Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-11 14:39 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
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 3.0.2 (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 | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | 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. |
Package: NanoMethViz |
Version: 3.0.2 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings NanoMethViz_3.0.2.tar.gz |
StartedAt: 2024-06-10 01:20:40 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 01:31:42 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 662.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: NanoMethViz.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings NanoMethViz_3.0.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/NanoMethViz.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘NanoMethViz/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘NanoMethViz’ version ‘3.0.2’ * 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++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking C++ specification ... OK Not all R platforms support C++20 * checking installed package size ... NOTE installed size is 6.9Mb sub-directories of 1Mb or more: libs 1.8Mb * 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 ... 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 43.766 2.052 45.854 get_exons_mus_musculus 13.210 0.460 13.670 get_exons_homo_sapiens 12.480 0.140 12.621 plot_gene 8.611 0.100 8.712 plot_gene_heatmap 6.870 0.024 6.895 plot_grange 6.243 0.044 6.286 plot_region 6.237 0.048 6.284 plot_agg_regions 5.316 0.044 5.361 plot_grange_heatmap 4.962 0.056 5.018 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/NanoMethViz.Rcheck/00check.log’ for details.
NanoMethViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL NanoMethViz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘NanoMethViz’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++20 g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c count_cg.cpp -o count_cg.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c modbam.cpp -o modbam.o modbam.cpp: In function ‘GenomicModPos parse_bam(const string&, const string&, const string&, const string&, const string&, int)’: modbam.cpp:394:44: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::basic_string_view<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 394 | while ( mod_string_end < mm_tok.size() && std::isalnum(mm_tok[mod_string_end]) ) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ modbam.cpp:400:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::basic_string_view<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 400 | if (mod_string_end == mm_tok.size() || mm_tok[mod_string_end] == '.') { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ modbam.cpp:425:17: warning: ‘parse_mode’ may be used uninitialized in this function [-Wmaybe-uninitialized] 425 | if (parse_mode == ParseMode::skip_low_prob) { | ^~ modbam.cpp:426:21: warning: ‘target_base’ may be used uninitialized in this function [-Wmaybe-uninitialized] 426 | if (seq.at(seq_ind) == target_base) { | ^~ g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.cpp -o utils.o g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o NanoMethViz.so RcppExports.o convert_methy_to_dss.o count_cg.o modbam.o utils.o -lz -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-bioc/R/site-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: x86_64-pc-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 580 ] > > proc.time() user system elapsed 156.017 12.455 114.492
NanoMethViz.Rcheck/NanoMethViz-Ex.timings
name | user | system | elapsed | |
NanoMethResult-class | 3.731 | 0.312 | 4.044 | |
bsseq_to_edger | 0.667 | 0.019 | 0.688 | |
bsseq_to_log_methy_ratio | 0.984 | 0.020 | 1.004 | |
cluster_regions | 4.298 | 0.192 | 4.490 | |
create_tabix_file | 0.184 | 0.004 | 0.188 | |
exons_to_genes | 0.246 | 0.011 | 0.259 | |
filter_methy | 1.879 | 0.048 | 1.922 | |
get_example_exons_mus_musculus | 0.208 | 0.012 | 0.221 | |
get_exons | 43.766 | 2.052 | 45.854 | |
get_exons_homo_sapiens | 12.480 | 0.140 | 12.621 | |
get_exons_mus_musculus | 13.21 | 0.46 | 13.67 | |
load_example_modbamresult | 0.224 | 0.003 | 0.227 | |
load_example_nanomethresult | 0.233 | 0.000 | 0.232 | |
methy | 0.003 | 0.000 | 0.002 | |
methy_col_names | 0.001 | 0.000 | 0.000 | |
methy_to_bsseq | 0.880 | 0.016 | 0.896 | |
methy_to_edger | 1.002 | 0.012 | 1.014 | |
modbam_to_tabix | 0.592 | 0.455 | 0.843 | |
plot_agg_genes | 1.721 | 0.012 | 1.732 | |
plot_agg_regions | 5.316 | 0.044 | 5.361 | |
plot_gene | 8.611 | 0.100 | 8.712 | |
plot_gene_heatmap | 6.870 | 0.024 | 6.895 | |
plot_grange | 6.243 | 0.044 | 6.286 | |
plot_grange_heatmap | 4.962 | 0.056 | 5.018 | |
plot_mds | 1.349 | 0.012 | 1.361 | |
plot_pca | 1.455 | 0.024 | 1.479 | |
plot_region | 6.237 | 0.048 | 6.284 | |
plot_region_heatmap | 4.815 | 0.008 | 4.823 | |
plot_violin | 2.391 | 0.036 | 2.427 | |
query_methy | 0.352 | 0.004 | 0.356 | |
region_methy_stats | 0.961 | 0.008 | 0.969 | |