Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:53 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 |
To the developers/maintainers of the SNPhood package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1910/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SNPhood 1.28.0 (landing page) Christian Arnold
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: SNPhood |
Version: 1.28.0 |
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SNPhood.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings SNPhood_1.28.0.tar.gz |
StartedAt: 2023-04-11 06:12:56 -0400 (Tue, 11 Apr 2023) |
EndedAt: 2023-04-11 06:21:09 -0400 (Tue, 11 Apr 2023) |
EllapsedTime: 493.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SNPhood.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SNPhood.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings SNPhood_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/SNPhood.Rcheck' * using R version 4.2.3 (2023-03-15 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'SNPhood/DESCRIPTION' ... OK * this is package 'SNPhood' version '1.28.0' * 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 appears to contain an email address not specified by mailto: nor contained in < > 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 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 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 64.44 2.11 67.70 plotAllelicBiasResults 18.30 0.11 18.42 plotAndSummarizeAllelicBiasTest 16.88 0.13 17.03 testForAllelicBiases 15.97 0.21 16.16 plotFDRResults 15.72 0.09 15.83 results 4.28 4.54 8.82 associateGenotypes 5.08 0.06 5.15 * 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 'F:/biocbuild/bbs-3.16-bioc/meat/SNPhood.Rcheck/00check.log' for details.
SNPhood.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL SNPhood ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-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 | 64.44 | 2.11 | 67.70 | |
annotation-methods | 0.28 | 0.02 | 0.29 | |
annotationBins | 0.17 | 0.00 | 0.17 | |
annotationBins2 | 1.28 | 0.03 | 1.31 | |
annotationDatasets | 1.14 | 0.00 | 1.14 | |
annotationReadGroups | 0.13 | 0.03 | 0.16 | |
annotationRegions | 0.15 | 0.00 | 0.16 | |
associateGenotypes | 5.08 | 0.06 | 5.15 | |
bins-methods | 1.19 | 0.00 | 1.19 | |
changeObjectIntegrityChecking | 0.15 | 0.00 | 0.16 | |
collectFiles | 0.05 | 0.00 | 0.04 | |
convertToAllelicFractions | 1.27 | 0.05 | 1.32 | |
counts-method | 0.20 | 0.04 | 0.25 | |
datasets-methods | 0.17 | 0.00 | 0.17 | |
deleteDatasets | 1.13 | 0.05 | 1.17 | |
deleteReadGroups | 0.15 | 0.00 | 0.16 | |
deleteRegions | 0.17 | 0.02 | 0.19 | |
enrichment-methods | 0.17 | 0.00 | 0.17 | |
getDefaultParameterList | 0 | 0 | 0 | |
mergeReadGroups | 0.21 | 0.00 | 0.20 | |
parameters-methods | 1.07 | 0.03 | 1.11 | |
plotAllelicBiasResults | 18.30 | 0.11 | 18.42 | |
plotAllelicBiasResultsOverview | 1.19 | 0.00 | 1.19 | |
plotAndCalculateCorrelationDatasets | 0.31 | 0.01 | 0.35 | |
plotAndCalculateWeakAndStrongGenotype | 0.74 | 0.05 | 0.78 | |
plotAndClusterMatrix | 1.57 | 0.06 | 1.64 | |
plotAndSummarizeAllelicBiasTest | 16.88 | 0.13 | 17.03 | |
plotBinCounts | 1.42 | 0.06 | 1.48 | |
plotClusterAverage | 1.64 | 0.02 | 1.66 | |
plotFDRResults | 15.72 | 0.09 | 15.83 | |
plotGenotypesPerCluster | 0.51 | 0.01 | 0.53 | |
plotGenotypesPerSNP | 1.61 | 0.10 | 1.71 | |
plotRegionCounts | 1.97 | 0.06 | 2.06 | |
readGroups-methods | 0.16 | 0.03 | 0.19 | |
regions-methods | 0.12 | 0.01 | 0.14 | |
renameBins | 1.19 | 0.02 | 1.21 | |
renameDatasets | 0.15 | 0.00 | 0.15 | |
renameReadGroups | 0.16 | 0.01 | 0.18 | |
renameRegions | 2.50 | 0.04 | 2.53 | |
results | 4.28 | 4.54 | 8.82 | |
testForAllelicBiases | 15.97 | 0.21 | 16.16 | |