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BioC 3.5: CHECK report for cellHTS2 on veracruz2

This page was generated on 2017-08-16 13:28:00 -0400 (Wed, 16 Aug 2017).

Package 184/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellHTS2 2.40.0
Joseph Barry
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/cellHTS2
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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


* 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.


cellHTS2.Rcheck/00install.out:

* 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)

cellHTS2.Rcheck/cellHTS2-Ex.timings:

nameusersystemelapsed
Bscore2.7260.0322.837
ROC-class0.2110.0070.229
ROC0.9170.0050.953
annotate0.8360.0030.866
bdgpbiomart0.1900.0060.202
buildCellHTS20.3900.0000.397
cellHTS-class1.1410.0211.196
configurationAsScreenPlot1.9020.0352.011
configure0.6570.0060.669
convertOldCellHTS0.5150.0040.538
convertWellCoordinates0.0010.0000.001
data-KcViab0.1100.0030.118
data-KcViabSmall0.0080.0030.010
data-dualCh0.0090.0020.012
data-oldKcViabSmall0.0080.0020.010
getDynamicRange0.6190.0050.649
getEnVisionRawData0.0850.0010.090
getMeasureRepAgreement0.4290.0040.441
getTopTable1.1980.0061.239
getZfactor0.4270.0070.447
imageScreen0.9860.0081.030
normalizePlates1.3770.0071.430
oneRowPerId0.0030.0000.003
plotSpatialEffects1.9900.0102.037
readHTAnalystData0.7860.0020.798
readPlateList0.6030.0040.638
rsa0.9080.0060.939
scoreReplicates0.7480.0050.762
scores2calls1.3900.0061.420
setSettings0.0070.0020.009
spatialNormalization2.0390.0112.106
summarizeChannels1.8170.0061.871
summarizeReplicates0.8870.0050.937
templateDescriptionFile0.0020.0010.002
updateCellHTS0.0950.0040.101
write.tabdel0.0670.0040.072
writeReport0.0140.0050.019
writeTab0.0170.0040.021