.0160.0000.014
hgCLengths0.0000.0000.001
hgu95Achroloc0.0680.0000.068
hgu95Achrom0.0560.0000.055
hgu95All0.060.000.06
hgu95Asym0.0600.0000.062
homoData-class0.0040.0000.004
htmlpage0.0240.0040.030
isValidkey000
makeAnchor0.0000.0000.001
organism1.0560.0001.059
p2LL000
pm.abstGrep1.0040.0082.217
pm.getabst0.9960.0002.134
pm.titles1.1600.0122.281
pmAbst2HTML0.0760.0040.450
pmid2MIAME0.0000.0000.001
pmidQuery0.0000.0000.001
probesByLL7.0930.1647.329
pubMedAbst-class0.0480.0040.552
pubmed0.0360.0000.509
readGEOAnn0.0000.0000.001
serializeEnv0.0000.0000.002
setRepository0.0000.0000.003
updateSymbolsToValidKeys0.0000.0000.001
usedChromGenes0.0720.0040.076