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This page was generated on 2021-11-24 15:05:08 -0500 (Wed, 24 Nov 2021).

CHECK results for netDx on nebbiolo2

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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:netDx.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings netDx_1.6.0.tar.gz
StartedAt: 2021-11-23 10:12:16 -0500 (Tue, 23 Nov 2021)
EndedAt: 2021-11-23 10:25:37 -0500 (Tue, 23 Nov 2021)
EllapsedTime: 800.5 seconds
RetCode: 0
Status:   OK  
CheckDir: netDx.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:netDx.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings netDx_1.6.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/netDx.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (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  7.4Mb
  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
createPSN_MultiData        32.989  0.765  43.247
buildPredictor             32.153  0.952  36.343
RR_featureTally             8.033  0.507   8.542
runFeatureSelection         7.593  0.551   4.797
compileFeatures             6.334  0.508  17.884
smoothMutations_LabelProp   6.178  0.146  28.919
thresholdSmoothedMutations  4.140  0.136  26.651
enrichLabelNets             1.638  0.022  46.818
getEnr                      0.929  0.056   8.443
makePSN_NamedMatrix         0.089  0.000   7.643
countIntType_batch          0.026  0.002   7.826
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/netDx.Rcheck/00check.log’
for details.



Installation output

netDx.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL netDx
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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)

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-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 ]
> 
> proc.time()
   user  system elapsed 
111.161   7.650 347.054 

Example timings

netDx.Rcheck/netDx-Ex.timings

nameusersystemelapsed
MB.pheno0.0070.0000.007
RR_featureTally8.0330.5078.542
avgNormDiff0.0440.0000.044
buildPredictor32.153 0.95236.343
buildPredictor_sparseGenetic1.0390.0202.566
callFeatSel0.1000.0160.116
callOverallSelectedFeatures0.0730.0000.073
cleanPathwayName0.0010.0000.000
cnv_GR0.0340.0000.034
cnv_TTstatus0.0050.0040.009
cnv_netPass0.0030.0000.003
cnv_netScores0.0010.0070.008
cnv_patientNetCount0.0970.0320.130
cnv_pheno0.0070.0000.008
compareShortestPath0.0160.0000.016
compileFeatureScores0.0060.0000.007
compileFeatures 6.334 0.50817.884
confmat0.0030.0010.004
confusionMatrix0.1260.0130.138
convertToMAE0.1680.0000.168
countIntType0.0010.0000.001
countIntType_batch0.0260.0027.826
countPatientsInNet0.0040.0000.004
createPSN_MultiData32.989 0.76543.247
dataList2List0.4110.0200.430
enrichLabelNets 1.638 0.02246.818
featScores0.0330.0120.045
fetchPathwayDefinitions1.1740.0321.492
genes0.0030.0000.002
getEMapInput1.0340.0201.092
getEMapInput_many0.9990.0201.056
getEnr0.9290.0568.443
getFeatureScores0.0160.0030.019
getFileSep000
getGMjar_path0.4300.0450.445
getNetConsensus0.0120.0000.012
getOR0.0020.0000.003
getPatientPredictions1.3950.0201.416
getPatientRankings0.0550.0000.055
getRegionOL0.4020.0000.402
getResults0.1290.0040.133
getSimilarity0.1980.0000.199
makePSN_NamedMatrix0.0890.0007.643
makePSN_RangeSets0.0140.0000.014
makeQueries0.0050.0000.005
makeSymmetric0.0010.0000.001
mapNamedRangesToSets0.0390.0000.039
modelres0.0020.0000.002
normDiff000
npheno0.0010.0000.001
pathwayList0.0010.0010.002
pathway_GR0.0820.0020.084
perfCalc0.0010.0000.001
pheno0.0070.0000.006
pheno_full0.0020.0000.002
plotEmap1.0430.0041.160
plotPerf1.2220.0231.243
plotPerf_multi0.0320.0000.032
predRes0.0030.0000.003
predictPatientLabels0.0060.0000.006
pruneNets0.0080.0000.008
randAlphanumString000
readPathways0.9730.0361.047
runFeatureSelection7.5930.5514.797
runQuery3.3300.2964.423
setupFeatureDB0.0880.0000.089
silh0.0000.0040.004
sim.eucscale0.3080.0040.311
sim.pearscale0.3700.0280.399
simpleCap0.0010.0000.001
smoothMutations_LabelProp 6.178 0.14628.919
sparsify20.7930.0160.808
sparsify31.7130.0601.772
splitTestTrain0.0210.0000.020
splitTestTrain_resampling0.0040.0000.003
tSNEPlotter0.6880.0240.712
thresholdSmoothedMutations 4.140 0.13626.651
toymodel0.8850.4481.333
updateNets0.0080.0000.008
writeNetsSIF0.0060.0000.006
writeQueryBatchFile0.0030.0000.003
writeQueryFile0.0040.0000.004
xpr0.0350.0080.043