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CHECK report for GenoGAM on tokay2

This page was generated on 2018-10-17 08:42:02 -0400 (Wed, 17 Oct 2018).

Package 586/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenoGAM 1.8.0
Georg Stricker
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/GenoGAM
Branch: RELEASE_3_7
Last Commit: 394e735
Last Changed Date: 2018-04-30 10:35:41 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenoGAM
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenoGAM.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GenoGAM_1.8.0.tar.gz
StartedAt: 2018-10-17 02:14:22 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:34:02 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 1179.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GenoGAM.Rcheck
Warnings: 1

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:GenoGAM.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GenoGAM_1.8.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/GenoGAM.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 'GenoGAM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GenoGAM' version '1.8.0'
* 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 'GenoGAM' can be installed ... WARNING
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUDhufI/R.INSTALL21c076577b23/GenoGAM/man/GenomicTiles-class.Rd:21: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUDhufI/R.INSTALL21c076577b23/GenoGAM/man/GenomicTiles.Rd:25: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUDhufI/R.INSTALL21c076577b23/GenoGAM/man/subsetByOverlaps-GenoGAMDataSet-GRanges-method.Rd:17: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUDhufI/R.INSTALL21c076577b23/GenoGAM/man/subsetByOverlaps-GenomicTiles-GRanges-method.Rd:16: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/GenoGAM.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* 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
.doCrossValidation: no visible global function definition for 'optim'
.loglik : <anonymous>: no visible global function definition for
  'dnbinom'
.pvals: no visible global function definition for 'pnorm'
.updateFormula: no visible global function definition for 'as.formula'
callBroadPeaks: no visible binding for global variable 'pval'
callPeaks: no visible binding for global variable 'fdr'
computeBroadPeakSignificance: no visible global function definition for
  'p.adjust'
computeBroadPeakSignificance: no visible binding for global variable
  'pval'
computeBroadPeakSignificance: no visible binding for global variable
  'region'
computeBroadPeakSignificance: no visible binding for global variable
  'estimate'
computePeakSignificance: no visible binding for global variable
  'zscore'
computePeakSignificance: no visible global function definition for
  'pnorm'
computeRegionSignificance: no visible global function definition for
  'p.adjust'
computeRegionSignificance: no visible binding for global variable
  'pvalue'
computeRegionSignificance: no visible binding for global variable
  'gene'
computeTileExtremes: no visible binding for global variable 'id'
computeZscore: no visible global function definition for 'pnorm'
extractSplines: no visible global function definition for
  'coefficients'
genogam: no visible global function definition for 'as.formula'
getExtremes: no visible binding for global variable 'position'
getFunctions: no visible global function definition for 'coefficients'
makeTestGenoGAM: no visible global function definition for 'runif'
parsePeaks : <anonymous>: no visible binding for global variable
  'position'
parsePeaks: no visible binding for global variable 'zscore'
plot.GenoGAM: no visible binding for global variable 'fit'
plotQC_GenoGAMDataSet: no visible global function definition for 'png'
plotQC_GenoGAMDataSet: no visible global function definition for 'par'
plotQC_GenoGAMDataSet: no visible global function definition for
  'abline'
plotQC_GenoGAMDataSet: no visible global function definition for
  'dev.off'
plotQC_hist: no visible global function definition for 'png'
plotQC_hist: no visible global function definition for 'par'
plotQC_hist: no visible global function definition for 'hist'
plotQC_hist: no visible global function definition for 'abline'
plotQC_hist: no visible global function definition for 'axis'
plotQC_hist: no visible global function definition for 'dev.off'
plot_base: no visible global function definition for 'par'
plot_base: no visible global function definition for 'plot'
plot_base: no visible global function definition for 'lines'
plot_base: no visible global function definition for 'abline'
plot_base: no visible global function definition for 'mtext'
writeToBroadPeaks: no visible global function definition for
  'write.table'
writeToNarrowPeaks: no visible global function definition for
  'write.table'
xsd : <anonymous>: no visible binding for global variable 'position'
xsd: no visible binding for global variable 'position'
Undefined global functions or variables:
  abline as.formula axis coefficients dev.off dnbinom estimate fdr fit
  gene hist id lines mtext optim p.adjust par plot png pnorm position
  pval pvalue region runif write.table zscore
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "axis", "hist", "lines", "mtext",
             "par", "plot")
  importFrom("stats", "as.formula", "coefficients", "dnbinom", "optim",
             "p.adjust", "pnorm", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 ... NOTE
S3 methods shown with full name in documentation object 'plot.GenoGAM':
  'plot.GenoGAM'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                               user system elapsed
GenomicTiles-metrics                           1.53   0.10   13.88
GenomicTiles-view                              0.68   0.00   34.62
computeSizeFactors                             0.65   0.00   11.89
getTile                                        0.64   0.01   23.31
subset-GenoGAMDataSet-method                   0.55   0.02   10.78
filterData                                     0.50   0.02   30.04
GenoGAMDataSet                                 0.45   0.00   13.39
subset-GenomicTiles-method                     0.45   0.00   10.43
getChunkIndex                                  0.39   0.01   30.69
untile                                         0.39   0.00   10.04
subsetByOverlaps-GenomicTiles-GRanges-method   0.33   0.00   10.14
getIndexCoordinates                            0.28   0.00   16.21
subsetByOverlaps-GenoGAMDataSet-GRanges-method 0.28   0.00   10.10
GenomicTiles                                   0.25   0.00   24.75
changeSettings                                 0.23   0.00   30.23
checkSettings                                  0.20   0.02   16.13
design                                         0.20   0.02   15.98
getCoordinates                                 0.17   0.02   10.26
makeTestGenomicTiles                           0.16   0.03    9.92
sizeFactors                                    0.19   0.00   10.34
tileSettings-elements                          0.18   0.00   41.45
tileSettings                                   0.18   0.00   11.87
dataRange                                      0.17   0.00   22.05
getIndex                                       0.17   0.00    9.44
makeTestGenoGAMDataSet                         0.15   0.00   14.53
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                               user system elapsed
GenomicTiles-metrics                           2.08   0.06   14.57
GenomicTiles-view                              0.79   0.05   32.84
computeSizeFactors                             0.83   0.00   13.68
getTile                                        0.75   0.00   14.47
GenoGAMDataSet                                 0.50   0.03    9.86
filterData                                     0.53   0.00   26.68
subset-GenoGAMDataSet-method                   0.45   0.01   13.80
subset-GenomicTiles-method                     0.46   0.00   12.70
subsetByOverlaps-GenoGAMDataSet-GRanges-method 0.42   0.00   12.49
getChunkIndex                                  0.39   0.01   12.53
GenomicTiles                                   0.38   0.00   24.31
getIndexCoordinates                            0.36   0.01   13.25
subsetByOverlaps-GenomicTiles-GRanges-method   0.34   0.02   14.18
untile                                         0.34   0.00   12.58
changeSettings                                 0.25   0.05   23.83
dataRange                                      0.23   0.01   11.81
design                                         0.20   0.02   13.56
getIndex                                       0.22   0.00   15.82
sizeFactors                                    0.19   0.02   12.33
makeTestGenoGAMDataSet                         0.20   0.00   12.94
checkSettings                                  0.19   0.00   20.15
getCoordinates                                 0.17   0.02   10.82
makeTestGenomicTiles                           0.19   0.00   11.56
tileSettings                                   0.18   0.00   14.87
tileSettings-elements                          0.16   0.00   12.97
* 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/GenoGAM.Rcheck/00check.log'
for details.

