Multiple platform build/check report for BioC 3.7 - CHECK report for CAGEr on tokay2

Package: CAGEr

Version: 1.22.3

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CAGEr.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CAGEr_1.22.3.tar.gz

StartedAt: 2018-10-17 00:51:57 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 01:04:31 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 754.4 seconds

RetCode: 0

Status: WARNINGS

CheckDir: CAGEr.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CAGEr.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CAGEr_1.22.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/CAGEr.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CAGEr/DESCRIPTION' ... OK
* this is package 'CAGEr' version '1.22.3'
* package encoding: UTF-8
* 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 'CAGEr' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpoZJFlU/R.INSTALL202caa96709/CAGEr/man/mapStats.Rd:28: file link 'mixedorder' in package 'gtools' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/CAGEr.Rcheck/00install.out' for details.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
clusterCTSS,CAGEset : getCTSSdataSE: no visible binding for '<<-'
  assignment to 'idx'
clusterCTSS,CAGEset : getCTSSdataSE: no visible binding for global
  variable 'idx'
clusterCTSS,CAGEset : getCTSSdatadf: no visible binding for '<<-'
  assignment to 'idx'
clusterCTSS,CAGEset : getCTSSdatadf: no visible binding for global
  variable 'idx'
clusterCTSS,CAGEset: no visible binding for global variable 'idx'
Undefined global functions or variables:
  idx
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
importPublicData           45.47   1.39   78.61
cumulativeCTSSdistribution 26.75   6.05   33.48
quantilePositions          19.49   0.61   20.10
aggregateTagClusters        9.25   0.15    9.41
clusterCTSS                 8.03   0.30    8.33
consensusClusters           6.69   0.56    7.25
distclu-functions           5.77   0.80    6.56
coverage-functions          5.43   0.42    5.86
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
importPublicData           35.20   1.82   51.79
cumulativeCTSSdistribution 25.06   5.93   41.07
quantilePositions          22.22   0.46   22.68
aggregateTagClusters       10.32   0.02   10.32
clusterCTSS                 9.32   0.57    9.89
distclu-functions           6.83   0.98   17.63
CAGEexp-class               4.65   0.56    5.20
coverage-functions          4.61   0.59    5.21
exportToBed                 4.81   0.00    5.53
* 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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/CAGEr.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/CAGEr_1.22.3.tar.gz && rm -rf CAGEr.buildbin-libdir && mkdir CAGEr.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CAGEr.buildbin-libdir CAGEr_1.22.3.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL CAGEr_1.22.3.zip && rm CAGEr_1.22.3.tar.gz CAGEr_1.22.3.zip
###
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100  783k  100  783k    0     0  12.5M      0 --:--:-- --:--:-- --:--:-- 14.4M

install for i386

* installing *source* package 'CAGEr' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CAGEr'
    finding HTML links ... done
    CAGEexp-class                           html  
    finding level-2 HTML links ... done

