Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 2128/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TEKRABber 1.10.0 (landing page) Yao-Chung Chen
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the TEKRABber package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TEKRABber.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: TEKRABber |
Version: 1.10.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TEKRABber.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TEKRABber_1.10.0.tar.gz |
StartedAt: 2024-12-21 11:42:45 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 12:00:05 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 1040.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TEKRABber.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TEKRABber.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TEKRABber_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/TEKRABber.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TEKRABber/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TEKRABber’ version ‘1.10.0’ * 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 ‘TEKRABber’ can be installed ... OK * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ... NOTE Problems with news in ‘NEWS.md’: No news entries found. * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘TEKRABber/R/zzz.R’: .onLoad calls: packageStartupMessage(paste(messages, collapse = "\n")) See section ‘Good practice’ in '?.onAttach'. appTEKRABber: no visible global function definition for ‘grid_page’ appTEKRABber: no visible global function definition for ‘grid_card_text’ appTEKRABber: no visible global function definition for ‘grid_card’ appTEKRABber: no visible global function definition for ‘card_header’ appTEKRABber: no visible global function definition for ‘card_body’ appTEKRABber: no visible global function definition for ‘selectizeInput’ appTEKRABber: no visible global function definition for ‘actionButton’ appTEKRABber: no visible global function definition for ‘plotlyOutput’ appTEKRABber: no visible global function definition for ‘plotOutput’ appTEKRABber : server: no visible global function definition for ‘renderPlotly’ appTEKRABber : server: no visible global function definition for ‘plot_ly’ appTEKRABber : server: no visible global function definition for ‘observeEvent’ appTEKRABber : server: no visible global function definition for ‘renderPlot’ appTEKRABber : server: no visible global function definition for ‘ggplot’ appTEKRABber : server: no visible global function definition for ‘aes’ appTEKRABber : server: no visible binding for global variable ‘gene’ appTEKRABber : server: no visible binding for global variable ‘TE’ appTEKRABber : server: no visible global function definition for ‘geom_point’ appTEKRABber : server: no visible global function definition for ‘labs’ appTEKRABber : server: no visible global function definition for ‘geom_smooth’ appTEKRABber : server: no visible global function definition for ‘theme_bw’ appTEKRABber : server: no visible global function definition for ‘ggtitle’ appTEKRABber : server: no visible global function definition for ‘ggviolin’ appTEKRABber : server: no visible global function definition for ‘ylab’ appTEKRABber : server: no visible global function definition for ‘xlab’ appTEKRABber : server: no visible global function definition for ‘theme’ appTEKRABber: no visible global function definition for ‘shinyApp’ corrOrthologTE: no visible binding for global variable ‘i’ corrOrthologTE: no visible binding for global variable ‘j’ corrOrthologTE: no visible global function definition for ‘cor.test’ orthologScale: no visible global function definition for ‘desc’ orthologScale: no visible binding for global variable ‘orthologyConfidence’ orthologScale: no visible binding for global variable ‘refLength’ orthologScale: no visible binding for global variable ‘compareLength’ orthologScale: no visible global function definition for ‘across’ orthologScale: no visible binding for global variable ‘refLen’ orthologScale: no visible binding for global variable ‘compareLen’ prepareRMSK: no visible binding for global variable ‘repEnd’ prepareRMSK: no visible binding for global variable ‘repStart’ prepareRMSK: no visible binding for global variable ‘repName’ prepareRMSK: no visible binding for global variable ‘repClass’ prepareRMSK: no visible binding for global variable ‘rLen’ prepareRMSK: no visible binding for global variable ‘cLen’ Undefined global functions or variables: TE across actionButton aes cLen card_body card_header compareLen compareLength cor.test desc gene geom_point geom_smooth ggplot ggtitle ggviolin grid_card grid_card_text grid_page i j labs observeEvent orthologyConfidence plotOutput plot_ly plotlyOutput rLen refLen refLength renderPlot renderPlotly repClass repEnd repName repStart selectizeInput shinyApp theme theme_bw xlab ylab Consider adding importFrom("stats", "cor.test") to your NAMESPACE file. * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed prepareRMSK 348.199 18.172 396.398 DECorrInputs 43.691 1.171 62.990 orthologScale 40.319 0.872 45.261 corrOrthologTE 40.303 0.518 41.509 DEgeneTE 27.649 0.431 29.028 appTEKRABber 27.252 0.430 28.700 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/TEKRABber.Rcheck/00check.log’ for details.
TEKRABber.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TEKRABber ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘TEKRABber’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rcpp_corr.cpp -o rcpp_corr.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o TEKRABber.so RcppExports.o rcpp_corr.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-TEKRABber/00new/TEKRABber/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (TEKRABber)
TEKRABber.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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("TEKRABber") Welcome to TEKRABber version 1.8.0 + New function: prepareRMSK() for getting repeatmasker + New parameter: `numCore` in corrOrthologTE() for parallel computing > test_check("TEKRABber") [ FAIL 0 | WARN 0 | SKIP 1 | PASS 10 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-corrOrthologTE.R:31:5' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 10 ] > > proc.time() user system elapsed 137.933 2.410 150.533
TEKRABber.Rcheck/TEKRABber-Ex.timings
name | user | system | elapsed | |
DECorrInputs | 43.691 | 1.171 | 62.990 | |
DEgeneTE | 27.649 | 0.431 | 29.028 | |
appTEKRABber | 27.252 | 0.430 | 28.700 | |
corrOrthologTE | 40.303 | 0.518 | 41.509 | |
ctInputDE | 0.306 | 0.010 | 0.327 | |
fetchDataHmChimp | 1.152 | 0.499 | 1.697 | |
hg38_panTro6_rmsk | 0.065 | 0.004 | 0.069 | |
orthologScale | 40.319 | 0.872 | 45.261 | |
prepareRMSK | 348.199 | 18.172 | 396.398 | |
speciesCounts | 0.525 | 0.013 | 0.543 | |