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CHECK report for RCAS on tokay2

This page was generated on 2018-10-17 08:42:37 -0400 (Wed, 17 Oct 2018).

Package 1193/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCAS 1.6.0
Bora Uyar
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/RCAS
Branch: RELEASE_3_7
Last Commit: c347094
Last Changed Date: 2018-04-30 10:35:43 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RCAS
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings RCAS_1.6.0.tar.gz
StartedAt: 2018-10-17 04:17:09 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:40:30 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 1400.8 seconds
RetCode: 0
Status:  OK  
CheckDir: RCAS.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings RCAS_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/RCAS.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 'RCAS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RCAS' version '1.6.0'
* 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 'RCAS' 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
Namespace in Imports field not imported from: 'DBI'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
getMotifSummaryTable                 52.14   0.32   52.49
runMotifRG                           46.69   0.33   47.04
getFeatureBoundaryCoverageMulti      20.77   0.83   21.61
calculateCoverageProfile             16.31   1.27   17.60
calculateCoverageProfileList         16.38   1.02   17.39
getTxdbFeaturesFromGRanges           15.77   0.33   16.10
calculateCoverageProfileListFromTxdb 14.95   0.47   15.42
summarizeQueryRegionsMulti           12.62   0.33   25.17
getTxdbFeatures                      12.26   0.15   12.42
plotFeatureBoundaryCoverage          11.96   0.13   12.09
getTargetedGenesTable                11.84   0.13   11.97
summarizeQueryRegions                11.64   0.15   11.80
getFeatureBoundaryCoverageBin        11.15   0.11   11.27
calculateCoverageProfileFromTxdb      9.32   0.65    9.97
getFeatureBoundaryCoverage            7.58   0.16    7.73
createDB                              3.07   0.05   26.09
runReportMetaAnalysis                 1.61   0.39    6.10
getIntervalOverlapMatrix              1.13   0.05   12.29
createOrthologousGeneSetList          0.88   0.07   15.07
retrieveOrthologs                     0.54   0.03    8.42
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                      user system elapsed
runMotifRG                           52.48   0.36   52.88
getMotifSummaryTable                 42.44   0.36   42.84
calculateCoverageProfileList         25.35   0.41   25.75
getFeatureBoundaryCoverageMulti      20.78   0.48   21.26
calculateCoverageProfileListFromTxdb 19.70   0.36   20.07
summarizeQueryRegionsMulti           17.86   0.33   35.64
calculateCoverageProfile             17.05   0.56   17.61
getTxdbFeaturesFromGRanges           14.39   0.16   14.55
calculateCoverageProfileFromTxdb     13.64   0.23   13.87
getFeatureBoundaryCoverageBin        13.48   0.16   13.64
getTxdbFeatures                      12.97   0.17   13.14
plotFeatureBoundaryCoverage          12.85   0.19   13.03
getFeatureBoundaryCoverage           12.58   0.14   12.72
summarizeQueryRegions                12.03   0.11   12.14
getTargetedGenesTable                10.75   0.16   10.91
createDB                              3.27   0.03   28.84
getIntervalOverlapMatrix              1.27   0.11   12.55
createOrthologousGeneSetList          0.90   0.03   18.08
retrieveOrthologs                     0.58   0.02    8.44
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/RCAS.Rcheck/00check.log'
for details.

Installation output

RCAS.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/RCAS_1.6.0.tar.gz && rm -rf RCAS.buildbin-libdir && mkdir RCAS.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RCAS.buildbin-libdir RCAS_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL RCAS_1.6.0.zip && rm RCAS_1.6.0.tar.gz RCAS_1.6.0.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1694k  100 1694k    0     0  21.5M      0 --:--:-- --:--:-- --:--:-- 23.9M

install for i386

* installing *source* package 'RCAS' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
  converting help for package 'RCAS'
    finding HTML links ... done
    calculateCoverageProfile                html  
    calculateCoverageProfileFromTxdb        html  
    calculateCoverageProfileList            html  
    calculateCoverageProfileListFromTxdb    html  
    createControlRegions                    html  
    createDB                                html  
    createOrthologousGeneSetList            html  
    deleteSampleDataFromDB                  html  
    discoverFeatureSpecificMotifs           html  
    extractSequences                        html  
    geneSets                                html  
    getFeatureBoundaryCoverage              html  
    getFeatureBoundaryCoverageBin           html  
    getFeatureBoundaryCoverageMulti         html  
    getIntervalOverlapMatrix                html  
    getMotifSummaryTable                    html  
    getTargetedGenesTable                   html  
    getTxdbFeatures                         html  
    getTxdbFeaturesFromGRanges              html  
    gff                                     html  
    importBed                               html  
    importBedFiles                          html  
    importGtf                               html  
    parseMsigdb                             html  
    plotFeatureBoundaryCoverage             html  
    printMsigdbDataset                      html  
    queryGff                                html  
    queryRegions                            html  
    retrieveOrthologs                       html  
    runGSEA                                 html  
    runMotifRG                              html  
    runReport                               html  
    runReportMetaAnalysis                   html  
    runTopGO                                html  
    summarizeDatabaseContent                html  
    summarizeQueryRegions                   html  
    summarizeQueryRegionsMulti              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
In R CMD INSTALL

install for x64

* installing *source* package 'RCAS' ...
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'RCAS' as RCAS_1.6.0.zip
* DONE (RCAS)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'RCAS' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

