Christian Arnold
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/SNPhood |
| Branch: master |
| Last Commit: f8f7c1f |
| Last Changed Date: 2019-10-29 13:40:06 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:43:42 -0500 (Thu, 16 Jan 2020).
| Package 1620/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SNPhood 1.17.0 Christian Arnold
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: SNPhood |
| Version: 1.17.0 |
| 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_1.17.0.tar.gz |
| StartedAt: 2020-01-16 09:04:24 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 09:21:49 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 1045.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SNPhood.Rcheck |
| Warnings: 0 |
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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_1.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SNPhood.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SNPhood/DESCRIPTION’ ... OK
* this is package ‘SNPhood’ version ‘1.17.0’
* 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 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
plotAndSummarizeAllelicBiasTest 139.633 60.242 57.680
plotAllelicBiasResults 135.304 52.972 63.648
plotFDRResults 132.642 54.541 57.829
testForAllelicBiases 131.700 54.310 58.036
analyzeSNPhood 180.740 4.669 198.400
results 9.766 12.546 22.355
annotationBins2 11.839 0.221 16.105
associateGenotypes 11.503 0.183 11.705
renameRegions 5.693 0.135 5.830
plotRegionCounts 5.256 0.169 10.754
plotAllelicBiasResultsOverview 1.913 0.082 5.554
* 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
‘/Users/biocbuild/bbs-3.11-bioc/meat/SNPhood.Rcheck/00check.log’
for details.
SNPhood.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SNPhood ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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)
SNPhood.Rcheck/SNPhood-Ex.timings
| name | user | system | elapsed | |
| analyzeSNPhood | 180.740 | 4.669 | 198.400 | |
| annotation-methods | 0.445 | 0.186 | 0.631 | |
| annotationBins | 1.180 | 0.039 | 1.218 | |
| annotationBins2 | 11.839 | 0.221 | 16.105 | |
| annotationDatasets | 0.249 | 0.078 | 0.346 | |
| annotationReadGroups | 0.260 | 0.057 | 0.316 | |
| annotationRegions | 1.292 | 0.039 | 1.332 | |
| associateGenotypes | 11.503 | 0.183 | 11.705 | |
| bins-methods | 1.360 | 0.077 | 1.438 | |
| changeObjectIntegrityChecking | 0.259 | 0.072 | 0.331 | |
| collectFiles | 0.045 | 0.002 | 0.047 | |
| convertToAllelicFractions | 0.260 | 0.026 | 0.285 | |
| counts-method | 0.396 | 0.034 | 0.430 | |
| datasets-methods | 0.257 | 0.055 | 0.316 | |
| deleteDatasets | 1.246 | 0.040 | 1.286 | |
| deleteReadGroups | 0.281 | 0.061 | 0.342 | |
| deleteRegions | 0.217 | 0.033 | 0.249 | |
| enrichment-methods | 0.269 | 0.090 | 0.359 | |
| getDefaultParameterList | 0.001 | 0.001 | 0.001 | |
| mergeReadGroups | 0.351 | 0.049 | 0.399 | |
| parameters-methods | 1.271 | 0.079 | 1.351 | |
| plotAllelicBiasResults | 135.304 | 52.972 | 63.648 | |
| plotAllelicBiasResultsOverview | 1.913 | 0.082 | 5.554 | |
| plotAndCalculateCorrelationDatasets | 0.372 | 0.073 | 0.467 | |
| plotAndCalculateWeakAndStrongGenotype | 3.513 | 0.147 | 3.665 | |
| plotAndClusterMatrix | 1.719 | 0.194 | 1.921 | |
| plotAndSummarizeAllelicBiasTest | 139.633 | 60.242 | 57.680 | |
| plotBinCounts | 3.153 | 0.073 | 3.229 | |
| plotClusterAverage | 1.106 | 0.063 | 1.169 | |
| plotFDRResults | 132.642 | 54.541 | 57.829 | |
| plotGenotypesPerCluster | 1.050 | 0.076 | 1.127 | |
| plotGenotypesPerSNP | 0.758 | 0.023 | 0.782 | |
| plotRegionCounts | 5.256 | 0.169 | 10.754 | |
| readGroups-methods | 0.23 | 0.08 | 0.31 | |
| regions-methods | 0.210 | 0.084 | 0.296 | |
| renameBins | 0.232 | 0.086 | 0.318 | |
| renameDatasets | 0.234 | 0.083 | 0.316 | |
| renameReadGroups | 1.398 | 0.055 | 1.453 | |
| renameRegions | 5.693 | 0.135 | 5.830 | |
| results | 9.766 | 12.546 | 22.355 | |
| testForAllelicBiases | 131.700 | 54.310 | 58.036 | |