Multiple platform build/check report for BioC 3.9 - CHECK report for SNPhood on tokay2

Package: SNPhood

Version: 1.13.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SNPhood.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SNPhood_1.13.0.tar.gz

StartedAt: 2019-02-09 06:03:48 -0500 (Sat, 09 Feb 2019)

EndedAt: 2019-02-09 06:19:53 -0500 (Sat, 09 Feb 2019)

EllapsedTime: 965.2 seconds

RetCode: 0

Status: WARNINGS

CheckDir: SNPhood.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SNPhood.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SNPhood_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SNPhood.Rcheck'
* using R Under development (unstable) (2019-01-10 r75962)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SNPhood/DESCRIPTION' ... OK
* this is package 'SNPhood' version '1.13.0'
* 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 'SNPhood' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpI71EYl/R.INSTALL255068424fb/SNPhood/man/collectFiles.Rd:46: file link 'path' in package 'Rsamtools' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SNPhood.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
* 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
.calcBinomTestVector: no visible binding for global variable 'pp'
Undefined global functions or variables:
  pp
* 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
analyzeSNPhood                  64.30   4.14  105.60
plotAllelicBiasResults          29.44   0.91   30.89
plotAndSummarizeAllelicBiasTest 26.69   0.94   27.69
plotFDRResults                  25.97   1.03   27.78
testForAllelicBiases            25.08   1.19   26.45
results                          6.37   2.34    8.72
plotRegionCounts                 4.08   0.08    7.00
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
analyzeSNPhood                  77.56   5.86   88.95
plotAllelicBiasResults          31.19   0.57   32.14
plotAndSummarizeAllelicBiasTest 28.25   0.32   29.09
plotFDRResults                  27.82   0.26   29.74
testForAllelicBiases            27.45   0.44   28.29
associateGenotypes               7.16   0.03    7.21
results                          3.72   1.92    5.64
plotRegionCounts                 3.75   0.14    6.32
plotAllelicBiasResultsOverview   2.97   0.12    5.01
* 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-3.9-bioc/meat/SNPhood.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/SNPhood_1.13.0.tar.gz && rm -rf SNPhood.buildbin-libdir && mkdir SNPhood.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SNPhood.buildbin-libdir SNPhood_1.13.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SNPhood_1.13.0.zip && rm SNPhood_1.13.0.tar.gz SNPhood_1.13.0.zip
###
##############################################################################
##############################################################################


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

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  2 3963k    2  112k    0     0   336k      0  0:00:11 --:--:--  0:00:11  341k
100 3963k  100 3963k    0     0  8739k      0 --:--:-- --:--:-- --:--:-- 8848k

install for i386

* installing *source* package 'SNPhood' ...
** R
** data
*** moving datasets to lazyload DB
Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SNPhood'
    finding HTML links ... done
    SNPhood-class                           html  
    SNPhood                                 html  
    SNPhood.o                               html  
    analyzeSNPhood                          html  
    finding level-2 HTML links ... done

    annotation-methods                      html  
    annotationBins                          html  
    annotationBins2                         html  
    annotationDatasets                      html  
    annotationReadGroups                    html  
    annotationRegions                       html  
    associateGenotypes                      html  
    bins-methods                            html  
    changeObjectIntegrityChecking           html  
    collectFiles                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpI71EYl/R.INSTALL255068424fb/SNPhood/man/collectFiles.Rd:46: file link 'path' in package 'Rsamtools' does not exist and so has been treated as a topic
    convertToAllelicFractions               html  
    counts-method                           html  
    datasets-methods                        html  
    deleteDatasets                          html  
    deleteReadGroups                        html  
    deleteRegions                           html  
    enrichment-methods                      html  
    getDefaultParameterList                 html  
    mergeReadGroups                         html  
    parameters-methods                      html  
    plotAllelicBiasResults                  html  
    plotAllelicBiasResultsOverview          html  
    plotAndCalculateCorrelationDatasets     html  
    plotAndCalculateWeakAndStrongGenotype   html  
    plotAndClusterMatrix                    html  
    plotAndSummarizeAllelicBiasTest         html  
    plotBinCounts                           html  
    plotClusterAverage                      html  
    plotFDRResults                          html  
    plotGenotypesPerCluster                 html  
    plotGenotypesPerSNP                     html  
    plotRegionCounts                        html  
    readGroups-methods                      html  
    regions-methods                         html  
    renameBins                              html  
    renameDatasets                          html  
    renameReadGroups                        html  
    renameRegions                           html  
    results                                 html  
    testForAllelicBiases                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'SNPhood' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SNPhood' as SNPhood_1.13.0.zip
* DONE (SNPhood)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SNPhood' successfully unpacked and MD5 sums checked