    CAGEr-class                             html  
    CAGEr-package                           html  
    CAGEr_Multicore                         html  
    CAGEset-class                           html  
    CTSS-class                              html  
    CTSSclusteringMethod                    html  
    CTSScoordinates                         html  
    CTSScumulativesTagClusters              html  
    CTSSnormalizedTpm                       html  
    CTSStagCount                            html  
    CTSStagCountTable                       html  
    CTSStoGenes                             html  
    CustomConsensusClusters                 html  
    FANTOM5humanSamples                     html  
    FANTOM5mouseSamples                     html  
    GeneExpDESeq2                           html  
    GeneExpSE                               html  
    QuantileWidthFunctions                  html  
    aggregateTagClusters                    html  
    annotateCTSS                            html  
    bam2CTSS                                html  
    byCtss                                  html  
    clusterAggregateAndSum                  html  
    clusterCTSS                             html  
    coerceInBSgenome                        html  
    consensusClusterConvertors              html  
    consensusClusters                       html  
    consensusClustersDESeq2                 html  
    consensusClustersQuantile               html  
    consensusClustersTpm                    html  
    coverage-functions                      html  
    cumulativeCTSSdistribution              html  
    distclu-functions                       html  
    exampleCAGEexp                          html  
    exampleCAGEset                          html  
    exampleZv9_annot                        html  
    exportCTSStoBedGraph                    html  
    exportToBed                             html  
    expressionClasses                       html  
    extractExpressionClass                  html  
    genomeName                              html  
    getCTSS                                 html  
    getExpressionProfiles                   html  
    getShiftingPromoters                    html  
    hanabi-class                            html  
    hanabi                                  html  
    hanabiPlot                              html  
    import.CAGEscanMolecule                 html  
    import.CTSS                             html  
    import.bam                              html  
    import.bam.ctss                         html  
    import.bedCTSS                          html  
    import.bedScore                         html  
    import.bedmolecule                      html  
    importPublicData                        html  
    inputFiles                              html  
    inputFilesType                          html  
    librarySizes                            html  
    loadFileIntoGPos                        html  
    mapStats                                html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpoZJFlU/R.INSTALL202caa96709/CAGEr/man/mapStats.Rd:28: file link 'mixedorder' in package 'gtools' does not exist and so has been treated as a topic
    mapStatsScopes                          html  
    mergeCAGEsets                           html  
    mergeSamples                            html  
    moleculesGR2CTSS                        html  
    normalizeTagCount                       html  
    parseCAGEscanBlocksToGrangeTSS          html  
    plot.hanabi                             html  
    plotAnnot                               html  
    plotCorrelation                         html  
    plotExpressionProfiles                  html  
    plotInterquantileWidth                  html  
    plotReverseCumulatives                  html  
    powerLaw                                html  
    quantilePositions                       html  
    ranges2annot                            html  
    ranges2genes                            html  
    ranges2names                            html  
    sampleLabels                            html  
    scoreShift                              html  
    seqNameTotalsSE                         html  
    setColors                               html  
    show-methods                            html  
    strandInvaders                          html  
    summariseChrExpr                        html  
    tagClusterConvertors                    html  
    tagClusters                             html  
    tagClustersQuantile                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'CAGEr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CAGEr' as CAGEr_1.22.3.zip
* DONE (CAGEr)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'CAGEr' successfully unpacked and MD5 sums checked
In R CMD INSTALL

name	user	system	elapsed
CAGEexp-class	2.80	1.03	3.83
CAGEr_Multicore	0.02	0.00	0.02
CAGEset-class	0.02	0.00	0.01
CTSS-class	0.01	0.00	0.02
CTSSclusteringMethod	0.02	0.00	0.01
CTSScoordinates	0.04	0.00	0.05
CTSSnormalizedTpm	0.79	0.04	0.83
CTSStagCount	0.21	0.03	0.25
CTSStagCountTable	0.02	0.00	0.01
CTSStoGenes	0.47	0.00	0.47
CustomConsensusClusters	1.03	0.05	1.08
GeneExpDESeq2	1.48	0.10	1.58
GeneExpSE	0	0	0
QuantileWidthFunctions	0.02	0.00	0.01
aggregateTagClusters	9.25	0.15	9.41
annotateCTSS	1.16	0.03	1.19
byCtss	0.01	0.00	0.01
clusterCTSS	8.03	0.30	8.33
consensusClusterConvertors	0.03	0.00	0.03
consensusClusters	6.69	0.56	7.25
consensusClustersDESeq2	0.08	0.00	0.08
consensusClustersTpm	0	0	0
coverage-functions	5.43	0.42	5.86
cumulativeCTSSdistribution	26.75	6.05	33.48
distclu-functions	5.77	0.80	6.56
exampleCAGEexp	0	0	0
exampleCAGEset	0.01	0.00	0.02
exportCTSStoBedGraph	1.66	0.06	1.78
exportToBed	3.16	0.02	3.17
expressionClasses	0	0	0
extractExpressionClass	0.01	0.00	0.02
genomeName	0	0	0
getCTSS	0.21	0.04	0.25
getExpressionProfiles	0.50	0.02	0.55
getShiftingPromoters	0.00	0.01	0.02
hanabi	0.22	0.21	0.42
hanabiPlot	0.42	0.29	0.72
import.CAGEscanMolecule	0	0	0
import.CTSS	0.05	0.02	0.06
import.bam	0	0	0
import.bedCTSS	0	0	0
import.bedScore	0	0	0
import.bedmolecule	0	0	0
importPublicData	45.47	1.39	78.61
inputFiles	0	0	0
inputFilesType	0	0	0
librarySizes	0	0	0
mapStats	0.16	0.03	0.19
mergeCAGEsets	1.72	0.05	1.77
mergeSamples	0.34	0.00	0.34
moleculesGR2CTSS	0.08	0.00	0.08
normalizeTagCount	0.28	0.00	0.28
parseCAGEscanBlocksToGrangeTSS	0.02	0.00	0.02
plotAnnot	1.95	0.03	2.09
plotCorrelation	0.42	0.00	0.42
plotExpressionProfiles	0.17	0.00	0.17
plotInterquantileWidth	0.27	0.00	0.27
plotReverseCumulatives	0.48	0.00	0.48
quantilePositions	19.49	0.61	20.10
ranges2annot	0.11	0.00	0.11
ranges2genes	0.03	0.00	0.03
ranges2names	0.05	0.00	0.05
sampleLabels	0	0	0
scoreShift	4.17	0.00	4.17
seqNameTotalsSE	0	0	0
setColors	0.42	0.01	0.44
strandInvaders	1.11	0.15	2.03
summariseChrExpr	0.82	0.00	0.81
tagClusterConvertors	0.37	0.00	0.38
tagClusters	0.06	0.00	0.06

