Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-26 12:06 -0400 (Tue, 26 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4821 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4610 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4553 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4539 |
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 2021/2319 | 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: 2025-08-25 21:40:57 -0400 (Mon, 25 Aug 2025) |
EndedAt: 2025-08-25 21:44:48 -0400 (Mon, 25 Aug 2025) |
EllapsedTime: 231.6 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 (2025-06-14 r88325) * 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 38.800 0.854 39.797 plotAllelicBiasResults 10.826 0.194 11.065 plotFDRResults 10.793 0.130 11.533 testForAllelicBiases 10.780 0.132 11.320 plotAndSummarizeAllelicBiasTest 10.265 0.142 10.687 * 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 | 38.800 | 0.854 | 39.797 | |
annotation-methods | 0.074 | 0.026 | 0.100 | |
annotationBins | 0.051 | 0.004 | 0.055 | |
annotationBins2 | 4.611 | 0.009 | 4.625 | |
annotationDatasets | 0.047 | 0.004 | 0.051 | |
annotationReadGroups | 0.451 | 0.010 | 0.462 | |
annotationRegions | 0.054 | 0.004 | 0.059 | |
associateGenotypes | 1.736 | 0.032 | 1.770 | |
bins-methods | 0.049 | 0.005 | 0.054 | |
changeObjectIntegrityChecking | 0.468 | 0.023 | 0.491 | |
collectFiles | 0.010 | 0.001 | 0.011 | |
convertToAllelicFractions | 0.062 | 0.003 | 0.065 | |
counts-method | 0.482 | 0.009 | 0.491 | |
datasets-methods | 0.048 | 0.006 | 0.055 | |
deleteDatasets | 0.055 | 0.006 | 0.060 | |
deleteReadGroups | 0.052 | 0.004 | 0.058 | |
deleteRegions | 0.467 | 0.011 | 0.478 | |
enrichment-methods | 0.056 | 0.004 | 0.060 | |
getDefaultParameterList | 0 | 0 | 0 | |
mergeReadGroups | 0.067 | 0.007 | 0.073 | |
parameters-methods | 0.049 | 0.007 | 0.056 | |
plotAllelicBiasResults | 10.826 | 0.194 | 11.065 | |
plotAllelicBiasResultsOverview | 0.273 | 0.004 | 0.278 | |
plotAndCalculateCorrelationDatasets | 0.559 | 0.024 | 0.601 | |
plotAndCalculateWeakAndStrongGenotype | 0.678 | 0.016 | 0.693 | |
plotAndClusterMatrix | 0.188 | 0.011 | 0.204 | |
plotAndSummarizeAllelicBiasTest | 10.265 | 0.142 | 10.687 | |
plotBinCounts | 0.374 | 0.006 | 0.380 | |
plotClusterAverage | 0.163 | 0.005 | 0.168 | |
plotFDRResults | 10.793 | 0.130 | 11.533 | |
plotGenotypesPerCluster | 0.134 | 0.006 | 0.140 | |
plotGenotypesPerSNP | 0.116 | 0.007 | 0.124 | |
plotRegionCounts | 0.516 | 0.012 | 0.532 | |
readGroups-methods | 0.049 | 0.008 | 0.056 | |
regions-methods | 0.065 | 0.011 | 0.076 | |
renameBins | 0.055 | 0.005 | 0.060 | |
renameDatasets | 0.503 | 0.018 | 0.524 | |
renameReadGroups | 0.046 | 0.005 | 0.052 | |
renameRegions | 0.640 | 0.028 | 0.674 | |
results | 0.730 | 2.399 | 3.156 | |
testForAllelicBiases | 10.780 | 0.132 | 11.320 | |