Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:45 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the netDx package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/netDx.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1263/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
netDx 1.4.3 (landing page) Shraddha Pai
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | ... NOT SUPPORTED ... | ||||||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: netDx |
Version: 1.4.3 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:netDx.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings netDx_1.4.3.tar.gz |
StartedAt: 2021-10-14 21:44:09 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 22:00:45 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 996.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: netDx.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:netDx.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings netDx_1.4.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/netDx.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘netDx/DESCRIPTION’ ... OK * this is package ‘netDx’ version ‘1.4.3’ * package encoding: UTF-8 * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘netDx’ can be installed ... OK * checking installed package size ... NOTE installed size is 7.3Mb sub-directories of 1Mb or more: extdata 5.9Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 confusionMatrix: no visible global function definition for ‘color2D.matplot’ Undefined global functions or variables: color2D.matplot * checking Rd files ... NOTE prepare_Rd: makeInputForEnrichmentMap.Rd:36-38: Dropping empty section \value * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘callOverallSelectedFeatures’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Documented arguments not in \usage in documentation object 'makeInputForEnrichmentMap': ‘featScores’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 data for ASCII and uncompressed saves ... WARNING Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress cnv_GR.rda 71Kb 59Kb xz cnv_patientNetCount.rda 72Kb 34Kb bzip2 cnv_pheno.rda 30Kb 23Kb xz xpr.rda 576Kb 408Kb xz * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed buildPredictor 45.010 1.407 50.527 createPSN_MultiData 40.920 0.784 63.875 buildPredictor_sparseGenetic 21.699 0.877 22.646 runFeatureSelection 8.956 0.937 6.035 compileFeatures 8.290 0.809 48.606 RR_featureTally 7.442 0.797 8.246 getPatientPredictions 5.873 0.010 5.889 plotPerf 5.342 0.016 5.362 runQuery 4.313 0.573 5.558 thresholdSmoothedMutations 4.267 0.197 32.704 smoothMutations_LabelProp 3.162 0.160 32.243 enrichLabelNets 2.046 0.065 129.332 getEnr 1.055 0.023 22.665 makePSN_NamedMatrix 0.092 0.007 21.051 countIntType_batch 0.031 0.006 22.039 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 3 WARNINGs, 5 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/netDx.Rcheck/00check.log’ for details.
netDx.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL netDx ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘netDx’ ... ** using staged installation ** R ** data ** inst ** 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 (netDx)
