| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:46 -0000 (Wed, 01 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
| 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 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1333/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| netDx 1.11.0 (landing page) Shraddha Pai
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | TIMEOUT | |||||||||
| Package: netDx |
| Version: 1.11.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:netDx.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings netDx_1.11.0.tar.gz |
| StartedAt: 2023-02-28 09:48:22 -0000 (Tue, 28 Feb 2023) |
| EndedAt: 2023-02-28 10:28:22 -0000 (Tue, 28 Feb 2023) |
| EllapsedTime: 2400.3 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: netDx.Rcheck |
| Warnings: NA |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:netDx.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings netDx_1.11.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/netDx.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘netDx/DESCRIPTION’ ... OK
* this is package ‘netDx’ version ‘1.11.0’
* 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 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 ... OK
* 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 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 28.883 1.632 48.931
createPSN_MultiData 25.236 1.000 53.958
RR_featureTally 21.234 0.684 21.920
sim.pearscale 11.196 0.040 11.237
smoothMutations_LabelProp 10.195 0.516 46.527
getSimilarity 8.028 0.012 8.040
runFeatureSelection 7.023 0.531 5.064
getPatientPredictions 7.012 0.040 7.054
compileFeatures 5.996 0.574 27.012
plotPerf 5.942 0.136 6.078
sparsify2 5.714 0.280 5.994
thresholdSmoothedMutations 3.809 0.188 40.722
enrichLabelNets 1.804 0.670 68.347
getEnr 0.799 0.184 12.285
makePSN_NamedMatrix 0.079 0.028 11.221
countIntType_batch 0.024 0.001 11.184
* 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 ...
‘RawDataConversion.Rmd’ using ‘UTF-8’... OK
‘ThreeWayClassifier.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ...
netDx.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL netDx ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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")
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 2 | SKIP 0 | PASS 39 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 39 ]
>
> proc.time()
user system elapsed
78.600 5.566 313.005
netDx.Rcheck/netDx-Ex.timings
| name | user | system | elapsed | |
| MB.pheno | 0.006 | 0.000 | 0.006 | |
| RR_featureTally | 21.234 | 0.684 | 21.920 | |
| avgNormDiff | 0.047 | 0.003 | 0.051 | |
| buildPredictor | 28.883 | 1.632 | 48.931 | |
| buildPredictor_sparseGenetic | 0.674 | 0.016 | 2.021 | |
| callFeatSel | 0.13 | 0.00 | 0.13 | |
| callOverallSelectedFeatures | 0.123 | 0.004 | 0.127 | |
| cleanPathwayName | 0.000 | 0.001 | 0.000 | |
| cnv_GR | 0.035 | 0.003 | 0.038 | |
| cnv_TTstatus | 0.003 | 0.012 | 0.014 | |
| cnv_netPass | 0.004 | 0.000 | 0.004 | |
| cnv_netScores | 0.009 | 0.004 | 0.013 | |
