flowDensity 1.4.0
Mehrnoush Malek
| 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/flowDensity | | 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 flowDensity.buildbin-libdir flowDensity.Rcheck && mkdir flowDensity.buildbin-libdir flowDensity.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowDensity.buildbin-libdir flowDensity_1.4.0.tar.gz >flowDensity.Rcheck\00install.out 2>&1 && cp flowDensity.Rcheck\00install.out flowDensity-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=flowDensity.buildbin-libdir --install="check:flowDensity-install.out" --force-multiarch --no-vignettes --timings flowDensity_1.4.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/flowDensity.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 'flowDensity/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowDensity' version '1.4.0'
* 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 'flowDensity' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
doc 1.0Mb
extdata 4.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'methods'
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
Namespace in Imports field not imported from: 'graphics'
All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'.densityGating' '.ellipseGating' 'nmRemove'
* 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 ... WARNING
Codoc mismatches from documentation object 'deGate':
deGate
Code: function(flow.frame, channel, n.sd = 1.5, use.percentile =
FALSE, percentile = 0.95, upper = NA, alpha = 0.1,
sd.threshold = FALSE, graphs = FALSE, all.cut = FALSE,
tinypeak.removal = 1/25, adjust.dens = 1)
Docs: function(flow.frame, channel, n.sd = 1.5, use.percentile =
FALSE, percentile = 0.95, upper = NA, alpha = 0.1,
sd.threshold = FALSE, graphs = FALSE, all.cut = FALSE,
tinypeak.removal = 1/25)
Argument names in code not in docs:
adjust.dens
Codoc mismatches from documentation object 'plotDens':
plotDens
Code: function(flow.frame, channels, col, main, xlab, ylab, pch =
".", s = FALSE, outdir, file.name, ...)
Docs: function(flow.frame, channels, col, main, xlab, ylab, pch =
".", s = FALSE, outdir, file.name, devn = TRUE, ...)
Argument names in docs not in code:
devn
Mismatches in argument names:
Position: 11 Code: ... Docs: devn
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'deGate':
'adjust.dens'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [10s] OK
** running examples for arch 'x64' ... [8s] 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: 2 WARNINGs, 3 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/flowDensity.Rcheck/00check.log'
for details.