Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-24 11:38 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4284 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
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 1384/2248 | 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 | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 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: 2024-07-24 01:55:06 -0400 (Wed, 24 Jul 2024) |
EndedAt: 2024-07-24 02:31:04 -0400 (Wed, 24 Jul 2024) |
EllapsedTime: 2157.6 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 4.4.1 (2024-06-14) * 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 21.303 0.624 24.297 createPSN_MultiData 19.651 1.272 31.939 RR_featureTally 8.535 0.424 8.959 runFeatureSelection 8.017 0.447 4.475 compileFeatures 6.545 0.441 22.207 smoothMutations_LabelProp 6.052 0.408 31.286 thresholdSmoothedMutations 3.897 0.388 27.344 enrichLabelNets 1.900 0.282 64.947 getEnr 0.853 0.208 10.536 makePSN_NamedMatrix 0.072 0.003 9.000 countIntType_batch 0.019 0.000 9.626 * 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 4.4.1 (2024-06-14) -- "Race for Your Life" 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 69.599 4.880 254.555
netDx.Rcheck/netDx-Ex.timings
name | user | system | elapsed | |
MB.pheno | 0.006 | 0.000 | 0.007 | |
RR_featureTally | 8.535 | 0.424 | 8.959 | |
avgNormDiff | 0.040 | 0.004 | 0.045 | |
buildPredictor | 21.303 | 0.624 | 24.297 | |
buildPredictor_sparseGenetic | 0.613 | 0.008 | 1.351 | |
callFeatSel | 0.071 | 0.000 | 0.071 | |
callOverallSelectedFeatures | 0.077 | 0.000 | 0.077 | |
cleanPathwayName | 0.001 | 0.000 | 0.000 | |
cnv_GR | 0.032 | 0.000 | 0.032 | |
cnv_TTstatus | 0.005 | 0.004 | 0.009 | |
cnv_netPass | 0.004 | 0.000 | 0.004 | |
cnv_netScores | 0.000 | 0.008 | 0.008 | |
cnv_patientNetCount | 0.106 | 0.024 | 0.130 | |
cnv_pheno | 0.009 | 0.000 | 0.009 | |
compareShortestPath | 0.029 | 0.000 | 0.028 | |
compileFeatureScores | 0.007 | 0.000 | 0.007 | |
compileFeatures | 6.545 | 0.441 | 22.207 | |
confmat | 0.003 | 0.000 | 0.002 | |
confusionMatrix | 0.108 | 0.009 | 0.115 | |
convertToMAE | 0.148 | 0.000 | 0.148 | |
countIntType | 0.001 | 0.000 | 0.002 | |
countIntType_batch | 0.019 | 0.000 | 9.626 | |
countPatientsInNet | 0.002 | 0.000 | 0.002 | |
createPSN_MultiData | 19.651 | 1.272 | 31.939 | |
dataList2List | 0.330 | 0.004 | 0.334 | |
enrichLabelNets | 1.900 | 0.282 | 64.947 | |
featScores | 0.050 | 0.004 | 0.054 | |
fetchPathwayDefinitions | 0.365 | 0.016 | 0.799 | |
genes | 0.002 | 0.000 | 0.002 | |
getEMapInput | 0.743 | 0.044 | 0.864 | |
getEMapInput_many | 0.745 | 0.072 | 0.893 | |
getEnr | 0.853 | 0.208 | 10.536 | |
getFeatureScores | 0.018 | 0.000 | 0.018 | |
getFileSep | 0 | 0 | 0 | |
getGMjar_path | 0.161 | 0.033 | 0.176 | |
getNetConsensus | 0.011 | 0.000 | 0.011 | |
getOR | 0.003 | 0.000 | 0.003 | |
getPatientPredictions | 1.708 | 0.084 | 1.792 | |
getPatientRankings | 0.072 | 0.028 | 0.100 | |
getRegionOL | 0.296 | 0.020 | 0.316 | |
getResults | 0.127 | 0.004 | 0.131 | |
getSimilarity | 0.197 | 0.000 | 0.198 | |
makePSN_NamedMatrix | 0.072 | 0.003 | 9.000 | |
makePSN_RangeSets | 0.014 | 0.001 | 0.014 | |
makeQueries | 0.007 | 0.000 | 0.007 | |
makeSymmetric | 0.001 | 0.000 | 0.001 | |
mapNamedRangesToSets | 0.033 | 0.000 | 0.032 | |
modelres | 0.002 | 0.000 | 0.002 | |
normDiff | 0.000 | 0.001 | 0.001 | |
npheno | 0.000 | 0.002 | 0.002 | |
pathwayList | 0.003 | 0.001 | 0.003 | |
pathway_GR | 0.059 | 0.007 | 0.067 | |
perfCalc | 0.002 | 0.001 | 0.003 | |
pheno | 0.009 | 0.000 | 0.009 | |
pheno_full | 0.002 | 0.000 | 0.002 | |
plotEmap | 0.726 | 0.088 | 1.209 | |
plotPerf | 2.063 | 0.164 | 2.227 | |
plotPerf_multi | 0.033 | 0.000 | 0.032 | |
predRes | 0.003 | 0.000 | 0.002 | |
predictPatientLabels | 0.006 | 0.000 | 0.005 | |
pruneNets | 0.008 | 0.000 | 0.008 | |
randAlphanumString | 0.001 | 0.000 | 0.000 | |
readPathways | 0.654 | 0.040 | 0.769 | |
runFeatureSelection | 8.017 | 0.447 | 4.475 | |
runQuery | 2.865 | 0.205 | 4.074 | |
setupFeatureDB | 0.094 | 0.000 | 0.104 | |
silh | 0.003 | 0.000 | 0.003 | |
sim.eucscale | 1.060 | 0.104 | 1.164 | |
sim.pearscale | 0.558 | 0.008 | 0.566 | |
simpleCap | 0 | 0 | 0 | |
smoothMutations_LabelProp | 6.052 | 0.408 | 31.286 | |
sparsify2 | 1.884 | 0.400 | 2.283 | |
sparsify3 | 1.915 | 0.292 | 2.206 | |
splitTestTrain | 0.016 | 0.008 | 0.024 | |
splitTestTrain_resampling | 0.006 | 0.000 | 0.006 | |
tSNEPlotter | 0.859 | 0.132 | 0.991 | |
thresholdSmoothedMutations | 3.897 | 0.388 | 27.344 | |
toymodel | 0.881 | 0.432 | 1.313 | |
updateNets | 0.003 | 0.004 | 0.007 | |
writeNetsSIF | 0.007 | 0.000 | 0.007 | |
writeQueryBatchFile | 0.003 | 0.000 | 0.003 | |
writeQueryFile | 0.007 | 0.000 | 0.006 | |
xpr | 0.041 | 0.004 | 0.045 | |