Shraddha Pai
| Snapshot Date: 2020-10-13 14:50:23 -0400 (Tue, 13 Oct 2020) |
| URL: https://git.bioconductor.org/packages/netDx |
| Branch: RELEASE_3_11 |
| Last Commit: e08c71c |
| Last Changed Date: 2020-10-12 17:37:46 -0400 (Mon, 12 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-14 11:57:11 -0400 (Wed, 14 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE netDx PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1186/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| netDx 1.0.4 Shraddha Pai
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped |
| Package: netDx |
| Version: 1.0.4 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:netDx.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings netDx_1.0.4.tar.gz |
| StartedAt: 2020-10-14 09:27:55 -0400 (Wed, 14 Oct 2020) |
| EndedAt: 2020-10-14 09:44:08 -0400 (Wed, 14 Oct 2020) |
| EllapsedTime: 973.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: netDx.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:netDx.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings netDx_1.0.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/netDx.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'netDx/DESCRIPTION' ... OK
* this is package 'netDx' version '1.0.4'
* 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 whether package 'netDx' can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.6Mb
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 ... 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 ... 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 30.50 1.59 53.01
createPSN_MultiData 25.49 0.89 43.83
buildPredictor_sparseGenetic 16.08 0.06 27.32
plotPerf 11.62 0.00 11.62
getPatientPredictions 11.09 0.01 11.32
RR_featureTally 8.42 2.52 10.94
thresholdSmoothedMutations 5.20 0.19 31.15
smoothMutations_LabelProp 4.42 0.22 35.42
enrichLabelNets 2.71 0.03 103.39
getEnr 1.14 0.00 15.94
compileFeatures 0.64 0.08 95.47
runFeatureSelection 0.52 0.03 6.58
makePSN_NamedMatrix 0.07 0.02 16.32
countIntType_batch 0.08 0.01 17.45
* 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: 1 WARNING, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/netDx.Rcheck/00check.log'
for details.
netDx.Rcheck/00install.out
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###
### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch netDx
###
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* installing to library 'C:/Users/biocbuild/bbs-3.11-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
converting help for package 'netDx'
finding HTML links ... done
MB.pheno html
RR_featureTally html
avgNormDiff html
buildPredictor html
buildPredictor_sparseGenetic html
callFeatSel html
cleanPathwayName html
cnv_GR html
cnv_TTstatus html
cnv_netPass html
cnv_netScores html
cnv_patientNetCount html
cnv_pheno html
compareShortestPath html
compileFeatureScores html
compileFeatures html
confmat html
convertProfileToNetworks html
countIntType html
countIntType_batch html
countPatientsInNet html
createPSN_MultiData html
dataList2List html
dot-get_cache html
enrichLabelNets html
featScores html
fetchPathwayDefinitions html
genes html
getCorrType html
getEMapInput html
getEMapInput_many html
getEnr html
getFeatureScores html
getFileSep html
getGMjar_path html
getNetConsensus html
getOR html
getPatientPredictions html
getPatientRankings html
getRegionOL html
getSimilarity html
makePSN_NamedMatrix html
makePSN_RangeSets html
makeQueries html
makeSymmetric html
mapNamedRangesToSets html
matrix_getIJ html
moveInteractionNets html
normDiff html
npheno html
pathwayList html
pathway_GR html
perfCalc html
pheno html
pheno_full html
plotEmap html
plotIntegratedPatientNetwork html
plotPerf html
plotPerf_multi html
plot_tSNE html
predRes html
predictPatientLabels html
pruneNet html
