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 11:42 -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 2137/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TPP 3.33.0 (landing page) Dorothee Childs
| 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 | OK | OK | OK | ![]() | ||||||||
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 TPP package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TPP.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: TPP |
Version: 3.33.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TPP.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TPP_3.33.0.tar.gz |
StartedAt: 2024-08-21 06:01:37 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 06:14:40 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 783.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TPP.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TPP.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TPP_3.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/TPP.Rcheck' * using R version 4.4.1 (2024-06-14 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 'TPP/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'TPP' version '3.33.0' * 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 'TPP' can be installed ... OK * checking installed package size ... NOTE installed size is 12.8Mb sub-directories of 1Mb or more: data 1.9Mb example_data 8.0Mb test_data 1.9Mb * 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 ... NOTE Problems with news in 'NEWS': Cannot process chunk/lines: Updated package vignette. Cannot process chunk/lines: Removed unit test that causes R CMD check to crash since the latest update of package 'testthat'. Cannot process chunk/lines: Fixed bug in plotColors for the case when no comparisons are specified * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: 'broom' All declared Imports should be used. Unexported objects imported by ':::' calls: 'doParallel:::.options' 'mefa:::rep.data.frame' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File 'TPP/R/TPP.R': .onLoad calls: packageStartupMessage(msgText, "\n") See section 'Good practice' in '?.onAttach'. fitSigmoidCCR: no visible global function definition for 'capture.output' modelSelector: no visible binding for global variable 'testHypothesis' modelSelector: no visible binding for global variable 'fitMetric' modelSelector: no visible binding for global variable 'minMetric' plot_fSta_distribution: no visible binding for global variable 'density' plot_pVal_distribution: no visible binding for global variable '..density..' tpp2dCreateTPPTRreference: no visible binding for global variable 'meltcurve_plot' tpp2dCreateTPPTRreference: no visible binding for global variable 'Protein_ID' tpp2dExport: no visible binding for global variable 'temperature' tpp2dImport: no visible binding for global variable 'temperature' tpp2dNormalize: no visible binding for global variable 'temperature' Undefined global functions or variables: ..density.. Protein_ID capture.output density fitMetric meltcurve_plot minMetric temperature testHypothesis Consider adding importFrom("stats", "density") importFrom("utils", "capture.output") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) analyzeTPPTR.Rd:146-147: Lost braces in \itemize; meant \describe ? checkRd: (-1) analyzeTPPTR.Rd:148: Lost braces in \itemize; meant \describe ? checkRd: (-1) analyzeTPPTR.Rd:149: Lost braces in \itemize; meant \describe ? checkRd: (-1) hdacCCR_data.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) hdacCCR_data.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) hdacTR_data.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) hdacTR_data.Rd:34: Lost braces in \itemize; meant \describe ? checkRd: (-1) hdacTR_data.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) hdacTR_data.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) tppccrCurveFit.Rd:42: Lost braces 42 | code{featureData(S)}. | ^ checkRd: (-1) tppccrImport.Rd:71-72: Lost braces in \itemize; meant \describe ? checkRd: (-1) tppccrImport.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) tppccrPlotCurves.Rd:45: Lost braces 45 | produced plots are stored in code{featureData(S)$plot}. | ^ checkRd: (-1) tpptrImport.Rd:76-77: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpptrImport.Rd:78: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpptrImport.Rd:79: Lost braces in \itemize; meant \describe ? * 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 sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed analyzeTPPTR 52.05 0.68 52.74 tppQCPlotsCorrelateExperiments 12.41 0.13 12.86 tpp2dCreateDRplots 12.20 0.20 12.41 tpptrSplineFitAndTest 11.92 0.14 34.21 tpp2dSplineFitAndTest 9.88 0.14 16.55 tppccrPlotCurves 8.22 0.17 9.18 tpptrPlotSplines 7.01 0.15 17.64 tpptrFTest 7.00 0.14 18.91 tpp2dCurveFit 7.03 0.07 7.09 tpp2dMerge2dRef 6.86 0.14 7.00 analyze2DTPP 6.32 0.24 6.57 tppccrResultTable 5.05 0.05 5.66 tpptrFitSplines 0.95 0.03 11.16 * 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: 5 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/TPP.Rcheck/00check.log' for details.
