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This page was generated on 2022-04-13 12:08:49 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for SNPhood on machv2


To the developers/maintainers of the SNPhood package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SNPhood.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1830/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNPhood 1.24.0  (landing page)
Christian Arnold
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/SNPhood
git_branch: RELEASE_3_14
git_last_commit: a479ac9
git_last_commit_date: 2021-10-26 12:23:28 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SNPhood
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SNPhood_1.24.0.tar.gz
StartedAt: 2022-04-12 18:45:18 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 19:00:35 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 917.4 seconds
RetCode: 0
Status:   OK  
CheckDir: SNPhood.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SNPhood_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/SNPhood.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SNPhood/DESCRIPTION’ ... OK
* this is package ‘SNPhood’ version ‘1.24.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SNPhood’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
* 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 < >
   use the Contact field instead
* 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
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
analyzeSNPhood                  162.951  2.717 166.138
plotAllelicBiasResults           52.303  0.270  52.613
plotAndSummarizeAllelicBiasTest  50.155  0.267  50.490
plotFDRResults                   49.006  0.213  49.260
testForAllelicBiases             48.674  0.242  48.956
results                           5.683 13.516  19.524
associateGenotypes               12.338  0.050  12.401
annotationBins2                  10.173  0.100  10.284
renameRegions                     7.412  0.019   7.436
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/SNPhood.Rcheck/00check.log’
for details.



Installation output

SNPhood.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SNPhood
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘SNPhood’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SNPhood)

Tests output


Example timings

SNPhood.Rcheck/SNPhood-Ex.timings

nameusersystemelapsed
analyzeSNPhood162.951 2.717166.138
annotation-methods0.6090.1490.758
annotationBins0.3730.0320.405
annotationBins210.173 0.10010.284
annotationDatasets0.3470.0090.355
annotationReadGroups0.3650.0360.403
annotationRegions1.3900.0341.425
associateGenotypes12.338 0.05012.401
bins-methods0.2890.0100.299
changeObjectIntegrityChecking0.4740.0350.510
collectFiles0.0550.0030.059
convertToAllelicFractions0.4540.0170.472
counts-method0.5650.0220.588
datasets-methods0.3260.0210.347
deleteDatasets1.2760.0121.288
deleteReadGroups0.3630.0250.387
deleteRegions0.4180.0170.435
enrichment-methods0.3880.0100.398
getDefaultParameterList0.0010.0000.001
mergeReadGroups1.4480.0141.463
parameters-methods0.3550.0150.370
plotAllelicBiasResults52.303 0.27052.613
plotAllelicBiasResultsOverview1.6790.0131.693
plotAndCalculateCorrelationDatasets1.6040.0651.672
plotAndCalculateWeakAndStrongGenotype1.1620.0291.195
plotAndClusterMatrix1.0070.0391.050
plotAndSummarizeAllelicBiasTest50.155 0.26750.490
plotBinCounts2.3150.0152.333
plotClusterAverage2.0650.0372.105
plotFDRResults49.006 0.21349.260
plotGenotypesPerCluster0.7320.0210.755
plotGenotypesPerSNP0.7950.0150.811
plotRegionCounts3.9500.0564.010
readGroups-methods1.3860.0051.390
regions-methods0.3750.0450.421
renameBins0.3870.0020.391
renameDatasets0.3930.0190.411
renameReadGroups1.4410.0231.465
renameRegions7.4120.0197.436
results 5.68313.51619.524
testForAllelicBiases48.674 0.24248.956