Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-07 11:39:57 -0400 (Fri, 07 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4755 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4489 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4520 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 2015/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SNPhood 1.34.0 (landing page) Christian Arnold
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | 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 | NA | |||||||||
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: 1.34.0 |
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SNPhood.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SNPhood_1.34.0.tar.gz |
StartedAt: 2024-06-06 11:41:06 -0400 (Thu, 06 Jun 2024) |
EndedAt: 2024-06-06 11:57:02 -0400 (Thu, 06 Jun 2024) |
EllapsedTime: 955.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SNPhood.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SNPhood.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SNPhood_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/SNPhood.Rcheck' * using R version 4.4.0 (2024-04-24 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'SNPhood/DESCRIPTION' ... OK * this is package 'SNPhood' version '1.34.0' * 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 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 68.81 6.47 83.98 plotAllelicBiasResults 19.73 0.38 20.11 plotAndSummarizeAllelicBiasTest 19.01 0.32 19.30 plotFDRResults 18.29 0.22 18.47 testForAllelicBiases 17.73 0.17 17.94 results 5.42 4.94 10.37 * 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 'F:/biocbuild/bbs-3.19-bioc/meat/SNPhood.Rcheck/00check.log' for details.
SNPhood.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL SNPhood ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 | 68.81 | 6.47 | 83.98 | |
annotation-methods | 0.32 | 0.09 | 0.41 | |
annotationBins | 0.27 | 0.02 | 0.28 | |
annotationBins2 | 1.33 | 0.12 | 1.45 | |
annotationDatasets | 0.09 | 0.10 | 0.19 | |
annotationReadGroups | 1.05 | 0.06 | 1.11 | |
annotationRegions | 0.10 | 0.06 | 0.16 | |
associateGenotypes | 4.59 | 0.08 | 4.72 | |
bins-methods | 0.17 | 0.05 | 0.22 | |
changeObjectIntegrityChecking | 1.08 | 0.11 | 1.19 | |
collectFiles | 0.05 | 0.00 | 0.05 | |
convertToAllelicFractions | 0.14 | 0.06 | 0.20 | |
counts-method | 1.06 | 0.05 | 1.10 | |
datasets-methods | 0.11 | 0.07 | 0.19 | |
deleteDatasets | 0.15 | 0.07 | 0.22 | |
deleteReadGroups | 1.02 | 0.01 | 1.03 | |
deleteRegions | 0.17 | 0.03 | 0.21 | |
enrichment-methods | 0.97 | 0.05 | 1.01 | |
getDefaultParameterList | 0 | 0 | 0 | |
mergeReadGroups | 0.14 | 0.08 | 0.22 | |
parameters-methods | 0.13 | 0.04 | 0.17 | |
plotAllelicBiasResults | 19.73 | 0.38 | 20.11 | |
plotAllelicBiasResultsOverview | 1.06 | 0.12 | 1.18 | |
plotAndCalculateCorrelationDatasets | 0.37 | 0.07 | 0.46 | |
plotAndCalculateWeakAndStrongGenotype | 2.08 | 0.11 | 2.15 | |
plotAndClusterMatrix | 0.74 | 0.15 | 0.89 | |
plotAndSummarizeAllelicBiasTest | 19.01 | 0.32 | 19.30 | |
plotBinCounts | 1.42 | 0.12 | 1.56 | |
plotClusterAverage | 0.54 | 0.11 | 0.64 | |
plotFDRResults | 18.29 | 0.22 | 18.47 | |
plotGenotypesPerCluster | 0.67 | 0.05 | 0.72 | |
plotGenotypesPerSNP | 0.49 | 0.03 | 0.52 | |
plotRegionCounts | 3.01 | 0.23 | 3.26 | |
readGroups-methods | 0.14 | 0.02 | 0.15 | |
regions-methods | 0.09 | 0.06 | 0.16 | |
renameBins | 0.19 | 0.06 | 0.25 | |
renameDatasets | 0.12 | 0.05 | 0.17 | |
renameReadGroups | 0.15 | 0.05 | 0.21 | |
renameRegions | 3.57 | 0.12 | 3.67 | |
results | 5.42 | 4.94 | 10.37 | |
testForAllelicBiases | 17.73 | 0.17 | 17.94 | |