Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-30 11:35:59 -0400 (Thu, 30 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 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
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 2184/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TPP2D 1.20.0 (landing page) Nils Kurzawa
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the TPP2D package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TPP2D.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: TPP2D |
Version: 1.20.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TPP2D.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TPP2D_1.20.0.tar.gz |
StartedAt: 2024-05-30 00:20:07 -0400 (Thu, 30 May 2024) |
EndedAt: 2024-05-30 00:22:16 -0400 (Thu, 30 May 2024) |
EllapsedTime: 129.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TPP2D.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TPP2D.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TPP2D_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/TPP2D.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TPP2D/DESCRIPTION’ ... OK * this is package ‘TPP2D’ version ‘1.20.0’ * 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 ‘TPP2D’ 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 ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.min_RSS_h0’ ‘.min_RSS_h1_slope_pEC50’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed computeFStatFromParams 5.951 0.104 6.116 fitAndEvalDataset 5.703 0.107 5.859 getModelParamsDf 5.619 0.099 5.759 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.19-bioc/meat/TPP2D.Rcheck/00check.log’ for details.
TPP2D.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TPP2D ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘TPP2D’ ... ** 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 (TPP2D)
TPP2D.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" 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. > Sys.setenv("R_TESTS" = "") > library(testthat) > library(TPP2D) Loading required package: dplyr Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union > > test_check("TPP2D") [1] "Warning: You have specificed B < 20, it is recommended to use at least B = 20 in order to obtain reliable results." | | | 0% | |======================================================================| 100% [ FAIL 0 | WARN 2 | SKIP 0 | PASS 18 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 18 ] > > proc.time() user system elapsed 6.873 0.369 7.309
TPP2D.Rcheck/TPP2D-Ex.timings
name | user | system | elapsed | |
TPP_importCheckConfigTable | 0.023 | 0.004 | 0.028 | |
annotateDataList | 0.845 | 0.039 | 0.892 | |
bootstrapNull | 0.080 | 0.012 | 2.354 | |
bootstrapNullAlternativeModel | 1.914 | 0.037 | 1.968 | |
bootstrapNullAlternativeModelFast | 2.022 | 0.030 | 2.074 | |
competeModels | 2.796 | 0.071 | 2.892 | |
computeFStatFromParams | 5.951 | 0.104 | 6.116 | |
computeFstat | 4.838 | 0.101 | 4.990 | |
configWide2Long | 0.006 | 0.001 | 0.008 | |
filterOutContaminants | 0.041 | 0.001 | 0.042 | |
findHits | 1.184 | 0.024 | 4.409 | |
fitAndEvalDataset | 5.703 | 0.107 | 5.859 | |
fitH0Model | 0.155 | 0.004 | 0.162 | |
fitH1Model | 0.896 | 0.015 | 0.917 | |
getFDR | 1.201 | 0.025 | 4.930 | |
getModelParamsDf | 5.619 | 0.099 | 5.759 | |
getPEC504Temperature | 0.342 | 0.010 | 0.357 | |
getPvalues | 0.635 | 0.019 | 4.535 | |
gg_qq | 0.060 | 0.001 | 0.062 | |
import2dDataset | 0.512 | 0.010 | 0.528 | |
import2dMain | 0.198 | 0.005 | 0.205 | |
plot2dTppFcHeatmap | 0.271 | 0.008 | 0.282 | |
plot2dTppFit | 0.353 | 0.006 | 0.362 | |
plot2dTppProfile | 0.342 | 0.007 | 0.354 | |
plot2dTppRelProfile | 0.368 | 0.006 | 0.377 | |
plot2dTppVolcano | 4.462 | 0.067 | 4.571 | |
recomputeSignalFromRatios | 0.057 | 0.002 | 0.058 | |
renameColumns | 0.511 | 0.008 | 0.521 | |
resolveAmbiguousProteinNames | 0.038 | 0.001 | 0.039 | |
runTPP2D | 1.486 | 0.018 | 1.513 | |
tpp2dExperiment-class | 0.000 | 0.001 | 0.000 | |