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BioC 3.0: CHECK report for annotate on moscato1

This page was generated on 2015-04-10 09:42:56 -0700 (Fri, 10 Apr 2015).

Package 39/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
annotate 1.44.0
Bioconductor Package Maintainer
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/annotate
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  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: 1.44.0
Command: rm -rf annotate.buildbin-libdir annotate.Rcheck && mkdir annotate.buildbin-libdir annotate.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=annotate.buildbin-libdir annotate_1.44.0.tar.gz >annotate.Rcheck\00install.out 2>&1 && cp annotate.Rcheck\00install.out annotate-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=annotate.buildbin-libdir --install="check:annotate-install.out" --force-multiarch --no-vignettes --timings annotate_1.44.0.tar.gz
StartedAt: 2015-04-09 22:32:10 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:38:27 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 376.1 seconds
RetCode: 0
Status:  OK  
CheckDir: annotate.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf annotate.buildbin-libdir annotate.Rcheck && mkdir annotate.buildbin-libdir annotate.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=annotate.buildbin-libdir annotate_1.44.0.tar.gz >annotate.Rcheck\00install.out 2>&1 && cp annotate.Rcheck\00install.out annotate-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=annotate.buildbin-libdir --install="check:annotate-install.out" --force-multiarch --no-vignettes --timings annotate_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/annotate.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'annotate/DESCRIPTION' ... OK
* this is package 'annotate' version '1.44.0'
* 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 'xpathSApply'
.blastSequencesToDNAMultipleAlignment: no visible global function
  definition for 'IRanges'
.blastSequencesToDataFrame: no visible global function definition for
  'xpathSApply'
.blastSequencesToDataFrame: no visible global function definition for
  'xmlToDataFrame'
.blastSequencesToDataFrame: no visible binding for global variable
  'xpathSApply'
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [82s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
chrCats        16.13   0.03   17.42
probesByLL      6.01   0.00    6.00
PWAmat          4.99   0.02    5.01
blastSequences  0.12   0.01   17.63
** running examples for arch 'x64' ... [80s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
chrCats        18.53   0.00   18.54
PWAmat          6.72   0.05    6.77
probesByLL      6.72   0.00    6.72
blastSequences  0.11   0.00   16.29
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'annotate_unit_tests.R' [8s]
 [9s] OK
** running tests for arch 'x64' ...
  Running 'annotate_unit_tests.R' [12s]
 [12s] 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-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_1.44.0.zip
* DONE (annotate)

annotate.Rcheck/examples_i386/annotate-Ex.timings:

nameusersystemelapsed
ACCNUMStats2.620.063.00
GO2heatmap0.200.030.24
GOmnplot0.140.000.14
HTMLPage-class000
LL2homology000
PMIDAmat0.160.002.12
PWAmat4.990.025.01
UniGeneQuery000
accessionToUID0.320.032.64
annPkgName000
aqListGOIDs0.490.050.53
blastSequences 0.12 0.0117.63
buildChromLocation1.920.002.06
buildPubMedAbst0.060.000.42
chrCats16.13 0.0317.42
chromLocation-class1.820.001.82
compatibleVersions0.110.040.14
dropECode0.140.000.14
entrezGeneByID000
entrezGeneQuery000
filterGOByOntology0.140.000.14
findNeighbors0.040.010.25
genbank0.220.001.20
getAnnMap0.130.020.14
getEvidence0.110.000.11
getGOTerm0.220.000.36
getOntology0.060.010.08
getPMInfo0.900.001.33
getSYMBOL0.20.00.3
getSeq4Acc0.020.000.26
hasGOannote0.080.000.08
hgByChroms0.020.000.01
hgCLengths000
hgu95Achroloc0.120.000.12
hgu95Achrom0.110.000.11
hgu95All0.130.000.13
hgu95Asym0.120.000.12
homoData-class000
htmlpage0.030.000.17
isValidkey000
makeAnchor000
organism1.950.001.95
p2LL000
pm.abstGrep1.230.012.37
pm.getabst1.570.002.73
pm.titles1.520.052.67
pmAbst2HTML0.060.000.55
pmid2MIAME000
pmidQuery000
probesByLL6.010.006.00
pubMedAbst-class0.040.000.77
pubmed0.020.020.39
readGEOAnn000
serializeEnv000
setRepository0.010.000.01
updateSymbolsToValidKeys000
usedChromGenes0.160.000.16

annotate.Rcheck/examples_x64/annotate-Ex.timings:

nameusersystemelapsed
ACCNUMStats2.480.052.53
GO2heatmap0.310.010.33
GOmnplot0.140.000.14
HTMLPage-class000
LL2homology000
PMIDAmat0.170.000.17
PWAmat6.720.056.77
UniGeneQuery000
accessionToUID0.300.042.83
annPkgName000
aqListGOIDs0.560.020.59
blastSequences 0.11 0.0016.29
buildChromLocation1.220.001.25
buildPubMedAbst0.030.000.40
chrCats18.53 0.0018.54
chromLocation-class1.250.031.28
compatibleVersions0.100.000.09
dropECode0.100.000.11
entrezGeneByID0.020.000.02
entrezGeneQuery000
filterGOByOntology0.090.000.09
findNeighbors0.050.020.06
genbank0.160.001.08
getAnnMap0.110.000.11
getEvidence0.070.000.08
getGOTerm0.210.030.23
getOntology0.060.030.09
getPMInfo1.620.002.05
getSYMBOL0.270.080.34
getSeq4Acc0.000.000.17
hasGOannote0.100.000.09
hgByChroms0.030.000.03
hgCLengths0.010.000.02
hgu95Achroloc0.130.000.14
hgu95Achrom0.090.000.09
hgu95All0.110.000.11
hgu95Asym0.090.000.11
homoData-class0.020.000.02
htmlpage0.050.000.07
isValidkey000
makeAnchor000
organism1.650.031.69
p2LL000
pm.abstGrep1.280.002.48
pm.getabst1.430.002.56
pm.titles1.300.012.41
pmAbst2HTML0.060.000.44
pmid2MIAME000
pmidQuery0.020.000.02
probesByLL6.720.006.72
pubMedAbst-class0.060.000.48
pubmed0.020.000.44
readGEOAnn000
serializeEnv000
setRepository000
updateSymbolsToValidKeys000
usedChromGenes0.070.040.09