BioC 3.3: CHECK report for rcellminer on linux2.bioconductor.org

Package: rcellminer

Version: 1.3.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings rcellminer_1.3.0.tar.gz

StartedAt: 2015-10-27 07:15:28 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:17:21 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 112.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: rcellminer.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings rcellminer_1.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/rcellminer.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rcellminer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rcellminer’ version ‘1.3.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rcellminer’ can be installed ... [7s/7s] OK
* checking installed package size ... NOTE
  installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    3.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘rcellminer’ for: ‘initialize’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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:
  ‘Drug_MOA_Key’
Undocumented data sets:
  ‘Drug_MOA_Key’
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
Undocumented arguments in documentation object 'plotStructures'
  ‘nscs’
Documented arguments not in \usage in documentation object 'plotStructures':
  ‘ids’

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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [53s/50s]
 [53s/50s] 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/rcellminer.Rcheck/00check.log’
for details.

* installing *source* package ‘rcellminer’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rcellminer)

name	user	system	elapsed
compareFingerprints	2.354	0.064	2.087
crossCors	0.007	0.000	0.007
crossCorsSpearman	0.001	0.000	0.000
getActivityRangeStats	0.024	0.000	0.024
getColumnQuantiles	0.002	0.000	0.002
getDrugActivityData	0.004	0.000	0.004
getDrugActivityRange	0.001	0.004	0.004
getDrugActivityRepeatData	0.002	0.000	0.003
getDrugMoaList	0.007	0.000	0.007
getDrugName	0.003	0.000	0.002
getFeatureDataFromMatList	1.911	0.125	2.123
getFingerprintList	0.191	0.008	0.081
getMedSenLineActivity	0.025	0.005	0.010
getMinDrugActivityRepeatCor	0.019	0.003	0.008
getMoaStr	0.061	0.000	0.020
getMoaToCompounds	0.019	0.000	0.006
getMolDataMatrices	0.522	0.065	0.466
getMolDataType	0.001	0.000	0.001
getNumDrugActivityRepeats	0.008	0.000	0.008
getNumMissingLines	0.005	0.000	0.004
getRsd	0.007	0.000	0.007
getSmiles	0.003	0.000	0.003
hasMoa	0.007	0.000	0.007
isPublic	0.002	0.000	0.002
loadCellminerPlotInfo	0.001	0.000	0.001
loadNciColorSet	0.002	0.000	0.002
passRuleOf5	0.102	0.000	0.074
passRuleOf5FromNsc	0.059	0.000	0.042
patternComparison	0.317	0.023	0.341
plotCellMiner	0.907	0.028	0.935
plotDrugActivityRepeats	0.719	0.060	0.780
plotDrugSets	0.029	0.000	0.028
plotStructures	1.669	0.045	0.920
plotStructuresFromNscs	0.944	0.039	0.398
rcdkplot	0.178	0.008	0.083
removeMolDataType	0.000	0.000	0.001
restrictFeatureMat	0.001	0.000	0.002
rowCors	0.001	0.000	0.002
runShinyApp	0.000	0.000	0.001
runShinyComparePlots	0	0	0
runShinyCompareStructures	0.001	0.000	0.000
runShinyCompoundBrowser	0.001	0.000	0.000
searchForNscs	0.011	0.000	0.011
selectCorrelatedRows	0.002	0.000	0.002
selectCorrelatedRows2	0.004	0.000	0.005