Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 2.14: CHECK report for cellHTS2 on moscato2

This page was generated on 2014-10-08 08:52:09 -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: rm -rf cellHTS2.buildbin-libdir && mkdir cellHTS2.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellHTS2.buildbin-libdir cellHTS2_2.28.0.tar.gz >cellHTS2-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=cellHTS2.buildbin-libdir --install="check:cellHTS2-install.out" --force-multiarch --no-vignettes --timings cellHTS2_2.28.0.tar.gz
StartedAt: 2014-10-07 23:29:22 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:37:48 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 505.7 seconds
RetCode: 0
Status:  OK  
CheckDir: cellHTS2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf cellHTS2.buildbin-libdir && mkdir cellHTS2.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellHTS2.buildbin-libdir cellHTS2_2.28.0.tar.gz >cellHTS2-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=cellHTS2.buildbin-libdir --install="check:cellHTS2-install.out" --force-multiarch --no-vignettes --timings cellHTS2_2.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/cellHTS2.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 whether package 'cellHTS2' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    KcViab   2.0Mb
    doc      1.7Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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:
  'RColorBrewer' 'genefilter' 'hwriter' 'locfit' '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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [49s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
Bscore 5.08      0    5.08
** running examples for arch 'x64' ... [49s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
Bscore  5.1      0     5.1
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test.R' [51s]
 [51s] OK
** running tests for arch 'x64' ...
  Running 'test.R' [56s]
 [57s] 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
  'E:/biocbld/bbs-2.14-bioc/meat/cellHTS2.Rcheck/00check.log'
for details.

cellHTS2.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'cellHTS2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cellHTS2' as cellHTS2_2.28.0.zip
* DONE (cellHTS2)

cellHTS2.Rcheck/examples_i386/cellHTS2-Ex.timings:

nameusersystemelapsed
Bscore5.080.005.08
ROC-class0.330.000.33
ROC1.540.001.55
annotate1.240.001.23
bdgpbiomart0.230.000.23
buildCellHTS20.530.000.53
cellHTS-class2.050.002.05
configurationAsScreenPlot1.910.001.92
configure0.890.020.90
convertOldCellHTS101
convertWellCoordinates000
data-KcViab0.170.000.18
data-KcViabSmall0.010.000.01
data-dualCh0.000.010.02
data-oldKcViabSmall0.020.000.01
getDynamicRange0.890.000.89
getEnVisionRawData0.030.000.03
getMeasureRepAgreement0.670.000.67
getTopTable2.150.002.15
getZfactor0.470.000.47
imageScreen1.760.001.76
normalizePlates2.440.002.44
oneRowPerId0.010.000.01
plotSpatialEffects2.730.012.76
readHTAnalystData1.120.001.12
readPlateList0.810.000.84
rsa1.280.001.28
scoreReplicates1.470.001.47
scores2calls1.790.021.81
setSettings000
spatialNormalization1.520.001.51
summarizeChannels2.650.002.66
summarizeReplicates1.360.001.35
templateDescriptionFile000
updateCellHTS0.130.000.12
write.tabdel0.060.010.08
writeReport0.020.000.02
writeTab0.030.000.03

cellHTS2.Rcheck/examples_x64/cellHTS2-Ex.timings:

nameusersystemelapsed
Bscore5.10.05.1
ROC-class0.390.000.39
ROC1.690.001.68
annotate1.240.001.25
bdgpbiomart0.210.000.21
buildCellHTS20.430.000.43
cellHTS-class2.140.012.16
configurationAsScreenPlot2.360.022.38
configure0.950.000.95
convertOldCellHTS1.340.001.35
convertWellCoordinates000
data-KcViab0.160.000.15
data-KcViabSmall0.010.000.02
data-dualCh0.020.000.01
data-oldKcViabSmall0.010.000.02
getDynamicRange0.880.000.87
getEnVisionRawData0.030.020.05
getMeasureRepAgreement0.720.000.72
getTopTable2.10.02.1
getZfactor0.530.000.53
imageScreen1.530.001.53
normalizePlates2.080.002.08
oneRowPerId000
plotSpatialEffects2.480.002.48
readHTAnalystData1.210.001.21
readPlateList0.830.010.86
rsa1.310.021.33
scoreReplicates1.40.01.4
scores2calls1.640.001.64
setSettings000
spatialNormalization1.590.011.61
summarizeChannels2.970.002.96
summarizeReplicates1.370.001.37
templateDescriptionFile000
updateCellHTS0.110.020.13
write.tabdel0.060.000.06
writeReport0.020.000.02
writeTab0.010.000.01