Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-08 11:45 -0400 (Mon, 08 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" | 4643 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4442 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4391 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 3833 |
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 1271/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mnem 1.21.0 (landing page) Martin Pirkl
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | NA | OK | WARNINGS | ||||||||||
To the developers/maintainers of the mnem package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mnem.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: mnem |
Version: 1.21.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:mnem.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings mnem_1.21.0.tar.gz |
StartedAt: 2024-07-06 06:33:19 -0000 (Sat, 06 Jul 2024) |
EndedAt: 2024-07-06 06:35:47 -0000 (Sat, 06 Jul 2024) |
EllapsedTime: 148.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: mnem.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:mnem.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings mnem_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/mnem.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mnem/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mnem’ version ‘1.21.0’ * 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 ‘mnem’ can be installed ... OK * used C++ compiler: ‘g++ (GCC) 10.3.1’ * checking installed package size ... NOTE installed size is 6.5Mb sub-directories of 1Mb or more: data 2.3Mb libs 3.8Mb * 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 loading without being on the library search path ... 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 createApp: no visible binding for global variable ‘..tmp’ nemEst2: no visible binding for global variable ‘n’ nemEst2: no visible binding for global variable ‘llbest’ scoreAdj: no visible binding for global variable ‘data’ Undefined global functions or variables: ..tmp data llbest n Consider adding importFrom("utils", "data") 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 ... WARNING Codoc mismatches from Rd file 'moreboxplot.Rd': moreboxplot Code: function(x, box = TRUE, dens = TRUE, scatter = "no", polygon = TRUE, sd = 0.1, dcol = NULL, scol = NULL, dlty = 1, dlwd = 1, spch = 1, gcol = rgb(0, 0, 0, 0.5), glty = 2, glen = 2001, gmin = -100, gmax = 100, ...) Docs: function(x, box = TRUE, dens = TRUE, scatter = "no", polygon = TRUE, sd = 0.1, dcol = NULL, scol = NULL, dlty = 1, dlwd = 1, spch = 1, gcol = rgb(0, 0, 0, 0.5), glty = 2, glen = 10, gmin = NA, gmax = NA, ...) Mismatches in argument default values: Name: 'glen' Code: 2001 Docs: 10 Name: 'gmin' Code: -100 Docs: NA Name: 'gmax' Code: 100 Docs: NA * 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 LazyData ... 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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, 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/mnem.Rcheck/00check.log’ for details.
mnem.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL mnem ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘mnem’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c mm.cpp -o mm.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o mnem.so RcppExports.o mm.o -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-mnem/00new/mnem/libs ** R ** data *** moving datasets to lazyload DB ** 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 (mnem)
mnem.Rcheck/tests/runTests.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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. > BiocGenerics:::testPackage("mnem") RUNIT TEST PROTOCOL -- Sat Jul 6 06:35:43 2024 *********************************************** Number of test functions: 0 Number of errors: 0 Number of failures: 0 1 Test Suite : mnem RUnit Tests - 0 test functions, 0 errors, 0 failures Number of test functions: 0 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 5.556 0.232 5.786
mnem.Rcheck/mnem-Ex.timings
name | user | system | elapsed | |
app | 0.002 | 0.000 | 0.001 | |
bootstrap | 0.579 | 0.016 | 0.596 | |
clustNEM | 2.167 | 0.055 | 2.229 | |
createApp | 0.000 | 0.001 | 0.001 | |
fitacc | 0.442 | 0.018 | 0.461 | |
fuzzyindex | 0.026 | 0.000 | 0.026 | |
getAffinity | 0.424 | 0.000 | 0.426 | |
getIC | 0.470 | 0.000 | 0.471 | |
hamSim | 0.006 | 0.000 | 0.006 | |
mnem | 0.422 | 0.000 | 0.424 | |
mnemh | 0.066 | 0.000 | 0.066 | |
mnemk | 0.471 | 0.003 | 0.476 | |
moreboxplot | 0.023 | 0.000 | 0.023 | |
nem | 0.001 | 0.000 | 0.001 | |
plot.bootmnem | 0.764 | 0.032 | 0.797 | |
plot.mnem | 0.674 | 0.016 | 0.691 | |
plot.mnem_mcmc | 0.598 | 0.004 | 0.604 | |
plot.mnem_sim | 0.097 | 0.000 | 0.097 | |
plotConvergence | 0.430 | 0.008 | 0.440 | |
plotConvergence.mnem | 0.448 | 0.008 | 0.457 | |
plotDnf | 0.042 | 0.003 | 0.045 | |
scoreAdj | 0.001 | 0.000 | 0.001 | |
simData | 0.005 | 0.000 | 0.006 | |
transitive.closure | 0.001 | 0.000 | 0.001 | |
transitive.reduction | 0.001 | 0.000 | 0.000 | |