Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:42 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 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 2241/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
vsclust 1.9.3 (landing page) Veit Schwammle
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the vsclust package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/vsclust.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: vsclust |
Version: 1.9.3 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:vsclust.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings vsclust_1.9.3.tar.gz |
StartedAt: 2024-12-24 06:08:27 -0500 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 06:14:39 -0500 (Tue, 24 Dec 2024) |
EllapsedTime: 372.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: vsclust.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:vsclust.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings vsclust_1.9.3.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/vsclust.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 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 'vsclust/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'vsclust' version '1.9.3' * 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 'vsclust' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.3.0' * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 ... WARNING 'library' or 'require' call not declared from: 'RDAVIDWebService' 'library' or 'require' call to 'RDAVIDWebService' in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE runFuncEnrich: no visible global function definition for 'compareCluster' runFuncEnrich: no visible global function definition for 'new' Undefined global functions or variables: compareCluster new Consider adding importFrom("methods", "new") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE prepare_Rd: vsclust-package.Rd:29-31: Dropping empty section \seealso prepare_Rd: vsclust-package.Rd:32-33: Dropping empty section \examples * 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 'E:/biocbuild/bbs-3.21-bioc/R/library/vsclust/libs/x64/vsclust.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 calcBHI 9.05 0.39 17.77 estimClust.plot 0.14 0.02 17.31 optimalClustNum 0.10 0.02 17.32 estimClustNum 0.03 0.01 13.83 ClustComp 0.02 0.01 9.12 runClustWrapper 0.03 0.00 9.05 * 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 WARNING, 4 NOTEs See 'E:/biocbuild/bbs-3.21-bioc/meat/vsclust.Rcheck/00check.log' for details.
vsclust.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL vsclust ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'vsclust' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vsclust_algo.cpp -o vsclust_algo.o vsclust_algo.cpp: In function 'double c_plusplus_means(const Rcpp::NumericMatrix&, Rcpp::NumericMatrix&, Rcpp::NumericVector&, Rcpp::NumericVector&, int, int, double, int, Rcpp::NumericMatrix&, double, Rcpp::IntegerVector&, double, double)': vsclust_algo.cpp:380:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 380 | if(verbose) | ^~ vsclust_algo.cpp:383:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 383 | ermin = new_fitness; | ^~~~~ g++ -std=gnu++17 -shared -s -static-libgcc -o vsclust.dll tmp.def RcppExports.o vsclust_algo.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-vsclust/00new/vsclust/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 (vsclust)
vsclust.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(vsclust) > > test_check("vsclust") Running cluster number 3 Running cluster number 4 Running cluster number 5 Running cluster number 6 Running cluster number 7 Running cluster number 8 Running cluster number 9 Running cluster number 10 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ] Warning message: In for (v in val) { : closing unused connection 5 (<-palomino7:11815) > > proc.time() user system elapsed 10.01 0.62 64.65
vsclust.Rcheck/vsclust-Ex.timings
name | user | system | elapsed | |
ClustComp | 0.02 | 0.01 | 9.12 | |
PrepareForVSClust | 0.17 | 0.00 | 0.17 | |
PrepareSEForVSClust | 0.96 | 0.10 | 1.08 | |
SignAnalysis | 0.03 | 0.00 | 0.03 | |
SignAnalysisPaired | 0.01 | 0.00 | 0.02 | |
SwitchOrder | 0.02 | 0.00 | 0.01 | |
averageCond | 0 | 0 | 0 | |
calcBHI | 9.05 | 0.39 | 17.77 | |
cvalidate.xiebeni | 0 | 0 | 0 | |
determine_fuzz | 0.02 | 0.00 | 0.02 | |
estimClust.plot | 0.14 | 0.02 | 17.31 | |
estimClustNum | 0.03 | 0.01 | 13.83 | |
mfuzz.plot | 0.05 | 0.00 | 0.04 | |
optimalClustNum | 0.10 | 0.02 | 17.32 | |
pcaWithVar | 0.02 | 0.00 | 0.01 | |
runClustWrapper | 0.03 | 0.00 | 9.05 | |
runVSClustApp | 0 | 0 | 0 | |
vsclust_algorithm | 0.02 | 0.00 | 0.01 | |