Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-21 13:23 -0400 (Fri, 21 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4690 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4404 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4353 |
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 |
Package 1961/2242 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SNPhood 1.35.0 (landing page) Christian Arnold
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the SNPhood package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: SNPhood |
Version: 1.35.0 |
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_1.35.0.tar.gz |
StartedAt: 2024-06-21 00:05:25 -0400 (Fri, 21 Jun 2024) |
EndedAt: 2024-06-21 00:08:55 -0400 (Fri, 21 Jun 2024) |
EllapsedTime: 210.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SNPhood.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SNPhood.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SNPhood/DESCRIPTION’ ... OK * this is package ‘SNPhood’ version ‘1.35.0’ * 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 contains an email address: 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 code 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 whether startup messages can be suppressed ... 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 35.987 0.520 37.037 plotAllelicBiasResults 9.609 0.113 9.723 plotAndSummarizeAllelicBiasTest 9.229 0.111 9.341 plotFDRResults 9.168 0.082 9.254 testForAllelicBiases 9.033 0.105 9.140 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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-3.20-bioc/meat/SNPhood.Rcheck/00check.log’ for details.
SNPhood.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SNPhood ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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 | 35.987 | 0.520 | 37.037 | |
annotation-methods | 0.090 | 0.023 | 0.113 | |
annotationBins | 0.069 | 0.004 | 0.073 | |
annotationBins2 | 3.998 | 0.006 | 4.004 | |
annotationDatasets | 0.061 | 0.004 | 0.065 | |
annotationReadGroups | 0.426 | 0.007 | 0.432 | |
annotationRegions | 0.071 | 0.004 | 0.075 | |
associateGenotypes | 1.505 | 0.034 | 1.540 | |
bins-methods | 0.059 | 0.005 | 0.063 | |
changeObjectIntegrityChecking | 0.084 | 0.013 | 0.097 | |
collectFiles | 0.007 | 0.000 | 0.008 | |
convertToAllelicFractions | 0.071 | 0.005 | 0.075 | |
counts-method | 0.422 | 0.011 | 0.432 | |
datasets-methods | 0.064 | 0.006 | 0.071 | |
deleteDatasets | 0.413 | 0.007 | 0.423 | |
deleteReadGroups | 0.074 | 0.004 | 0.078 | |
deleteRegions | 0.469 | 0.008 | 0.477 | |
enrichment-methods | 0.075 | 0.003 | 0.078 | |
getDefaultParameterList | 0.000 | 0.001 | 0.000 | |
mergeReadGroups | 0.088 | 0.007 | 0.095 | |
parameters-methods | 0.073 | 0.006 | 0.079 | |
plotAllelicBiasResults | 9.609 | 0.113 | 9.723 | |
plotAllelicBiasResultsOverview | 0.288 | 0.005 | 0.294 | |
plotAndCalculateCorrelationDatasets | 0.510 | 0.011 | 0.520 | |
plotAndCalculateWeakAndStrongGenotype | 0.601 | 0.011 | 0.612 | |
plotAndClusterMatrix | 0.188 | 0.009 | 0.197 | |
plotAndSummarizeAllelicBiasTest | 9.229 | 0.111 | 9.341 | |
plotBinCounts | 0.355 | 0.006 | 0.362 | |
plotClusterAverage | 0.580 | 0.026 | 0.607 | |
plotFDRResults | 9.168 | 0.082 | 9.254 | |
plotGenotypesPerCluster | 0.147 | 0.007 | 0.154 | |
plotGenotypesPerSNP | 0.127 | 0.004 | 0.131 | |
plotRegionCounts | 0.516 | 0.021 | 0.537 | |
readGroups-methods | 0.064 | 0.004 | 0.068 | |
regions-methods | 0.065 | 0.003 | 0.067 | |
renameBins | 0.066 | 0.001 | 0.067 | |
renameDatasets | 0.068 | 0.004 | 0.072 | |
renameReadGroups | 0.065 | 0.004 | 0.067 | |
renameRegions | 0.950 | 0.011 | 0.961 | |
results | 0.690 | 2.194 | 2.890 | |
testForAllelicBiases | 9.033 | 0.105 | 9.140 | |