Multiple platform build/check report for BioC 3.12 - CHECK report for netDx on merida1

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### Running command:
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###   /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_1.2.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/netDx.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.2.2’
* 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  7.2Mb
  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 ... WARNING
Undocumented code objects:
  ‘replacePattern’
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 ... 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               41.494  1.279  51.292
createPSN_MultiData          36.245  0.511  56.192
buildPredictor_sparseGenetic 22.269  0.412  22.770
runFeatureSelection           8.805  0.863   6.029
RR_featureTally               8.247  0.695   8.953
compileFeatures               7.703  0.823  43.113
getPatientPredictions         5.750  0.028   5.795
plotPerf                      5.466  0.042   5.526
runQuery                      4.240  0.581   5.559
thresholdSmoothedMutations    3.263  0.197  27.107
smoothMutations_LabelProp     3.004  0.156  27.196
enrichLabelNets               1.859  0.060 111.343
getEnr                        0.827  0.018  18.705
makePSN_NamedMatrix           0.087  0.007  19.804
countIntType_batch            0.031  0.007  18.852
* 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: 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/netDx.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL netDx
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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)
> 
> test_check("netDx")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
 23.329   1.460  77.067

Example timings

name	user	system	elapsed
MB.pheno	0.009	0.002	0.011
RR_featureTally	8.247	0.695	8.953
avgNormDiff	0.030	0.003	0.033
buildPredictor	41.494	1.279	51.292
buildPredictor_sparseGenetic	22.269	0.412	22.770
callFeatSel	0.164	0.002	0.167
cleanPathwayName	0.001	0.000	0.001
cnv_GR	0.044	0.004	0.048
cnv_TTstatus	0.011	0.029	0.041
cnv_netPass	0.005	0.002	0.006
cnv_netScores	0.007	0.018	0.025
cnv_patientNetCount	0.148	0.123	0.310
cnv_pheno	0.010	0.003	0.013
compareShortestPath	0.024	0.004	0.028
compileFeatureScores	0.011	0.002	0.013
compileFeatures	7.703	0.823	43.113
confmat	0.003	0.002	0.006
countIntType	0.003	0.001	0.004
countIntType_batch	0.031	0.007	18.852
countPatientsInNet	0.003	0.002	0.005
createPSN_MultiData	36.245	0.511	56.192
enrichLabelNets	1.859	0.060	111.343
featScores	0.060	0.061	0.123
fetchPathwayDefinitions	1.479	0.016	1.662
genes	0.005	0.003	0.007
getEMapInput	1.576	0.020	1.642
getEMapInput_many	1.337	0.047	1.428
getEnr	0.827	0.018	18.705
getFeatureScores	0.020	0.002	0.022
getGMjar_path	0.582	0.050	0.636
getNetConsensus	0.022	0.001	0.022
getOR	0.004	0.002	0.005
getPatientPredictions	5.750	0.028	5.795
getPatientRankings	0.107	0.003	0.150
getRegionOL	0.607	0.008	0.618
getSimilarity	0.156	0.002	0.158
makePSN_NamedMatrix	0.087	0.007	19.804
makePSN_RangeSets	0.014	0.003	0.016
makeQueries	0.011	0.003	0.014
makeSymmetric	0.002	0.000	0.003
mapNamedRangesToSets	0.073	0.003	0.077
normDiff	0.000	0.001	0.001
npheno	0.003	0.003	0.006
pathwayList	0.005	0.014	0.019
pathway_GR	0.165	0.008	0.174
perfCalc	0.004	0.002	0.006
pheno	0.010	0.002	0.013
pheno_full	0.003	0.002	0.005
plotEmap	1.588	0.025	1.700
plotPerf	5.466	0.042	5.526
plotPerf_multi	0.050	0.002	0.053
predRes	0.003	0.002	0.004
predictPatientLabels	0.010	0.001	0.012
pruneNets	0.012	0.004	0.015
readPathways	1.498	0.026	1.609
runFeatureSelection	8.805	0.863	6.029
runQuery	4.240	0.581	5.559
setupFeatureDB	0.070	0.007	0.076
silh	0.005	0.003	0.008
sim.eucscale	0.536	0.003	0.541
sim.pearscale	0.921	0.005	0.929
simpleCap	0.001	0.000	0.000
smoothMutations_LabelProp	3.004	0.156	27.196
sparsify2	0.423	0.084	0.506
sparsify3	0.244	0.004	0.248
splitTestTrain	0.009	0.001	0.011
splitTestTrain_resampling	0.004	0.001	0.005
thresholdSmoothedMutations	3.263	0.197	27.107
updateNets	0.009	0.002	0.012
writeNetsSIF	0.009	0.002	0.012
writeQueryBatchFile	0.005	0.002	0.008
writeQueryFile	0.005	0.002	0.007
xpr	0.027	0.044	0.071

CHECK report for netDx on merida1

Summary

Command output

Installation output

Tests output

Example timings