| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-30 11:35 -0400 (Thu, 30 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4988 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4718 |
| 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 687/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| epialleleR 1.20.0 (landing page) Oleksii Nikolaienko
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for epialleleR in R Universe. | ||||||||||||||
|
To the developers/maintainers of the epialleleR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epialleleR.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: epialleleR |
| Version: 1.20.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:epialleleR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings epialleleR_1.20.0.tar.gz |
| StartedAt: 2026-04-29 23:49:08 -0400 (Wed, 29 Apr 2026) |
| EndedAt: 2026-04-29 23:52:17 -0400 (Wed, 29 Apr 2026) |
| EllapsedTime: 189.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: epialleleR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:epialleleR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings epialleleR_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/epialleleR.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-30 03:49:08 UTC
* checking for file ‘epialleleR/DESCRIPTION’ ... OK
* this is package ‘epialleleR’ version ‘1.20.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘epialleleR’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking C++ specification ... INFO
specified C++17
* checking installed package size ... INFO
installed size is 9.9Mb
sub-directories of 1Mb or more:
extdata 2.3Mb
libs 7.3Mb
* 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 loading without being on the library search path ... 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 ... INFO
GNU make is a SystemRequirements.
* 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
File ‘/home/biocbuild/bbs-3.23-bioc/R/site-library/epialleleR/libs/epialleleR.so’:
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (C)
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
generateVcfReport 18.09 1.364 19.776
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/epialleleR.Rcheck/00check.log’
for details.
epialleleR.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL epialleleR
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘epialleleR’ ...
** this is package ‘epialleleR’ version ‘1.20.0’
** using staged installation
** libs
specified C++17
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c rcpp_call_methylation.cpp -o rcpp_call_methylation.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c rcpp_check_bam.cpp -o rcpp_check_bam.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c rcpp_cx_report.cpp -o rcpp_cx_report.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c rcpp_extract_patterns.cpp -o rcpp_extract_patterns.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c rcpp_fep.cpp -o rcpp_fep.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c rcpp_get_base_freqs.cpp -o rcpp_get_base_freqs.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c rcpp_get_xm_beta.cpp -o rcpp_get_xm_beta.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c rcpp_match_target.cpp -o rcpp_match_target.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c rcpp_mhl_report.cpp -o rcpp_mhl_report.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c rcpp_read_bam.cpp -o rcpp_read_bam.o
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/range/concepts.hpp:26,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/range/size_type.hpp:20,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/range/size.hpp:21,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/range/functions.hpp:20,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:41,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/concept/interval_associator.hpp:11,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/associative_interval_container.hpp:18,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/interval_base_set.hpp:24,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/interval_set.hpp:14,
from rcpp_read_bam.cpp:3:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
rcpp_read_bam.cpp: In function ‘T_granges load_intervals(Rcpp::DataFrame&, const bam_hdr_t*)’:
rcpp_read_bam.cpp:61:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
61 | for (int i=0; i<seqlevels.size(); i++) { // for every BED seqlevel
| ~^~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/assert.hpp:35,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/continuous_interval.hpp:13,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/type_traits/interval_type_default.hpp:13,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/interval.hpp:12,
