Christian Arnold
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/SNPhood |
| Branch: RELEASE_3_9 |
| Last Commit: a7e7b13 |
| Last Changed Date: 2019-05-02 11:53:58 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:56:39 -0400 (Wed, 16 Oct 2019).
| Package 1551/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SNPhood 1.14.0 Christian Arnold
| malbec2 | Linux (Ubuntu 18.04.2 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: 1.14.0 |
| 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_1.14.0.tar.gz |
| StartedAt: 2019-10-16 07:01:09 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 07:16:09 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 899.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SNPhood.Rcheck |
| Warnings: 0 |
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### Running 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_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SNPhood.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.14.0’
* 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 < >
* 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 or elapsed time > 5s
user system elapsed
plotFDRResults 137.432 65.354 54.149
plotAllelicBiasResults 137.297 60.316 60.052
testForAllelicBiases 134.526 61.781 53.887
plotAndSummarizeAllelicBiasTest 133.837 60.698 54.630
analyzeSNPhood 146.405 4.482 159.587
results 8.903 11.703 20.615
annotationBins2 10.940 0.172 14.170
associateGenotypes 7.747 0.116 7.863
plotRegionCounts 5.123 0.225 10.164
* 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-3.9-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/3.6/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 | 146.405 | 4.482 | 159.587 | |
| annotation-methods | 0.451 | 0.209 | 0.660 | |
| annotationBins | 0.234 | 0.036 | 0.270 | |
| annotationBins2 | 10.940 | 0.172 | 14.170 | |
| annotationDatasets | 0.178 | 0.043 | 0.222 | |
| annotationReadGroups | 0.229 | 0.032 | 0.261 | |
| annotationRegions | 0.252 | 0.051 | 0.302 | |
| associateGenotypes | 7.747 | 0.116 | 7.863 | |
| bins-methods | 0.991 | 0.064 | 1.055 | |
| changeObjectIntegrityChecking | 1.226 | 0.069 | 1.293 | |
| collectFiles | 0.051 | 0.002 | 0.053 | |
| convertToAllelicFractions | 1.106 | 0.034 | 1.141 | |
| counts-method | 0.306 | 0.053 | 0.360 | |
| datasets-methods | 0.248 | 0.095 | 0.343 | |
| deleteDatasets | 0.284 | 0.091 | 0.374 | |
| deleteReadGroups | 0.194 | 0.084 | 0.278 | |
| deleteRegions | 0.301 | 0.092 | 0.393 | |
| enrichment-methods | 0.278 | 0.104 | 0.381 | |
| getDefaultParameterList | 0.001 | 0.001 | 0.001 | |
| mergeReadGroups | 0.447 | 0.108 | 0.554 | |
| parameters-methods | 0.262 | 0.118 | 0.380 | |
| plotAllelicBiasResults | 137.297 | 60.316 | 60.052 | |
| plotAllelicBiasResultsOverview | 2.298 | 0.129 | 4.514 | |
| plotAndCalculateCorrelationDatasets | 0.345 | 0.108 | 0.454 | |
| plotAndCalculateWeakAndStrongGenotype | 1.406 | 0.081 | 1.489 | |
| plotAndClusterMatrix | 2.296 | 0.141 | 2.439 | |
| plotAndSummarizeAllelicBiasTest | 133.837 | 60.698 | 54.630 | |
| plotBinCounts | 3.453 | 0.085 | 3.540 | |
| plotClusterAverage | 1.997 | 0.087 | 2.085 | |
| plotFDRResults | 137.432 | 65.354 | 54.149 | |
| plotGenotypesPerCluster | 0.981 | 0.148 | 1.130 | |
| plotGenotypesPerSNP | 0.839 | 0.161 | 1.001 | |
| plotRegionCounts | 5.123 | 0.225 | 10.164 | |
| readGroups-methods | 0.218 | 0.048 | 0.267 | |
| regions-methods | 0.231 | 0.108 | 0.357 | |
| renameBins | 0.242 | 0.100 | 0.343 | |
| renameDatasets | 0.254 | 0.053 | 0.307 | |
| renameReadGroups | 0.244 | 0.084 | 0.328 | |
| renameRegions | 4.113 | 0.207 | 4.322 | |
| results | 8.903 | 11.703 | 20.615 | |
| testForAllelicBiases | 134.526 | 61.781 | 53.887 | |