BioC 3.4: CHECK report for genomation on moscato1

Package: genomation

Version: 1.5.5

Command: rm -rf genomation.buildbin-libdir genomation.Rcheck && mkdir genomation.buildbin-libdir genomation.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomation.buildbin-libdir genomation_1.5.5.tar.gz >genomation.Rcheck\00install.out 2>&1 && cp genomation.Rcheck\00install.out genomation-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=genomation.buildbin-libdir --install="check:genomation-install.out" --force-multiarch --no-vignettes --timings genomation_1.5.5.tar.gz

StartedAt: 2016-09-20 09:02:42 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 09:09:51 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 429.2 seconds

RetCode: 0

Status:  OK

CheckDir: genomation.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf genomation.buildbin-libdir genomation.Rcheck && mkdir genomation.buildbin-libdir genomation.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomation.buildbin-libdir genomation_1.5.5.tar.gz >genomation.Rcheck\00install.out 2>&1 && cp genomation.Rcheck\00install.out genomation-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=genomation.buildbin-libdir --install="check:genomation-install.out" --force-multiarch --no-vignettes --timings genomation_1.5.5.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/genomation.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'genomation/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genomation' version '1.5.5'
* package encoding: latin1
* 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 'genomation' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.2Mb
    libs      2.4Mb
* 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
Namespace in Imports field not imported from: 'RUnit'
  All declared Imports should be used.
Unexported object imported by a ':::' call: 'BiocGenerics:::testPackage'
  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
plotGeneAnnotation,list: no visible binding for global variable
  'SampleName'
plotGeneAnnotation,list: no visible binding for global variable 'value'
Undefined global functions or variables:
  SampleName value
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.4-bioc/meat/genomation.buildbin-libdir/genomation/libs/i386/genomation.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following directory looks like a leftover from 'knitr':
  'cache'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'genomation_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'genomation_unit_tests.R'
 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: 5 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/genomation.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'genomation' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c idxstats.cpp -o idxstats.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o genomation.dll tmp.def RcppExports.o idxstats.o -LD:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/lib/i386 -lhts -lz -pthread -lws2_32 -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/genomation.buildbin-libdir/genomation/libs/i386
** 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 'genomation' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=c++0x -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c idxstats.cpp -o idxstats.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o genomation.dll tmp.def RcppExports.o idxstats.o -LD:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/lib/x64 -lhts -lz -pthread -lws2_32 -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/genomation.buildbin-libdir/genomation/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genomation' as genomation_1.5.5.zip
* DONE (genomation)

name	user	system	elapsed
AnnotationByGeneParts-methods	0.46	0.04	0.51
ScoreMatrix-methods	3.35	0.08	3.43
ScoreMatrixBin-methods	0.64	0.00	0.64
ScoreMatrixList-methods	0.80	0.02	0.81
annotateWithFeature-methods	0.03	0.01	0.04
annotateWithFeatureFlank-methods	0.18	0.00	0.19
annotateWithGeneParts-methods	0.38	0.00	0.37
binMatrix-methods	0.17	0.02	0.27
convertBed2Exons-methods	0.08	0.00	0.08
convertBed2Introns-methods	0.07	0.00	0.07
findFeatureComb-methods	0.28	0.00	0.28
getFeatsWithTargetsStats-methods	0.35	0.01	0.36
getFlanks-methods	0.10	0.00	0.11
getRandomEnrichment-methods	0.02	0.00	0.02
getTargetAnnotationStats-methods	0.34	0.00	0.34
gffToGRanges	0.11	0.00	0.11
heatMatrix	1.13	0.07	1.18
heatMeta	1.10	0.04	1.16
intersectScoreMatrixList-methods	0.24	0.00	0.23
multiHeatMatrix	0.86	0.05	0.90
orderBy-methods	0.98	0.05	1.44
patternMatrix-methods	0.13	0.00	0.12
plotGeneAnnotation-methods	0.67	0.03	0.70
plotMeta	0.81	0.09	0.91
plotTargetAnnotation-methods	0.34	0.02	0.36
readBed	0.02	0.04	0.09
readBroadPeak	0.03	0.02	0.05
readFeatureFlank-methods	0.13	0.00	0.12
readGeneric	0.04	0.00	0.05
readNarrowPeak	0.02	0.03	0.05
readTranscriptFeatures-methods	0.17	0.02	0.18
scaleScoreMatrix-methods	0.16	0.01	0.17
scaleScoreMatrixList	0.87	0.02	0.89

name	user	system	elapsed
AnnotationByGeneParts-methods	0.55	0.05	0.60
ScoreMatrix-methods	4.62	0.17	4.79
ScoreMatrixBin-methods	0.79	0.05	0.84
ScoreMatrixList-methods	1.11	0.01	1.12
annotateWithFeature-methods	0.05	0.00	0.05
annotateWithFeatureFlank-methods	0.25	0.02	0.26
annotateWithGeneParts-methods	0.45	0.01	0.47
binMatrix-methods	0.22	0.00	0.22
convertBed2Exons-methods	0.10	0.00	0.09
convertBed2Introns-methods	0.10	0.00	0.09
findFeatureComb-methods	0.37	0.00	0.37
getFeatsWithTargetsStats-methods	0.49	0.00	0.49
getFlanks-methods	0.14	0.00	0.14
getRandomEnrichment-methods	0.01	0.00	0.01
getTargetAnnotationStats-methods	0.42	0.03	0.46
gffToGRanges	0.13	0.00	0.14
heatMatrix	0.86	0.10	0.95
heatMeta	0.73	0.06	0.80
intersectScoreMatrixList-methods	0.33	0.01	0.34
multiHeatMatrix	1.11	0.05	1.16
orderBy-methods	1.12	0.02	1.14
patternMatrix-methods	0.13	0.01	0.14
plotGeneAnnotation-methods	1.23	0.03	1.26
plotMeta	0.61	0.10	0.70
plotTargetAnnotation-methods	0.40	0.01	0.42
readBed	0.07	0.02	0.08
readBroadPeak	0.04	0.00	0.05
readFeatureFlank-methods	0.14	0.00	0.14
readGeneric	0.05	0.01	0.06
readNarrowPeak	0.03	0.02	0.05
readTranscriptFeatures-methods	0.2	0.0	0.2
scaleScoreMatrix-methods	0.2	0.0	0.2
scaleScoreMatrixList	1.21	0.00	1.22