BioC 2.13: CHECK report for plateCore on moscato1
This page was generated on 2014-04-05 09:49:56 -0700 (Sat, 05 Apr 2014).
plateCore 1.20.0 Errol Strain
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/plateCore | Last Changed Rev: 81642 / Revision: 88450 | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ OK ] | OK |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
Summary
Package: plateCore
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Version: 1.20.0
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Command: rm -rf plateCore.buildbin-libdir && mkdir plateCore.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=plateCore.buildbin-libdir plateCore_1.20.0.tar.gz >plateCore-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=plateCore.buildbin-libdir --install="check:plateCore-install.out" --force-multiarch --no-vignettes --timings plateCore_1.20.0.tar.gz && mv plateCore.buildbin-libdir/* plateCore.Rcheck/ && rmdir plateCore.buildbin-libdir
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StartedAt: 2014-04-05 05:51:56 -0700 (Sat, 05 Apr 2014)
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EndedAt: 2014-04-05 05:57:35 -0700 (Sat, 05 Apr 2014)
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EllapsedTime: 338.9 seconds
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RetCode: 0
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Status: OK
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CheckDir: plateCore.Rcheck
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Warnings: 0
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Command output
* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/plateCore.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'plateCore/DESCRIPTION' ... OK
* this is package 'plateCore' version '1.20.0'
* 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 'plateCore' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'flowCore' 'lattice'
A package should be listed in only one of these fields.
* 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:
'flowViz' 'latticeExtra'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
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
panel.xyplot.flowPlate: warning in filterBoundary(filter =
filter[[nm]], parameters = c(channel.x.name, channel.y.name), frame =
frames[[nm]]): partial argument match of 'filter' to 'filter.object'
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
'plateCoreVig.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [93s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
summaryStats-methods 12.45 0.00 12.45
applyControlGates-methods 10.80 0.00 10.80
mfiPlot-methods 9.32 0.00 9.31
fpbind-methods 7.77 0.00 7.77
on-methods 6.83 0.00 6.88
compensate-methods 5.54 0.05 5.58
** running examples for arch 'x64' ... [132s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
summaryStats-methods 17.77 0.02 17.78
applyControlGates-methods 14.08 0.00 14.08
mfiPlot-methods 13.49 0.02 13.51
on-methods 10.92 0.00 10.92
fpbind-methods 9.97 0.00 9.97
fixAutoFl-methods 6.68 0.02 6.71
compensate-methods 5.65 0.00 5.65
plotPlate-methods 5.39 0.01 5.39
* 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
NOTE: There were 4 notes.
See
'D:/biocbld/bbs-2.13-bioc/meat/plateCore.Rcheck/00check.log'
for details.
plateCore.Rcheck/00install.out:
install for i386
* installing *source* package 'plateCore' ...
** R
** data
** 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 'plateCore' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'plateCore' as plateCore_1.20.0.zip
* DONE (plateCore)
plateCore.Rcheck/examples_i386/plateCore-Ex.timings:
name | user | system | elapsed
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Subset-methods | 3.98 | 0.00 | 3.97 |
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applyControlGates-methods | 10.8 | 0.0 | 10.8 |
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compensate-methods | 5.54 | 0.05 | 5.58 |
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compensationSet | 0.2 | 0.0 | 0.2 |
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densityplot-methods | 1.15 | 0.02 | 1.17 |
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fixAutoFl-methods | 4.87 | 0.03 | 4.94 |
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flowPlate-class | 2.48 | 0.02 | 2.52 |
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flowPlate-method | 2.51 | 0.01 | 2.52 |
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fpbind-methods | 7.77 | 0.00 | 7.77 |
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getGroups-methods | 1.68 | 0.00 | 1.68 |
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gutterPlot-methods | 1.51 | 0.00 | 1.52 |
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mfiPlot-methods | 9.32 | 0.00 | 9.31 |
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on-methods | 6.83 | 0.00 | 6.88 |
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panel.densityplot.flowPlate | 1.41 | 0.02 | 1.42 |
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panel.xyplot.flowPlate | 1.12 | 0.00 | 1.12 |
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plateCore-package | 2.21 | 0.00 | 2.22 |
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plateSet-methods | 2.42 | 0.00 | 2.41 |
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plotPlate-methods | 3.06 | 0.00 | 3.06 |
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prepanel.densityplot.flowPlate | 1.35 | 0.01 | 1.35 |
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prepanel.xyplot.flowPlate | 1.07 | 0.00 | 1.08 |
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setControlGates-methods | 3 | 0 | 3 |
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summaryStats-methods | 12.45 | 0.00 | 12.45 |
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wellAnnotation-methods | 1.23 | 0.00 | 1.23 |
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xyplot-methods | 1.17 | 0.00 | 1.17 |
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plateCore.Rcheck/examples_x64/plateCore-Ex.timings:
name | user | system | elapsed
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Subset-methods | 4.76 | 0.03 | 4.79 |
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applyControlGates-methods | 14.08 | 0.00 | 14.08 |
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compensate-methods | 5.65 | 0.00 | 5.65 |
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compensationSet | 0.36 | 0.00 | 0.36 |
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densityplot-methods | 2.01 | 0.00 | 2.01 |
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fixAutoFl-methods | 6.68 | 0.02 | 6.71 |
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flowPlate-class | 4.01 | 0.00 | 4.01 |
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flowPlate-method | 4.17 | 0.02 | 4.18 |
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fpbind-methods | 9.97 | 0.00 | 9.97 |
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getGroups-methods | 1.76 | 0.02 | 1.78 |
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gutterPlot-methods | 1.89 | 0.01 | 1.91 |
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mfiPlot-methods | 13.49 | 0.02 | 13.51 |
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on-methods | 10.92 | 0.00 | 10.92 |
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panel.densityplot.flowPlate | 2.30 | 0.01 | 2.36 |
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panel.xyplot.flowPlate | 1.85 | 0.00 | 1.85 |
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plateCore-package | 3.20 | 0.04 | 3.45 |
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plateSet-methods | 3.02 | 0.00 | 3.03 |
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plotPlate-methods | 5.39 | 0.01 | 5.39 |
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prepanel.densityplot.flowPlate | 2.2 | 0.0 | 2.2 |
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prepanel.xyplot.flowPlate | 1.99 | 0.00 | 2.00 |
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setControlGates-methods | 4.09 | 0.00 | 4.09 |
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summaryStats-methods | 17.77 | 0.02 | 17.78 |
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wellAnnotation-methods | 2.03 | 0.00 | 2.03 |
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xyplot-methods | 2.24 | 0.03 | 2.29 |
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