pruneNet_pctX html
pruneNets html
randAlphanumString html
readPathways html
runFeatureSelection html
runQuery html
setupFeatureDB html
silh html
sim.eucscale html
sim.pearscale html
simpleCap html
smoothMutations_LabelProp html
sparsify2 html
sparsify3 html
splitTestTrain html
splitTestTrain_resampling html
thresholdSmoothedMutations html
updateNets html
writeNetsSIF html
writeQueryBatchFile html
writeQueryFile html
writeWeightedNets html
xpr html
** 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)
Making 'packages.html' ... done
netDx.Rcheck/tests/testthat.Rout
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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)
>
> test_check("netDx")
== testthat results ===========================================================
[ OK: 15 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
19.03 0.84 80.89
netDx.Rcheck/netDx-Ex.timings
| name | user | system | elapsed | |
| MB.pheno | 0.02 | 0.00 | 0.02 | |
| RR_featureTally | 8.42 | 2.52 | 10.94 | |
| avgNormDiff | 0.01 | 0.00 | 0.02 | |
| buildPredictor | 30.50 | 1.59 | 53.01 | |
| buildPredictor_sparseGenetic | 16.08 | 0.06 | 27.32 | |
| callFeatSel | 0.09 | 0.00 | 0.09 | |
| cleanPathwayName | 0 | 0 | 0 | |
| cnv_GR | 0.03 | 0.00 | 0.03 | |
| cnv_TTstatus | 0.00 | 0.02 | 0.02 | |
| cnv_netPass | 0 | 0 | 0 | |
| cnv_netScores | 0.02 | 0.00 | 0.01 | |
| cnv_patientNetCount | 0.12 | 0.03 | 0.15 | |
| cnv_pheno | 0.02 | 0.00 | 0.02 | |
| compareShortestPath | 0.03 | 0.00 | 0.03 | |
| compileFeatureScores | 0.01 | 0.00 | 0.02 | |
| compileFeatures | 0.64 | 0.08 | 95.47 | |
| confmat | 0.00 | 0.02 | 0.01 | |
| countIntType | 0 | 0 | 0 | |
| countIntType_batch | 0.08 | 0.01 | 17.45 | |
| countPatientsInNet | 0 | 0 | 0 | |
| createPSN_MultiData | 25.49 | 0.89 | 43.83 | |
| enrichLabelNets | 2.71 | 0.03 | 103.39 | |
| featScores | 0.07 | 0.02 | 0.08 | |
| fetchPathwayDefinitions | 1.17 | 0.07 | 1.23 | |
| genes | 0 | 0 | 0 | |
| getEMapInput | 1.28 | 0.09 | 1.72 | |
| getEMapInput_many | 1.02 | 0.02 | 1.03 | |
| getEnr | 1.14 | 0.00 | 15.94 | |
| getFeatureScores | 0.03 | 0.00 | 0.03 | |
| getGMjar_path | 0.29 | 0.03 | 0.45 | |
| getNetConsensus | 0.02 | 0.00 | 0.01 | |
| getOR | 0 | 0 | 0 | |
| getPatientPredictions | 11.09 | 0.01 | 11.32 | |
| getPatientRankings | 0.11 | 0.00 | 0.11 | |
| getRegionOL | 0.51 | 0.00 | 0.51 | |
| getSimilarity | 0.18 | 0.00 | 0.17 | |
| makePSN_NamedMatrix | 0.07 | 0.02 | 16.32 | |
| makePSN_RangeSets | 0.02 | 0.00 | 0.01 | |
| makeQueries | 0.02 | 0.00 | 0.02 | |
| makeSymmetric | 0 | 0 | 0 | |
| mapNamedRangesToSets | 0.06 | 0.00 | 0.06 | |
| normDiff | 0 | 0 | 0 | |
| npheno | 0 | 0 | 0 | |
| pathwayList | 0.01 | 0.00 | 0.02 | |
| pathway_GR | 0.16 | 0.00 | 0.15 | |
| perfCalc | 0 | 0 | 0 | |
| pheno | 0.03 | 0.00 | 0.03 | |
| pheno_full | 0 | 0 | 0 | |
| plotEmap | 1.77 | 0.03 | 1.80 | |
| plotPerf | 11.62 | 0.00 | 11.62 | |
| plotPerf_multi | 0.05 | 0.00 | 0.05 | |
| predRes | 0 | 0 | 0 | |
| predictPatientLabels | 0.01 | 0.00 | 0.02 | |
| pruneNets | 0.02 | 0.00 | 0.01 | |
| readPathways | 1.03 | 0.02 | 1.05 | |
| runFeatureSelection | 0.52 | 0.03 | 6.58 | |
| runQuery | 0.37 | 0.03 | 4.79 | |
| setupFeatureDB | 0.11 | 0.00 | 0.11 | |
| silh | 0.00 | 0.01 | 0.02 | |
| sim.eucscale | 0.94 | 0.00 | 0.94 | |
| sim.pearscale | 0.83 | 0.00 | 0.83 | |
| simpleCap | 0 | 0 | 0 | |
| smoothMutations_LabelProp | 4.42 | 0.22 | 35.42 | |
| sparsify2 | 0.48 | 0.03 | 0.51 | |
| sparsify3 | 0.41 | 0.02 | 0.42 | |
| splitTestTrain | 0.02 | 0.00 | 0.02 | |
| splitTestTrain_resampling | 0.01 | 0.00 | 0.02 | |
| thresholdSmoothedMutations | 5.20 | 0.19 | 31.15 | |
| updateNets | 0 | 0 | 0 | |
| writeNetsSIF | 0.00 | 0.01 | 0.01 | |
| writeQueryBatchFile | 0.02 | 0.00 | 0.02 | |
| writeQueryFile | 0 | 0 | 0 | |
| xpr | 0.03 | 0.00 | 0.03 | |