Installation output

GenoGAM.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/GenoGAM_1.8.0.tar.gz && rm -rf GenoGAM.buildbin-libdir && mkdir GenoGAM.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenoGAM.buildbin-libdir GenoGAM_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL GenoGAM_1.8.0.zip && rm GenoGAM_1.8.0.tar.gz GenoGAM_1.8.0.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
 79 2105k   79 1680k    0     0  18.8M      0 --:--:-- --:--:-- --:--:-- 20.0M
100 2105k  100 2105k    0     0  22.6M      0 --:--:-- --:--:-- --:--:-- 24.1M

install for i386

* installing *source* package 'GenoGAM' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Note: break used in wrong context: no loop is visible 
Note: break used in wrong context: no loop is visible 
Note: break used in wrong context: no loop is visible 
** help
*** installing help indices
  converting help for package 'GenoGAM'
    finding HTML links ... done
    GenoGAM-class                           html  
    GenoGAM-methods                         html  
    GenoGAM-view                            html  
    GenoGAM                                 html  
    GenoGAMDataSet-brackets                 html  
    GenoGAMDataSet-class                    html  
    GenoGAMDataSet                          html  
    GenoGAMDataSetToDataFrame               html  
    GenoGAMSettings-class                   html  
    GenoGAMSettings                         html  
    GenomicTiles-brackets                   html  
    GenomicTiles-class                      html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUDhufI/R.INSTALL21c076577b23/GenoGAM/man/GenomicTiles-class.Rd:21: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    GenomicTiles-metrics                    html  
    GenomicTiles-view                       html  
    GenomicTiles                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUDhufI/R.INSTALL21c076577b23/GenoGAM/man/GenomicTiles.Rd:25: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    asDataFrame                             html  
    callPeaks                               html  
    changeSettings                          html  
    checkSettings                           html  
    computeRegionSignificance               html  
    computeSignificance                     html  
    computeSizeFactors                      html  
    dataRange                               html  
    design                                  html  
    filterData                              html  
    fitGenoGAM                              html  
    getChunkIndex                           html  
    getCoordinates                          html  
    getIndex                                html  
    getIndexCoordinates                     html  
    getTile                                 html  
    makeTestGenoGAM                         html  
    makeTestGenoGAMDataSet                  html  
    makeTestGenomicTiles                    html  
    plot.GenoGAM                            html  
    qualityCheck                            html  
    sizeFactors                             html  
    subset-GenoGAM-method                   html  
    subset-GenoGAMDataSet-method            html  
    subset-GenomicTiles-method              html  
    subsetByOverlaps-GenoGAM-ANY-method     html  
    subsetByOverlaps-GenoGAMDataSet-GRanges-method
                                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUDhufI/R.INSTALL21c076577b23/GenoGAM/man/subsetByOverlaps-GenoGAMDataSet-GRanges-method.Rd:17: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
    subsetByOverlaps-GenomicTiles-GRanges-method
                                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpUDhufI/R.INSTALL21c076577b23/GenoGAM/man/subsetByOverlaps-GenomicTiles-GRanges-method.Rd:16: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
    tileSettings-elements                   html  
    tileSettings                            html  
    untile                                  html  
    writeToBEDFile                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GenoGAM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenoGAM' as GenoGAM_1.8.0.zip
* DONE (GenoGAM)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'GenoGAM' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings

GenoGAM.Rcheck/examples_i386/GenoGAM-Ex.timings

nameusersystemelapsed
GenoGAM-methods0.10.00.1
GenoGAM-view0.090.000.09
GenoGAMDataSet 0.45 0.0013.39
GenomicTiles-metrics 1.53 0.1013.88
GenomicTiles-view 0.68 0.0034.62
GenomicTiles 0.25 0.0024.75
callPeaks1.750.072.44
changeSettings 0.23 0.0030.23
checkSettings 0.20 0.0216.13
computeRegionSignificance0.190.000.19
computeSignificance0.020.000.01
computeSizeFactors 0.65 0.0011.89
dataRange 0.17 0.0022.05
design 0.20 0.0215.98
filterData 0.50 0.0230.04
fitGenoGAM000
getChunkIndex 0.39 0.0130.69
getCoordinates 0.17 0.0210.26
getIndex0.170.009.44
getIndexCoordinates 0.28 0.0016.21
getTile 0.64 0.0123.31
makeTestGenoGAM0.020.000.02
makeTestGenoGAMDataSet 0.15 0.0014.53
makeTestGenomicTiles0.160.039.92
sizeFactors 0.19 0.0010.34
subset-GenoGAM-method0.090.000.10
subset-GenoGAMDataSet-method 0.55 0.0210.78
subset-GenomicTiles-method 0.45 0.0010.43
subsetByOverlaps-GenoGAM-ANY-method0.050.000.05
subsetByOverlaps-GenoGAMDataSet-GRanges-method 0.28 0.0010.10
subsetByOverlaps-GenomicTiles-GRanges-method 0.33 0.0010.14
tileSettings-elements 0.18 0.0041.45
tileSettings 0.18 0.0011.87
untile 0.39 0.0010.04

GenoGAM.Rcheck/examples_x64/GenoGAM-Ex.timings

nameusersystemelapsed
GenoGAM-methods0.060.000.06
GenoGAM-view0.060.000.06
GenoGAMDataSet0.500.039.86
GenomicTiles-metrics 2.08 0.0614.57
GenomicTiles-view 0.79 0.0532.84
GenomicTiles 0.38 0.0024.31
callPeaks0.830.030.86
changeSettings 0.25 0.0523.83
checkSettings 0.19 0.0020.15
computeRegionSignificance0.20.00.2
computeSignificance0.020.000.01
computeSizeFactors 0.83 0.0013.68
dataRange 0.23 0.0111.81
design 0.20 0.0213.56
filterData 0.53 0.0026.68
fitGenoGAM000
getChunkIndex 0.39 0.0112.53
getCoordinates 0.17 0.0210.82
getIndex 0.22 0.0015.82
getIndexCoordinates 0.36 0.0113.25
getTile 0.75 0.0014.47
makeTestGenoGAM0.020.000.01
makeTestGenoGAMDataSet 0.20 0.0012.94
makeTestGenomicTiles 0.19 0.0011.56
sizeFactors 0.19 0.0212.33
subset-GenoGAM-method0.060.020.08
subset-GenoGAMDataSet-method 0.45 0.0113.80
subset-GenomicTiles-method 0.46 0.0012.70
subsetByOverlaps-GenoGAM-ANY-method0.090.000.09
subsetByOverlaps-GenoGAMDataSet-GRanges-method 0.42 0.0012.49
subsetByOverlaps-GenomicTiles-GRanges-method 0.34 0.0214.18
tileSettings-elements 0.16 0.0012.97
tileSettings 0.18 0.0014.87
untile 0.34 0.0012.58