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This page was generated on 2023-10-16 11:36:25 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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

Package 1431/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oneSENSE 1.22.0  (landing page)
Yong Kee Tan
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/oneSENSE
git_branch: RELEASE_3_17
git_last_commit: b80268f
git_last_commit_date: 2023-04-25 10:55:17 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for oneSENSE on palomino3


To the developers/maintainers of the oneSENSE package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: oneSENSE
Version: 1.22.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:oneSENSE.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings oneSENSE_1.22.0.tar.gz
StartedAt: 2023-10-16 04:57:25 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 04:58:43 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 78.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: oneSENSE.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:oneSENSE.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings oneSENSE_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/oneSENSE.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'oneSENSE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'oneSENSE' version '1.22.0'
* 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
* 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 ... 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
Warning in matrix(dataX, nrow = Bins, ncol = dim(dataX)[2]) :
  data length differs from size of matrix: [22500 != 250 x 15]
Warning in matrix(dataX, nrow = Bins, ncol = dim(dataX)[2]) :
  data length differs from size of matrix: [22500 != 250 x 15]
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 'F:/biocbuild/bbs-3.17-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: 1 ERROR, 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc/meat/oneSENSE.Rcheck/00check.log'
for details.


Installation output

oneSENSE.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL oneSENSE
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'oneSENSE' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (oneSENSE)

Tests output


Example timings

oneSENSE.Rcheck/oneSENSE-Ex.timings

nameusersystemelapsed
FCStSNE000
OneSmapperFlour0.120.030.52
OneSmapperFreq10.480.110.88