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CHECK report for flowVS on tokay1

This page was generated on 2019-04-13 11:25:17 -0400 (Sat, 13 Apr 2019).

Package 553/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowVS 1.14.1
Ariful Azad
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/flowVS
Branch: RELEASE_3_8
Last Commit: 8527e3b
Last Changed Date: 2019-01-04 13:33:17 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowVS
Version: 1.14.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowVS.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings flowVS_1.14.1.tar.gz
StartedAt: 2019-04-13 02:19:43 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:23:09 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 205.6 seconds
RetCode: 0
Status:  OK  
CheckDir: flowVS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowVS.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings flowVS_1.14.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/flowVS.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowVS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowVS' version '1.14.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'flowVS' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bartlettTestMicro: no visible binding for global variable 'var'
curvPeaks: no visible global function definition for 'density'
curvPeaks: no visible global function definition for 'quantile'
curvPeaks: no visible global function definition for 'approxfun'
curvPeaks: no visible global function definition for 'optimize'
densityPeaks: no visible global function definition for 'quantile'
densityPeaks: no visible global function definition for 'density'
densityPeaks: no visible global function definition for 'median'
densityPeaks: no visible global function definition for 'var'
densityPeaks: no visible global function definition for 'colorRamp'
densityPeaks: no visible global function definition for 'rgb'
densityPeaks: no visible global function definition for 'polygon'
densityPeaks: no visible global function definition for 'lines'
densityPeaks: no visible global function definition for 'abline'
densityPeaks: no visible global function definition for 'dev.copy2pdf'
flowVS1D: no visible global function definition for 'median'
lymphs: no visible global function definition for 'as.formula'
lymphs: no visible global function definition for 'colorRampPalette'
microVS: no visible global function definition for 'quantile'
microVS: no visible global function definition for 'points'
optimStat: no visible global function definition for 'optimize'
optimStat: no visible global function definition for 'points'
peakStats1D: no visible global function definition for 'median'
plotMeanSd : mediwind: no visible global function definition for
  'median'
plotMeanSd: no visible global function definition for 'quantile'
plotMeanSd: no visible global function definition for 'lines'
Undefined global functions or variables:
  abline approxfun as.formula colorRamp colorRampPalette density
  dev.copy2pdf lines median optimize points polygon quantile rgb var
Consider adding
  importFrom("grDevices", "colorRamp", "colorRampPalette",
             "dev.copy2pdf", "rgb")
  importFrom("graphics", "abline", "lines", "points", "polygon")
  importFrom("stats", "approxfun", "as.formula", "density", "median",
             "optimize", "quantile", "var")
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' ... NOTE
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
microVS    6.10   0.00     6.1
plotMeanSd 5.64   0.06     5.7
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
microVS    8.12   0.10    8.22
plotMeanSd 6.68   0.01    6.70
* 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-3.8-bioc/meat/flowVS.Rcheck/00check.log'
for details.



Installation output

flowVS.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/flowVS_1.14.1.tar.gz && rm -rf flowVS.buildbin-libdir && mkdir flowVS.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowVS.buildbin-libdir flowVS_1.14.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL flowVS_1.14.1.zip && rm flowVS_1.14.1.tar.gz flowVS_1.14.1.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 3440k  100 3440k    0     0  32.5M      0 --:--:-- --:--:-- --:--:-- 33.9M

install for i386

* installing *source* package 'flowVS' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowVS'
    finding HTML links ... done
    HD                                      html  
    estParamFlowVS                          html  
    flowVS-package                          html  
    lymphs                                  html  
    microVS                                 html  
    plotMeanSd                              html  
    transFlowVS                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'flowVS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowVS' as flowVS_1.14.1.zip
* DONE (flowVS)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'flowVS' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

flowVS.Rcheck/examples_i386/flowVS-Ex.timings

nameusersystemelapsed
estParamFlowVS0.030.000.30
lymphs0.620.060.68
microVS6.10.06.1
plotMeanSd5.640.065.70
transFlowVS0.040.000.05

flowVS.Rcheck/examples_x64/flowVS-Ex.timings

nameusersystemelapsed
estParamFlowVS0.030.010.05
lymphs1.060.001.06
microVS8.120.108.22
plotMeanSd6.680.016.70
transFlowVS0.050.000.05