plateCore 1.28.0
Errol Strain
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/plateCore | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf plateCore.buildbin-libdir plateCore.Rcheck && mkdir plateCore.buildbin-libdir plateCore.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=plateCore.buildbin-libdir plateCore_1.28.0.tar.gz >plateCore.Rcheck\00install.out 2>&1 && cp plateCore.Rcheck\00install.out plateCore-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=plateCore.buildbin-libdir --install="check:plateCore-install.out" --force-multiarch --no-vignettes --timings plateCore_1.28.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/plateCore.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'plateCore/DESCRIPTION' ... OK
* this is package 'plateCore' version '1.28.0'
* 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
** 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 ... 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.
* 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'
fixAutoFl,flowPlate : .local: no visible binding for global variable
'Sample.Type'
fpbind,flowPlate-flowPlate : .local : <anonymous>: no visible binding
for global variable 'name'
setControlGates,flowPlate : .local: no visible binding for global
variable 'Sample.Type'
setControlGates,flowPlate : .local: no visible binding for global
variable 'Channel'
setControlGates,flowPlate : .local : <anonymous>: no visible binding
for global variable 'Well.Id'
setControlGates,flowPlate : .local : <anonymous>: no visible binding
for global variable 'plateName'
setControlGates,flowPlate : .local : <anonymous>: no visible binding
for global variable 'name'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'flowPlate,ANY,ANY,ANY'
generic '[[' and siglist 'flowPlate,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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' ... [82s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mfiPlot-methods 8.73 0.01 8.75
applyControlGates-methods 8.62 0.01 8.63
summaryStats-methods 7.71 0.00 7.71
on-methods 6.62 0.00 6.62
** running examples for arch 'x64' ... [89s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mfiPlot-methods 9.77 0.01 9.78
applyControlGates-methods 9.38 0.00 9.38
summaryStats-methods 9.19 0.00 9.19
on-methods 6.29 0.00 6.57
fixAutoFl-methods 5.23 0.03 5.26
* 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: 1 WARNING, 3 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/plateCore.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'plateCore' ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "flowStats" for requests: %on%
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "flowStats" for requests: %on%
install for x64
* installing *source* package 'plateCore' ...
** testing if installed package can be loaded
No methods found in "flowStats" for requests: %on%
* MD5 sums
packaged installation of 'plateCore' as plateCore_1.28.0.zip
* DONE (plateCore)