Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:39 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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 1401/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
NanoMethViz 3.0.1 (landing page) Shian Su
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the NanoMethViz package: - 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: 3.0.1 |
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_3.0.1.tar.gz |
StartedAt: 2024-05-06 23:22:08 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 23:25:29 -0400 (Mon, 06 May 2024) |
EllapsedTime: 201.6 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_3.0.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/NanoMethViz.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-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 Ventura 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘NanoMethViz/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘NanoMethViz’ version ‘3.0.1’ * 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 ‘NanoMethViz’ can be installed ... OK * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * 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 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 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 ... NOTE read_methy_lines: no visible global function definition for ‘read.delim’ Undefined global functions or variables: read.delim Consider adding importFrom("utils", "read.delim") 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 ... 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 17.192 0.805 18.057 get_exons_mus_musculus 4.966 0.252 5.222 get_exons_homo_sapiens 4.913 0.249 5.187 * 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-mac-arm64/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-arm64/Resources/library’ * installing *source* package ‘NanoMethViz’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++20 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c count_cg.cpp -o count_cg.o clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c modbam.cpp -o modbam.o clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o NanoMethViz.so RcppExports.o convert_methy_to_dss.o count_cg.o modbam.o utils.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/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 version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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 579 ] > > proc.time() user system elapsed 57.503 3.387 40.787
NanoMethViz.Rcheck/NanoMethViz-Ex.timings
name | user | system | elapsed | |
NanoMethResult-class | 1.691 | 0.237 | 1.928 | |
bsseq_to_edger | 0.290 | 0.009 | 0.299 | |
bsseq_to_log_methy_ratio | 0.823 | 0.011 | 0.834 | |
cluster_regions | 1.084 | 0.029 | 1.115 | |
create_tabix_file | 0.081 | 0.011 | 0.094 | |
exons_to_genes | 0.094 | 0.002 | 0.095 | |
filter_methy | 0.848 | 0.061 | 0.910 | |
get_example_exons_mus_musculus | 0.083 | 0.002 | 0.084 | |
get_exons | 17.192 | 0.805 | 18.057 | |
get_exons_homo_sapiens | 4.913 | 0.249 | 5.187 | |
get_exons_mus_musculus | 4.966 | 0.252 | 5.222 | |
load_example_modbamresult | 0.087 | 0.002 | 0.089 | |
load_example_nanomethresult | 0.082 | 0.002 | 0.084 | |
methy | 0.001 | 0.000 | 0.000 | |
methy_col_names | 0 | 0 | 0 | |
methy_to_bsseq | 0.373 | 0.009 | 0.381 | |
methy_to_edger | 0.577 | 0.080 | 0.657 | |
modbam_to_tabix | 0.194 | 0.098 | 0.232 | |
plot_agg_genes | 0.662 | 0.021 | 0.685 | |
plot_agg_regions | 1.813 | 0.080 | 1.894 | |
plot_gene | 3.220 | 0.083 | 3.304 | |
plot_gene_heatmap | 2.016 | 0.066 | 2.083 | |
plot_grange | 1.861 | 0.035 | 1.897 | |
plot_grange_heatmap | 1.448 | 0.036 | 1.484 | |
plot_mds | 0.527 | 0.013 | 0.542 | |
plot_pca | 0.518 | 0.011 | 0.531 | |
plot_region | 1.741 | 0.034 | 1.775 | |
plot_region_heatmap | 1.430 | 0.031 | 1.461 | |
plot_violin | 0.834 | 0.021 | 0.856 | |
query_methy | 0.125 | 0.003 | 0.128 | |
region_methy_stats | 0.330 | 0.008 | 0.338 | |