BioC 3.2: CHECK report for annotate on oaxaca
This page was generated on 2015-08-24 10:54:56 -0700 (Mon, 24 Aug 2015).
annotate 1.47.4 Bioconductor Package Maintainer
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/annotate | Last Changed Rev: 106549 / Revision: 107696 | Last Changed Date: 2015-07-19 10:01:15 -0700 (Sun, 19 Jul 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |  |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK |  |
Summary
Package: annotate |
Version: 1.47.4 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotate_1.47.4.tar.gz |
StartedAt: 2015-08-23 21:38:10 -0700 (Sun, 23 Aug 2015) |
EndedAt: 2015-08-23 21:41:52 -0700 (Sun, 23 Aug 2015) |
EllapsedTime: 222.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: annotate.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings annotate_1.47.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/annotate.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annotate/DESCRIPTION’ ... OK
* this is package ‘annotate’ version ‘1.47.4’
* 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 ‘annotate’ can be installed ... [11s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘Biostrings’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘AnnotationDbi:::makeFlatBimapUsingSelect’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.blastSequencesToDNAMultipleAlignment: no visible global function
definition for ‘IRanges’
.blastSequencesToDataFrame: no visible global function definition for
‘xmlToDataFrame’
getGOChildren: no visible binding for global variable ‘GOMFCHILDREN’
getGOChildren: no visible binding for global variable ‘GOBPCHILDREN’
getGOChildren: no visible binding for global variable ‘GOCCCHILDREN’
getGOOntology: no visible binding for global variable ‘GOTERM’
getGOParents: no visible binding for global variable ‘GOMFPARENTS’
getGOParents: no visible binding for global variable ‘GOBPPARENTS’
getGOParents: no visible binding for global variable ‘GOCCPARENTS’
getGOTerm: no visible binding for global variable ‘GOTERM’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [42s/97s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
chrCats 15.768 0.200 16.297
blastSequences 0.184 0.005 43.359
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘annotate_unit_tests.R’ [9s/9s]
[9s/9s] 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
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.2-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:
name | user | system | elapsed
|
ACCNUMStats | 2.525 | 0.030 | 2.559 |
|
GO2heatmap | 0.217 | 0.010 | 0.228 |
|
GOmnplot | 0.129 | 0.004 | 0.134 |
|
HTMLPage-class | 0.001 | 0.000 | 0.001 |
|
LL2homology | 0.001 | 0.000 | 0.001 |
|
PMIDAmat | 0.168 | 0.004 | 0.252 |
|
PWAmat | 4.156 | 0.088 | 4.251 |
|
UniGeneQuery | 0.002 | 0.000 | 0.002 |
|
accessionToUID | 0.266 | 0.014 | 2.098 |
|
annPkgName | 0.001 | 0.000 | 0.002 |
|
aqListGOIDs | 0.755 | 0.042 | 0.801 |
|
blastSequences | 0.184 | 0.005 | 43.359 |
|
buildChromLocation | 2.236 | 0.040 | 2.296 |
|
buildPubMedAbst | 0.039 | 0.001 | 0.370 |
|
chrCats | 15.768 | 0.200 | 16.297 |
|
chromLocation-class | 2.327 | 0.011 | 2.362 |
|
compatibleVersions | 0.097 | 0.003 | 0.102 |
|
dropECode | 0.081 | 0.002 | 0.084 |
|
entrezGeneByID | 0.001 | 0.001 | 0.002 |
|
entrezGeneQuery | 0.001 | 0.000 | 0.002 |
|
filterGOByOntology | 0.122 | 0.005 | 0.127 |
|
findNeighbors | 0.043 | 0.003 | 0.101 |
|
genbank | 0.170 | 0.007 | 1.472 |
|
getAnnMap | 0.122 | 0.013 | 0.273 |
|
getEvidence | 0.072 | 0.001 | 0.074 |
|
getGOTerm | 0.256 | 0.007 | 0.296 |
|
getOntology | 0.075 | 0.002 | 0.076 |
|
getPMInfo | 0.675 | 0.003 | 1.074 |
|
getSYMBOL | 0.204 | 0.013 | 0.295 |
|
getSeq4Acc | 0.003 | 0.001 | 0.608 |
|
hasGOannote | 0.050 | 0.002 | 0.051 |
|
hgByChroms | 0.018 | 0.004 | 0.022 |
|
hgCLengths | 0.002 | 0.000 | 0.003 |
|
hgu95Achroloc | 0.085 | 0.010 | 0.095 |
|
hgu95Achrom | 0.072 | 0.009 | 0.092 |
|
hgu95All | 0.078 | 0.009 | 0.092 |
|
hgu95Asym | 0.076 | 0.009 | 0.086 |
|
homoData-class | 0.004 | 0.000 | 0.005 |
|
htmlpage | 0.036 | 0.002 | 0.039 |
|
isValidkey | 0.001 | 0.000 | 0.001 |
|
makeAnchor | 0.001 | 0.000 | 0.001 |
|
organism | 2.445 | 0.018 | 2.471 |
|
p2LL | 0.000 | 0.000 | 0.001 |
|
pm.abstGrep | 1.079 | 0.017 | 2.687 |
|
pm.getabst | 0.985 | 0.014 | 2.586 |
|
pm.titles | 1.047 | 0.012 | 2.977 |
|
pmAbst2HTML | 0.057 | 0.002 | 0.942 |
|
pmid2MIAME | 0 | 0 | 0 |
|
pmidQuery | 0.001 | 0.000 | 0.001 |
|
pubMedAbst-class | 0.033 | 0.001 | 0.386 |
|
pubmed | 0.015 | 0.001 | 0.354 |
|
readGEOAnn | 0.001 | 0.000 | 0.001 |
|
serializeEnv | 0.002 | 0.000 | 0.002 |
|
setRepository | 0.003 | 0.000 | 0.004 |
|
updateSymbolsToValidKeys | 0.000 | 0.001 | 0.001 |
|
usedChromGenes | 0.093 | 0.010 | 0.103 |
|