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This page was generated on 2022-10-19 13:20:54 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 nebbiolo1


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 1878/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNPhood 1.26.0  (landing page)
Christian Arnold
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/SNPhood
git_branch: RELEASE_3_15
git_last_commit: 7c587a3
git_last_commit_date: 2022-04-26 11:27:57 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SNPhood
Version: 1.26.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings SNPhood_1.26.0.tar.gz
StartedAt: 2022-10-18 21:55:31 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 22:05:07 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 576.3 seconds
RetCode: 0
Status:   OK  
CheckDir: SNPhood.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings SNPhood_1.26.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/SNPhood.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SNPhood/DESCRIPTION’ ... OK
* this is package ‘SNPhood’ version ‘1.26.0’
* 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 ... 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                  103.426  6.596 111.240
plotAllelicBiasResults           28.714  0.295  27.312
plotAndSummarizeAllelicBiasTest  28.656  0.256  27.531
testForAllelicBiases             28.276  0.227  27.097
plotFDRResults                   28.102  0.195  26.985
results                           2.804 10.535  13.338
annotationBins2                  11.224  0.134  11.378
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/SNPhood.Rcheck/00check.log’
for details.



Installation output

SNPhood.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL SNPhood
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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
analyzeSNPhood103.426 6.596111.240
annotation-methods0.2500.1040.353
annotationBins0.1800.0320.212
annotationBins211.224 0.13411.378
annotationDatasets0.1510.0520.202
annotationReadGroups0.1480.0200.168
annotationRegions1.0240.0121.036
associateGenotypes4.2130.0604.273
bins-methods0.1460.0280.174
changeObjectIntegrityChecking0.2250.0000.225
collectFiles0.030.000.03
convertToAllelicFractions0.2020.0040.207
counts-method0.2580.0000.258
datasets-methods0.1810.0200.201
deleteDatasets1.0940.0041.098
deleteReadGroups0.1700.0160.186
deleteRegions0.2140.0120.226
enrichment-methods0.1930.0120.205
getDefaultParameterList0.0010.0000.000
mergeReadGroups0.2100.0160.226
parameters-methods0.1770.0160.193
plotAllelicBiasResults28.714 0.29527.312
plotAllelicBiasResultsOverview1.9610.0281.989
plotAndCalculateCorrelationDatasets0.2440.0360.280
plotAndCalculateWeakAndStrongGenotype0.7330.0720.805
plotAndClusterMatrix1.7360.0561.792
plotAndSummarizeAllelicBiasTest28.656 0.25627.531
plotBinCounts1.2580.0521.311
plotClusterAverage1.6220.0321.654
plotFDRResults28.102 0.19526.985
plotGenotypesPerCluster0.4330.0640.498
plotGenotypesPerSNP0.4190.0000.419
plotRegionCounts1.9340.0311.965
readGroups-methods0.1860.0040.191
regions-methods1.6080.0161.623
renameBins0.1690.0610.230
renameDatasets0.1790.0040.183
renameReadGroups0.1900.0030.194
renameRegions2.9230.0152.939
results 2.80410.53513.338
testForAllelicBiases28.276 0.22727.097