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This page was generated on 2024-06-21 13:21 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4690
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4404
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
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 2031/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
stJoincount 1.7.0  (landing page)
Jiarong Song
Snapshot Date: 2024-06-20 14:00 -0400 (Thu, 20 Jun 2024)
git_url: https://git.bioconductor.org/packages/stJoincount
git_branch: devel
git_last_commit: 1b562c6
git_last_commit_date: 2024-04-30 11:45:38 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for stJoincount on nebbiolo2

To the developers/maintainers of the stJoincount package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/stJoincount.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: stJoincount
Version: 1.7.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:stJoincount.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings stJoincount_1.7.0.tar.gz
StartedAt: 2024-06-21 04:13:54 -0400 (Fri, 21 Jun 2024)
EndedAt: 2024-06-21 04:20:45 -0400 (Fri, 21 Jun 2024)
EllapsedTime: 410.7 seconds
RetCode: 0
Status:   OK  
CheckDir: stJoincount.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:stJoincount.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings stJoincount_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/stJoincount.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘stJoincount/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘stJoincount’ version ‘1.7.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘stJoincount’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 loading without being on the library search path ... 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/stJoincount.Rcheck/00check.log’
for details.


Installation output

stJoincount.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL stJoincount
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘stJoincount’ ...
** 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 (stJoincount)

Tests output

stJoincount.Rcheck/tests/testthat.Rout


R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(stJoincount)
> 
> test_check("stJoincount")
No optimal number found, using n = 110 instead.
In this case, there may be minor deviations in the subsequent calculation process.
        The results are for reference only
No optimal number found, using n = 110 instead.
In this case, there may be minor deviations in the subsequent calculation process.
        The results are for reference only
No optimal number found, using n = 110 instead.
In this case, there may be minor deviations in the subsequent calculation process.
        The results are for reference only
No optimal number found, using n = 110 instead.
In this case, there may be minor deviations in the subsequent calculation process.
        The results are for reference only
No optimal number found, using n = 110 instead.
In this case, there may be minor deviations in the subsequent calculation process.
        The results are for reference only
No optimal number found, using n = 110 instead.
In this case, there may be minor deviations in the subsequent calculation process.
        The results are for reference only
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 39 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 39 ]
> 
> proc.time()
   user  system elapsed 
 25.503   0.928  26.422 

Example timings

stJoincount.Rcheck/stJoincount-Ex.timings

nameusersystemelapsed
customDict0.0020.0000.003
dataPrepFromSeurat0.1090.0080.117
dataPrepFromSpE0.2050.0040.210
extentBuffer1.2030.0001.203
joincountAnalysis1.3480.0041.353
mosaicIntPlot1.7140.0321.746
rasterPrep0.0230.0000.023
rasterizeEachCluster1.3410.0001.340
resolutionCalc0.0210.0000.021
zscoreMatrix1.3260.0001.325
zscorePlot1.3630.0161.379