Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:40 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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To the developers/maintainers of the famat package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/famat.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 650/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
famat 1.9.0 (landing page) Mathieu Charles
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: famat |
Version: 1.9.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:famat.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings famat_1.9.0.tar.gz |
StartedAt: 2023-02-28 03:08:41 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 03:15:16 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 395.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: famat.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:famat.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings famat_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/famat.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘famat/DESCRIPTION’ ... OK * this is package ‘famat’ version ‘1.9.0’ * 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 ‘famat’ 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 dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘BiasedUrn’ ‘mgcv’ ‘stats’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Getenvir: no visible binding for global variable ‘MPINetData’ Undefined global functions or variables: MPINetData * 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘famat-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: interactions > ### Title: Interactions between genes and metabolites > ### Aliases: interactions > > ### ** Examples > > ## load example data > data(listk) > data(listr) > data(listw) > > interactions_result=interactions(listk,listr,listw) Error in names(no_path) <- (names(tagged) = c("from", "link", "to", "path", : 'names' attribute [6] must be the same length as the vector [0] Calls: interactions -> filter_inter Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Backtrace: ▆ 1. └─famat::interactions(listk, listr, listw) at test-compl_data.R:6:0 2. └─famat:::filter_inter(interac) ── Error ('test-interactions.R:6'): (code run outside of `test_that()`) ──────── Error in `names(no_path) <- (names(tagged) = c("from", "link", "to", "path", "tag", "type"))`: 'names' attribute [6] must be the same length as the vector [0] Backtrace: ▆ 1. └─famat::interactions(listk, listr, listw) at test-interactions.R:6:0 2. └─famat:::filter_inter(interac) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘famat.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘famat.Rmd’ using rmarkdown Quitting from lines 79-84 (famat.Rmd) Error: processing vignette 'famat.Rmd' failed with diagnostics: 'names' attribute [6] must be the same length as the vector [0] --- failed re-building ‘famat.Rmd’ SUMMARY: processing the following file failed: ‘famat.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 3 ERRORs, 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/famat.Rcheck/00check.log’ for details.
famat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL famat ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘famat’ ... ** using staged installation ** R ** data ** 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 (famat)
famat.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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(famat) > > test_check("famat") [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-compl_data.R:6'): (code run outside of `test_that()`) ────────── Error in `names(no_path) <- (names(tagged) = c("from", "link", "to", "path", "tag", "type"))`: 'names' attribute [6] must be the same length as the vector [0] Backtrace: ▆ 1. └─famat::interactions(listk, listr, listw) at test-compl_data.R:6:0 2. └─famat:::filter_inter(interac) ── Error ('test-interactions.R:6'): (code run outside of `test_that()`) ──────── Error in `names(no_path) <- (names(tagged) = c("from", "link", "to", "path", "tag", "type"))`: 'names' attribute [6] must be the same length as the vector [0] Backtrace: ▆ 1. └─famat::interactions(listk, listr, listw) at test-interactions.R:6:0 2. └─famat:::filter_inter(interac) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ] Error: Test failures Execution halted
famat.Rcheck/famat-Ex.timings
name | user | system | elapsed | |
compl_data | 123.159 | 4.344 | 129.973 | |