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This page was generated on 2021-10-15 15:06:54 -0400 (Fri, 15 Oct 2021).

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? here 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 1801/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNPhood 1.22.0  (landing page)
Christian Arnold
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/SNPhood
git_branch: RELEASE_3_13
git_last_commit: 562991f
git_last_commit_date: 2021-05-19 12:16:25 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SNPhood_1.22.0.tar.gz
StartedAt: 2021-10-15 00:12:14 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 00:25:13 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 779.2 seconds
RetCode: 0
Status:   OK  
CheckDir: SNPhood.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SNPhood_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/SNPhood.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.22.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ... 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 < >
   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                  138.146  2.180 140.707
plotAllelicBiasResults           42.545  0.216  42.830
plotAndSummarizeAllelicBiasTest  41.856  0.161  42.059
plotFDRResults                   41.190  0.125  41.347
testForAllelicBiases             39.359  0.142  39.529
results                           4.983 12.203  17.506
associateGenotypes               10.788  0.043  10.838
annotationBins2                   9.802  0.091   9.905
renameRegions                     5.731  0.022   5.757
* 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-3.13-bioc/meat/SNPhood.Rcheck/00check.log’
for details.



Installation output

SNPhood.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SNPhood
###
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* 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
analyzeSNPhood138.146 2.180140.707
annotation-methods0.4920.0860.580
annotationBins0.3000.0250.325
annotationBins29.8020.0919.905
annotationDatasets0.3200.0150.335
annotationReadGroups1.2040.0251.229
annotationRegions0.2500.0210.272
associateGenotypes10.788 0.04310.838
bins-methods0.3280.0180.348
changeObjectIntegrityChecking1.1810.0201.204
collectFiles0.0360.0020.038
convertToAllelicFractions0.3370.0150.351
counts-method0.4630.0190.483
datasets-methods0.3640.0280.392
deleteDatasets1.0360.0141.050
deleteReadGroups0.3330.0250.362
deleteRegions1.2670.0221.298
enrichment-methods0.2770.0120.290
getDefaultParameterList0.0010.0000.001
mergeReadGroups0.4570.0140.474
parameters-methods0.2880.0180.308
plotAllelicBiasResults42.545 0.21642.830
plotAllelicBiasResultsOverview1.4390.0151.454
plotAndCalculateCorrelationDatasets0.3790.0080.389
plotAndCalculateWeakAndStrongGenotype2.0510.0382.093
plotAndClusterMatrix0.8540.0220.881
plotAndSummarizeAllelicBiasTest41.856 0.16142.059
plotBinCounts2.1310.0222.155
plotClusterAverage0.9090.0190.929
plotFDRResults41.190 0.12541.347
plotGenotypesPerCluster0.6220.0180.641
plotGenotypesPerSNP0.7240.0310.756
plotRegionCounts3.2360.0423.281
readGroups-methods0.2670.0050.273
regions-methods0.2740.0190.293
renameBins1.1610.0181.180
renameDatasets0.3090.0020.311
renameReadGroups0.3430.0350.378
renameRegions5.7310.0225.757
results 4.98312.20317.506
testForAllelicBiases39.359 0.14239.529