BioC 3.5: CHECK report for cellHTS2 on malbec2

Package: cellHTS2

Version: 2.40.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings cellHTS2_2.40.0.tar.gz

StartedAt: 2017-10-17 21:48:40 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 21:52:20 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 220.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: cellHTS2.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings cellHTS2_2.40.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/cellHTS2.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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  5.8Mb
  sub-directories of 1Mb or more:
    KcViab   2.0Mb
    doc      1.6Mb
* 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 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
  ‘/home/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	2.396	0.012	2.416
ROC-class	0.244	0.008	0.253
ROC	0.924	0.000	0.927
annotate	0.736	0.004	0.741
bdgpbiomart	0.180	0.000	0.179
buildCellHTS2	0.420	0.000	0.422
cellHTS-class	1.180	0.012	1.195
configurationAsScreenPlot	2.028	0.024	2.052
configure	0.704	0.000	0.707
convertOldCellHTS	0.508	0.000	0.506
convertWellCoordinates	0.000	0.000	0.001
data-KcViab	0.124	0.004	0.127
data-KcViabSmall	0.012	0.000	0.011
data-dualCh	0.012	0.000	0.012
data-oldKcViabSmall	0.008	0.004	0.013
getDynamicRange	0.660	0.004	0.665
getEnVisionRawData	0.068	0.000	0.068
getMeasureRepAgreement	0.496	0.000	0.497
getTopTable	0.948	0.000	0.950
getZfactor	0.320	0.000	0.319
imageScreen	0.776	0.000	0.779
normalizePlates	1.056	0.000	1.060
oneRowPerId	0.004	0.000	0.003
plotSpatialEffects	1.544	0.000	1.541
readHTAnalystData	0.664	0.000	0.664
readPlateList	0.436	0.000	0.437
rsa	0.740	0.004	0.745
scoreReplicates	0.728	0.000	0.724
scores2calls	0.976	0.000	0.978
setSettings	0.004	0.000	0.004
spatialNormalization	1.632	0.000	1.631
summarizeChannels	1.432	0.000	1.433
summarizeReplicates	0.732	0.000	0.731
templateDescriptionFile	0.004	0.000	0.002
updateCellHTS	0.132	0.000	0.132
write.tabdel	0.080	0.000	0.079
writeReport	0.012	0.000	0.011
writeTab	0.016	0.000	0.016