Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:46 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 742/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
fobitools 1.13.0 (landing page) Pol Castellano-Escuder
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the fobitools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fobitools.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: fobitools |
Version: 1.13.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:fobitools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings fobitools_1.13.0.tar.gz |
StartedAt: 2024-08-21 05:00:25 -0000 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 05:05:39 -0000 (Wed, 21 Aug 2024) |
EllapsedTime: 314.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: fobitools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:fobitools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings fobitools_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/fobitools.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) 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 ‘fobitools/DESCRIPTION’ ... OK * this is package ‘fobitools’ version ‘1.13.0’ * 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 ‘fobitools’ 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 annotate_foods: no visible binding for global variable ‘FOOD_NAME’ annotate_foods: no visible binding for global variable ‘FOOD_ID’ annotate_foods: no visible binding for global variable ‘words’ annotate_foods: no visible binding for global variable ‘words_joint’ annotate_foods: no visible binding for global variable ‘id_code’ annotate_foods: no visible binding for global variable ‘name’ annotate_foods: no visible binding for global variable ‘ref’ annotate_foods: no visible binding for global variable ‘detect’ annotate_foods: no visible binding for global variable ‘.’ annotate_foods: no visible binding for global variable ‘match_score’ fobi_graph: no visible binding for global variable ‘is_a_code’ fobi_graph: no visible binding for global variable ‘id_code’ fobi_graph: no visible binding for global variable ‘Contains’ fobi_graph: no visible binding for global variable ‘Property’ fobi_graph: no visible binding for global variable ‘name’ fobi_graph: no visible binding for global variable ‘BiomarkerOf’ fobi_graph: no visible binding for global variable ‘is_a_name’ fobi_graph: no visible binding for global variable ‘subOntology’ id_convert: no visible binding for global variable ‘BiomarkerOf’ id_convert: no visible binding for global variable ‘name’ id_convert: no visible binding for global variable ‘FOBI’ id_convert: no visible binding for global variable ‘HMDB’ id_convert: no visible binding for global variable ‘KEGG’ id_convert: no visible binding for global variable ‘PubChemCID’ id_convert: no visible binding for global variable ‘InChIKey’ id_convert: no visible binding for global variable ‘InChICode’ id_convert: no visible binding for global variable ‘ChemSpider’ id_convert: no visible binding for global variable ‘metaboliteNames’ id_convert: no visible binding for global variable ‘presence’ id_convert: no visible binding for global variable ‘.’ msea: no visible binding for global variable ‘BiomarkerOf’ msea: no visible binding for global variable ‘id_BiomarkerOf’ msea: no visible binding for global variable ‘name’ msea: no visible binding for global variable ‘FOBI’ msea: no visible binding for global variable ‘is_a_code’ msea: no visible binding for global variable ‘is_a_name’ msea: no visible binding for global variable ‘.’ msea: no visible global function definition for ‘unstack’ msea: no visible binding for global variable ‘pathway’ msea: no visible binding for global variable ‘size’ msea: no visible binding for global variable ‘className’ msea: no visible binding for global variable ‘classSize’ msea: no visible binding for global variable ‘log2err’ msea: no visible binding for global variable ‘ES’ msea: no visible binding for global variable ‘NES’ msea: no visible binding for global variable ‘pval’ msea: no visible binding for global variable ‘padj’ msea: no visible binding for global variable ‘leadingEdge’ ora: no visible binding for global variable ‘BiomarkerOf’ ora: no visible binding for global variable ‘id_BiomarkerOf’ ora: no visible binding for global variable ‘name’ ora: no visible binding for global variable ‘FOBI’ ora: no visible binding for global variable ‘is_a_code’ ora: no visible binding for global variable ‘is_a_name’ ora: no visible binding for global variable ‘.’ ora: no visible global function definition for ‘unstack’ ora: no visible binding for global variable ‘pathway’ ora: no visible binding for global variable ‘size’ ora: no visible binding for global variable ‘overlapGenes’ ora: no visible binding for global variable ‘className’ ora: no visible binding for global variable ‘classSize’ ora: no visible binding for global variable ‘overlap’ ora: no visible binding for global variable ‘pval’ ora: no visible binding for global variable ‘padj’ ora: no visible binding for global variable ‘overlapMetabolites’ parse_fobi: no visible binding for global variable ‘V2’ parse_fobi: no visible binding for global variable ‘V1’ parse_fobi: no visible binding for global variable ‘gf’ parse_fobi: no visible binding for global variable ‘name’ parse_fobi: no visible binding for global variable ‘id_code’ parse_fobi: no visible binding for global variable ‘Contains’ parse_fobi: no visible binding for global variable ‘disjoint_from’ parse_fobi: no visible binding for global variable ‘FOBI:050339’ parse_fobi: no visible binding for global variable ‘ChemSpider’ parse_fobi: no visible binding for global variable ‘KEGG’ parse_fobi: no visible binding for global variable ‘is_a_code’ parse_fobi: no visible binding for global variable ‘id_BiomarkerOf’ parse_fobi: no visible binding for global variable ‘id_Contains’ Undefined global functions or variables: . BiomarkerOf ChemSpider Contains ES FOBI FOBI:050339 FOOD_ID FOOD_NAME HMDB InChICode InChIKey KEGG NES Property PubChemCID V1 V2 className classSize detect disjoint_from gf id_BiomarkerOf id_Contains id_code is_a_code is_a_name leadingEdge log2err match_score metaboliteNames name overlap overlapGenes overlapMetabolites padj pathway presence pval ref size subOntology unstack words words_joint Consider adding importFrom("methods", "className") importFrom("utils", "unstack") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 ... NOTE Note: found 199 marked UTF-8 strings * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... NOTE The following directory looks like a leftover from 'knitr': ‘figure’ Please remove from your package. * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed parse_fobi 35.186 0.474 41.849 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/fobitools.Rcheck/00check.log’ for details.
fobitools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL fobitools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘fobitools’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (fobitools)
fobitools.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: 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(testthat) > library(fobitools) > > test_check("fobitools") 100% annotated 0.449 sec elapsed 100% annotated 0.366 sec elapsed 100% annotated 11.427 sec elapsed [ FAIL 0 | WARN 7 | SKIP 0 | PASS 73 ] [ FAIL 0 | WARN 7 | SKIP 0 | PASS 73 ] > > proc.time() user system elapsed 145.865 5.682 175.281
fobitools.Rcheck/fobitools-Ex.timings
name | user | system | elapsed | |
ORA | 0.442 | 0.028 | 0.472 | |
annotate_foods | 0.530 | 0.032 | 0.579 | |
fobi_graph | 0.904 | 0.036 | 0.948 | |
id_convert | 0.129 | 0.004 | 0.133 | |
msea | 2.072 | 0.211 | 2.198 | |
parse_fobi | 35.186 | 0.474 | 41.849 | |