Sergio Picart-Armada
| Snapshot Date: 2024-10-09 14:00 -0400 (Wed, 09 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/FELLA |
| git_branch: RELEASE_3_19 |
| git_last_commit: ec13672 |
| git_last_commit_date: 2024-04-30 11:04:43 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-11 20:41 -0400 (Fri, 11 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4529 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4479 |
| 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 715/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FELLA 1.24.0 (landing page) Sergio Picart-Armada
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the FELLA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FELLA.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: FELLA |
| Version: 1.24.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FELLA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FELLA_1.24.0.tar.gz |
| StartedAt: 2024-10-10 05:10:37 -0400 (Thu, 10 Oct 2024) |
| EndedAt: 2024-10-10 05:18:32 -0400 (Thu, 10 Oct 2024) |
| EllapsedTime: 475.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FELLA.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FELLA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FELLA_1.24.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/FELLA.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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FELLA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FELLA’ version ‘1.24.0’
* 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 ‘FELLA’ 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
buildGraphFromKEGGREST: no visible global function definition for
‘capture.output’
Undefined global functions or variables:
capture.output
Consider adding
importFrom("utils", "capture.output")
to your NAMESPACE file.
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'dot-params.Rd':
‘databaseDir’ ‘internalDir’ ‘object’ ‘data’ ‘type’ ‘level’ ‘method’
‘methods’ ‘approx’ ‘loadMatrix’ ‘threshold’
‘thresholdConnectedComponent’ ‘plimit’ ‘nlimit’ ‘niter’ ‘layout’
‘graph’ ‘GOterm’ ‘GONamesAsLabels’ ‘LabelLengthAtPlot’
‘godata.options’ ‘mart.options’ ‘p.adjust’ ‘dampingFactor’ ‘t.df’
‘compounds’ ‘compoundsBackground’ ‘NamesAsLabels’ ‘capPscores’
Documented arguments not in \usage in Rd file 'infere.con2ec.Rd':
‘gene2enyzme’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
data-funs 15.711 0.488 19.665
enrich-funs 6.768 0.142 8.488
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc/meat/FELLA.Rcheck/00check.log’
for details.
FELLA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FELLA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘FELLA’ ... ** 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 (FELLA)
FELLA.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(testthat)
> library(FELLA)
>
> test_check("FELLA")
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[ FAIL 0 | WARN 12 | SKIP 0 | PASS 168 ]
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 168 ]
>
> proc.time()
user system elapsed
81.205 6.136 136.739
FELLA.Rcheck/FELLA-Ex.timings
| name | user | system | elapsed | |
| FELLA | 0.610 | 0.113 | 0.926 | |
| FELLA.sample | 0.021 | 0.002 | 0.027 | |
| checkArguments | 0.003 | 0.001 | 0.004 | |
| data-funs | 15.711 | 0.488 | 19.665 | |
| enrich-funs | 6.768 | 0.142 | 8.488 | |
| export-funs | 0.428 | 0.018 | 0.523 | |
| getBackground | 0.807 | 0.029 | 0.982 | |
| getCom | 0.020 | 0.003 | 0.026 | |
| getExcluded | 0.023 | 0.005 | 0.033 | |
| getGraph | 0.020 | 0.002 | 0.027 | |
| getInfo | 0.036 | 0.003 | 0.046 | |
| getInput | 0.024 | 0.004 | 0.033 | |
| getMatrix | 0.036 | 0.003 | 0.046 | |
| getName | 0.020 | 0.002 | 0.025 | |
| getPscores | 0.053 | 0.005 | 0.066 | |
| getPvaluesSize | 0.040 | 0.003 | 0.046 | |
| getStatus | 0.020 | 0.003 | 0.028 | |
| getSums | 0.447 | 0.016 | 0.515 | |
| getValid | 0.042 | 0.006 | 0.049 | |
| infere.con2ec | 0.004 | 0.001 | 0.005 | |
| input.sample | 0.002 | 0.002 | 0.005 | |
| is.FELLA.DATA | 0.020 | 0.002 | 0.025 | |
| is.FELLA.USER | 0.041 | 0.005 | 0.053 | |
| largestcc | 0.224 | 0.004 | 0.246 | |
| launchApp | 0 | 0 | 0 | |
| listApprox | 0.001 | 0.000 | 0.001 | |
| listCategories | 0.001 | 0.000 | 0.001 | |
| listInternalDatabases | 0.001 | 0.001 | 0.004 | |
| listMethods | 0.001 | 0.000 | 0.001 | |
| mytriangle | 0.101 | 0.005 | 0.123 | |
| plotBipartite | 0.120 | 0.007 | 0.145 | |
| plotLegend | 0.063 | 0.005 | 0.080 | |
| sanitise | 0.001 | 0.001 | 0.001 | |