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This page was generated on 2022-01-14 13:06:51 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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 oneSENSE on tokay2


To the developers/maintainers of the oneSENSE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/oneSENSE.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 1335/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oneSENSE 1.16.0  (landing page)
Yong Kee Tan
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/oneSENSE
git_branch: RELEASE_3_14
git_last_commit: 9a0de26
git_last_commit_date: 2021-10-26 12:36:37 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: oneSENSE
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:oneSENSE.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings oneSENSE_1.16.0.tar.gz
StartedAt: 2022-01-13 23:35:15 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 23:37:27 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 132.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: oneSENSE.Rcheck
Warnings: NA

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:oneSENSE.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings oneSENSE_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/oneSENSE.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 'oneSENSE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'oneSENSE' version '1.16.0'
* 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 'oneSENSE' 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'oneSENSE-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: OneSmapperFreq2
> ### Title: Frequency Heatplot Generation Part 2
> ### Aliases: OneSmapperFreq2
> 
> ### ** Examples
> 
> 
> dir2 <-system.file('extdata/fcs_Out',package='oneSENSE')
> file5 <- system.file('extdata/myFFdatas.rds', package = 'oneSENSE')
> FFdata1 <- readRDS(file5)
> OneSmapperFreq2(dir2, 250, FFdata1) #remove hash symbol to run
No scatter mode specifed:
  Setting the mode to markers
  Read more about this attribute -> https://plotly.com/r/reference/#scatter-mode
Warning: 'export' is deprecated.
Use 'orca' instead.
See help("Deprecated")
Error in shell.exec(url) : 
  file association for 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/oneSENSE/extdata/grouptwo.png' not available or invalid
Calls: OneSmapperFreq2 -> browseURL -> shell.exec
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'oneSENSE-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: OneSmapperFreq2
> ### Title: Frequency Heatplot Generation Part 2
> ### Aliases: OneSmapperFreq2
> 
> ### ** Examples
> 
> 
> dir2 <-system.file('extdata/fcs_Out',package='oneSENSE')
> file5 <- system.file('extdata/myFFdatas.rds', package = 'oneSENSE')
> FFdata1 <- readRDS(file5)
> OneSmapperFreq2(dir2, 250, FFdata1) #remove hash symbol to run
No scatter mode specifed:
  Setting the mode to markers
  Read more about this attribute -> https://plotly.com/r/reference/#scatter-mode
Warning: 'export' is deprecated.
Use 'orca' instead.
See help("Deprecated")
Error in shell.exec(url) : 
  file association for 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/oneSENSE/extdata/grouptwo.png' not available or invalid
Calls: OneSmapperFreq2 -> browseURL -> shell.exec
Execution halted
* 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 ERRORs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/oneSENSE.Rcheck/00check.log'
for details.


Installation output

oneSENSE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/oneSENSE_1.16.0.tar.gz && rm -rf oneSENSE.buildbin-libdir && mkdir oneSENSE.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=oneSENSE.buildbin-libdir oneSENSE_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL oneSENSE_1.16.0.zip && rm oneSENSE_1.16.0.tar.gz oneSENSE_1.16.0.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 1625k  100 1625k    0     0  4616k      0 --:--:-- --:--:-- --:--:-- 4632k

install for i386

* installing *source* package 'oneSENSE' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'oneSENSE'
    finding HTML links ... done
    FCStSNE                                 html  
    OneSmapperFlour                         html  
    OneSmapperFreq1                         html  
    OneSmapperFreq2                         html  
    getCoords                               html  
    getParameters                           html  
    oneSENSE_GUI                            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 'oneSENSE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'oneSENSE' as oneSENSE_1.16.0.zip
* DONE (oneSENSE)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'oneSENSE' successfully unpacked and MD5 sums checked

Tests output


Example timings

oneSENSE.Rcheck/examples_i386/oneSENSE-Ex.timings

nameusersystemelapsed
FCStSNE000
OneSmapperFlour0.050.002.55
OneSmapperFreq10.410.120.54

oneSENSE.Rcheck/examples_x64/oneSENSE-Ex.timings

nameusersystemelapsed
FCStSNE000
OneSmapperFlour0.060.000.55
OneSmapperFreq10.360.120.48