Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:02:53 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 412/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
combi 1.16.0 (landing page) Stijn Hawinkel
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the combi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/combi.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: combi |
Version: 1.16.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:combi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings combi_1.16.0.tar.gz |
StartedAt: 2024-05-31 02:29:55 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 02:37:40 -0400 (Fri, 31 May 2024) |
EllapsedTime: 465.1 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: combi.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:combi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings combi_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/combi.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * 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 ‘combi/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘combi’ version ‘1.16.0’ * 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 ‘combi’ 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 ... NOTE Package in Depends field not imported from: ‘DBI’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function call to a different package: .C("spline_value", ..., PACKAGE = "cobs") See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE addLink: no visible binding for global variable ‘species’ convPlot: no visible binding for global variable ‘Iteration’ convPlot: no visible binding for global variable ‘Value’ convPlot: no visible binding for global variable ‘Variable’ convPlot: no visible binding for global variable ‘Colour’ inflPlot: no visible binding for global variable ‘h’ inflPlot: no visible binding for global variable ‘LatentVariable’ inflPlot: no visible binding for global variable ‘value’ Undefined global functions or variables: Colour Iteration LatentVariable Value Variable h species value * 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 * 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: 7. └─combi:::estIndepModel(...) 8. ├─base::suppressWarnings(...) 9. │ └─base::withCallingHandlers(...) 10. └─combi:::estMeanVarTrend(...) 11. └─stats::optimize(...) 12. └─stats (local) `<fn>`(-16.5139598160924) 13. └─combi (local) f(arg, ...) 14. ├─base::suppressWarnings(...) 15. │ └─base::withCallingHandlers(...) 16. └─cobs::cobs(...) 17. └─cobs::drqssbc2(...) [ FAIL 1 | WARN 13 | SKIP 0 | PASS 19 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/combi.Rcheck/00check.log’ for details.
combi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL combi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘combi’ ... ** 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 (combi)
combi.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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(combi) Loading required package: DBI > test_check("combi") [ FAIL 1 | WARN 13 | SKIP 0 | PASS 19 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-combiinput.R:30:5'): combi runs when NAs present in data matrix and allowMissingess = TRUE ── Error in `drqssbc2(x, y, w, pw = pw, knots = knots, degree = degree, Tlambda = if (select.lambda) lambdaSet else lambda, constraint = constraint, ptConstr = ptConstr, maxiter = maxiter, trace = trace - 1, nrq, nl1, neqc, niqc, nvar, tau = tau, select.lambda = select.lambda, give.pseudo.x = keep.x.ps, rq.tol = rq.tol, tol.0res = tol.0res, print.warn = print.warn)`: The problem is degenerate for the range of lambda specified. Backtrace: ▆ 1. ├─testthat::expect_s3_class(...) at test-combiinput.R:30:5 2. │ └─testthat::quasi_label(enquo(object), arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─combi::combi(...) 5. └─base::lapply(...) 6. └─combi (local) FUN(X[[i]], ...) 7. └─combi:::estIndepModel(...) 8. ├─base::suppressWarnings(...) 9. │ └─base::withCallingHandlers(...) 10. └─combi:::estMeanVarTrend(...) 11. └─stats::optimize(...) 12. └─stats (local) `<fn>`(-16.5139598160924) 13. └─combi (local) f(arg, ...) 14. ├─base::suppressWarnings(...) 15. │ └─base::withCallingHandlers(...) 16. └─cobs::cobs(...) 17. └─cobs::drqssbc2(...) [ FAIL 1 | WARN 13 | SKIP 0 | PASS 19 ] Error: Test failures Execution halted
combi.Rcheck/combi-Ex.timings
name | user | system | elapsed | |
addLink | 1.233 | 0.056 | 1.290 | |
checkMeanVarTrend | 3.463 | 0.040 | 3.503 | |
combi | 0.021 | 0.000 | 0.021 | |
convPlot | 0.679 | 0.056 | 0.735 | |
extractCoords | 0.045 | 0.012 | 0.057 | |
extractData | 0.028 | 0.000 | 0.028 | |
inflPlot | 0.550 | 0.036 | 0.586 | |
plot.combi | 1.772 | 0.032 | 1.804 | |
print.combi | 0.042 | 0.003 | 0.046 | |