| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:12 -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 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 1342/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| netDx 1.10.0 (landing page) Shraddha Pai
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| Package: netDx |
| Version: 1.10.0 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:netDx.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings netDx_1.10.0.tar.gz |
| StartedAt: 2023-04-10 22:20:28 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 23:00:28 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 2400.1 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: netDx.Rcheck |
| Warnings: NA |
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### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:netDx.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings netDx_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/netDx.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘netDx/DESCRIPTION’ ... OK
* this is package ‘netDx’ version ‘1.10.0’
* 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 loading without being on the library search path ... 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 22.432 1.747 26.282
createPSN_MultiData 20.377 1.531 31.521
RR_featureTally 8.260 0.596 8.857
runFeatureSelection 8.092 0.514 4.672
compileFeatures 7.052 0.678 21.889
smoothMutations_LabelProp 7.083 0.396 28.967
thresholdSmoothedMutations 3.379 0.192 24.264
enrichLabelNets 2.022 0.192 58.553
getEnr 0.867 0.165 9.510
makePSN_NamedMatrix 0.081 0.002 9.088
countIntType_batch 0.022 0.013 9.917
* 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-3.16-bioc/R/bin/R CMD INSTALL netDx ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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
69.544 5.154 244.218
netDx.Rcheck/netDx-Ex.timings
| name | user | system | elapsed | |
| MB.pheno | 0.002 | 0.003 | 0.007 | |
| RR_featureTally | 8.260 | 0.596 | 8.857 | |
| avgNormDiff | 0.042 | 0.004 | 0.046 | |
| buildPredictor | 22.432 | 1.747 | 26.282 | |
| buildPredictor_sparseGenetic | 0.763 | 0.072 | 2.345 | |
| callFeatSel | 0.097 | 0.016 | 0.114 | |
| callOverallSelectedFeatures | 0.075 | 0.020 | 0.095 | |
| cleanPathwayName | 0 | 0 | 0 | |
| cnv_GR | 0.030 | 0.004 | 0.034 | |
| cnv_TTstatus | 0.005 | 0.004 | 0.009 | |
| cnv_netPass | 0.003 | 0.000 | 0.003 | |
| cnv_netScores | 0.001 | 0.007 | 0.009 | |
| cnv_patientNetCount | 0.097 | 0.044 | 0.142 | |
| cnv_pheno | 0.011 | 0.000 | 0.010 | |
| compareShortestPath | 0.073 | 0.028 | 0.101 | |
| compileFeatureScores | 0.003 | 0.004 | 0.007 | |
| compileFeatures | 7.052 | 0.678 | 21.889 | |
| confmat | 0.001 | 0.004 | 0.005 | |
| confusionMatrix | 0.091 | 0.008 | 0.099 | |
| convertToMAE | 0.136 | 0.004 | 0.140 | |
| countIntType | 0.002 | 0.000 | 0.001 | |
| countIntType_batch | 0.022 | 0.013 | 9.917 | |
| countPatientsInNet | 0.003 | 0.001 | 0.004 | |
| createPSN_MultiData | 20.377 | 1.531 | 31.521 | |
| dataList2List | 0.375 | 0.009 | 0.384 | |
| enrichLabelNets | 2.022 | 0.192 | 58.553 | |
| featScores | 0.036 | 0.012 | 0.048 | |
| fetchPathwayDefinitions | 0.321 | 0.008 | 0.594 | |
| genes | 0.003 | 0.000 | 0.002 | |
| getEMapInput | 0.718 | 0.048 | 0.808 | |
| getEMapInput_many | 0.744 | 0.057 | 0.842 | |
| getEnr | 0.867 | 0.165 | 9.510 | |
| getFeatureScores | 0.015 | 0.000 | 0.016 | |
| getFileSep | 0 | 0 | 0 | |
| getGMjar_path | 0.145 | 0.021 | 0.133 | |
| getNetConsensus | 0.013 | 0.004 | 0.016 | |
| getOR | 0.000 | 0.002 | 0.003 | |
| getPatientPredictions | 1.686 | 0.049 | 1.735 | |
| getPatientRankings | 0.075 | 0.008 | 0.083 | |
| getRegionOL | 0.3 | 0.0 | 0.3 | |
| getResults | 0.118 | 0.008 | 0.125 | |
| getSimilarity | 0.193 | 0.000 | 0.192 | |
| makePSN_NamedMatrix | 0.081 | 0.002 | 9.088 | |
| makePSN_RangeSets | 0.017 | 0.000 | 0.017 | |
| makeQueries | 0.008 | 0.000 | 0.007 | |
| makeSymmetric | 0.002 | 0.000 | 0.001 | |
| mapNamedRangesToSets | 0.034 | 0.000 | 0.033 | |
| modelres | 0.003 | 0.000 | 0.003 | |
| normDiff | 0.001 | 0.000 | 0.001 | |
| npheno | 0.002 | 0.000 | 0.002 | |
| pathwayList | 0.003 | 0.000 | 0.003 | |
| pathway_GR | 0.062 | 0.004 | 0.066 | |
| perfCalc | 0.002 | 0.000 | 0.002 | |
| pheno | 0.015 | 0.004 | 0.018 | |
| pheno_full | 0.000 | 0.003 | 0.003 | |
| plotEmap | 0.694 | 0.060 | 0.878 | |
| plotPerf | 1.30 | 0.06 | 1.36 | |
| plotPerf_multi | 0.036 | 0.012 | 0.048 | |
| predRes | 0.002 | 0.001 | 0.004 | |
| predictPatientLabels | 0.005 | 0.002 | 0.007 | |
| pruneNets | 0.009 | 0.000 | 0.009 | |
| randAlphanumString | 0.001 | 0.000 | 0.001 | |
| readPathways | 0.670 | 0.048 | 0.764 | |
| runFeatureSelection | 8.092 | 0.514 | 4.672 | |
| runQuery | 3.067 | 0.235 | 4.235 | |
| setupFeatureDB | 0.069 | 0.004 | 0.073 | |
| silh | 0.003 | 0.000 | 0.003 | |
| sim.eucscale | 0.303 | 0.052 | 0.354 | |
| sim.pearscale | 0.378 | 0.020 | 0.397 | |
| simpleCap | 0 | 0 | 0 | |
| smoothMutations_LabelProp | 7.083 | 0.396 | 28.967 | |
| sparsify2 | 0.933 | 0.088 | 1.021 | |
| sparsify3 | 1.097 | 0.000 | 1.097 | |
| splitTestTrain | 0.021 | 0.000 | 0.020 | |
| splitTestTrain_resampling | 0.005 | 0.000 | 0.005 | |
| tSNEPlotter | 0.911 | 0.020 | 0.930 | |
| thresholdSmoothedMutations | 3.379 | 0.192 | 24.264 | |
| toymodel | 0.794 | 0.516 | 1.309 | |
| updateNets | 0.002 | 0.003 | 0.005 | |
| writeNetsSIF | 0.005 | 0.000 | 0.005 | |
| writeQueryBatchFile | 0.003 | 0.000 | 0.002 | |
| writeQueryFile | 0.006 | 0.000 | 0.005 | |
| xpr | 0.034 | 0.008 | 0.042 | |