Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-10-03 11:49 -0400 (Thu, 03 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4716 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
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 1378/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
NanoMethViz 3.1.5 (landing page) Shian Su
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
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 NanoMethViz package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NanoMethViz.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: NanoMethViz |
Version: 3.1.5 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings NanoMethViz_3.1.5.tar.gz |
StartedAt: 2024-10-03 07:27:23 -0000 (Thu, 03 Oct 2024) |
EndedAt: 2024-10-03 07:40:28 -0000 (Thu, 03 Oct 2024) |
EllapsedTime: 785.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: NanoMethViz.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings NanoMethViz_3.1.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/NanoMethViz.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 ‘NanoMethViz/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘NanoMethViz’ version ‘3.1.5’ * 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 ‘NanoMethViz’ can be installed ... OK * used C++ compiler: ‘g++ (GCC) 10.3.1’ * checking C++ specification ... OK Not all R platforms support C++20 * checking installed package size ... NOTE installed size is 11.4Mb sub-directories of 1Mb or more: libs 4.9Mb * 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 whether startup messages can be suppressed ... 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 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 get_exons 56.954 1.602 58.931 filter_methy 30.448 0.292 30.799 get_exons_homo_sapiens 18.285 0.347 18.665 get_exons_mus_musculus 18.399 0.164 18.596 plot_gene 12.684 0.080 12.789 plot_gene_heatmap 10.311 0.124 10.455 plot_grange 8.888 0.068 8.972 plot_region 8.784 0.055 8.856 plot_grange_heatmap 7.360 0.060 7.433 plot_region_heatmap 7.301 0.048 7.363 cluster_regions 6.838 0.243 7.096 plot_agg_regions 7.030 0.023 7.066 NanoMethResult-class 4.729 0.272 5.012 * 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-3.20-bioc/meat/NanoMethViz.Rcheck/00check.log’ for details.
NanoMethViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL NanoMethViz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘NanoMethViz’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++20 g++ -std=gnu++20 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++20 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o g++ -std=gnu++20 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c count_cg.cpp -o count_cg.o g++ -std=gnu++20 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c genome.cpp -o genome.o g++ -std=gnu++20 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c modbam.cpp -o modbam.o g++ -std=gnu++20 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c utils.cpp -o utils.o g++ -std=gnu++20 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o NanoMethViz.so RcppExports.o convert_methy_to_dss.o count_cg.o genome.o modbam.o utils.o -lz -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-NanoMethViz/00new/NanoMethViz/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (NanoMethViz)
NanoMethViz.Rcheck/tests/testthat.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. > library(testthat) > library(NanoMethViz) Loading required package: ggplot2 > > test_check("NanoMethViz") Starting 2 test processes [ FAIL 0 | WARN 0 | SKIP 0 | PASS 628 ] > > proc.time() user system elapsed 260.151 10.436 173.792
NanoMethViz.Rcheck/NanoMethViz-Ex.timings
name | user | system | elapsed | |
NanoMethResult-class | 4.729 | 0.272 | 5.012 | |
bsseq_to_edger | 0.760 | 0.040 | 0.806 | |
bsseq_to_log_methy_ratio | 1.249 | 0.036 | 1.287 | |
cluster_regions | 6.838 | 0.243 | 7.096 | |
create_tabix_file | 1.836 | 0.020 | 1.863 | |
exons_to_genes | 0.369 | 0.000 | 0.369 | |
filter_methy | 30.448 | 0.292 | 30.799 | |
get_example_exons_mus_musculus | 0.311 | 0.008 | 0.321 | |
get_exons | 56.954 | 1.602 | 58.931 | |
get_exons_homo_sapiens | 18.285 | 0.347 | 18.665 | |
get_exons_mus_musculus | 18.399 | 0.164 | 18.596 | |
load_example_modbamresult | 0.499 | 0.004 | 0.504 | |
load_example_nanomethresult | 0.302 | 0.004 | 0.306 | |
methy | 0.003 | 0.000 | 0.003 | |
methy_col_names | 0.000 | 0.000 | 0.001 | |
methy_to_bsseq | 1.068 | 0.028 | 1.098 | |
methy_to_edger | 1.222 | 0.016 | 1.241 | |
modbam_to_tabix | 0.545 | 0.214 | 0.653 | |
plot_agg_genes | 2.469 | 0.004 | 2.476 | |
plot_agg_regions | 7.030 | 0.023 | 7.066 | |
plot_gene | 12.684 | 0.080 | 12.789 | |
plot_gene_heatmap | 10.311 | 0.124 | 10.455 | |
plot_grange | 8.888 | 0.068 | 8.972 | |
plot_grange_heatmap | 7.360 | 0.060 | 7.433 | |
plot_mds | 1.682 | 0.016 | 1.701 | |
plot_pca | 1.779 | 0.016 | 1.798 | |
plot_region | 8.784 | 0.055 | 8.856 | |
plot_region_heatmap | 7.301 | 0.048 | 7.363 | |
plot_violin | 3.038 | 0.036 | 3.081 | |
query_methy | 0.482 | 0.000 | 0.484 | |
region_methy_stats | 1.274 | 0.004 | 1.279 | |