Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-09 21:31 -0500 (Sat, 09 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 2170/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TPP 3.34.0 (landing page) Dorothee Childs
| teran2 | Linux (Ubuntu 24.04.1 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: 3.34.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TPP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TPP_3.34.0.tar.gz |
StartedAt: 2024-11-09 15:27:02 -0500 (Sat, 09 Nov 2024) |
EndedAt: 2024-11-09 15:32:57 -0500 (Sat, 09 Nov 2024) |
EllapsedTime: 355.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TPP.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TPP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TPP_3.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/TPP.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-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 Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TPP/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TPP’ version ‘3.34.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘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 8.058 0.057 8.116 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/TPP.Rcheck/00check.log’ for details.
TPP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TPP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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. > 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, saveRDS, 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 61.575 1.415 63.080
TPP.Rcheck/TPP-Ex.timings
name | user | system | elapsed | |
analyze2DTPP | 1.467 | 0.027 | 1.496 | |
analyzeTPPCCR | 0.989 | 0.014 | 1.004 | |
analyzeTPPTR | 8.058 | 0.057 | 8.116 | |
tpp2dAddAdditionalInfo | 0.006 | 0.001 | 0.007 | |
tpp2dCalcFractAbundance | 0.673 | 0.040 | 0.713 | |
tpp2dComputeFoldChanges | 0.089 | 0.002 | 0.090 | |
tpp2dCreateDRplots | 2.542 | 0.030 | 2.572 | |
tpp2dCurveFit | 1.497 | 0.019 | 1.516 | |
tpp2dExport | 0.020 | 0.001 | 0.022 | |
tpp2dImport | 0.083 | 0.002 | 0.085 | |
tpp2dMerge2dRef | 1.729 | 0.023 | 1.754 | |
tpp2dNormalize | 0.159 | 0.002 | 0.161 | |
tpp2dSplineFitAndTest | 3.034 | 0.029 | 3.064 | |
tpp2dSplinePlot | 0.003 | 0.000 | 0.003 | |
tpp2dTRReferenceObject | 0.005 | 0.001 | 0.006 | |
tppDefaultTheme | 0.092 | 0.001 | 0.093 | |
tppExport | 0.123 | 0.011 | 0.135 | |
tppQCPlotsCorrelateExperiments | 3.485 | 0.038 | 3.527 | |
tppccrCurveFit | 1.109 | 0.011 | 1.121 | |
tppccrImport | 0.031 | 0.001 | 0.032 | |
tppccrNormalize | 0.038 | 0.002 | 0.039 | |
tppccrNormalizeToReference | 0.047 | 0.002 | 0.050 | |
tppccrPlotCurves | 1.492 | 0.021 | 1.516 | |
tppccrResultTable | 0.927 | 0.028 | 0.958 | |
tppccrTransform | 0.043 | 0.002 | 0.045 | |
tpptrAnalyzeMeltingCurves | 0.096 | 0.003 | 0.099 | |
tpptrCurveFit | 0.238 | 0.005 | 0.244 | |
tpptrDefaultNormReqs | 0.085 | 0.002 | 0.087 | |
tpptrFTest | 2.56 | 0.02 | 2.58 | |
tpptrFitSplines | 0.339 | 0.007 | 0.347 | |
tpptrImport | 0.049 | 0.002 | 0.050 | |
tpptrNormalize | 0.108 | 0.001 | 0.109 | |
tpptrPlotSplines | 2.603 | 0.012 | 2.615 | |
tpptrSplineFitAndTest | 4.691 | 0.033 | 4.726 | |
tpptrTidyUpESets | 0.084 | 0.005 | 0.088 | |