BioC 3.3: CHECK report for annotate on windows2.bioconductor.org
This page was generated on 2015-10-27 12:13:52 -0400 (Tue, 27 Oct 2015).
annotate 1.49.0 Bioconductor Package Maintainer
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/annotate | Last Changed Rev: 109592 / Revision: 109948 | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK |  |
Summary
Package: annotate
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Version: 1.49.0
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Command: rm -rf annotate.buildbin-libdir annotate.Rcheck && mkdir annotate.buildbin-libdir annotate.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=annotate.buildbin-libdir annotate_1.49.0.tar.gz >annotate.Rcheck\00install.out 2>&1 && cp annotate.Rcheck\00install.out annotate-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=annotate.buildbin-libdir --install="check:annotate-install.out" --force-multiarch --no-vignettes --timings annotate_1.49.0.tar.gz
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StartedAt: 2015-10-27 00:34:55 -0400 (Tue, 27 Oct 2015)
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EndedAt: 2015-10-27 00:39:30 -0400 (Tue, 27 Oct 2015)
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EllapsedTime: 274.4 seconds
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RetCode: 0
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Status: OK
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CheckDir: annotate.Rcheck
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Warnings: 0
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Command output
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### Running command:
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### rm -rf annotate.buildbin-libdir annotate.Rcheck && mkdir annotate.buildbin-libdir annotate.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=annotate.buildbin-libdir annotate_1.49.0.tar.gz >annotate.Rcheck\00install.out 2>&1 && cp annotate.Rcheck\00install.out annotate-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=annotate.buildbin-libdir --install="check:annotate-install.out" --force-multiarch --no-vignettes --timings annotate_1.49.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/annotate.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'annotate/DESCRIPTION' ... OK
* this is package 'annotate' version '1.49.0'
* 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 whether package 'annotate' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
Undefined global functions or variables:
GOBPCHILDREN GOBPPARENTS GOCCCHILDREN GOCCPARENTS GOMFCHILDREN
GOMFPARENTS GOTERM IRanges xmlToDataFrame
* 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 ...
** running examples for arch 'i386' ... [90s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
chrCats 8.97 0.03 9.92
accessionToUID 4.84 2.23 7.66
genbank 3.57 1.45 5.17
pm.getabst 3.30 1.44 5.26
pm.titles 3.64 0.94 5.14
blastSequences 0.06 0.00 31.30
** running examples for arch 'x64' ... [81s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
chrCats 11.75 0.02 11.77
accessionToUID 2.82 2.17 18.23
blastSequences 0.05 0.00 18.10
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'annotate_unit_tests.R' [5s]
[5s] OK
** running tests for arch 'x64' ...
Running 'annotate_unit_tests.R' [6s]
[6s] 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
'c:/biocbld/bbs-3.3-bioc/meat/annotate.Rcheck/00check.log'
for details.
annotate.Rcheck/00install.out:
install for i386
* 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
install for x64
* installing *source* package 'annotate' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'annotate' as annotate_1.49.0.zip
* DONE (annotate)
annotate.Rcheck/examples_i386/annotate-Ex.timings:
name | user | system | elapsed
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ACCNUMStats | 1.38 | 0.04 | 1.42 |
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GO2heatmap | 0.11 | 0.02 | 0.12 |
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GOmnplot | 0.06 | 0.00 | 0.06 |
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HTMLPage-class | 0 | 0 | 0 |
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LL2homology | 0 | 0 | 0 |
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PMIDAmat | 0.18 | 0.00 | 0.21 |
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PWAmat | 3.88 | 0.08 | 3.95 |
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UniGeneQuery | 0 | 0 | 0 |
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accessionToUID | 4.84 | 2.23 | 7.66 |
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annPkgName | 0 | 0 | 0 |
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aqListGOIDs | 0.46 | 0.02 | 4.43 |
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blastSequences | 0.06 | 0.00 | 31.30 |
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buildChromLocation | 0.89 | 0.03 | 0.92 |
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buildPubMedAbst | 0.11 | 0.01 | 0.24 |
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chrCats | 8.97 | 0.03 | 9.92 |
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chromLocation-class | 0.98 | 0.02 | 1.00 |
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compatibleVersions | 0.02 | 0.02 | 0.03 |
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dropECode | 0.01 | 0.01 | 0.03 |
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entrezGeneByID | 0 | 0 | 0 |
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entrezGeneQuery | 0 | 0 | 0 |
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filterGOByOntology | 0.06 | 0.00 | 0.06 |
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findNeighbors | 0.02 | 0.00 | 0.13 |
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genbank | 3.57 | 1.45 | 5.17 |
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getAnnMap | 0.02 | 0.00 | 0.31 |
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getEvidence | 0.03 | 0.00 | 0.03 |
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getGOTerm | 0.16 | 0.02 | 1.86 |
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getOntology | 0.03 | 0.02 | 0.05 |
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getPMInfo | 0.48 | 0.06 | 0.65 |
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getSYMBOL | 0.08 | 0.00 | 0.39 |
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getSeq4Acc | 0.00 | 0.00 | 0.06 |
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hasGOannote | 0.01 | 0.00 | 0.06 |
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hgByChroms | 0.00 | 0.01 | 0.02 |
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hgCLengths | 0.02 | 0.00 | 0.02 |
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hgu95Achroloc | 0.06 | 0.00 | 0.06 |
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hgu95Achrom | 0.06 | 0.00 | 0.06 |
