| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-04-29 11:40:40 -0400 (Mon, 29 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4752 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4518 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4475 |
| 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 1.11.0 (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 | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: condiments |
| Version: 1.11.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:condiments.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings condiments_1.11.0.tar.gz |
| StartedAt: 2024-04-29 04:52:35 -0000 (Mon, 29 Apr 2024) |
| EndedAt: 2024-04-29 05:01:45 -0000 (Mon, 29 Apr 2024) |
| EllapsedTime: 551.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: condiments.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:condiments.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings condiments_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/condiments.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘condiments/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘condiments’ version ‘1.11.0’
* 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 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
.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 5.704 0.000 5.717
topologyTest 5.592 0.032 5.635
* 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
‘/home/biocbuild/bbs-3.19-bioc/meat/condiments.Rcheck/00check.log’
for details.
condiments.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL condiments ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
> 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
207.208 5.398 213.119
condiments.Rcheck/condiments-Ex.timings
| name | user | system | elapsed | |
| create_differential_topology | 0.006 | 0.000 | 0.006 | |
| differentiationTest | 2.856 | 0.052 | 2.917 | |
| fateSelectionTest | 2.283 | 0.036 | 2.323 | |
| fateSelectionTest_multipleSamples | 3.087 | 0.026 | 3.119 | |
| imbalance_score | 0.289 | 0.004 | 0.295 | |
| merge_sds | 0.486 | 0.000 | 0.487 | |
| nLineages | 0.394 | 0.000 | 0.395 | |
| progressionTest | 0.483 | 0.004 | 0.491 | |
| progressionTest_multipleSamples | 0.472 | 0.008 | 0.481 | |
| slingshot_conditions | 0.997 | 0.004 | 1.003 | |
| topologyTest | 5.592 | 0.032 | 5.635 | |
| topologyTest_multipleSamples | 5.704 | 0.000 | 5.717 | |
| weights_from_pst | 0.394 | 0.000 | 0.395 | |