| cnv_patientNetCount | 0.212 | 0.048 | 0.260 | |
| cnv_pheno | 0.013 | 0.000 | 0.013 | |
| compareShortestPath | 0.027 | 0.000 | 0.027 | |
| compileFeatureScores | 0.009 | 0.001 | 0.011 | |
| compileFeatures | 5.996 | 0.574 | 27.012 | |
| confmat | 0.003 | 0.001 | 0.003 | |
| confusionMatrix | 0.117 | 0.000 | 0.117 | |
| convertToMAE | 0.162 | 0.007 | 0.169 | |
| countIntType | 0.001 | 0.001 | 0.002 | |
| countIntType_batch | 0.024 | 0.001 | 11.184 | |
| countPatientsInNet | 0.003 | 0.000 | 0.003 | |
| createPSN_MultiData | 25.236 | 1.000 | 53.958 | |
| dataList2List | 0.388 | 0.036 | 0.424 | |
| enrichLabelNets | 1.804 | 0.670 | 68.347 | |
| featScores | 0.043 | 0.004 | 0.046 | |
| fetchPathwayDefinitions | 0.449 | 0.043 | 2.318 | |
| genes | 0.004 | 0.000 | 0.004 | |
| getEMapInput | 1.031 | 0.176 | 1.433 | |
| getEMapInput_many | 1.088 | 0.264 | 1.572 | |
| getEnr | 0.799 | 0.184 | 12.285 | |
| getFeatureScores | 0.016 | 0.000 | 0.016 | |
| getFileSep | 0 | 0 | 0 | |
| getGMjar_path | 0.219 | 0.012 | 0.197 | |
| getNetConsensus | 0.017 | 0.000 | 0.017 | |
| getOR | 0.004 | 0.000 | 0.004 | |
| getPatientPredictions | 7.012 | 0.040 | 7.054 | |
| getPatientRankings | 0.082 | 0.004 | 0.088 | |
| getRegionOL | 0.429 | 0.024 | 0.453 | |
| getResults | 0.158 | 0.004 | 0.162 | |
| getSimilarity | 8.028 | 0.012 | 8.040 | |
| makePSN_NamedMatrix | 0.079 | 0.028 | 11.221 | |
| makePSN_RangeSets | 0.015 | 0.000 | 0.015 | |
| makeQueries | 0.011 | 0.000 | 0.011 | |
| makeSymmetric | 0.000 | 0.001 | 0.001 | |
| mapNamedRangesToSets | 0.047 | 0.005 | 0.052 | |
| modelres | 0.004 | 0.000 | 0.004 | |
| normDiff | 0.000 | 0.002 | 0.002 | |
| npheno | 0.001 | 0.002 | 0.003 | |
| pathwayList | 0.002 | 0.002 | 0.005 | |
| pathway_GR | 0.094 | 0.009 | 0.103 | |
| perfCalc | 0.001 | 0.001 | 0.002 | |
| pheno | 0.009 | 0.002 | 0.011 | |
| pheno_full | 0.003 | 0.000 | 0.003 | |
| plotEmap | 1.090 | 0.260 | 2.015 | |
| plotPerf | 5.942 | 0.136 | 6.078 | |
| plotPerf_multi | 0.043 | 0.008 | 0.051 | |
| predRes | 0.004 | 0.000 | 0.004 | |
| predictPatientLabels | 0.011 | 0.000 | 0.010 | |
| pruneNets | 0.012 | 0.000 | 0.012 | |
| randAlphanumString | 0 | 0 | 0 | |
| readPathways | 1.053 | 0.132 | 1.873 | |
| runFeatureSelection | 7.023 | 0.531 | 5.064 | |
| runQuery | 3.032 | 0.317 | 4.580 | |
| setupFeatureDB | 0.068 | 0.012 | 0.081 | |
| silh | 0.003 | 0.004 | 0.007 | |
| sim.eucscale | 0.590 | 0.032 | 0.623 | |
| sim.pearscale | 11.196 | 0.040 | 11.237 | |
| simpleCap | 0 | 0 | 0 | |
| smoothMutations_LabelProp | 10.195 | 0.516 | 46.527 | |
| sparsify2 | 5.714 | 0.280 | 5.994 | |
| sparsify3 | 1.084 | 0.012 | 1.096 | |
| splitTestTrain | 0.025 | 0.000 | 0.026 | |
| splitTestTrain_resampling | 0.007 | 0.000 | 0.007 | |
| tSNEPlotter | 1.419 | 0.000 | 1.418 | |
| thresholdSmoothedMutations | 3.809 | 0.188 | 40.722 | |
| toymodel | 1.264 | 1.004 | 2.268 | |
| updateNets | 0.005 | 0.004 | 0.009 | |
| writeNetsSIF | 0.009 | 0.000 | 0.009 | |
| writeQueryBatchFile | 0.004 | 0.000 | 0.004 | |
| writeQueryFile | 0.007 | 0.000 | 0.007 | |
| xpr | 0.032 | 0.015 | 0.047 | |