BioC 3.2: CHECK report for genomation on moscato1

Package: genomation

Version: 1.2.2

Command: rm -rf genomation.buildbin-libdir genomation.Rcheck && mkdir genomation.buildbin-libdir genomation.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomation.buildbin-libdir genomation_1.2.2.tar.gz >genomation.Rcheck\00install.out 2>&1 && cp genomation.Rcheck\00install.out genomation-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=genomation.buildbin-libdir --install="check:genomation-install.out" --force-multiarch --no-vignettes --timings genomation_1.2.2.tar.gz

StartedAt: 2016-04-23 02:42:34 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:53:02 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 628.2 seconds

RetCode: 0

Status:  OK

CheckDir: genomation.Rcheck

Warnings: 0

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### Running command:
###
###   rm -rf genomation.buildbin-libdir genomation.Rcheck && mkdir genomation.buildbin-libdir genomation.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomation.buildbin-libdir genomation_1.2.2.tar.gz >genomation.Rcheck\00install.out 2>&1 && cp genomation.Rcheck\00install.out genomation-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=genomation.buildbin-libdir --install="check:genomation-install.out" --force-multiarch --no-vignettes --timings genomation_1.2.2.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/genomation.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.2.2'
* 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 ... NOTE
Found the following non-portable file paths:
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixBinExample_407baab934d04322bb38d0d0ac9fb116.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixBinExample_407baab934d04322bb38d0d0ac9fb116.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixBinExample_407baab934d04322bb38d0d0ac9fb116.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixExample_2de29d7f21b635496f4db157edb50190.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixExample_2de29d7f21b635496f4db157edb50190.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixExample_2de29d7f21b635496f4db157edb50190.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixList_ebb306060f1abf836664f37d612280d2.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixList_ebb306060f1abf836664f37d612280d2.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/ScoreMatrixList_ebb306060f1abf836664f37d612280d2.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/annotateCtcf_ab2ac4372bba7029e15e15cd549d146d.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/annotateCtcf_ab2ac4372bba7029e15e15cd549d146d.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/annotateCtcf_ab2ac4372bba7029e15e15cd549d146d.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/annotateTargetList_38eb770337221ca3080607d368160ddb.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/annotateTargetList_38eb770337221ca3080607d368160ddb.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/annotateTargetList_38eb770337221ca3080607d368160ddb.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/annotationHubExample1_360864ac1c5055bfc67acf4dd8c3335d.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/annotationHubExample1_360864ac1c5055bfc67acf4dd8c3335d.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/annotationHubExample1_360864ac1c5055bfc67acf4dd8c3335d.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/ctcfScoreMatrixList_679c632949390e24b9324cb97719d730.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/ctcfScoreMatrixList_679c632949390e24b9324cb97719d730.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/ctcfScoreMatrixList_679c632949390e24b9324cb97719d730.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/eadAllPeaks_842772f2b9d10ebfcfe47f14c8d0585a.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/eadAllPeaks_842772f2b9d10ebfcfe47f14c8d0585a.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/eadAllPeaks_842772f2b9d10ebfcfe47f14c8d0585a.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/findFeatureComb_bf52dc550c6f2c305953de86dca5d0ae.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/findFeatureComb_bf52dc550c6f2c305953de86dca5d0ae.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/findFeatureComb_bf52dc550c6f2c305953de86dca5d0ae.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/genomationDataInfo_abff89e4650670ad4e0429220b0f24d1.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/genomationDataInfo_abff89e4650670ad4e0429220b0f24d1.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/genomationDataInfo_abff89e4650670ad4e0429220b0f24d1.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/genomationInfo_3695e0cbaa0a6203c8c39c1f259a22e7.RData
