Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:04 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 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 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 | |||||||||
palomino7 | 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: 3.0.2 |
Command: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NanoMethViz.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings NanoMethViz_3.0.2.tar.gz |
StartedAt: 2024-07-22 04:24:09 -0400 (Mon, 22 Jul 2024) |
EndedAt: 2024-07-22 04:35:42 -0400 (Mon, 22 Jul 2024) |
EllapsedTime: 693.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: NanoMethViz.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NanoMethViz.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings NanoMethViz_3.0.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/NanoMethViz.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * 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 '3.0.2' * 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 whether package 'NanoMethViz' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * checking C++ specification ... OK Not all R platforms support C++20 * checking installed package size ... NOTE installed size is 6.2Mb 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 ... 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 for x64 is not available File 'E:/biocbuild/bbs-3.19-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 42.30 2.89 45.82 get_exons_mus_musculus 14.49 0.66 15.23 get_exons_homo_sapiens 14.03 1.06 15.06 plot_gene 12.02 0.33 12.33 plot_gene_heatmap 10.29 0.37 10.66 plot_region 8.42 0.29 8.67 plot_grange 8.35 0.30 8.62 NanoMethResult-class 6.41 2.16 8.64 plot_region_heatmap 7.60 0.14 7.74 plot_grange_heatmap 7.28 0.14 7.41 plot_agg_regions 5.98 0.13 6.14 cluster_regions 5.55 0.07 5.61 * 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 'E:/biocbuild/bbs-3.19-bioc/meat/NanoMethViz.Rcheck/00check.log' for details.
NanoMethViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL NanoMethViz ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'NanoMethViz' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' using C++20 g++ -std=gnu++20 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-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"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-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"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-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"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-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:394:44: warning: comparison of integer expressions of different signedness: 'int' and 'std::basic_string_view<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 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 long unsigned int'} [-Wsign-compare] 400 | if (mod_string_end == mm_tok.size() || mm_tok[mod_string_end] == '.') { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ modbam.cpp:437:21: warning: 'target_base' may be used uninitialized [-Wmaybe-uninitialized] 437 | if (seq.at(seq_ind) == target_base) { | ^~ modbam.cpp:368:14: note: 'target_base' was declared here 368 | char target_base; | ^~~~~~~~~~~ modbam.cpp:425:17: warning: 'parse_mode' may be used uninitialized [-Wmaybe-uninitialized] 425 | if (parse_mode == ParseMode::skip_low_prob) { | ^~ modbam.cpp:371:19: note: 'parse_mode' was declared here 371 | ParseMode parse_mode; | ^~~~~~~~~~ In file included from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_iterator.h:85, from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_algobase.h:67, from C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/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/13.2.0/include/c++/bits/alloc_traits.h:539:21, 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/13.2.0/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/13.2.0/include/c++/bits/stl_vector.h:1289:21, inlined from 'GenomicModPos parse_bam(const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, int)' at modbam.cpp:430:46: C:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/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:367:14: note: 'current_base' was declared here 367 | char current_base; | ^~~~~~~~~~~~ g++ -std=gnu++20 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-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 modbam.o utils.o -lz -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-NanoMethViz/00new/NanoMethViz/libs/x64 ** 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 ** 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 ucrt) -- "Race for Your Life" 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 0 | PASS 580 ] > > proc.time() user system elapsed 17.48 1.26 146.73
NanoMethViz.Rcheck/NanoMethViz-Ex.timings
name | user | system | elapsed | |
NanoMethResult-class | 6.41 | 2.16 | 8.64 | |
bsseq_to_edger | 1.03 | 0.07 | 1.17 | |
bsseq_to_log_methy_ratio | 1.61 | 0.03 | 2.07 | |
cluster_regions | 5.55 | 0.07 | 5.61 | |
create_tabix_file | 0.92 | 0.40 | 1.18 | |
exons_to_genes | 0.45 | 0.03 | 0.48 | |
filter_methy | 3.15 | 0.16 | 3.44 | |
get_example_exons_mus_musculus | 0.35 | 0.02 | 0.37 | |
get_exons | 42.30 | 2.89 | 45.82 | |
get_exons_homo_sapiens | 14.03 | 1.06 | 15.06 | |
get_exons_mus_musculus | 14.49 | 0.66 | 15.23 | |
load_example_modbamresult | 0.40 | 0.01 | 0.42 | |
load_example_nanomethresult | 0.53 | 0.02 | 0.55 | |
methy | 0 | 0 | 0 | |
methy_col_names | 0 | 0 | 0 | |
methy_to_bsseq | 1.32 | 0.06 | 1.44 | |
methy_to_edger | 1.31 | 0.05 | 1.47 | |
modbam_to_tabix | 2.08 | 0.82 | 2.43 | |
plot_agg_genes | 2.44 | 0.11 | 2.55 | |
plot_agg_regions | 5.98 | 0.13 | 6.14 | |
plot_gene | 12.02 | 0.33 | 12.33 | |
plot_gene_heatmap | 10.29 | 0.37 | 10.66 | |
plot_grange | 8.35 | 0.30 | 8.62 | |
plot_grange_heatmap | 7.28 | 0.14 | 7.41 | |
plot_mds | 2.09 | 0.03 | 2.26 | |
plot_pca | 2.53 | 0.09 | 2.69 | |
plot_region | 8.42 | 0.29 | 8.67 | |
plot_region_heatmap | 7.60 | 0.14 | 7.74 | |
plot_violin | 3.29 | 0.11 | 3.40 | |
query_methy | 0.66 | 0.01 | 0.66 | |
region_methy_stats | 1.20 | 0.05 | 1.25 | |