RCAS.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(RCAS)
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Loading required package: DT
Loading required package: data.table
Loading required package: topGO
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: graph
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:data.table':

    first, second

The following object is masked from 'package:plotly':

    rename

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:data.table':

    shift

The following object is masked from 'package:plotly':

    slice

The following object is masked from 'package:grDevices':

    windows


Attaching package: 'AnnotationDbi'

The following object is masked from 'package:plotly':

    select


Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

The following object is masked from 'package:IRanges':

    members

Loading required package: motifRG
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:graph':

    complement

The following object is masked from 'package:base':

    strsplit

Loading required package: seqLogo
Loading required package: grid

Attaching package: 'grid'

The following object is masked from 'package:topGO':

    depth

Loading required package: BSgenome
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

The following object is masked from 'package:plotly':

    export

Loading required package: BSgenome.Hsapiens.UCSC.hg19

> 
> test_check("RCAS")
TGGAGA 1.002297e-06 
 Refine  TGGAGA 12.49218 : 12.70132 11.92052 12.4026 11.25875 12.16159 TRUE 524 171 502 170 
New motif:  TGGAGA 
== testthat results  ===========================================================
OK: 102 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 105.37    4.59  132.20

RCAS.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(RCAS)
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Loading required package: DT
Loading required package: data.table
Loading required package: topGO
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: graph
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:data.table':

    first, second

The following object is masked from 'package:plotly':

    rename

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:data.table':

    shift

The following object is masked from 'package:plotly':

    slice

The following object is masked from 'package:grDevices':

    windows


Attaching package: 'AnnotationDbi'

The following object is masked from 'package:plotly':

    select


Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

The following object is masked from 'package:IRanges':

    members

Loading required package: motifRG
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:graph':

    complement

The following object is masked from 'package:base':

    strsplit

Loading required package: seqLogo
Loading required package: grid

Attaching package: 'grid'

The following object is masked from 'package:topGO':

    depth

Loading required package: BSgenome
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

The following object is masked from 'package:plotly':

    export

Loading required package: BSgenome.Hsapiens.UCSC.hg19

> 
> test_check("RCAS")
TGGAGA 1.399627e-06 
Skip pattern  TTTCTT TTTTTA TTTTCT 
 Refine  TGGAGA 12.1978 : 11.67676 12.4157 12.14834 13.34848 12.38413 TRUE 524 176 502 169 
New motif:  TGGAGA 
== testthat results  ===========================================================
OK: 102 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 113.15    1.85  137.46

Example timings

RCAS.Rcheck/examples_i386/RCAS-Ex.timings

nameusersystemelapsed
calculateCoverageProfile16.31 1.2717.60
calculateCoverageProfileFromTxdb9.320.659.97
calculateCoverageProfileList16.38 1.0217.39
calculateCoverageProfileListFromTxdb14.95 0.4715.42
createControlRegions0.250.000.25
createDB 3.07 0.0526.09
createOrthologousGeneSetList 0.88 0.0715.07
discoverFeatureSpecificMotifs000
extractSequences1.140.141.28
getFeatureBoundaryCoverage7.580.167.73
getFeatureBoundaryCoverageBin11.15 0.1111.27
getFeatureBoundaryCoverageMulti20.77 0.8321.61
getIntervalOverlapMatrix 1.13 0.0512.29
getMotifSummaryTable52.14 0.3252.49
getTargetedGenesTable11.84 0.1311.97
getTxdbFeatures12.26 0.1512.42
getTxdbFeaturesFromGRanges15.77 0.3316.10
importBed0.230.000.23
importBedFiles0.860.080.94
importGtf0.020.000.02
parseMsigdb0.000.000.06
plotFeatureBoundaryCoverage11.96 0.1312.09
printMsigdbDataset0.080.000.10
queryGff0.690.060.75
retrieveOrthologs0.540.038.42
runGSEA1.660.081.74
runMotifRG46.69 0.3347.04
runReport000
runReportMetaAnalysis1.610.396.10
runTopGO000
summarizeQueryRegions11.64 0.1511.80
summarizeQueryRegionsMulti12.62 0.3325.17

RCAS.Rcheck/examples_x64/RCAS-Ex.timings

nameusersystemelapsed
calculateCoverageProfile17.05 0.5617.61
calculateCoverageProfileFromTxdb13.64 0.2313.87
calculateCoverageProfileList25.35 0.4125.75
calculateCoverageProfileListFromTxdb19.70 0.3620.07
createControlRegions0.280.000.28
createDB 3.27 0.0328.84
createOrthologousGeneSetList 0.90 0.0318.08
discoverFeatureSpecificMotifs000
extractSequences1.860.172.08
getFeatureBoundaryCoverage12.58 0.1412.72
getFeatureBoundaryCoverageBin13.48 0.1613.64
getFeatureBoundaryCoverageMulti20.78 0.4821.26
getIntervalOverlapMatrix 1.27 0.1112.55
getMotifSummaryTable42.44 0.3642.84
getTargetedGenesTable10.75 0.1610.91
getTxdbFeatures12.97 0.1713.14
getTxdbFeaturesFromGRanges14.39 0.1614.55
importBed0.450.030.48
importBedFiles1.440.011.45
importGtf000
parseMsigdb000
plotFeatureBoundaryCoverage12.85 0.1913.03
printMsigdbDataset0.100.000.09
queryGff0.680.060.75
retrieveOrthologs0.580.028.44
runGSEA1.160.081.23
runMotifRG52.48 0.3652.88
runReport0.020.000.01
runReportMetaAnalysis1.340.452.80
runTopGO000
summarizeQueryRegions12.03 0.1112.14
summarizeQueryRegionsMulti17.86 0.3335.64