flowBin 1.12.0
Kieran O'Neill
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/flowBin | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf flowBin.buildbin-libdir flowBin.Rcheck && mkdir flowBin.buildbin-libdir flowBin.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowBin.buildbin-libdir flowBin_1.12.0.tar.gz >flowBin.Rcheck\00install.out 2>&1 && cp flowBin.Rcheck\00install.out flowBin-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=flowBin.buildbin-libdir --install="check:flowBin-install.out" --force-multiarch --no-vignettes --timings flowBin_1.12.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/flowBin.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 'flowBin/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowBin' version '1.12.0'
* 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 'flowBin' 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 ... NOTE
Package in Depends field not imported from: 'flowCore'
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
.getBinExpr.def : getBinFrame: no visible global function definition
for 'exprs<-'
.getBinExpr.def : getBinFrame: no visible global function definition
for 'exprs'
.getBinExpr.def : scaleData: no visible global function definition for
'pData'
.getBinExpr.def : getOnePopExpr : extractOneTube : <anonymous>: no
visible global function definition for 'exprs'
.getBinExpr.def : getOnePopExpr : extractOneTube: no visible global
function definition for 'pData'
.getBinExpr.def : getOneBinMeds : <anonymous>: no visible global
function definition for 'median'
.getBinExpr.def : getOneBinMeds : <anonymous>: no visible global
function definition for 'exprs'
.getBinExpr.def : getOneBinMeds: no visible global function definition
for 'pData'
checkQNorm.func: no visible global function definition for 'flowSet'
checkQNorm.func: no visible global function definition for 'par'
checkQNorm.func: no visible binding for global variable 'sd'
flowFPBin.def: no visible global function definition for 'flowSet'
kMeansBin.def: no visible global function definition for 'exprs'
kMeansBin.def: no visible global function definition for 'pData'
kMeansBin.def: no visible global function definition for 'kmeans'
mapBinsKNN.def : mapClustersKNN: no visible global function definition
for 'exprs'
mapBinsKNN.def: no visible global function definition for
'capture.output'
mapBinsKNN.def: no visible global function definition for 'parLapply'
medianFI: no visible global function definition for 'median'
medianFIDist: no visible global function definition for 'median'
proportionPositive: no visible global function definition for
'quantile'
qnorm.func : normCol : <anonymous>: no visible global function
definition for 'exprs'
qnorm.func : normCol : getCol: no visible global function definition
for 'exprs'
qnorm.func : normCol : getCol: no visible global function definition
for 'runif'
qnorm.func : normCol : setCol: no visible global function definition
for 'exprs'
qnorm.func : normCol : setCol: no visible global function definition
for 'exprs<-'
checkQNorm,FlowSample-FlowSample: no visible global function definition
for 'flowSet'
checkQNorm,FlowSample-FlowSample: no visible global function definition
for 'par'
checkQNorm,FlowSample-FlowSample: no visible binding for global
variable 'sd'
flowFPBin,FlowSample: no visible global function definition for
'flowSet'
getBinExpr,BinnedFlowSample : getBinFrame: no visible global function
definition for 'exprs<-'
getBinExpr,BinnedFlowSample : getBinFrame: no visible global function
definition for 'exprs'
getBinExpr,BinnedFlowSample : scaleData: no visible global function
definition for 'pData'
getBinExpr,BinnedFlowSample : getOnePopExpr : extractOneTube :
<anonymous>: no visible global function definition for 'exprs'
getBinExpr,BinnedFlowSample : getOnePopExpr : extractOneTube: no
visible global function definition for 'pData'
getBinExpr,BinnedFlowSample : getOneBinMeds : <anonymous>: no visible
global function definition for 'median'
getBinExpr,BinnedFlowSample : getOneBinMeds : <anonymous>: no visible
global function definition for 'exprs'
getBinExpr,BinnedFlowSample : getOneBinMeds: no visible global function
definition for 'pData'
kMeansBin,FlowSample: no visible global function definition for 'exprs'
kMeansBin,FlowSample: no visible global function definition for 'pData'
kMeansBin,FlowSample: no visible global function definition for
'kmeans'
mapBinsKNN,FlowSample : mapClustersKNN: no visible global function
definition for 'exprs'
mapBinsKNN,FlowSample: no visible global function definition for
'capture.output'
mapBinsKNN,FlowSample: no visible global function definition for
'parLapply'
quantileNormalise,FlowSample : normCol : <anonymous>: no visible global
function definition for 'exprs'
quantileNormalise,FlowSample : normCol : getCol: no visible global
function definition for 'exprs'
quantileNormalise,FlowSample : normCol : getCol: no visible global
function definition for 'runif'
quantileNormalise,FlowSample : normCol : setCol: no visible global
function definition for 'exprs'
quantileNormalise,FlowSample : normCol : setCol: no visible global
function definition for 'exprs<-'
show,FlowSample: no visible global function definition for 'str'
Undefined global functions or variables:
capture.output exprs exprs<- flowSet kmeans median pData par
parLapply quantile runif sd str
Consider adding
importFrom("graphics", "par")
importFrom("stats", "kmeans", "median", "quantile", "runif", "sd")
importFrom("utils", "capture.output", "str")
to your NAMESPACE file.
* 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
flowBin 6.96 0.01 6.97
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getBinExpr 8.66 0.02 8.67
flowBin 7.28 0.00 7.28
* 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 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/flowBin.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'flowBin' ...
** 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 'flowBin' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowBin' as flowBin_1.12.0.zip
* DONE (flowBin)