name	user	system	elapsed
CAGEexp-class	4.65	0.56	5.20
CAGEr_Multicore	0.03	0.00	0.04
CAGEset-class	0.01	0.00	0.01
CTSS-class	0.03	0.00	0.03
CTSSclusteringMethod	0.02	0.00	0.02
CTSScoordinates	0.08	0.02	0.09
CTSSnormalizedTpm	1.26	0.12	1.39
CTSStagCount	0.35	0.00	0.35
CTSStagCountTable	0.01	0.00	0.01
CTSStoGenes	0.72	0.00	0.72
CustomConsensusClusters	1.36	0.03	1.39
GeneExpDESeq2	1.89	0.08	1.97
GeneExpSE	0.02	0.00	0.02
QuantileWidthFunctions	0	0	0
aggregateTagClusters	10.32	0.02	10.32
annotateCTSS	1.46	0.00	1.46
byCtss	0	0	0
clusterCTSS	9.32	0.57	9.89
consensusClusterConvertors	0.03	0.00	0.03
consensusClusters	4.11	0.66	4.77
consensusClustersDESeq2	0.18	0.00	0.19
consensusClustersTpm	0.02	0.00	0.01
coverage-functions	4.61	0.59	5.21
cumulativeCTSSdistribution	25.06	5.93	41.07
distclu-functions	6.83	0.98	17.63
exampleCAGEexp	0	0	0
exampleCAGEset	0.02	0.00	0.02
exportCTSStoBedGraph	2.75	0.02	2.76
exportToBed	4.81	0.00	5.53
expressionClasses	0	0	0
extractExpressionClass	0.01	0.00	0.02
genomeName	0	0	0
getCTSS	0.33	0.03	0.36
getExpressionProfiles	0.39	0.00	0.39
getShiftingPromoters	0	0	0
hanabi	0.20	0.03	0.24
hanabiPlot	0.27	0.04	0.31
import.CAGEscanMolecule	0	0	0
import.CTSS	0.05	0.00	0.04
import.bam	0	0	0
import.bedCTSS	0	0	0
import.bedScore	0	0	0
import.bedmolecule	0	0	0
importPublicData	35.20	1.82	51.79
inputFiles	0.02	0.00	0.01
inputFilesType	0	0	0
librarySizes	0	0	0
mapStats	0.33	0.00	0.33
mergeCAGEsets	2.78	0.08	2.86
mergeSamples	0.38	0.00	0.38
moleculesGR2CTSS	0.11	0.00	0.11
normalizeTagCount	0.48	0.00	0.48
parseCAGEscanBlocksToGrangeTSS	0.02	0.00	0.02
plotAnnot	2.06	0.00	2.06
plotCorrelation	0.55	0.00	0.55
plotExpressionProfiles	0.15	0.00	0.15
plotInterquantileWidth	0.33	0.00	0.33
plotReverseCumulatives	0.63	0.00	0.63
quantilePositions	22.22	0.46	22.68
ranges2annot	0.10	0.00	0.09
ranges2genes	0.04	0.00	0.05
ranges2names	0.05	0.00	0.05
sampleLabels	0	0	0
scoreShift	4.58	0.00	4.58
seqNameTotalsSE	0.01	0.00	0.01
setColors	0.27	0.00	0.27
strandInvaders	0.95	0.07	1.01
summariseChrExpr	0.52	0.00	0.52
tagClusterConvertors	0.27	0.00	0.27
tagClusters	0.05	0.00	0.05

CHECK report for CAGEr on tokay2

Summary

Command output

Installation output

Tests output

Example timings