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  genomation/vignettes/GenomationManual-knitr_cache/html/genomationInfo_3695e0cbaa0a6203c8c39c1f259a22e7.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/getFiles_annotation_86cfb90bd357dcfc651cab92d9823674.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/getFiles_annotation_86cfb90bd357dcfc651cab92d9823674.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/getFiles_annotation_86cfb90bd357dcfc651cab92d9823674.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrix1_f8336a1a5116f1b86620fd302e8b9408.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrix1_f8336a1a5116f1b86620fd302e8b9408.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrix1_f8336a1a5116f1b86620fd302e8b9408.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrix2_347ab9775397b5a07a1ed9de95acb239.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrix2_347ab9775397b5a07a1ed9de95acb239.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrix2_347ab9775397b5a07a1ed9de95acb239.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrixScales_71d0aa8c912f8fe69e7d1ecdc0f097f3.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrixScales_71d0aa8c912f8fe69e7d1ecdc0f097f3.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/heatMatrixScales_71d0aa8c912f8fe69e7d1ecdc0f097f3.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/listgenomationData_d524ebd9f9d0df78338f47cd513a1d47.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/listgenomationData_d524ebd9f9d0df78338f47cd513a1d47.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/listgenomationData_d524ebd9f9d0df78338f47cd513a1d47.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/multiHeatMatrix1_c7efcff4a3ac59f1eaf47704452cd6a4.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/multiHeatMatrix1_c7efcff4a3ac59f1eaf47704452cd6a4.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/multiHeatMatrix1_c7efcff4a3ac59f1eaf47704452cd6a4.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/multiHeatMatrix2_c69d020b751522773ecae22277116057.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/multiHeatMatrix2_c69d020b751522773ecae22277116057.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/multiHeatMatrix2_c69d020b751522773ecae22277116057.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/plotGeneAnnotation_1e9123ea4c14593569413355f4239810.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/plotGeneAnnotation_1e9123ea4c14593569413355f4239810.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/plotGeneAnnotation_1e9123ea4c14593569413355f4239810.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/plotScaledProfile_221dff85157171b89489f997b066e614.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/plotScaledProfile_221dff85157171b89489f997b066e614.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/plotScaledProfile_221dff85157171b89489f997b066e614.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/readAllPeaks_annotation_f9baf0f20ccefedc5fcdce26c381694c.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readAllPeaks_annotation_f9baf0f20ccefedc5fcdce26c381694c.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readAllPeaks_annotation_f9baf0f20ccefedc5fcdce26c381694c.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/readCtcfPeaks_5253032fac7ff35f47ceedabb6d4462f.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readCtcfPeaks_5253032fac7ff35f47ceedabb6d4462f.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readCtcfPeaks_5253032fac7ff35f47ceedabb6d4462f.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/readFeatureFlank_bf6a16b8efaa6ad29ed1c8eb9bb89164.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readFeatureFlank_bf6a16b8efaa6ad29ed1c8eb9bb89164.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readFeatureFlank_bf6a16b8efaa6ad29ed1c8eb9bb89164.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric1_0f3f99fcd18ffaa95dd8f8b8535cabfc.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric1_0f3f99fcd18ffaa95dd8f8b8535cabfc.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric1_0f3f99fcd18ffaa95dd8f8b8535cabfc.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric2_2f1afcdcc436bb9c0d84974cc8350472.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric2_2f1afcdcc436bb9c0d84974cc8350472.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric2_2f1afcdcc436bb9c0d84974cc8350472.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric3_9e3bfb6d08a5b935053150708fec0350.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric3_9e3bfb6d08a5b935053150708fec0350.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric3_9e3bfb6d08a5b935053150708fec0350.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric4_0291f02c1f4a870ed4ecb7fb196bdc42.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric4_0291f02c1f4a870ed4ecb7fb196bdc42.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readGeneric4_0291f02c1f4a870ed4ecb7fb196bdc42.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/readGff1_5339cf7ec2738db2eedd4de15411f7e9.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readGff2_afa5c88910bddbc7aebbcf6fdefd0ed4.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readTranscriptFeatures_e96ede3e983d7c27cd16c354caa80074.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/readTranscriptFeatures_e96ede3e983d7c27cd16c354caa80074.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/readTranscriptFeatures_e96ede3e983d7c27cd16c354caa80074.rdx
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  genomation/vignettes/GenomationManual-knitr_cache/html/selectBamChipseq_a020bd4daa8bb3169ad8d4fd3b5d193e.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/selectBamChipseq_a020bd4daa8bb3169ad8d4fd3b5d193e.rdx
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  genomation/vignettes/GenomationManual-knitr_cache/html/unnamed-chunk-1_1318f7ba667fd22a634972bd79226a56.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/unnamed-chunk-1_1318f7ba667fd22a634972bd79226a56.rdx
  genomation/vignettes/GenomationManual-knitr_cache/html/visualizeFeatureComb_d4f9175c506720034cedfa8eb544f233.RData
  genomation/vignettes/GenomationManual-knitr_cache/html/visualizeFeatureComb_d4f9175c506720034cedfa8eb544f233.rdb
  genomation/vignettes/GenomationManual-knitr_cache/html/visualizeFeatureComb_d4f9175c506720034cedfa8eb544f233.rdx