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hgu95All | 0.07 | 0.00 | 0.06 |
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hgu95Asym | 0.06 | 0.00 | 0.07 |
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homoData-class | 0.01 | 0.00 | 0.01 |
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htmlpage | 0.00 | 0.00 | 0.03 |
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isValidkey | 0 | 0 | 0 |
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makeAnchor | 0 | 0 | 0 |
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organism | 0.92 | 0.02 | 0.94 |
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p2LL | 0 | 0 | 0 |
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pm.abstGrep | 3.11 | 1.23 | 4.89 |
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pm.getabst | 3.30 | 1.44 | 5.26 |
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pm.titles | 3.64 | 0.94 | 5.14 |
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pmAbst2HTML | 0.11 | 0.03 | 0.33 |
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pmid2MIAME | 0 | 0 | 0 |
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pmidQuery | 0 | 0 | 0 |
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pubMedAbst-class | 0.12 | 0.02 | 0.50 |
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pubmed | 0.13 | 0.09 | 0.34 |
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readGEOAnn | 0 | 0 | 0 |
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serializeEnv | 0.01 | 0.00 | 0.02 |
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setRepository | 0 | 0 | 0 |
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updateSymbolsToValidKeys | 0 | 0 | 0 |
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usedChromGenes | 0.08 | 0.00 | 0.08 |
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annotate.Rcheck/examples_x64/annotate-Ex.timings:
name | user | system | elapsed
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ACCNUMStats | 1.47 | 0.03 | 1.58 |
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GO2heatmap | 0.14 | 0.00 | 0.14 |
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GOmnplot | 0.08 | 0.00 | 0.08 |
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HTMLPage-class | 0 | 0 | 0 |
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LL2homology | 0 | 0 | 0 |
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PMIDAmat | 0.23 | 0.01 | 0.25 |
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PWAmat | 3.11 | 0.07 | 3.17 |
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UniGeneQuery | 0.02 | 0.00 | 0.02 |
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accessionToUID | 2.82 | 2.17 | 18.23 |
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annPkgName | 0 | 0 | 0 |
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aqListGOIDs | 0.30 | 0.03 | 0.33 |
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blastSequences | 0.05 | 0.00 | 18.10 |
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buildChromLocation | 1.11 | 0.03 | 1.14 |
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buildPubMedAbst | 0.08 | 0.03 | 0.17 |
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chrCats | 11.75 | 0.02 | 11.77 |
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chromLocation-class | 1.08 | 0.00 | 1.08 |
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compatibleVersions | 0.03 | 0.00 | 0.03 |
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dropECode | 0.05 | 0.00 | 0.05 |
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entrezGeneByID | 0 | 0 | 0 |
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entrezGeneQuery | 0 | 0 | 0 |
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filterGOByOntology | 0.08 | 0.00 | 0.08 |
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findNeighbors | 0.02 | 0.00 | 0.02 |
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genbank | 2.14 | 1.64 | 3.89 |
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getAnnMap | 0.03 | 0.00 | 0.03 |
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getEvidence | 0.05 | 0.00 | 0.05 |
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getGOTerm | 0.15 | 0.01 | 0.17 |
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getOntology | 0.03 | 0.00 | 0.03 |
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getPMInfo | 0.61 | 0.08 | 0.78 |
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getSYMBOL | 0.13 | 0.00 | 0.12 |
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getSeq4Acc | 0.00 | 0.00 | 0.05 |
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hasGOannote | 0.03 | 0.00 | 0.03 |
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hgByChroms | 0.02 | 0.00 | 0.02 |
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hgCLengths | 0 | 0 | 0 |
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hgu95Achroloc | 0.06 | 0.00 | 0.06 |
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hgu95Achrom | 0.05 | 0.00 | 0.05 |
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hgu95All | 0.06 | 0.00 | 0.06 |
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hgu95Asym | 0.04 | 0.00 | 0.05 |
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homoData-class | 0 | 0 | 0 |
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htmlpage | 0.05 | 0.00 | 0.04 |
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isValidkey | 0 | 0 | 0 |
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makeAnchor | 0 | 0 | 0 |
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organism | 1.08 | 0.00 | 1.08 |
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p2LL | 0 | 0 | 0 |
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pm.abstGrep | 2.78 | 1.53 | 4.91 |
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pm.getabst | 2.90 | 1.17 | 4.71 |
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pm.titles | 2.62 | 1.04 | 4.21 |
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pmAbst2HTML | 0.10 | 0.01 | 0.61 |
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pmid2MIAME | 0 | 0 | 0 |
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pmidQuery | 0 | 0 | 0 |
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pubMedAbst-class | 0.08 | 0.03 | 0.20 |
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pubmed | 0.18 | 0.03 | 0.30 |
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readGEOAnn | 0 | 0 | 0 |
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serializeEnv | 0 | 0 | 0 |
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setRepository | 0.02 | 0.00 | 0.01 |
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updateSymbolsToValidKeys | 0 | 0 | 0 |
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usedChromGenes | 0.06 | 0.00 | 0.06 |
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