Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1886/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scMitoMut 1.2.0 (landing page) Wenjie Sun
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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. |
Package: scMitoMut |
Version: 1.2.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scMitoMut.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scMitoMut_1.2.0.tar.gz |
StartedAt: 2024-12-20 09:18:00 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 09:20:38 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 158.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scMitoMut.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scMitoMut.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scMitoMut_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scMitoMut.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scMitoMut/DESCRIPTION’ ... OK * this is package ‘scMitoMut’ version ‘1.2.0’ * 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 ‘scMitoMut’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 ... 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 export_dt 11.518 4.374 17.760 plot_heatmap 11.270 1.706 14.201 plot_af_coverage 4.886 0.346 6.484 get_pval 4.205 0.333 5.932 filter_loc 4.270 0.263 5.870 run_model_fit 4.250 0.222 6.388 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/scMitoMut.Rcheck/00check.log’ for details.
scMitoMut.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scMitoMut ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘scMitoMut’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c em_bm.cpp -o em_bm.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mle_bb.cpp -o mle_bb.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o scMitoMut.so RcppExports.o em_bm.o mle_bb.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 9.034 0.739 12.705
scMitoMut.Rcheck/scMitoMut-Ex.timings
name | user | system | elapsed | |
export_dt | 11.518 | 4.374 | 17.760 | |
filter_loc | 4.270 | 0.263 | 5.870 | |
get_pval | 4.205 | 0.333 | 5.932 | |
open_h5_file | 0.524 | 0.042 | 0.636 | |
parse_mgatk | 1.496 | 0.122 | 1.853 | |
parse_table | 0.528 | 0.037 | 0.648 | |
plot_af_coverage | 4.886 | 0.346 | 6.484 | |
plot_heatmap | 11.270 | 1.706 | 14.201 | |
print.mtmutObj | 0.594 | 0.076 | 0.747 | |
process_locus_bmbb | 0.728 | 0.170 | 1.062 | |
rm_mtmutObj | 0.551 | 0.038 | 0.645 | |
run_model_fit | 4.250 | 0.222 | 6.388 | |
subset_cell | 0.636 | 0.120 | 0.853 | |