Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 2122/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TPP2D 1.21.0 (landing page) Nils Kurzawa
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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: 1.21.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TPP2D.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TPP2D_1.21.0.tar.gz |
StartedAt: 2024-06-10 11:23:05 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 11:30:37 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 451.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TPP2D.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TPP2D.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TPP2D_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/TPP2D.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'TPP2D/DESCRIPTION' ... OK * this is package 'TPP2D' version '1.21.0' * 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 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 5.60 0.11 5.70 getModelParamsDf 5.38 0.13 5.50 findHits 1.04 0.11 15.47 getFDR 0.93 0.03 14.28 getPvalues 0.48 0.07 13.69 bootstrapNull 0.09 0.03 11.70 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/TPP2D.Rcheck/00check.log' for details.
TPP2D.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL TPP2D ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 6.68 10.18 16.84
TPP2D.Rcheck/TPP2D-Ex.timings
name | user | system | elapsed | |
TPP_importCheckConfigTable | 0.03 | 0.01 | 0.05 | |
annotateDataList | 0.55 | 0.11 | 0.69 | |
bootstrapNull | 0.09 | 0.03 | 11.70 | |
bootstrapNullAlternativeModel | 1.62 | 0.05 | 1.67 | |
bootstrapNullAlternativeModelFast | 1.80 | 0.03 | 1.83 | |
competeModels | 2.81 | 0.05 | 2.86 | |
computeFStatFromParams | 5.60 | 0.11 | 5.70 | |
computeFstat | 4.08 | 0.14 | 4.22 | |
configWide2Long | 0 | 0 | 0 | |
filterOutContaminants | 0.03 | 0.01 | 0.05 | |
findHits | 1.04 | 0.11 | 15.47 | |
fitAndEvalDataset | 4.77 | 0.11 | 4.88 | |
fitH0Model | 0.10 | 0.02 | 0.12 | |
fitH1Model | 0.82 | 0.03 | 0.85 | |
getFDR | 0.93 | 0.03 | 14.28 | |
getModelParamsDf | 5.38 | 0.13 | 5.50 | |
getPEC504Temperature | 0.41 | 0.00 | 0.40 | |
getPvalues | 0.48 | 0.07 | 13.69 | |
gg_qq | 0.04 | 0.00 | 0.04 | |
import2dDataset | 0.47 | 0.00 | 0.47 | |
import2dMain | 0.22 | 0.02 | 0.23 | |
plot2dTppFcHeatmap | 0.20 | 0.08 | 0.28 | |
plot2dTppFit | 0.25 | 0.00 | 0.25 | |
plot2dTppProfile | 0.25 | 0.00 | 0.25 | |
plot2dTppRelProfile | 0.25 | 0.01 | 0.27 | |
plot2dTppVolcano | 3.51 | 0.11 | 3.61 | |
recomputeSignalFromRatios | 0.05 | 0.02 | 0.06 | |
renameColumns | 0.5 | 0.0 | 0.5 | |
resolveAmbiguousProteinNames | 0.03 | 0.00 | 0.03 | |
runTPP2D | 1.62 | 0.05 | 1.67 | |
tpp2dExperiment-class | 0 | 0 | 0 | |