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This page was generated on 2021-11-24 15:06:12 -0500 (Wed, 24 Nov 2021).

CHECK results for netDx on machv2

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? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1284/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netDx 1.6.0  (landing page)
Shraddha Pai
Snapshot Date: 2021-11-23 04:15:06 -0500 (Tue, 23 Nov 2021)
git_url: https://git.bioconductor.org/packages/netDx
git_branch: RELEASE_3_14
git_last_commit: 85f6f3b
git_last_commit_date: 2021-10-26 12:57:05 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64... NOT SUPPORTED ...
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: netDx
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:netDx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings netDx_1.6.0.tar.gz
StartedAt: 2021-11-23 19:23:51 -0500 (Tue, 23 Nov 2021)
EndedAt: 2021-11-23 19:41:12 -0500 (Tue, 23 Nov 2021)
EllapsedTime: 1041.0 seconds
RetCode: 0
Status:   OK  
CheckDir: netDx.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:netDx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings netDx_1.6.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/netDx.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netDx/DESCRIPTION’ ... OK
* this is package ‘netDx’ version ‘1.6.0’
* 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  7.3Mb
  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 ... 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             50.923  1.492  56.491
createPSN_MultiData        45.408  0.746  61.980
smoothMutations_LabelProp  11.533  0.538  43.364
runFeatureSelection         9.690  0.938   6.399
RR_featureTally             9.068  1.176  10.259
compileFeatures             7.175  0.680  29.254
getPatientPredictions       6.622  0.012   6.640
plotPerf                    6.160  0.014   6.178
thresholdSmoothedMutations  5.526  0.243  37.274
runQuery                    4.623  0.568   5.821
toymodel                    2.252  2.929   5.315
enrichLabelNets             1.518  0.062  72.190
getEnr                      0.646  0.022  13.057
makePSN_NamedMatrix         0.145  0.008  11.981
countIntType_batch          0.028  0.006  12.135
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/netDx.Rcheck/00check.log’
for details.



Installation output

netDx.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL netDx
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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)

Tests output

netDx.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 ]
> 
> proc.time()
   user  system elapsed 
110.445   6.424 362.322 

Example timings

netDx.Rcheck/netDx-Ex.timings

nameusersystemelapsed
MB.pheno0.0120.0030.015
RR_featureTally 9.068 1.17610.259
avgNormDiff0.0830.0030.085
buildPredictor50.923 1.49256.491
buildPredictor_sparseGenetic1.7400.0682.256
callFeatSel0.1950.0020.198
callOverallSelectedFeatures0.1960.0290.225
cleanPathwayName0.0000.0010.001
cnv_GR0.0620.0020.064
cnv_TTstatus0.0140.0430.058
cnv_netPass0.0050.0020.007
cnv_netScores0.0100.0300.079
cnv_patientNetCount0.2330.1550.388
cnv_pheno0.0140.0030.016
compareShortestPath0.0300.0040.033
compileFeatureScores0.0110.0020.012
compileFeatures 7.175 0.68029.254
confmat0.0020.0010.003
confusionMatrix0.1070.0120.182
convertToMAE0.2400.0060.247
countIntType0.0010.0010.018
countIntType_batch 0.028 0.00612.135
countPatientsInNet0.0030.0020.005
createPSN_MultiData45.408 0.74661.980
dataList2List0.7050.0180.724
enrichLabelNets 1.518 0.06272.190
featScores0.0510.0660.116
fetchPathwayDefinitions1.6950.0241.989
genes0.0050.0020.006
getEMapInput1.8060.0301.911
getEMapInput_many1.6860.0551.795
getEnr 0.646 0.02213.057
getFeatureScores0.0270.0020.029
getFileSep0.0010.0000.001
getGMjar_path0.6620.0570.732
getNetConsensus0.0250.0010.026
getOR0.0030.0020.006
getPatientPredictions6.6220.0126.640
getPatientRankings0.0990.0020.102
getRegionOL0.7520.0050.757
getResults0.2290.0040.233
getSimilarity0.2420.0020.245
makePSN_NamedMatrix 0.145 0.00811.981
makePSN_RangeSets0.0190.0020.021
makeQueries0.0100.0020.012
makeSymmetric0.0020.0000.002
mapNamedRangesToSets0.0900.0020.093
modelres0.0030.0020.005
normDiff0.0010.0010.002
npheno0.0040.0020.005
pathwayList0.0030.0080.011
pathway_GR0.2100.0100.221
perfCalc0.0020.0010.003
pheno0.0130.0020.015
pheno_full0.0040.0020.006
plotEmap1.7370.0261.918
plotPerf6.1600.0146.178
plotPerf_multi0.0490.0020.052
predRes0.0040.0020.007
predictPatientLabels0.0090.0010.010
pruneNets0.0140.0040.018
randAlphanumString0.0000.0010.001
readPathways1.9090.0822.174
runFeatureSelection9.6900.9386.399
runQuery4.6230.5685.821
setupFeatureDB0.1060.0080.147
silh0.0040.0030.008
sim.eucscale0.5490.0060.556
sim.pearscale1.0110.0181.030
simpleCap0.0000.0000.001
smoothMutations_LabelProp11.533 0.53843.364
sparsify20.5310.0590.592
sparsify30.4070.0160.423
splitTestTrain0.0300.0010.031
splitTestTrain_resampling0.0060.0020.008
tSNEPlotter1.5350.0301.569
thresholdSmoothedMutations 5.526 0.24337.274
toymodel2.2522.9295.315
updateNets0.0070.0010.008
writeNetsSIF0.0070.0010.009
writeQueryBatchFile0.0040.0010.005
writeQueryFile0.0060.0020.008
xpr0.0640.0270.092