BioC 3.5: CHECK report for cellHTS2 on veracruz2

Package: cellHTS2

Version: 2.40.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cellHTS2_2.40.0.tar.gz

StartedAt: 2017-08-16 00:41:06 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:45:00 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 233.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: cellHTS2.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cellHTS2_2.40.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/cellHTS2.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellHTS2/DESCRIPTION’ ... OK
* this is package ‘cellHTS2’ version ‘2.40.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘RColorBrewer’ ‘Biobase’ ‘genefilter’ ‘splots’ ‘vsn’ ‘hwriter’
  ‘locfit’ ‘grid’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘cellHTS2’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    KcViab   2.0Mb
    doc      1.8Mb
* 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 ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘genefilter’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘Biobase:::.showAnnotatedDataFrame’
  See the note in ?`:::` about the use of this operator.
* 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 ... WARNING
Unknown package ‘cellHTS’ in Rd xrefs
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
  ‘GO.db’ ‘KEGG.db’
* 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: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/cellHTS2.Rcheck/00check.log’
for details.

* installing *source* package ‘cellHTS2’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cellHTS2)

name	user	system	elapsed
Bscore	2.726	0.032	2.837
ROC-class	0.211	0.007	0.229
ROC	0.917	0.005	0.953
annotate	0.836	0.003	0.866
bdgpbiomart	0.190	0.006	0.202
buildCellHTS2	0.390	0.000	0.397
cellHTS-class	1.141	0.021	1.196
configurationAsScreenPlot	1.902	0.035	2.011
configure	0.657	0.006	0.669
convertOldCellHTS	0.515	0.004	0.538
convertWellCoordinates	0.001	0.000	0.001
data-KcViab	0.110	0.003	0.118
data-KcViabSmall	0.008	0.003	0.010
data-dualCh	0.009	0.002	0.012
data-oldKcViabSmall	0.008	0.002	0.010
getDynamicRange	0.619	0.005	0.649
getEnVisionRawData	0.085	0.001	0.090
getMeasureRepAgreement	0.429	0.004	0.441
getTopTable	1.198	0.006	1.239
getZfactor	0.427	0.007	0.447
imageScreen	0.986	0.008	1.030
normalizePlates	1.377	0.007	1.430
oneRowPerId	0.003	0.000	0.003
plotSpatialEffects	1.990	0.010	2.037
readHTAnalystData	0.786	0.002	0.798
readPlateList	0.603	0.004	0.638
rsa	0.908	0.006	0.939
scoreReplicates	0.748	0.005	0.762
scores2calls	1.390	0.006	1.420
setSettings	0.007	0.002	0.009
spatialNormalization	2.039	0.011	2.106
summarizeChannels	1.817	0.006	1.871
summarizeReplicates	0.887	0.005	0.937
templateDescriptionFile	0.002	0.001	0.002
updateCellHTS	0.095	0.004	0.101
write.tabdel	0.067	0.004	0.072
writeReport	0.014	0.005	0.019
writeTab	0.017	0.004	0.021