Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-16 11:41 -0400 (Tue, 16 Jul 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" | 4677 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
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 2087/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TEKRABber 1.9.0 (landing page) Yao-Chung Chen
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino6 | 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 | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | 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: 1.9.0 |
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TEKRABber.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TEKRABber_1.9.0.tar.gz |
StartedAt: 2024-07-16 04:58:21 -0400 (Tue, 16 Jul 2024) |
EndedAt: 2024-07-16 05:16:51 -0400 (Tue, 16 Jul 2024) |
EllapsedTime: 1109.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TEKRABber.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TEKRABber.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TEKRABber_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/TEKRABber.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 'TEKRABber/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'TEKRABber' version '1.9.0' * 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 'TEKRABber' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * 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 for x64 is not available File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/TEKRABber/libs/x64/TEKRABber.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed prepareRMSK 290.28 21.69 365.31 orthologScale 80.72 2.86 95.16 DECorrInputs 67.68 1.72 83.65 corrOrthologTE 37.15 0.68 54.25 DEgeneTE 24.78 0.62 25.37 appTEKRABber 23.25 0.64 45.91 * 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 'C:/Users/biocbuild/bbs-3.20-bioc/meat/TEKRABber.Rcheck/00check.log' for details.
TEKRABber.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL TEKRABber ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'TEKRABber' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' g++ -std=gnu++17 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_corr.cpp -o rcpp_corr.o rcpp_corr.cpp:23: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 23 | #pragma omp parallel for | g++ -std=gnu++17 -shared -s -static-libgcc -o TEKRABber.dll tmp.def RcppExports.o rcpp_corr.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-TEKRABber/00new/TEKRABber/libs/x64 ** 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 (TEKRABber)
TEKRABber.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("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 167.71 3.84 198.09
TEKRABber.Rcheck/TEKRABber-Ex.timings
name | user | system | elapsed | |
DECorrInputs | 67.68 | 1.72 | 83.65 | |
DEgeneTE | 24.78 | 0.62 | 25.37 | |
appTEKRABber | 23.25 | 0.64 | 45.91 | |
corrOrthologTE | 37.15 | 0.68 | 54.25 | |
ctInputDE | 0.10 | 0.04 | 0.14 | |
fetchDataHmChimp | 0.64 | 0.25 | 0.89 | |
hg38_panTro6_rmsk | 0.03 | 0.05 | 0.08 | |
orthologScale | 80.72 | 2.86 | 95.16 | |
prepareRMSK | 290.28 | 21.69 | 365.31 | |
speciesCounts | 0.21 | 0.01 | 0.22 | |