from rcpp_read_bam.cpp:2:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp: In instantiation of ‘static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::concepts::usage_requirements<boost::DefaultConstructible<int> >]’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:137:5: required from ‘struct boost::DefaultConstructible<int>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:135:3: required from ‘struct boost::DefaultConstructibleConcept<int>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of ‘template<class Model> boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints<Model, (& Model::constraints)>*) [with Model = boost::DefaultConstructibleConcept<int>]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:42:5: required from ‘const bool boost::concepts::not_satisfied<boost::DefaultConstructibleConcept<int> >::value’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:45:51: required from ‘struct boost::concepts::not_satisfied<boost::DefaultConstructibleConcept<int> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp:72:8: required from ‘struct boost::concepts::requirement_<void (*)(boost::DefaultConstructibleConcept<int>)>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/continuous_interval.hpp:45:9: required from ‘boost::icl::discrete_interval<DomainT, Compare>::discrete_interval(const DomainT&, const DomainT&, boost::icl::interval_bounds, boost::icl::discrete_interval<DomainT, Compare>*) [with DomainT = int; Compare = std::less]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/discrete_interval.hpp:120:16: required from ‘static boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::interval_type boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::construct(const domain_type&, const domain_type&, boost::icl::interval_bounds) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>; domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/concept/interval.hpp:254:52: required from ‘typename boost::enable_if<boost::icl::has_dynamic_bounds<Type>, Type>::type boost::icl::construct(const typename interval_traits<Type>::domain_type&, const typename interval_traits<Type>::domain_type&, interval_bounds) [with Type = discrete_interval<int, std::less>; typename boost::enable_if<has_dynamic_bounds<Type>, Type>::type = discrete_interval<int, std::less>; typename interval_traits<Type>::domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/interval.hpp:91:47: required from ‘static boost::icl::interval<DomainT, Compare>::interval_type boost::icl::interval<DomainT, Compare>::closed(const DomainT&, const DomainT&) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>]’
rcpp_read_bam.cpp:73:58: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp:50:47: warning: ‘this’ pointer is null [-Wnonnull]
50 | static void failed() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:31,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/detail/concept_check.hpp:11,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/continuous_interval.hpp:14:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/usage.hpp:20:5: note: in a call to non-static member function ‘boost::concepts::usage_requirements<Model>::~usage_requirements() [with Model = boost::DefaultConstructible<int>]’
20 | ~usage_requirements() { ((Model*)0)->~Model(); }
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp: In instantiation of ‘static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::DefaultConstructibleConcept<int>]’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/continuous_interval.hpp:45:9: required from ‘boost::icl::discrete_interval<DomainT, Compare>::discrete_interval(const DomainT&, const DomainT&, boost::icl::interval_bounds, boost::icl::discrete_interval<DomainT, Compare>*) [with DomainT = int; Compare = std::less]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/discrete_interval.hpp:120:16: required from ‘static boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::interval_type boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::construct(const domain_type&, const domain_type&, boost::icl::interval_bounds) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>; domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/concept/interval.hpp:254:52: required from ‘typename boost::enable_if<boost::icl::has_dynamic_bounds<Type>, Type>::type boost::icl::construct(const typename interval_traits<Type>::domain_type&, const typename interval_traits<Type>::domain_type&, interval_bounds) [with Type = discrete_interval<int, std::less>; typename boost::enable_if<has_dynamic_bounds<Type>, Type>::type = discrete_interval<int, std::less>; typename interval_traits<Type>::domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/interval.hpp:91:47: required from ‘static boost::icl::interval<DomainT, Compare>::interval_type boost::icl::interval<DomainT, Compare>::closed(const DomainT&, const DomainT&) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>]’
rcpp_read_bam.cpp:73:58: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp:50:47: warning: ‘this’ pointer is null [-Wnonnull]
50 | static void failed() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/aux_/integral_wrapper.hpp:22,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/int.hpp:20,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/lambda_fwd.hpp:23,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/aux_/na_spec.hpp:18,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/if.hpp:19,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/type_traits/interval_type_default.hpp:11:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:135:17: note: in a call to non-static member function ‘boost::DefaultConstructibleConcept<int>::~DefaultConstructibleConcept()’
135 | BOOST_concept(DefaultConstructible,(TT))
| ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
29 | # define BOOST_PP_CAT_I(a, b) a ## b
