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 12:05 -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 1390/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
NanoMethViz 3.2.0 (landing page) Shian Su
| 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 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: 3.2.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NanoMethViz.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings NanoMethViz_3.2.0.tar.gz |
StartedAt: 2024-12-20 04:00:26 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 04:13:11 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 765.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: NanoMethViz.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NanoMethViz.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings NanoMethViz_3.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/NanoMethViz.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'NanoMethViz/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'NanoMethViz' version '3.2.0' * 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 whether package 'NanoMethViz' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.3.0' * checking C++ specification ... OK Not all R platforms support C++20 * checking installed package size ... NOTE installed size is 7.7Mb sub-directories of 1Mb or more: libs 1.2Mb * 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 ... 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/NanoMethViz/libs/x64/NanoMethViz.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed get_exons 49.14 3.56 53.69 filter_methy 19.87 0.22 20.19 get_exons_mus_musculus 16.83 0.63 17.42 get_exons_homo_sapiens 14.27 1.19 15.45 plot_gene 11.91 0.61 12.49 plot_gene_heatmap 10.67 0.27 10.90 NanoMethResult-class 6.80 1.75 8.71 plot_grange 7.84 0.41 8.25 plot_region 8.03 0.22 8.24 plot_agg_regions 7.56 0.34 7.89 plot_region_heatmap 7.06 0.28 7.32 plot_grange_heatmap 6.77 0.26 7.02 cluster_regions 6.48 0.19 6.69 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/NanoMethViz.Rcheck/00check.log' for details.
NanoMethViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL NanoMethViz ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'NanoMethViz' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' using C++20 g++ -std=gnu++20 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++20 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o g++ -std=gnu++20 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c count_cg.cpp -o count_cg.o g++ -std=gnu++20 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c genome.cpp -o genome.o genome.cpp: In member function 'bool Genome::check_if_motif(const std::string&, int, const std::string&, int)': genome.cpp:43:21: warning: variable 'chrom_view' set but not used [-Wunused-but-set-variable] 43 | string_view chrom_view = this->bases_at(chrom, motif_start, motif_end); | ^~~~~~~~~~ g++ -std=gnu++20 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c modbam.cpp -o modbam.o modbam.cpp: In function 'GenomicModPos parse_bam(const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, int)': modbam.cpp:331:44: warning: comparison of integer expressions of different signedness: 'int' and 'std::basic_string_view<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 331 | while ( mod_string_end < mm_tok.size() && std::isalnum(mm_tok[mod_string_end]) ) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ modbam.cpp:339:40: warning: comparison of integer expressions of different signedness: 'int' and 'std::basic_string_view<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 339 | if (mod_string_end == mm_tok.size() || mm_tok[mod_string_end] == '?') { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ modbam.cpp:363:17: warning: 'target_base' may be used uninitialized [-Wmaybe-uninitialized] 363 | if (seq.at(seq_ind) == target_base) { | ^~ modbam.cpp:305:14: note: 'target_base' was declared here 305 | char target_base; | ^~~~~~~~~~~ modbam.cpp:364:21: warning: 'parse_mode' may be used uninitialized [-Wmaybe-uninitialized] 364 | switch (parse_mode) { | ^~~~~~ modbam.cpp:308:19: note: 'parse_mode' was declared here 308 | ParseMode parse_mode; | ^~~~~~~~~~ In file included from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_iterator.h:85, from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_algobase.h:67, from c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\algorithm:60, from modbam.cpp:1: In function 'constexpr decltype (::new(void*(0)) _Tp) std::construct_at(_Tp*, _Args&& ...) [with _Tp = char; _Args = {const char&}]', inlined from 'static constexpr void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = char; _Args = {const char&}; _Tp = char]' at c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\alloc_traits.h:540:21, inlined from 'constexpr void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const char&}; _Tp = char; _Alloc = std::allocator<char>]' at c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\vector.tcc:468:28, inlined from 'constexpr void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = char; _Alloc = std::allocator<char>]' at c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_vector.h:1292:21, inlined from 'GenomicModPos parse_bam(const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, int)' at modbam.cpp:368:50: c:\rtools44\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\13.3.0\include\c++\bits\stl_construct.h:97:14: warning: 'current_base' may be used uninitialized [-Wmaybe-uninitialized] 97 | { return ::new((void*)__location) _Tp(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ modbam.cpp: In function 'GenomicModPos parse_bam(const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, int)': modbam.cpp:304:14: note: 'current_base' was declared here 304 | char current_base; | ^~~~~~~~~~~~ g++ -std=gnu++20 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o g++ -shared -s -static-libgcc -o NanoMethViz.dll tmp.def RcppExports.o convert_methy_to_dss.o count_cg.o genome.o modbam.o utils.o -lz -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-NanoMethViz/00new/NanoMethViz/libs/x64 ** 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 ** 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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 3 | PASS 457 ] ══ Skipped tests (3) ═══════════════════════════════════════════════════════════ • empty test (3): 'test-cluster_regions.R:1:1', 'test-plot_agg_regions.R:1:1', 'test-plot_region_heatmap.R:28:1' [ FAIL 0 | WARN 0 | SKIP 3 | PASS 457 ] > > proc.time() user system elapsed 17.40 1.26 172.29
NanoMethViz.Rcheck/NanoMethViz-Ex.timings
name | user | system | elapsed | |
NanoMethResult-class | 6.80 | 1.75 | 8.71 | |
bsseq_to_edger | 0.93 | 0.03 | 1.99 | |
bsseq_to_log_methy_ratio | 1.60 | 0.03 | 1.70 | |
cluster_regions | 6.48 | 0.19 | 6.69 | |
create_tabix_file | 2.14 | 0.50 | 2.64 | |
exons_to_genes | 0.42 | 0.02 | 0.44 | |
filter_methy | 19.87 | 0.22 | 20.19 | |
get_example_exons_mus_musculus | 0.30 | 0.01 | 0.31 | |
get_exons | 49.14 | 3.56 | 53.69 | |
get_exons_homo_sapiens | 14.27 | 1.19 | 15.45 | |
get_exons_mus_musculus | 16.83 | 0.63 | 17.42 | |
load_example_modbamresult | 0.54 | 0.01 | 0.57 | |
load_example_nanomethresult | 0.30 | 0.03 | 0.33 | |
methy | 0 | 0 | 0 | |
methy_col_names | 0 | 0 | 0 | |
methy_to_bsseq | 1.14 | 0.08 | 1.28 | |
methy_to_edger | 1.59 | 0.08 | 1.72 | |
modbam_to_tabix | 2.63 | 0.79 | 3.05 | |
plot_agg_genes | 1.94 | 0.08 | 2.01 | |
plot_agg_regions | 7.56 | 0.34 | 7.89 | |
plot_gene | 11.91 | 0.61 | 12.49 | |
plot_gene_heatmap | 10.67 | 0.27 | 10.90 | |
plot_grange | 7.84 | 0.41 | 8.25 | |
plot_grange_heatmap | 6.77 | 0.26 | 7.02 | |
plot_mds | 2.18 | 0.05 | 2.28 | |
plot_pca | 2.02 | 0.06 | 2.11 | |
plot_region | 8.03 | 0.22 | 8.24 | |
plot_region_heatmap | 7.06 | 0.28 | 7.32 | |
plot_violin | 3.16 | 0.14 | 3.32 | |
query_methy | 0.58 | 0.05 | 0.62 | |
region_methy_stats | 1.36 | 0.04 | 1.42 | |