Kieran O'Neill
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/flowBin |
| Branch: RELEASE_3_11 |
| Last Commit: 8e86624 |
| Last Changed Date: 2020-04-27 14:37:48 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:34 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE flowBin PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 604/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| flowBin 1.24.0 Kieran O'Neill
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: flowBin |
| Version: 1.24.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowBin.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings flowBin_1.24.0.tar.gz |
| StartedAt: 2020-10-17 04:04:05 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 04:06:04 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 119.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: flowBin.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowBin.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings flowBin_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/flowBin.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.24.0'
* 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
* 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
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getBinExpr 5.78 0.03 5.82
flowBin 5.45 0.06 5.51
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getBinExpr 7.16 0.02 7.17
flowBin 6.15 0.00 6.16
* 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-3.11-bioc/meat/flowBin.Rcheck/00check.log'
for details.
flowBin.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/flowBin_1.24.0.tar.gz && rm -rf flowBin.buildbin-libdir && mkdir flowBin.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowBin.buildbin-libdir flowBin_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL flowBin_1.24.0.zip && rm flowBin_1.24.0.tar.gz flowBin_1.24.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 158k 100 158k 0 0 962k 0 --:--:-- --:--:-- --:--:-- 1006k
install for i386
* installing *source* package 'flowBin' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'flowBin'
finding HTML links ... done
BinnedFlowSample html
FlowSample html
amlsample html
checkQNorm html
eventsInBins html
flowBin html
flowFPBin html
getBinExpr html
kMeansBin html
mapBinsKNN html
quantileNormalise html
removeSparseBins html
show-methods html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'flowBin' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowBin' as flowBin_1.24.0.zip
* DONE (flowBin)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'flowBin' successfully unpacked and MD5 sums checked
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flowBin.Rcheck/examples_i386/flowBin-Ex.timings
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flowBin.Rcheck/examples_x64/flowBin-Ex.timings
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