Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-30 12:34:52 -0400 (Thu, 30 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
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 1374/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
netDx 1.17.0 (landing page) Shraddha Pai
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
To the developers/maintainers of the netDx package: - 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 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: netDx |
Version: 1.17.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:netDx.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings netDx_1.17.0.tar.gz |
StartedAt: 2024-05-29 22:19:54 -0400 (Wed, 29 May 2024) |
EndedAt: 2024-05-29 22:57:02 -0400 (Wed, 29 May 2024) |
EllapsedTime: 2228.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: netDx.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:netDx.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings netDx_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/netDx.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘netDx/DESCRIPTION’ ... OK * this is package ‘netDx’ version ‘1.17.0’ * 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 7.4Mb sub-directories of 1Mb or more: extdata 6.0Mb * 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 ... NOTE Found the following CITATION file in a non-standard place: CITATION.cff Most likely ‘inst/CITATION’ should be used instead. * 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 loading without being on the library search path ... 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 ... OK * checking Rd files ... NOTE checkRd: (-1) getEnr.Rd:53: Lost braces; missing escapes or markup? 53 | {(+,-),(-,+),(-,-)} interactions. | ^ checkRd: (-1) predict.Rd:27: Lost braces; missing escapes or markup? 27 | e.g. keys could include {'clinical','rna','methylation'}, and values within 'rna' could include pathway names {'cell cycle', 'DNA repair'}, etc., | ^ checkRd: (-1) predict.Rd:27: Lost braces; missing escapes or markup? 27 | e.g. keys could include {'clinical','rna','methylation'}, and values within 'rna' could include pathway names {'cell cycle', 'DNA repair'}, etc., | ^ * 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 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 buildPredictor 25.959 0.960 29.003 createPSN_MultiData 20.534 1.107 33.048 RR_featureTally 10.751 0.967 11.719 runFeatureSelection 7.609 0.412 4.494 smoothMutations_LabelProp 7.199 0.568 32.506 compileFeatures 6.598 0.496 21.595 thresholdSmoothedMutations 3.574 0.125 26.045 enrichLabelNets 2.085 0.207 57.874 getEnr 0.772 0.044 10.612 makePSN_NamedMatrix 0.082 0.001 9.066 countIntType_batch 0.014 0.021 9.973 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/netDx.Rcheck/00check.log’ for details.
netDx.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL netDx ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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") TT_STATUS STATUS TEST TRAIN LumA 52 178 notLumA 52 243 PRED_CLASS STATUS LumA notLumA LumA 41 11 notLumA 17 35 [1] TRUE [ FAIL 0 | WARN 0 | SKIP 0 | PASS 39 ] > > proc.time() user system elapsed 67.850 4.589 257.698
netDx.Rcheck/netDx-Ex.timings
name | user | system | elapsed | |
MB.pheno | 0.005 | 0.001 | 0.005 | |
RR_featureTally | 10.751 | 0.967 | 11.719 | |