netDx.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(netDx) Attaching package: 'netDx' The following object is masked from 'package:stats': predict > > test_check("netDx") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ] > > proc.time() user system elapsed 27.139 1.799 93.526
netDx.Rcheck/netDx-Ex.timings
name | user | system | elapsed | |
MB.pheno | 0.006 | 0.002 | 0.008 | |
RR_featureTally | 7.442 | 0.797 | 8.246 | |
avgNormDiff | 0.036 | 0.004 | 0.039 | |
buildPredictor | 45.010 | 1.407 | 50.527 | |
buildPredictor_sparseGenetic | 21.699 | 0.877 | 22.646 | |
callFeatSel | 0.115 | 0.002 | 0.116 | |
cleanPathwayName | 0.001 | 0.000 | 0.001 | |
cnv_GR | 0.031 | 0.001 | 0.032 | |
cnv_TTstatus | 0.009 | 0.022 | 0.031 | |
cnv_netPass | 0.004 | 0.001 | 0.005 | |
cnv_netScores | 0.008 | 0.019 | 0.028 | |
cnv_patientNetCount | 0.127 | 0.116 | 0.243 | |
cnv_pheno | 0.011 | 0.003 | 0.013 | |
compareShortestPath | 0.028 | 0.004 | 0.032 | |
compileFeatureScores | 0.009 | 0.001 | 0.012 | |
compileFeatures | 8.290 | 0.809 | 48.606 | |
confmat | 0.003 | 0.001 | 0.004 | |
countIntType | 0.003 | 0.001 | 0.004 | |
countIntType_batch | 0.031 | 0.006 | 22.039 | |
countPatientsInNet | 0.004 | 0.002 | 0.006 | |
createPSN_MultiData | 40.920 | 0.784 | 63.875 | |
enrichLabelNets | 2.046 | 0.065 | 129.332 | |
featScores | 0.056 | 0.068 | 0.124 | |
fetchPathwayDefinitions | 1.624 | 0.028 | 1.869 | |
genes | 0.002 | 0.001 | 0.004 | |
getEMapInput | 1.621 | 0.022 | 1.700 | |
getEMapInput_many | 1.390 | 0.045 | 1.489 | |
getEnr | 1.055 | 0.023 | 22.665 | |
getFeatureScores | 0.024 | 0.002 | 0.026 | |
getGMjar_path | 0.720 | 0.059 | 0.758 | |
getNetConsensus | 0.021 | 0.000 | 0.021 | |
getOR | 0.007 | 0.003 | 0.008 | |
getPatientPredictions | 5.873 | 0.010 | 5.889 | |
getPatientRankings | 0.145 | 0.003 | 0.148 | |
getRegionOL | 0.526 | 0.003 | 0.530 | |
getSimilarity | 0.186 | 0.003 | 0.189 | |
makePSN_NamedMatrix | 0.092 | 0.007 | 21.051 | |
makePSN_RangeSets | 0.015 | 0.001 | 0.017 | |
makeQueries | 0.011 | 0.003 | 0.013 | |
makeSymmetric | 0.002 | 0.001 | 0.003 | |
mapNamedRangesToSets | 0.057 | 0.003 | 0.061 | |
normDiff | 0.001 | 0.000 | 0.002 | |
npheno | 0.002 | 0.001 | 0.004 | |
pathwayList | 0.003 | 0.008 | 0.010 | |
pathway_GR | 0.136 | 0.004 | 0.140 | |
perfCalc | 0.002 | 0.001 | 0.004 | |
pheno | 0.011 | 0.002 | 0.011 | |
pheno_full | 0.003 | 0.002 | 0.003 | |
plotEmap | 1.523 | 0.021 | 1.652 | |
plotPerf | 5.342 | 0.016 | 5.362 | |
plotPerf_multi | 0.056 | 0.002 | 0.059 | |
predRes | 0.003 | 0.001 | 0.005 | |
predictPatientLabels | 0.015 | 0.002 | 0.016 | |
pruneNets | 0.012 | 0.005 | 0.016 | |
readPathways | 1.748 | 0.107 | 1.958 | |
runFeatureSelection | 8.956 | 0.937 | 6.035 | |
runQuery | 4.313 | 0.573 | 5.558 | |
setupFeatureDB | 0.054 | 0.006 | 0.061 | |
silh | 0.003 | 0.001 | 0.005 | |
sim.eucscale | 0.444 | 0.004 | 0.450 | |
sim.pearscale | 0.959 | 0.030 | 0.989 | |
simpleCap | 0.000 | 0.000 | 0.001 | |
smoothMutations_LabelProp | 3.162 | 0.160 | 32.243 | |
sparsify2 | 0.417 | 0.051 | 0.469 | |
sparsify3 | 0.388 | 0.016 | 0.404 | |
splitTestTrain | 0.016 | 0.002 | 0.018 | |
splitTestTrain_resampling | 0.004 | 0.001 | 0.005 | |
thresholdSmoothedMutations | 4.267 | 0.197 | 32.704 | |
updateNets | 0.006 | 0.002 | 0.009 | |
writeNetsSIF | 0.007 | 0.001 | 0.009 | |
writeQueryBatchFile | 0.005 | 0.003 | 0.008 | |
writeQueryFile | 0.006 | 0.003 | 0.009 | |
xpr | 0.028 | 0.052 | 0.080 | |