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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 2024/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
speckle 1.6.0  (landing page)
Belinda Phipson
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/speckle
git_branch: RELEASE_3_20
git_last_commit: 5919895
git_last_commit_date: 2024-10-29 11:16:44 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 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 speckle on nebbiolo2

To the developers/maintainers of the speckle package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/speckle.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: speckle
Version: 1.6.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:speckle.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings speckle_1.6.0.tar.gz
StartedAt: 2024-12-20 05:43:42 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 05:48:19 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 277.3 seconds
RetCode: 0
Status:   OK  
CheckDir: speckle.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:speckle.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings speckle_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/speckle.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘speckle/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘speckle’ version ‘1.6.0’
* 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 ‘speckle’ 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 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 ... NOTE
.extractSCE: no visible global function definition for ‘colData<-’
Undefined global functions or variables:
  colData<-
* 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
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/speckle.Rcheck/00check.log’
for details.


Installation output

speckle.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘speckle’ ...
** using staged installation
** R
** data
** 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 (speckle)

Tests output

speckle.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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(speckle)
> 
> test_check("speckle")
Performing arcsin square root transformation of 
                    proportions
Performing logit transformation of proportions
Using classic mode.
NULL
Performing logit transformation of proportions
NULL
Performing arcsin square root transformation of proportions
group variable has 2 levels, t-tests will be performed
Performing logit transformation of proportions
Performing logit transformation of proportions
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 18 ]

══ Skipped tests (10) ══════════════════════════════════════════════════════════
• On CRAN (10): 'test-convertData.R:26:3', 'test-getTransformedProps.R:35:3',
  'test-normCounts.R:13:3', 'test-plotCellTypeMeanVar.R:24:3',
  'test-plotCellTypeProps.R:23:3', 'test-plotCellTypePropsMeanVar.R:30:3',
  'test-propeller.R:42:3', 'test-propeller.anova.R:54:3',
  'test-propeller.ttest.R:49:3', 'test-speckle_example_data.R:11:3'

[ FAIL 0 | WARN 0 | SKIP 10 | PASS 18 ]
Deleting unused snapshots:
• convertData/converted_data.json
• getTransformedProps/transformed_props.json
• normCounts/lnorm_y2.json
• propeller.anova/propeller_anova_table.json
• propeller.ttest/propeller_ttest_table.json
• propeller/propeller_table.json
• speckle_example_data/speckle_example_data.json
> 
> proc.time()
   user  system elapsed 
 11.051   0.782  11.821 

Example timings

speckle.Rcheck/speckle-Ex.timings

nameusersystemelapsed
convertDataToList0.0370.0030.040
estimateBetaParam000
estimateBetaParamsFromCounts0.0030.0000.003
getTransformedProps0.0350.0050.040
ggplotColors0.0090.0000.009
normCounts0.0290.0030.032
plotCellTypeMeanVar0.0940.0120.106
plotCellTypeProps0.2660.0070.273
plotCellTypePropsMeanVar0.0220.0000.022
propeller0.0330.0010.034
propeller.anova0.0410.0020.042
propeller.ttest0.0380.0000.038
speckle_example_data0.0210.0090.030