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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_1.4.3.tar.gz
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* 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               45.010  1.407  50.527
createPSN_MultiData          40.920  0.784  63.875
buildPredictor_sparseGenetic 21.699  0.877  22.646
runFeatureSelection           8.956  0.937   6.035
compileFeatures               8.290  0.809  48.606
RR_featureTally               7.442  0.797   8.246
getPatientPredictions         5.873  0.010   5.889
plotPerf                      5.342  0.016   5.362
runQuery                      4.313  0.573   5.558
thresholdSmoothedMutations    4.267  0.197  32.704
smoothMutations_LabelProp     3.162  0.160  32.243
enrichLabelNets               2.046  0.065 129.332
getEnr                        1.055  0.023  22.665
makePSN_NamedMatrix           0.092  0.007  21.051
countIntType_batch            0.031  0.006  22.039
* 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.