Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-07-12 17:40 -0400 (Fri, 12 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
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 424/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
condiments 1.12.0  (landing page)
Hector Roux de Bezieux
Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 Jul 2024)
git_url: https://git.bioconductor.org/packages/condiments
git_branch: RELEASE_3_19
git_last_commit: 9b27d5c
git_last_commit_date: 2024-04-30 11:32:42 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for condiments on merida1

To the developers/maintainers of the condiments package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/condiments.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: condiments
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:condiments.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings condiments_1.12.0.tar.gz
StartedAt: 2024-07-11 02:27:03 -0400 (Thu, 11 Jul 2024)
EndedAt: 2024-07-11 02:43:17 -0400 (Thu, 11 Jul 2024)
EllapsedTime: 974.3 seconds
RetCode: 0
Status:   OK  
CheckDir: condiments.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:condiments.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings condiments_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/condiments.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘condiments/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘condiments’ version ‘1.12.0’
* 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 ‘condiments’ 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 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 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
.condition_sling: no visible binding for global variable ‘.’
.condition_sling : <anonymous>: no visible binding for global variable
  ‘.’
.distinct_inputs: no visible binding for global variable ‘Samples’
.distinct_inputs: no visible binding for global variable ‘.’
.fateSelectionTest: no visible binding for global variable ‘pair’
.fateSelectionTest: no visible binding for global variable ‘statistic’
.fateSelectionTest: no visible binding for global variable ‘p.value’
.multiple_samples: no visible binding for global variable ‘p.value’
.progressionTest: no visible binding for global variable ‘lineage’
.progressionTest: no visible binding for global variable ‘statistic’
.progressionTest: no visible binding for global variable ‘p.value’
.topologyTest_multipleSamples: no visible binding for global variable
  ‘p.value’
fateSelectionTest_multipleSamples,SlingshotDataSet: no visible binding
  for global variable ‘condition’
progressionTest_multipleSamples,SlingshotDataSet: no visible binding
  for global variable ‘condition’
Undefined global functions or variables:
  . Samples condition lineage p.value pair statistic
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
topologyTest_multipleSamples 9.387  0.081  11.365
topologyTest                 9.191  0.121  11.213
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/condiments.Rcheck/00check.log’
for details.


Installation output

condiments.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL condiments
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘condiments’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (condiments)

Tests output

condiments.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> library(condiments)
> library(testthat)
> test_check("condiments")
note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 2 unique complexity parameters in default grid. Truncating the grid to 2 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 2 unique complexity parameters in default grid. Truncating the grid to 2 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 112 ]
> 
> proc.time()
   user  system elapsed 
305.849   7.432 375.484 

Example timings

condiments.Rcheck/condiments-Ex.timings

nameusersystemelapsed
create_differential_topology0.0090.0010.012
differentiationTest3.5490.1024.439
fateSelectionTest3.6810.1794.610
fateSelectionTest_multipleSamples4.1030.0664.999
imbalance_score0.4620.0210.572
merge_sds0.7310.0180.901
nLineages0.6100.0100.727
progressionTest0.8180.0281.031
progressionTest_multipleSamples0.7320.0480.936
slingshot_conditions1.5500.0271.891
topologyTest 9.191 0.12111.213
topologyTest_multipleSamples 9.387 0.08111.365
weights_from_pst0.6520.0150.785