avgNormDiff | 0.051 | 0.000 | 0.051 | |
buildPredictor | 25.959 | 0.960 | 29.003 | |
buildPredictor_sparseGenetic | 0.78 | 0.00 | 1.94 | |
callFeatSel | 0.084 | 0.000 | 0.084 | |
callOverallSelectedFeatures | 0.093 | 0.012 | 0.105 | |
cleanPathwayName | 0 | 0 | 0 | |
cnv_GR | 0.041 | 0.000 | 0.041 | |
cnv_TTstatus | 0.002 | 0.007 | 0.009 | |
cnv_netPass | 0.005 | 0.000 | 0.004 | |
cnv_netScores | 0.006 | 0.004 | 0.009 | |
cnv_patientNetCount | 0.110 | 0.028 | 0.138 | |
cnv_pheno | 0.009 | 0.000 | 0.010 | |
compareShortestPath | 0.104 | 0.000 | 0.104 | |
compileFeatureScores | 0.009 | 0.000 | 0.009 | |
compileFeatures | 6.598 | 0.496 | 21.595 | |
confmat | 0.002 | 0.000 | 0.002 | |
confusionMatrix | 0.107 | 0.000 | 0.107 | |
convertToMAE | 0.140 | 0.016 | 0.156 | |
countIntType | 0.002 | 0.000 | 0.002 | |
countIntType_batch | 0.014 | 0.021 | 9.973 | |
countPatientsInNet | 0.004 | 0.000 | 0.004 | |
createPSN_MultiData | 20.534 | 1.107 | 33.048 | |
dataList2List | 0.376 | 0.035 | 0.412 | |
enrichLabelNets | 2.085 | 0.207 | 57.874 | |
featScores | 0.023 | 0.005 | 0.027 | |
fetchPathwayDefinitions | 0.371 | 0.056 | 0.685 | |
genes | 0.003 | 0.000 | 0.003 | |
getEMapInput | 0.773 | 0.112 | 0.918 | |
getEMapInput_many | 0.757 | 0.064 | 0.852 | |
getEnr | 0.772 | 0.044 | 10.612 | |
getFeatureScores | 0.015 | 0.000 | 0.015 | |
getFileSep | 0 | 0 | 0 | |
getGMjar_path | 0.138 | 0.022 | 0.141 | |
getNetConsensus | 0.013 | 0.000 | 0.013 | |
getOR | 0.004 | 0.000 | 0.003 | |
getPatientPredictions | 1.822 | 0.120 | 1.943 | |
getPatientRankings | 0.087 | 0.012 | 0.099 | |
getRegionOL | 0.327 | 0.027 | 0.355 | |
getResults | 0.134 | 0.004 | 0.138 | |
getSimilarity | 0.196 | 0.003 | 0.200 | |
makePSN_NamedMatrix | 0.082 | 0.001 | 9.066 | |
makePSN_RangeSets | 0.014 | 0.000 | 0.014 | |
makeQueries | 0.007 | 0.000 | 0.008 | |
makeSymmetric | 0.001 | 0.000 | 0.001 | |
mapNamedRangesToSets | 0.032 | 0.000 | 0.032 | |
modelres | 0.002 | 0.000 | 0.002 | |
normDiff | 0.001 | 0.000 | 0.001 | |
npheno | 0.002 | 0.000 | 0.002 | |
pathwayList | 0.001 | 0.001 | 0.003 | |
pathway_GR | 0.061 | 0.001 | 0.063 | |
perfCalc | 0.002 | 0.001 | 0.002 | |
pheno | 0.008 | 0.000 | 0.008 | |
pheno_full | 0.001 | 0.000 | 0.002 | |
plotEmap | 0.812 | 0.035 | 1.014 | |
plotPerf | 1.226 | 0.004 | 1.230 | |
plotPerf_multi | 0.037 | 0.000 | 0.037 | |
predRes | 0.003 | 0.000 | 0.003 | |
predictPatientLabels | 0.006 | 0.000 | 0.006 | |
pruneNets | 0.005 | 0.004 | 0.009 | |
randAlphanumString | 0.001 | 0.000 | 0.001 | |
readPathways | 0.747 | 0.021 | 0.800 | |
runFeatureSelection | 7.609 | 0.412 | 4.494 | |
runQuery | 2.893 | 0.198 | 4.052 | |
setupFeatureDB | 0.063 | 0.000 | 0.064 | |
silh | 0.003 | 0.000 | 0.003 | |
sim.eucscale | 0.268 | 0.008 | 0.276 | |
sim.pearscale | 0.559 | 0.020 | 0.579 | |
simpleCap | 0.000 | 0.000 | 0.001 | |
smoothMutations_LabelProp | 7.199 | 0.568 | 32.506 | |
sparsify2 | 1.217 | 0.408 | 1.625 | |
sparsify3 | 2.289 | 0.304 | 2.593 | |
splitTestTrain | 0.016 | 0.004 | 0.020 | |
splitTestTrain_resampling | 0.006 | 0.000 | 0.006 | |
tSNEPlotter | 0.844 | 0.016 | 0.860 | |
thresholdSmoothedMutations | 3.574 | 0.125 | 26.045 | |
toymodel | 0.796 | 0.440 | 1.237 | |
updateNets | 0.003 | 0.004 | 0.007 | |
writeNetsSIF | 0.006 | 0.000 | 0.006 | |
writeQueryBatchFile | 0.003 | 0.000 | 0.003 | |
writeQueryFile | 0.006 | 0.000 | 0.006 | |
xpr | 0.036 | 0.008 | 0.044 | |