Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:39:35 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 1371/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
NanoMethViz 2.99.4 (landing page) Shian Su
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
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. |
Package: NanoMethViz |
Version: 2.99.4 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NanoMethViz_2.99.4.tar.gz |
StartedAt: 2024-03-02 07:34:09 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 07:55:08 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 1258.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: NanoMethViz.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NanoMethViz_2.99.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/NanoMethViz.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘NanoMethViz/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘NanoMethViz’ version ‘2.99.4’ * 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... OK Not all R platforms support C++20 * checking installed package size ... NOTE installed size is 5.3Mb * 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 R 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 plot_violin: no visible binding for global variable ‘methy_data’ Undefined global functions or variables: methy_data * 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 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 81.826 8.394 111.895 get_exons_mus_musculus 24.818 2.027 33.040 get_exons_homo_sapiens 20.495 1.116 25.360 plot_gene_heatmap 17.618 0.299 20.870 plot_agg_regions 12.873 0.212 15.166 plot_grange_heatmap 12.535 0.164 14.829 plot_region_heatmap 12.426 0.155 14.648 NanoMethResult-class 9.755 1.685 13.521 cluster_regions 8.112 0.202 9.737 plot_agg_genes 5.804 0.255 7.019 plot_violin 5.010 0.093 5.878 plot_gene 4.679 0.084 5.531 plot_grange 4.494 0.068 5.337 filter_methy 4.000 0.550 5.421 plot_region 4.134 0.064 5.033 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/NanoMethViz.Rcheck/00check.log’ for details.
NanoMethViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NanoMethViz ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘NanoMethViz’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++20 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o clang++ -arch x86_64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c count_cg.cpp -o count_cg.o clang++ -arch x86_64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c modbam.cpp -o modbam.o clang++ -arch x86_64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o clang++ -arch x86_64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o NanoMethViz.so RcppExports.o convert_methy_to_dss.o count_cg.o modbam.o utils.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-NanoMethViz/00new/NanoMethViz/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 (NanoMethViz)
NanoMethViz.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 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. > library(testthat) > library(NanoMethViz) Loading required package: ggplot2 > > test_check("NanoMethViz") Starting 2 test processes [ FAIL 0 | WARN 0 | SKIP 0 | PASS 572 ] > > proc.time() user system elapsed 354.092 16.438 304.882
NanoMethViz.Rcheck/NanoMethViz-Ex.timings
name | user | system | elapsed | |
NanoMethResult-class | 9.755 | 1.685 | 13.521 | |
bsseq_to_edger | 1.503 | 0.055 | 1.820 | |
bsseq_to_log_methy_ratio | 2.404 | 0.066 | 3.138 | |
cluster_regions | 8.112 | 0.202 | 9.737 | |
create_tabix_file | 0.420 | 0.056 | 0.591 | |
exons_to_genes | 0.692 | 0.020 | 0.811 | |
filter_methy | 4.000 | 0.550 | 5.421 | |
get_example_exons_mus_musculus | 0.604 | 0.016 | 0.757 | |
get_exons | 81.826 | 8.394 | 111.895 | |
get_exons_homo_sapiens | 20.495 | 1.116 | 25.360 | |
get_exons_mus_musculus | 24.818 | 2.027 | 33.040 | |
load_example_nanomethresult | 0.596 | 0.016 | 0.672 | |
methy | 0.004 | 0.001 | 0.005 | |
methy_col_names | 0.001 | 0.001 | 0.001 | |
methy_to_bsseq | 2.148 | 0.053 | 2.556 | |
methy_to_edger | 2.319 | 0.052 | 2.683 | |
modbam_to_tabix | 0.999 | 0.360 | 1.444 | |
plot_agg_genes | 5.804 | 0.255 | 7.019 | |
plot_agg_regions | 12.873 | 0.212 | 15.166 | |
plot_gene | 4.679 | 0.084 | 5.531 | |
plot_gene_heatmap | 17.618 | 0.299 | 20.870 | |
plot_grange | 4.494 | 0.068 | 5.337 | |
plot_grange_heatmap | 12.535 | 0.164 | 14.829 | |
plot_mds | 3.095 | 0.079 | 3.537 | |
plot_pca | 3.088 | 0.061 | 3.510 | |
plot_region | 4.134 | 0.064 | 5.033 | |
plot_region_heatmap | 12.426 | 0.155 | 14.648 | |
plot_violin | 5.010 | 0.093 | 5.878 | |
query_methy | 0.862 | 0.018 | 1.016 | |
region_methy_stats | 1.985 | 0.029 | 2.312 | |