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BioC 2.14: CHECK report for cellHTS2 on petty

This page was generated on 2014-10-08 08:58:04 -0700 (Wed, 08 Oct 2014).

Package 126/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellHTS2 2.28.0
Joseph Barry
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/cellHTS2
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: cellHTS2
Version: 2.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cellHTS2_2.28.0.tar.gz
StartedAt: 2014-10-07 21:06:01 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 21:16:55 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 653.8 seconds
RetCode: 0
Status:  OK 
CheckDir: cellHTS2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cellHTS2_2.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/cellHTS2.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellHTS2/DESCRIPTION’ ... OK
* this is package ‘cellHTS2’ version ‘2.28.0’
* 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 ... [43s/46s] OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc      1.7Mb
    KcViab   2.0Mb
* 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
Packages in Depends field not imported from:
  ‘genefilter’ ‘hwriter’ ‘locfit’ ‘RColorBrewer’ ‘splots’
  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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotate,cellHTS: warning in read.table(file.path(path, file), sep =
  "\t", header = TRUE, stringsAsFactors = FALSE, na.string = "", quote
  = "", fill = FALSE): partial argument match of 'na.string' to
  'na.strings'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 ... [98s/99s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
Bscore             8.277  0.081   8.786
summarizeChannels  6.067  0.020   6.112
plotSpatialEffects 5.205  0.030   5.271
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test.R’ [98s/102s]
 [98s/102s] 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

NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/cellHTS2.Rcheck/00check.log’
for details.

cellHTS2.Rcheck/00install.out:

* installing *source* package ‘cellHTS2’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘lines’ from package ‘graphics’ in package ‘cellHTS2’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cellHTS2)

cellHTS2.Rcheck/cellHTS2-Ex.timings:

nameusersystemelapsed
Bscore8.2770.0818.786
ROC-class0.7000.0190.755
ROC3.4710.0153.514
annotate2.6750.0102.687
bdgpbiomart0.3980.0180.417
buildCellHTS20.9730.0070.998
cellHTS-class4.3690.0644.455
configurationAsScreenPlot4.7170.0674.794
configure1.9510.0091.971
convertOldCellHTS2.1240.0112.146
convertWellCoordinates0.0020.0000.002
data-KcViab0.2720.0150.286
data-KcViabSmall0.0210.0080.029
data-dualCh0.0230.0080.031
data-oldKcViabSmall0.0200.0090.029
getDynamicRange1.8320.0151.866
getEnVisionRawData0.1340.0030.142
getMeasureRepAgreement1.4530.0101.466
getTopTable3.6470.0153.670
getZfactor1.0810.0131.100
imageScreen3.1330.0153.154
normalizePlates4.3800.0204.488
oneRowPerId0.0070.0000.007
plotSpatialEffects5.2050.0305.271
readHTAnalystData2.5400.0072.563
readPlateList1.8650.0111.879
rsa2.7080.0112.720
scoreReplicates2.9510.0112.966
scores2calls3.2940.0153.319
setSettings0.0110.0050.016
spatialNormalization3.2610.0133.277
summarizeChannels6.0670.0206.112
summarizeReplicates3.0390.0143.107
templateDescriptionFile0.0040.0010.005
updateCellHTS0.2750.0100.285
write.tabdel0.1300.0110.140
writeReport0.0220.0090.032
writeTab0.0360.0090.045