TPP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL TPP ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'TPP' ... ** 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 (TPP)
TPP.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 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. > library(testthat) > library(TPP) Loading required package: Biobase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: dplyr Attaching package: 'dplyr' The following object is masked from 'package:Biobase': combine The following objects are masked from 'package:BiocGenerics': combine, intersect, setdiff, union 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 Loading required package: magrittr Attaching package: 'magrittr' The following objects are masked from 'package:testthat': equals, is_less_than, not Loading required package: tidyr Attaching package: 'tidyr' The following object is masked from 'package:magrittr': extract The following object is masked from 'package:testthat': matches > > test_check("TPP") [[1]] [[2]] [[3]] [[1]] [[2]] [[3]] [[1]] [[2]] [[3]] [[1]] [[2]] [[3]] [[1]] [[2]] [[3]] [[1]] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 303 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 303 ] > > proc.time() user system elapsed 202.67 7.28 438.31
TPP.Rcheck/TPP-Ex.timings
name | user | system | elapsed | |
analyze2DTPP | 6.32 | 0.24 | 6.57 | |
analyzeTPPCCR | 3.90 | 0.08 | 3.98 | |
analyzeTPPTR | 52.05 | 0.68 | 52.74 | |
tpp2dAddAdditionalInfo | 0.03 | 0.00 | 0.03 | |
tpp2dCalcFractAbundance | 2.45 | 0.16 | 2.61 | |
tpp2dComputeFoldChanges | 0.52 | 0.00 | 0.51 | |
tpp2dCreateDRplots | 12.20 | 0.20 | 12.41 | |
tpp2dCurveFit | 7.03 | 0.07 | 7.09 | |
tpp2dExport | 0.07 | 0.01 | 0.08 | |
tpp2dImport | 0.39 | 0.03 | 0.42 | |
tpp2dMerge2dRef | 6.86 | 0.14 | 7.00 | |
tpp2dNormalize | 0.73 | 0.00 | 0.74 | |
tpp2dSplineFitAndTest | 9.88 | 0.14 | 16.55 | |
tpp2dSplinePlot | 0.0 | 0.0 | 0.2 | |
tpp2dTRReferenceObject | 0.01 | 0.02 | 0.17 | |
tppDefaultTheme | 0.33 | 0.00 | 0.34 | |
tppExport | 0.26 | 0.03 | 1.59 | |
tppQCPlotsCorrelateExperiments | 12.41 | 0.13 | 12.86 | |
tppccrCurveFit | 4.39 | 0.07 | 4.50 | |
tppccrImport | 0.15 | 0.00 | 0.16 | |
tppccrNormalize | 0.21 | 0.02 | 0.22 | |
tppccrNormalizeToReference | 0.23 | 0.00 | 0.29 | |
tppccrPlotCurves | 8.22 | 0.17 | 9.18 | |
tppccrResultTable | 5.05 | 0.05 | 5.66 | |
tppccrTransform | 0.25 | 0.00 | 0.26 | |
tpptrAnalyzeMeltingCurves | 0.53 | 0.03 | 0.61 | |
tpptrCurveFit | 1.20 | 0.05 | 1.25 | |
tpptrDefaultNormReqs | 0.50 | 0.01 | 0.51 | |
tpptrFTest | 7.00 | 0.14 | 18.91 | |
tpptrFitSplines | 0.95 | 0.03 | 11.16 | |
tpptrImport | 0.22 | 0.00 | 0.22 | |
tpptrNormalize | 0.46 | 0.00 | 0.72 | |
tpptrPlotSplines | 7.01 | 0.15 | 17.64 | |
tpptrSplineFitAndTest | 11.92 | 0.14 | 34.21 | |
tpptrTidyUpESets | 0.44 | 0.01 | 0.45 | |