Kieran O'Neill
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/flowBin |
| Branch: RELEASE_3_6 |
| Last Commit: 3e4b819 |
| Last Changed Date: 2017-10-30 12:40:10 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:11:47 -0400 (Thu, 12 Apr 2018).
| Package 471/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| flowBin 1.14.0 Kieran O'Neill
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: flowBin |
| Version: 1.14.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings flowBin_1.14.0.tar.gz |
| StartedAt: 2018-04-11 23:28:15 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 23:29:23 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 67.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: flowBin.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings flowBin_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/flowBin.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowBin/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowBin’ version ‘1.14.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
flowBin 5.620 0.012 5.635
getBinExpr 5.324 0.016 5.345
* 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
‘/home/biocbuild/bbs-3.6-bioc/meat/flowBin.Rcheck/00check.log’
for details.
flowBin.Rcheck/00install.out
* 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 * DONE (flowBin)
flowBin.Rcheck/flowBin-Ex.timings
| name | user | system | elapsed | |
| checkQNorm | 0.932 | 0.024 | 0.955 | |
| flowBin | 5.620 | 0.012 | 5.635 | |
| flowFPBin | 0.348 | 0.004 | 0.353 | |
| getBinExpr | 5.324 | 0.016 | 5.345 | |
| kMeansBin | 0.372 | 0.000 | 0.374 | |
| mapBinsKNN | 0.236 | 0.008 | 0.248 | |
| quantileNormalise | 0.408 | 0.004 | 0.415 | |