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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 flowCHIC on tokay2


To the developers/maintainers of the flowCHIC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowCHIC.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 653/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowCHIC 1.28.0  (landing page)
Author: Joachim Schumann
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/flowCHIC
git_branch: RELEASE_3_14
git_last_commit: 03c4f45
git_last_commit_date: 2021-10-26 12:16:56 -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: flowCHIC
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowCHIC.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings flowCHIC_1.28.0.tar.gz
StartedAt: 2022-01-23 19:15:56 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 19:21:10 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 313.9 seconds
RetCode: 0
Status:   OK  
CheckDir: flowCHIC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowCHIC.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings flowCHIC_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/flowCHIC.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 'flowCHIC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowCHIC' version '1.28.0'
* package encoding: UTF-8
* 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 'flowCHIC' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
fcs_to_img,character: warning in hexbin(x, y, xbin = 128): partial
  argument match of 'xbin' to 'xbins'
img_sub,character: warning in hexbin(x, y, xbin = xbin): partial
  argument match of 'xbin' to 'xbins'
fcs_to_img,character: no visible global function definition for 'png'
fcs_to_img,character: no visible binding for global variable 'count'
fcs_to_img,character: no visible global function definition for
  'dev.off'
img_sub,character: no visible global function definition for 'png'
img_sub,character: no visible binding for global variable 'count'
img_sub,character: no visible global function definition for 'dev.off'
plot_nmds,data.frame-data.frame: no visible global function definition
  for 'as.dist'
plot_nmds,data.frame-data.frame: no visible global function definition
  for 'par'
plot_nmds,data.frame-data.frame: no visible global function definition
  for 'hclust'
plot_nmds,data.frame-data.frame: no visible global function definition
  for 'points'
plot_nmds,data.frame-data.frame: no visible global function definition
  for 'text'
plot_nmds,data.frame-data.frame: no visible global function definition
  for 'legend'
Undefined global functions or variables:
  as.dist count dev.off hclust legend par png points text
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "par", "points", "text")
  importFrom("stats", "as.dist", "hclust")
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
calculate_overlaps_xor 8.47   2.21   15.21
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
calculate_overlaps_xor 7.74   2.24    14.8
plot_nmds              4.56   0.82    34.8
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/flowCHIC.Rcheck/00check.log'
for details.



Installation output

flowCHIC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/flowCHIC_1.28.0.tar.gz && rm -rf flowCHIC.buildbin-libdir && mkdir flowCHIC.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowCHIC.buildbin-libdir flowCHIC_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL flowCHIC_1.28.0.zip && rm flowCHIC_1.28.0.tar.gz flowCHIC_1.28.0.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 3126k  100 3126k    0     0  3873k      0 --:--:-- --:--:-- --:--:-- 3879k

install for i386

* installing *source* package 'flowCHIC' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowCHIC'
    finding HTML links ... done
    Results_overlaps                        html  
    Results_overlaps_incol                  html  
    Results_overlaps_mix                    html  
    Results_xor                             html  
    Results_xor_incol                       html  
    Results_xor_mix                         html  
    abiotic_incol                           html  
    calculate_overlaps_xor                  html  
    fcs_to_img                              html  
    flowCHIC_package                        html  
    img_sub                                 html  
    plot_nmds                               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 'flowCHIC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowCHIC' as flowCHIC_1.28.0.zip
* DONE (flowCHIC)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'flowCHIC' successfully unpacked and MD5 sums checked

Tests output


Example timings

flowCHIC.Rcheck/examples_i386/flowCHIC-Ex.timings

nameusersystemelapsed
calculate_overlaps_xor 8.47 2.2115.21
fcs_to_img1.080.651.74
img_sub1.900.432.33
plot_nmds3.700.704.48

flowCHIC.Rcheck/examples_x64/flowCHIC-Ex.timings

nameusersystemelapsed
calculate_overlaps_xor 7.74 2.2414.80
fcs_to_img1.210.531.74
img_sub1.690.372.06
plot_nmds 4.56 0.8234.80