| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:35:57 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 704/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FELLA 1.22.0 (landing page) Sergio Picart-Armada
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | TIMEOUT | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.22.0 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:FELLA.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings FELLA_1.22.0.tar.gz |
| StartedAt: 2024-04-15 22:45:37 -0400 (Mon, 15 Apr 2024) |
| EndedAt: 2024-04-15 23:25:37 -0400 (Mon, 15 Apr 2024) |
| EllapsedTime: 2400.4 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: FELLA.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:FELLA.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings FELLA_1.22.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/FELLA.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘FELLA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FELLA’ version ‘1.22.0’
* 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 R 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
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 ... 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
data-funs 5.983 0.312 6.295
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘musmusculus.Rmd’ using ‘UTF-8’... OK
‘quickstart.Rmd’ using ‘UTF-8’... failed
‘zebrafish.Rmd’ using ‘UTF-8’... OK
‘FELLA.Rnw’ using ‘UTF-8’... OK
ERROR
Errors in running code in vignettes:
when running code in ‘quickstart.Rmd’
...
> input.fail <- paste0(" ", input.full)
> defineCompounds(compounds = input.fail, data = FELLA.sample)
No background compounds specified. Default background will be used.
Warning in defineCompounds(compounds = input.fail, data = FELLA.sample) :
Some compounds were introduced as affected but they do not belong to the background. These compounds will be excluded from the analysis. Use 'getExcluded' to see them.
When sourcing ‘quickstart.R’:
Error: None of the specified compounds appear in the available KEGG data.
Execution halted
* checking re-building of vignette outputs ...
FELLA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL FELLA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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")
|
| | 0%
|
|============== | 20%
|
|============================ | 40%
|
|========================================== | 60%
|
|======================================================== | 80%
|
|======================================================================| 100%
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
|
| | 0%
|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
|========================================== | 60%
|
|================================================= | 70%
|
|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 168 ]
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 168 ]
>
> proc.time()
user system elapsed
32.909 3.335 69.060
FELLA.Rcheck/FELLA-Ex.timings
| name | user | system | elapsed | |
| FELLA | 0.240 | 0.011 | 0.251 | |
| FELLA.sample | 0.011 | 0.000 | 0.011 | |
| checkArguments | 0.002 | 0.000 | 0.002 | |
| data-funs | 5.983 | 0.312 | 6.295 | |
| enrich-funs | 2.817 | 0.012 | 2.829 | |
| export-funs | 0.184 | 0.000 | 0.185 | |
| getBackground | 0.287 | 0.008 | 0.295 | |
| getCom | 0.010 | 0.000 | 0.011 | |
| getExcluded | 0.012 | 0.000 | 0.012 | |
| getGraph | 0.01 | 0.00 | 0.01 | |
| getInfo | 0.01 | 0.00 | 0.01 | |
| getInput | 0.012 | 0.000 | 0.011 | |
| getMatrix | 0.015 | 0.004 | 0.019 | |
| getName | 0.021 | 0.000 | 0.021 | |
| getPscores | 0.025 | 0.004 | 0.030 | |
| getPvaluesSize | 0.021 | 0.000 | 0.021 | |
| getStatus | 0.011 | 0.000 | 0.010 | |
| getSums | 0.416 | 0.044 | 0.459 | |
| getValid | 0.022 | 0.000 | 0.022 | |
| infere.con2ec | 0.002 | 0.000 | 0.002 | |
| input.sample | 0.001 | 0.000 | 0.000 | |
| is.FELLA.DATA | 0.012 | 0.004 | 0.015 | |
| is.FELLA.USER | 0.017 | 0.008 | 0.025 | |
| largestcc | 0.090 | 0.012 | 0.101 | |
| launchApp | 0 | 0 | 0 | |
| listApprox | 0.000 | 0.000 | 0.001 | |
| listCategories | 0 | 0 | 0 | |
| listInternalDatabases | 0.001 | 0.000 | 0.001 | |
| listMethods | 0 | 0 | 0 | |
| mytriangle | 0.030 | 0.012 | 0.042 | |
| plotBipartite | 0.056 | 0.004 | 0.060 | |
| plotLegend | 0.025 | 0.004 | 0.028 | |
| sanitise | 0.000 | 0.000 | 0.001 | |