name	user	system	elapsed
analyzeSNPhood	64.30	4.14	105.60
annotation-methods	0.95	0.14	1.09
annotationBins	0.93	0.06	1.00
annotationBins2	1.13	0.25	2.89
annotationDatasets	1.23	0.08	1.36
annotationReadGroups	0.94	0.03	0.97
annotationRegions	0.20	0.05	0.25
associateGenotypes	4.11	0.01	4.16
bins-methods	0.94	0.14	1.07
changeObjectIntegrityChecking	0.20	0.02	0.22
collectFiles	0.03	0.00	0.03
convertToAllelicFractions	0.25	0.03	0.28
counts-method	1.24	0.05	1.29
datasets-methods	0.39	0.01	0.41
deleteDatasets	0.36	0.07	0.42
deleteReadGroups	0.25	0.12	0.37
deleteRegions	1.05	0.05	1.10
enrichment-methods	0.17	0.06	0.23
getDefaultParameterList	0	0	0
mergeReadGroups	0.24	0.06	0.30
parameters-methods	0.23	0.08	0.31
plotAllelicBiasResults	29.44	0.91	30.89
plotAllelicBiasResultsOverview	1.69	0.14	3.55
plotAndCalculateCorrelationDatasets	1.17	0.14	1.31
plotAndCalculateWeakAndStrongGenotype	0.89	0.06	0.96
plotAndClusterMatrix	0.73	0.06	0.79
plotAndSummarizeAllelicBiasTest	26.69	0.94	27.69
plotBinCounts	3.45	0.16	3.61
plotClusterAverage	0.82	0.01	0.83
plotFDRResults	25.97	1.03	27.78
plotGenotypesPerCluster	0.57	0.33	0.90
plotGenotypesPerSNP	0.61	0.05	0.66
plotRegionCounts	4.08	0.08	7.00
readGroups-methods	0.28	0.01	0.30
regions-methods	0.27	0.07	0.33
renameBins	1.28	0.03	1.31
renameDatasets	0.30	0.03	0.33
renameReadGroups	0.32	0.03	0.36
renameRegions	1.38	0.08	1.45
results	6.37	2.34	8.72
testForAllelicBiases	25.08	1.19	26.45

name	user	system	elapsed
analyzeSNPhood	77.56	5.86	88.95
annotation-methods	0.28	0.07	0.36
annotationBins	0.32	0.04	0.34
annotationBins2	1.58	0.07	3.49
annotationDatasets	1.18	0.02	1.25
annotationReadGroups	0.14	0.08	0.22
annotationRegions	0.30	0.03	0.32
associateGenotypes	7.16	0.03	7.21
bins-methods	0.29	0.02	0.31
changeObjectIntegrityChecking	0.32	0.04	0.36
collectFiles	0.03	0.00	0.03
convertToAllelicFractions	1.30	0.02	1.31
counts-method	0.41	0.03	0.44
datasets-methods	0.20	0.03	0.23
deleteDatasets	0.19	0.05	0.24
deleteReadGroups	0.14	0.06	0.20
deleteRegions	0.18	0.05	0.23
enrichment-methods	0.29	0.00	0.28
getDefaultParameterList	0	0	0
mergeReadGroups	1.25	0.00	1.25
parameters-methods	0.18	0.04	0.24
plotAllelicBiasResults	31.19	0.57	32.14
plotAllelicBiasResultsOverview	2.97	0.12	5.01
plotAndCalculateCorrelationDatasets	1.39	0.08	1.47
plotAndCalculateWeakAndStrongGenotype	1.34	0.08	1.43
plotAndClusterMatrix	1.10	0.08	1.17
plotAndSummarizeAllelicBiasTest	28.25	0.32	29.09
plotBinCounts	2.44	0.08	2.52
plotClusterAverage	0.82	0.05	0.87
plotFDRResults	27.82	0.26	29.74
plotGenotypesPerCluster	0.76	0.04	0.81
plotGenotypesPerSNP	1.75	0.07	1.83
plotRegionCounts	3.75	0.14	6.32
readGroups-methods	0.25	0.04	0.29
regions-methods	0.30	0.04	0.34
renameBins	0.20	0.07	0.27
renameDatasets	0.20	0.06	0.26
renameReadGroups	1.10	0.01	1.11
renameRegions	1.72	0.07	1.78
results	3.72	1.92	5.64
testForAllelicBiases	27.45	0.44	28.29

CHECK report for SNPhood on tokay2

Summary

Command output

Installation output

Tests output

Example timings