Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-01 12:06 -0400 (Wed, 01 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4843 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4631 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4575 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
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 2035/2337 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SNPhood 1.39.0 (landing page) Christian Arnold
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.39.0 |
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_1.39.0.tar.gz |
StartedAt: 2025-09-30 21:49:55 -0400 (Tue, 30 Sep 2025) |
EndedAt: 2025-09-30 21:53:53 -0400 (Tue, 30 Sep 2025) |
EllapsedTime: 237.5 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_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SNPhood.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SNPhood/DESCRIPTION’ ... OK * this is package ‘SNPhood’ version ‘1.39.0’ * 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: analyzeSNPhood.Rd: BamFile-class, BamFileList-class collectFiles.Rd: BamFile-class, BamFileList-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 39.536 0.728 40.469 plotAllelicBiasResults 11.909 0.205 12.121 plotAndSummarizeAllelicBiasTest 10.885 0.158 11.078 plotFDRResults 10.721 0.169 10.969 testForAllelicBiases 10.643 0.135 10.807 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.22-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/4.5-arm64/Resources/library’ * installing *source* package ‘SNPhood’ ... ** this is package ‘SNPhood’ version ‘1.39.0’ ** 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 | 39.536 | 0.728 | 40.469 | |
annotation-methods | 0.071 | 0.021 | 0.091 | |
annotationBins | 0.046 | 0.010 | 0.057 | |
annotationBins2 | 4.483 | 0.012 | 4.509 | |
annotationDatasets | 0.042 | 0.006 | 0.049 | |
annotationReadGroups | 0.046 | 0.011 | 0.057 | |
annotationRegions | 0.052 | 0.010 | 0.067 | |
associateGenotypes | 1.835 | 0.092 | 1.932 | |
bins-methods | 0.042 | 0.011 | 0.053 | |
changeObjectIntegrityChecking | 0.050 | 0.007 | 0.056 | |
collectFiles | 0.011 | 0.001 | 0.011 | |
convertToAllelicFractions | 0.060 | 0.006 | 0.065 | |
counts-method | 0.554 | 0.032 | 0.594 | |
datasets-methods | 0.048 | 0.024 | 0.072 | |
deleteDatasets | 0.059 | 0.009 | 0.070 | |
deleteReadGroups | 0.052 | 0.011 | 0.070 | |
deleteRegions | 0.502 | 0.023 | 0.534 | |
enrichment-methods | 0.052 | 0.014 | 0.066 | |
getDefaultParameterList | 0 | 0 | 0 | |
mergeReadGroups | 0.067 | 0.010 | 0.077 | |
parameters-methods | 0.050 | 0.011 | 0.061 | |
plotAllelicBiasResults | 11.909 | 0.205 | 12.121 | |
plotAllelicBiasResultsOverview | 0.362 | 0.025 | 0.389 | |
plotAndCalculateCorrelationDatasets | 0.568 | 0.017 | 0.585 | |
plotAndCalculateWeakAndStrongGenotype | 0.226 | 0.014 | 0.240 | |
plotAndClusterMatrix | 0.218 | 0.035 | 0.253 | |
plotAndSummarizeAllelicBiasTest | 10.885 | 0.158 | 11.078 | |
plotBinCounts | 0.513 | 0.020 | 0.533 | |
plotClusterAverage | 0.251 | 0.013 | 0.264 | |
plotFDRResults | 10.721 | 0.169 | 10.969 | |
plotGenotypesPerCluster | 0.181 | 0.020 | 0.201 | |
plotGenotypesPerSNP | 0.134 | 0.014 | 0.147 | |
plotRegionCounts | 0.617 | 0.018 | 0.635 | |
readGroups-methods | 0.085 | 0.028 | 0.112 | |
regions-methods | 0.047 | 0.010 | 0.056 | |
renameBins | 0.545 | 0.020 | 0.566 | |
renameDatasets | 0.047 | 0.010 | 0.057 | |
renameReadGroups | 0.052 | 0.011 | 0.063 | |
renameRegions | 0.641 | 0.032 | 0.675 | |
results | 0.674 | 2.168 | 2.869 | |
testForAllelicBiases | 10.643 | 0.135 | 10.807 | |