Back to Multiple platform build/check report for BioC 3.13
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2021-10-13 15:06:00 -0400 (Wed, 13 Oct 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 1263/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netDx 1.4.3  (landing page)
Shraddha Pai
Snapshot Date: 2021-10-12 04:50:13 -0400 (Tue, 12 Oct 2021)
git_url: https://git.bioconductor.org/packages/netDx
git_branch: RELEASE_3_13
git_last_commit: 4f053f2
git_last_commit_date: 2021-08-18 18:41:08 -0400 (Wed, 18 Aug 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64... NOT SUPPORTED ...
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: netDx
Version: 1.4.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:netDx.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings netDx_1.4.3.tar.gz
StartedAt: 2021-10-12 21:35:54 -0400 (Tue, 12 Oct 2021)
EndedAt: 2021-10-12 21:52:40 -0400 (Tue, 12 Oct 2021)
EllapsedTime: 1006.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: netDx.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:netDx.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings netDx_1.4.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/netDx.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.4.3’
* 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 ... 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 ... NOTE
confusionMatrix: no visible global function definition for
  ‘color2D.matplot’
Undefined global functions or variables:
  color2D.matplot
* checking Rd files ... NOTE
prepare_Rd: makeInputForEnrichmentMap.Rd:36-38: Dropping empty section \value
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘callOverallSelectedFeatures’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'makeInputForEnrichmentMap':
  ‘featScores’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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               44.729  1.370  50.299
createPSN_MultiData          40.854  0.762  64.953
buildPredictor_sparseGenetic 21.702  0.816  22.588
runFeatureSelection           9.136  0.849   6.161
compileFeatures               8.130  0.877  50.340
RR_featureTally               7.867  0.781   8.661
getPatientPredictions         5.710  0.010   5.725
plotPerf                      5.347  0.021   5.380
runQuery                      4.338  0.573   5.503
thresholdSmoothedMutations    4.417  0.210  33.235
smoothMutations_LabelProp     3.329  0.143  32.429
enrichLabelNets               2.091  0.070 133.321
getEnr                        1.071  0.019  23.126
makePSN_NamedMatrix           0.107  0.009  21.464
countIntType_batch            0.029  0.005  21.518
* 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: 3 WARNINGs, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/netDx.Rcheck/00check.log’
for details.



Installation output

netDx.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/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 4.1.1 (2021-08-10) -- "Kick Things"
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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
 26.860   1.769  93.983 

Example timings

netDx.Rcheck/netDx-Ex.timings

nameusersystemelapsed
MB.pheno0.0090.0020.011
RR_featureTally7.8670.7818.661
avgNormDiff0.0380.0010.040
buildPredictor44.729 1.37050.299
buildPredictor_sparseGenetic21.702 0.81622.588
callFeatSel0.1910.0020.193
cleanPathwayName0.0000.0000.001
cnv_GR0.0460.0020.049
cnv_TTstatus0.0110.0290.040
cnv_netPass0.0030.0010.005
cnv_netScores0.0090.0270.037
cnv_patientNetCount0.1600.1410.301
cnv_pheno0.0070.0020.008
compareShortestPath0.0250.0040.028
compileFeatureScores0.0090.0010.011
compileFeatures 8.130 0.87750.340
confmat0.0040.0030.007
countIntType0.0020.0010.003
countIntType_batch 0.029 0.00521.518
countPatientsInNet0.0040.0020.006
createPSN_MultiData40.854 0.76264.953
enrichLabelNets 2.091 0.070133.321
featScores0.0630.0680.130
fetchPathwayDefinitions1.5640.0291.811
genes0.0030.0020.005
getEMapInput1.4900.0341.584
getEMapInput_many1.5800.0441.681
getEnr 1.071 0.01923.126
getFeatureScores0.0200.0020.022
getGMjar_path0.6660.0550.699
getNetConsensus0.0210.0000.022
getOR0.0040.0020.006
getPatientPredictions5.7100.0105.725
getPatientRankings0.1210.0030.124
getRegionOL0.4160.0030.420
getSimilarity0.1970.0020.198
makePSN_NamedMatrix 0.107 0.00921.464
makePSN_RangeSets0.0100.0020.013
makeQueries0.0060.0010.008
makeSymmetric0.0010.0000.002
mapNamedRangesToSets0.0440.0010.046
normDiff0.0010.0000.002
npheno0.0020.0010.003
pathwayList0.0030.0120.016
pathway_GR0.1760.0050.182
perfCalc0.0030.0010.004
pheno0.0130.0020.015
pheno_full0.0020.0010.004
plotEmap1.5600.0281.690
plotPerf5.3470.0215.380
plotPerf_multi0.0470.0020.049
predRes0.0030.0020.004
predictPatientLabels0.0100.0020.012
pruneNets0.0100.0030.012
readPathways1.4340.0961.638
runFeatureSelection9.1360.8496.161
runQuery4.3380.5735.503
setupFeatureDB0.0560.0070.063
silh0.0050.0040.008
sim.eucscale0.5360.0060.541
sim.pearscale0.8510.0380.890
simpleCap0.0010.0000.000
smoothMutations_LabelProp 3.329 0.14332.429
sparsify20.3440.0680.412
sparsify30.4130.0300.443
splitTestTrain0.0140.0020.016
splitTestTrain_resampling0.0050.0020.006
thresholdSmoothedMutations 4.417 0.21033.235
updateNets0.0100.0020.012
writeNetsSIF0.0120.0030.015
writeQueryBatchFile0.0040.0030.007
writeQueryFile0.0040.0020.005
xpr0.0240.0330.058