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BioC 3.6: CHECK report for twoddpcr on tokay1

This page was generated on 2017-08-16 13:37:34 -0400 (Wed, 16 Aug 2017).

Package 1372/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
twoddpcr 1.1.3
Anthony Chiu
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/twoddpcr
Last Changed Rev: 131666 / Revision: 131943
Last Changed Date: 2017-07-31 07:42:29 -0400 (Mon, 31 Jul 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: twoddpcr
Version: 1.1.3
Command: rm -rf twoddpcr.buildbin-libdir twoddpcr.Rcheck && mkdir twoddpcr.buildbin-libdir twoddpcr.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=twoddpcr.buildbin-libdir twoddpcr_1.1.3.tar.gz >twoddpcr.Rcheck\00install.out 2>&1 && cp twoddpcr.Rcheck\00install.out twoddpcr-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=twoddpcr.buildbin-libdir --install="check:twoddpcr-install.out" --force-multiarch --no-vignettes --timings twoddpcr_1.1.3.tar.gz
StartedAt: 2017-08-16 02:59:56 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 03:04:07 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 251.4 seconds
RetCode: 0
Status:  OK  
CheckDir: twoddpcr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf twoddpcr.buildbin-libdir twoddpcr.Rcheck && mkdir twoddpcr.buildbin-libdir twoddpcr.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=twoddpcr.buildbin-libdir twoddpcr_1.1.3.tar.gz >twoddpcr.Rcheck\00install.out 2>&1 && cp twoddpcr.Rcheck\00install.out twoddpcr-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=twoddpcr.buildbin-libdir --install="check:twoddpcr-install.out" --force-multiarch --no-vignettes --timings twoddpcr_1.1.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/twoddpcr.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'twoddpcr/DESCRIPTION' ... OK
* this is package 'twoddpcr' version '1.1.3'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 'twoddpcr' can be installed ... OK
* checking installed package size ... OK
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* 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 ... 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' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
knnClassify      11.22   0.13   11.34
flatPlot          6.28   0.15    6.44
dropletPlot       6.28   0.02    6.30
ggplot.well       6.00   0.18    6.17
renormalisePlate  5.12   0.03    5.16
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
knnClassify      10.88   0.03   11.14
renormalisePlate  6.97   0.06    7.03
ggplot.well       6.25   0.20    6.45
dropletPlot       6.10   0.08    6.17
flatPlot          5.89   0.16    6.04
sdRain            5.87   0.00    5.88
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* 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: OK

twoddpcr.Rcheck/00install.out:


install for i386

* installing *source* package 'twoddpcr' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'twoddpcr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'twoddpcr' as twoddpcr_1.1.3.zip
* DONE (twoddpcr)

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

nameusersystemelapsed
amplitudes0.640.000.64
basicsSummary000
castSummary0.070.000.06
classCov0.140.010.16
classMeans0.110.000.11
classStats0.120.000.12
clusterCentres1.200.081.29
copiesSummary0.030.000.03
ddpcrPlate-class0.430.000.42
ddpcrWell-class0.050.000.05
ddpcrWell-methods0.440.000.44
dropletPlot6.280.026.30
exportTable0.090.000.11
extractPlateName000
extractWellNames000
facetPlot2.950.113.06
flatPlot6.280.156.44
fullCopiesSummary0.020.000.02
fullCountsSummary0.030.000.03
ggplot.well6.000.186.17
gridClassify2.230.042.28
heatPlot2.410.102.50
kmeansClassify1.450.011.47
knnClassify11.22 0.1311.34
mahalanobisRain0.810.030.85
mutantCopiesSummary000
numDroplets0.470.000.47
parseClusterCounts0.020.000.01
plateClassification1.400.001.41
plateClassificationMethod0.440.000.44
plateSummary3.130.003.12
positiveCounts0.040.000.05
readCSVDataFrame0.020.000.01
relabelClasses0.160.000.15
removeDropletClasses1.160.001.16
renormalisePlate5.120.035.16
sdRain3.920.013.94
setChannelNames0.020.000.02
setDropletVolume000
sortDataFrame000
sortWells0.450.000.45
thresholdClassify2.030.022.05
wellClassification0.040.000.03
wellClassificationMethod0.040.000.04
whiteTheme1.630.011.64
wildTypeCopiesSummary0.010.000.02

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

nameusersystemelapsed
amplitudes0.710.000.70
basicsSummary000
castSummary0.060.000.06
classCov0.180.000.17
classMeans0.090.000.09
classStats0.240.000.24
clusterCentres1.330.001.32
copiesSummary0.040.000.05
ddpcrPlate-class0.410.000.41
ddpcrWell-class0.060.000.06
ddpcrWell-methods0.50.00.5
dropletPlot6.100.086.17
exportTable0.120.000.14
extractPlateName000
extractWellNames000
facetPlot3.330.033.36
flatPlot5.890.166.04
fullCopiesSummary0.020.000.02
fullCountsSummary0.030.000.03
ggplot.well6.250.206.45
gridClassify2.560.062.62
heatPlot3.310.053.38
kmeansClassify2.510.022.53
knnClassify10.88 0.0311.14
mahalanobisRain1.450.001.45
mutantCopiesSummary000
numDroplets0.750.000.75
parseClusterCounts0.010.000.01
plateClassification1.970.062.03
plateClassificationMethod0.530.000.53
plateSummary3.530.003.53
positiveCounts0.140.000.14
readCSVDataFrame0.030.000.03
relabelClasses0.190.000.19
removeDropletClasses1.120.001.12
renormalisePlate6.970.067.03
sdRain5.870.005.88
setChannelNames000
setDropletVolume000
sortDataFrame000
sortWells0.730.000.74
thresholdClassify3.070.003.09
wellClassification0.040.000.05
wellClassificationMethod0.070.000.06
whiteTheme2.010.002.02
wildTypeCopiesSummary000