Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:47 -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 1871/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scMitoMut 1.3.1 (landing page) Wenjie Sun
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the scMitoMut package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scMitoMut.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: scMitoMut |
Version: 1.3.1 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:scMitoMut.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scMitoMut_1.3.1.tar.gz |
StartedAt: 2024-12-24 10:58:20 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 10:59:36 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 76.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scMitoMut.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:scMitoMut.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scMitoMut_1.3.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/scMitoMut.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scMitoMut/DESCRIPTION’ ... OK * this is package ‘scMitoMut’ version ‘1.3.1’ * 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 ‘scMitoMut’ can be installed ... OK * used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ * 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 ...Warning: program compiled against libxml 212 using older 211 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 export_dt: no visible binding for global variable ‘af’ export_dt: no visible binding for global variable ‘fwd_depth’ export_dt: no visible binding for global variable ‘rev_depth’ export_dt: no visible binding for global variable ‘coverage’ export_dt: no visible binding for global variable ‘alt_count’ export_dt: no visible binding for global variable ‘alt_depth’ export_dt: no visible binding for global variable ‘mut_status’ export_dt: no visible binding for global variable ‘cell_barcode’ export_dt: no visible binding for global variable ‘n’ export_dt: no visible binding for global variable ‘loc’ filter_loc: no visible binding for global variable ‘mut_cell_n’ plot_locus: no visible binding for global variable ‘alt_depth’ plot_locus: no visible binding for global variable ‘depth’ plot_locus: no visible binding for global variable ‘af’ plot_locus: no visible binding for global variable ‘highlight’ process_locus_bb: no visible binding for global variable ‘alt_depth’ process_locus_bb: no visible binding for global variable ‘fwd_depth’ process_locus_bb: no visible binding for global variable ‘rev_depth’ process_locus_bm: no visible binding for global variable ‘alt_depth’ process_locus_bm: no visible binding for global variable ‘fwd_depth’ process_locus_bm: no visible binding for global variable ‘rev_depth’ process_locus_summary: no visible binding for global variable ‘alt_depth’ process_locus_summary: no visible binding for global variable ‘fwd_depth’ process_locus_summary: no visible binding for global variable ‘rev_depth’ read_locus: no visible binding for global variable ‘cell_barcode’ read_locus: no visible binding for global variable ‘fwd_depth’ read_locus: no visible binding for global variable ‘rev_depth’ read_locus: no visible binding for global variable ‘coverage’ read_locus: no visible binding for global variable ‘alt’ read_locus: no visible binding for global variable ‘af’ read_mgatk: no visible binding for global variable ‘fwd_depth’ read_mgatk: no visible binding for global variable ‘rev_depth’ Undefined global functions or variables: af alt alt_count alt_depth cell_barcode coverage depth fwd_depth highlight loc mut_cell_n mut_status n rev_depth * 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 line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... 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 plot_heatmap 6.975 0.835 6.804 export_dt 6.778 0.905 6.438 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/scMitoMut.Rcheck/00check.log’ for details.
scMitoMut.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL scMitoMut ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘scMitoMut’ ... ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppArmadillo/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppArmadillo/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c em_bm.cpp -o em_bm.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppArmadillo/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c mle_bb.cpp -o mle_bb.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o scMitoMut.so RcppExports.o em_bm.o mle_bb.o -lopenblas -lgfortran -lm -lz -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-scMitoMut/00new/scMitoMut/libs ** 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 ** 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 (scMitoMut)
scMitoMut.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 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. > # 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(scMitoMut) > > test_check("scMitoMut") chrM.200 chrM.204 chrM.310 chrM.824 chrM.1000 chrM.1001 chrM.1227 chrM.2285 chrM.6081 chrM.9429 chrM.9728 chrM.9804 chrM.9840 chrM.12889 chrM.16093 chrM.16147 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ] > > proc.time() user system elapsed 5.807 0.207 5.851
scMitoMut.Rcheck/scMitoMut-Ex.timings
name | user | system | elapsed | |
export_dt | 6.778 | 0.905 | 6.438 | |
filter_loc | 3.063 | 0.075 | 3.217 | |
get_pval | 2.937 | 0.119 | 2.968 | |
open_h5_file | 0.39 | 0.00 | 0.39 | |
parse_mgatk | 1.100 | 0.011 | 1.115 | |
parse_table | 0.376 | 0.008 | 0.385 | |
plot_af_coverage | 3.357 | 0.097 | 3.321 | |
plot_heatmap | 6.975 | 0.835 | 6.804 | |
print.mtmutObj | 0.413 | 0.060 | 0.474 | |
process_locus_bmbb | 0.507 | 0.024 | 0.526 | |
rm_mtmutObj | 0.406 | 0.007 | 0.415 | |
run_model_fit | 2.976 | 0.035 | 2.961 | |
subset_cell | 0.485 | 0.107 | 0.491 | |