| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| 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 424/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| condiments 1.12.0 (landing page) Hector Roux de Bezieux
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| 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: 2024-06-10 11:37:42 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 11:49:37 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 715.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: condiments.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* 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 4.530 0.070 6.866
topologyTest 4.431 0.078 6.880
* 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.
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-arm64/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)
condiments.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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
167.631 7.768 265.521
condiments.Rcheck/condiments-Ex.timings
| name | user | system | elapsed | |
| create_differential_topology | 0.005 | 0.001 | 0.006 | |
| differentiationTest | 2.868 | 0.077 | 4.575 | |
| fateSelectionTest | 1.832 | 0.096 | 2.864 | |
| fateSelectionTest_multipleSamples | 2.937 | 0.065 | 4.643 | |
| imbalance_score | 0.232 | 0.018 | 0.371 | |
| merge_sds | 0.384 | 0.014 | 0.572 | |
| nLineages | 0.296 | 0.009 | 0.496 | |
| progressionTest | 0.366 | 0.019 | 0.608 | |
| progressionTest_multipleSamples | 0.376 | 0.025 | 0.604 | |
| slingshot_conditions | 0.758 | 0.018 | 1.196 | |
| topologyTest | 4.431 | 0.078 | 6.880 | |
| topologyTest_multipleSamples | 4.530 | 0.070 | 6.866 | |
| weights_from_pst | 0.344 | 0.013 | 0.513 | |