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 11:41 -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 955/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
HiLDA 1.19.0 (landing page) Zhi Yang
| 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 HiLDA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiLDA.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: HiLDA |
Version: 1.19.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HiLDA.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings HiLDA_1.19.0.tar.gz |
StartedAt: 2024-08-21 01:42:11 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 01:46:36 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 265.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: HiLDA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HiLDA.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings HiLDA_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/HiLDA.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 'HiLDA/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'HiLDA' version '1.19.0' * 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 'HiLDA' 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 ... 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 ... OK * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/HiLDA/libs/x64/HiLDA.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 hildaTest 101.18 0.13 101.37 hildaGlobalResult 48.97 0.12 49.20 hildaReadMPFile 16.64 1.22 18.34 * 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/HiLDA.Rcheck/00check.log' for details.
HiLDA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL HiLDA ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'HiLDA' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/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 EMalgorithm.cpp -o EMalgorithm.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/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 checkBoundary.cpp -o checkBoundary.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/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 convertFromToVector.cpp -o convertFromToVector.o g++ -std=gnu++17 -shared -s -static-libgcc -o HiLDA.dll tmp.def EMalgorithm.o RcppExports.o checkBoundary.o convertFromToVector.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-HiLDA/00new/HiLDA/libs/x64 ** R ** 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 (HiLDA)
HiLDA.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(HiLDA) Loading required package: ggplot2 > > test_check("HiLDA") #trial: 1; #iteration: 42; time(s): 0.09; convergence: TRUE; loglikelihood: -8202.5086 #trial: 2; #iteration: 21; time(s): 0.08; convergence: TRUE; loglikelihood: -8202.3184 #trial: 3; #iteration: 20; time(s): 0.07; convergence: TRUE; loglikelihood: -8202.3184 #trial: 4; #iteration: 15; time(s): 0.03; convergence: TRUE; loglikelihood: -8202.3188 #trial: 5; #iteration: 26; time(s): 0.07; convergence: TRUE; loglikelihood: -8202.3188 #trial: 6; #iteration: 16; time(s): 0.02; convergence: TRUE; loglikelihood: -8202.3184 #trial: 7; #iteration: 18; time(s): 0.05; convergence: TRUE; loglikelihood: -8202.3184 #trial: 8; #iteration: 20; time(s): 0.03; convergence: TRUE; loglikelihood: -8202.3183 #trial: 9; #iteration: 13; time(s): 0.05; convergence: TRUE; loglikelihood: -8202.3184 #trial: 10; #iteration: 22; time(s): 0.04; convergence: TRUE; loglikelihood: -8202.3185 [ FAIL 0 | WARN 2 | SKIP 0 | PASS 4 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 4 ] > > proc.time() user system elapsed 2.73 0.32 3.11
HiLDA.Rcheck/HiLDA-Ex.timings
name | user | system | elapsed | |
hildaBarplot | 1.46 | 0.08 | 1.53 | |
hildaDiffPlot | 1.01 | 0.05 | 1.06 | |
hildaGlobalResult | 48.97 | 0.12 | 49.20 | |
hildaLocalResult | 0.01 | 0.00 | 0.02 | |
hildaPlotSignature | 0.47 | 0.03 | 0.50 | |
hildaReadMPFile | 16.64 | 1.22 | 18.34 | |
hildaRhat | 0.02 | 0.00 | 0.02 | |
hildaTest | 101.18 | 0.13 | 101.37 | |
pmBarplot | 1.22 | 0.15 | 1.38 | |
pmMultiBarplot | 1.46 | 0.00 | 1.47 | |
pmPlotSignature | 1.01 | 0.10 | 1.11 | |
pmgetSignature | 0.39 | 0.01 | 0.40 | |
visPMS | 0.52 | 0.05 | 0.56 | |