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'genomation' 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
Unexported objects imported by ':::' calls:
  'BiocGenerics:::testPackage' 'GenomicAlignments:::invertRleStrand'
  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
heatMeta: no visible binding for global variable 'a'
ScoreMatrixBin,GRanges-GRanges : .local: no visible global function
  definition for 'runValue'
plotGeneAnnotation,list: no visible binding for global variable
  'SampleName'
plotGeneAnnotation,list: no visible binding for global variable 'value'
randomizeFeature,GRanges : <anonymous>: no visible global function
  definition for 'Rle'
randomizeFeature,GRanges: no visible global function definition for
  'runValue'
* 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 Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* 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' ... [57s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
AnnotationByGeneParts-methods 1.23   0.07   24.65
** running examples for arch 'x64' ... [39s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
ScoreMatrix-methods 5.93   0.13    6.05
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'genomation_unit_tests.R' [31s]
 [32s] OK
** running tests for arch 'x64' ...
  Running 'genomation_unit_tests.R' [47s]
 [48s] 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: 4 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/genomation.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'genomation' ...
** 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' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genomation' as genomation_1.2.2.zip
* DONE (genomation)

name	user	system	elapsed
AnnotationByGeneParts-methods	1.23	0.07	24.65
ScoreMatrix-methods	3.93	0.07	4.01
ScoreMatrixBin-methods	0.99	0.02	1.00
ScoreMatrixList-methods	1.65	0.00	1.65
annotateWithFeature-methods	0.06	0.00	0.07
annotateWithFeatureFlank-methods	0.31	0.00	0.31
annotateWithGeneParts-methods	0.59	0.00	0.60
binMatrix-methods	0.39	0.00	0.39
convertBed2Exons-methods	0.14	0.00	0.14
convertBed2Introns-methods	0.16	0.00	0.16
findFeatureComb-methods	0.59	0.00	0.59
getFeatsWithTargetsStats-methods	0.67	0.00	0.67
getFlanks-methods	0.22	0.00	0.22
getRandomEnrichment-methods	0.00	0.02	0.02
getTargetAnnotationStats-methods	0.67	0.00	0.67
gffToGRanges	0.15	0.00	0.15
heatMatrix	1.70	0.14	1.84
heatMeta	1.41	0.04	1.45
intersectScoreMatrixList-methods	0.59	0.00	0.60
multiHeatMatrix	0.87	0.08	0.95
orderBy-methods	1.14	0.00	1.14
patternMatrix-methods	0.26	0.03	0.30
plotGeneAnnotation-methods	0.96	0.03	0.98
plotMeta	0.92	0.03	0.95
plotTargetAnnotation-methods	0.45	0.02	0.47
readBed	0.06	0.06	0.13
readBroadPeak	0.05	0.03	0.08
readFeatureFlank-methods	0.22	0.02	0.23
readGeneric	0.07	0.00	0.08
readNarrowPeak	0.05	0.03	0.08
readTranscriptFeatures-methods	0.36	0.02	0.37
scaleScoreMatrix-methods	0.29	0.00	0.30
scaleScoreMatrixList	1.17	0.01	1.18

name	user	system	elapsed
AnnotationByGeneParts-methods	1.28	0.06	2.84
ScoreMatrix-methods	5.93	0.13	6.05
ScoreMatrixBin-methods	1.14	0.01	1.16
ScoreMatrixList-methods	1.57	0.05	1.62
annotateWithFeature-methods	0.05	0.00	0.04
annotateWithFeatureFlank-methods	0.25	0.00	0.25
annotateWithGeneParts-methods	0.53	0.00	0.53
binMatrix-methods	0.4	0.0	0.4
convertBed2Exons-methods	0.14	0.00	0.14
convertBed2Introns-methods	0.1	0.0	0.1
findFeatureComb-methods	0.56	0.00	0.56
getFeatsWithTargetsStats-methods	0.50	0.05	0.54
getFlanks-methods	0.14	0.00	0.14
getRandomEnrichment-methods	0	0	0
getTargetAnnotationStats-methods	0.58	0.03	0.61
gffToGRanges	0.12	0.00	0.12
heatMatrix	1.72	0.04	1.77
heatMeta	1.34	0.07	1.40
intersectScoreMatrixList-methods	0.33	0.03	0.36
multiHeatMatrix	1.27	0.06	1.33
orderBy-methods	1.15	0.02	1.17
patternMatrix-methods	0.19	0.00	0.18
plotGeneAnnotation-methods	1.17	0.01	1.18
plotMeta	1.24	0.05	1.30
plotTargetAnnotation-methods	0.75	0.03	0.78
readBed	0.11	0.03	0.14
readBroadPeak	0.07	0.02	0.07
readFeatureFlank-methods	0.21	0.00	0.22
readGeneric	0.05	0.01	0.06
readNarrowPeak	0.03	0.02	0.05
readTranscriptFeatures-methods	0.23	0.01	0.25
scaleScoreMatrix-methods	0.27	0.00	0.26
scaleScoreMatrixList	1.14	0.02	1.15