Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:06:15 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for flowVS on tokay2


To the developers/maintainers of the flowVS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowVS.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 677/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowVS 1.26.0  (landing page)
Ariful Azad
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/flowVS
git_branch: RELEASE_3_14
git_last_commit: 3e78d21
git_last_commit_date: 2021-10-26 13:09:01 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: flowVS
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowVS.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings flowVS_1.26.0.tar.gz
StartedAt: 2022-01-23 19:26:16 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 19:29:27 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 191.0 seconds
RetCode: 0
Status:   OK  
CheckDir: flowVS.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowVS.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings flowVS_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/flowVS.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.26.0'
* 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 '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
** running examples for arch 'x64' ... 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 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/flowVS.Rcheck/00check.log'
for details.



Installation output

flowVS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/flowVS_1.26.0.tar.gz && rm -rf flowVS.buildbin-libdir && mkdir flowVS.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowVS.buildbin-libdir flowVS_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL flowVS_1.26.0.zip && rm flowVS_1.26.0.tar.gz flowVS_1.26.0.zip
###
##############################################################################
##############################################################################


  % 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 3441k  100 3441k    0     0  5850k      0 --:--:-- --:--:-- --:--:-- 5863k

install for i386

* installing *source* package 'flowVS' ...
** using staged installation
** 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 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 'flowVS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowVS' as flowVS_1.26.0.zip
* DONE (flowVS)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'flowVS' successfully unpacked and MD5 sums checked

Tests output


Example timings

flowVS.Rcheck/examples_i386/flowVS-Ex.timings

nameusersystemelapsed
estParamFlowVS0.050.000.05
lymphs0.870.020.89
microVS2.720.424.13
plotMeanSd1.660.031.69
transFlowVS0.050.000.05

flowVS.Rcheck/examples_x64/flowVS-Ex.timings

nameusersystemelapsed
estParamFlowVS0.050.000.05
lymphs1.170.021.19
microVS2.470.012.49
plotMeanSd1.870.001.88
transFlowVS0.030.000.03