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/concept_def.hpp:23:12: note: in expansion of macro ‘BOOST_PP_CAT’
23 | struct BOOST_PP_CAT(name,Concept) \
| ^~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:135:3: note: in expansion of macro ‘BOOST_concept’
135 | BOOST_concept(DefaultConstructible,(TT))
| ^~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp: In instantiation of ‘static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::concepts::usage_requirements<boost::LessThanComparable<int> >]’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:243:5: required from ‘struct boost::LessThanComparable<int>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:241:3: required from ‘struct boost::LessThanComparableConcept<int>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of ‘template<class Model> boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints<Model, (& Model::constraints)>*) [with Model = boost::LessThanComparableConcept<int>]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:42:5: required from ‘const bool boost::concepts::not_satisfied<boost::LessThanComparableConcept<int> >::value’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:45:51: required from ‘struct boost::concepts::not_satisfied<boost::LessThanComparableConcept<int> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp:72:8: required from ‘struct boost::concepts::requirement_<void (*)(boost::LessThanComparableConcept<int>)>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/continuous_interval.hpp:46:9: required from ‘boost::icl::discrete_interval<DomainT, Compare>::discrete_interval(const DomainT&, const DomainT&, boost::icl::interval_bounds, boost::icl::discrete_interval<DomainT, Compare>*) [with DomainT = int; Compare = std::less]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/discrete_interval.hpp:120:16: required from ‘static boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::interval_type boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::construct(const domain_type&, const domain_type&, boost::icl::interval_bounds) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>; domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/concept/interval.hpp:254:52: required from ‘typename boost::enable_if<boost::icl::has_dynamic_bounds<Type>, Type>::type boost::icl::construct(const typename interval_traits<Type>::domain_type&, const typename interval_traits<Type>::domain_type&, interval_bounds) [with Type = discrete_interval<int, std::less>; typename boost::enable_if<has_dynamic_bounds<Type>, Type>::type = discrete_interval<int, std::less>; typename interval_traits<Type>::domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/interval.hpp:91:47: required from ‘static boost::icl::interval<DomainT, Compare>::interval_type boost::icl::interval<DomainT, Compare>::closed(const DomainT&, const DomainT&) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>]’
rcpp_read_bam.cpp:73:58: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp:50:47: warning: ‘this’ pointer is null [-Wnonnull]
50 | static void failed() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/usage.hpp:20:5: note: in a call to non-static member function ‘boost::concepts::usage_requirements<Model>::~usage_requirements() [with Model = boost::LessThanComparable<int>]’
20 | ~usage_requirements() { ((Model*)0)->~Model(); }
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp: In instantiation of ‘static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::LessThanComparableConcept<int>]’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/continuous_interval.hpp:46:9: required from ‘boost::icl::discrete_interval<DomainT, Compare>::discrete_interval(const DomainT&, const DomainT&, boost::icl::interval_bounds, boost::icl::discrete_interval<DomainT, Compare>*) [with DomainT = int; Compare = std::less]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/discrete_interval.hpp:120:16: required from ‘static boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::interval_type boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::construct(const domain_type&, const domain_type&, boost::icl::interval_bounds) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>; domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/concept/interval.hpp:254:52: required from ‘typename boost::enable_if<boost::icl::has_dynamic_bounds<Type>, Type>::type boost::icl::construct(const typename interval_traits<Type>::domain_type&, const typename interval_traits<Type>::domain_type&, interval_bounds) [with Type = discrete_interval<int, std::less>; typename boost::enable_if<has_dynamic_bounds<Type>, Type>::type = discrete_interval<int, std::less>; typename interval_traits<Type>::domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/interval.hpp:91:47: required from ‘static boost::icl::interval<DomainT, Compare>::interval_type boost::icl::interval<DomainT, Compare>::closed(const DomainT&, const DomainT&) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>]’
rcpp_read_bam.cpp:73:58: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp:50:47: warning: ‘this’ pointer is null [-Wnonnull]
50 | static void failed() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:241:17: note: in a call to non-static member function ‘boost::LessThanComparableConcept<int>::~LessThanComparableConcept()’
241 | BOOST_concept(LessThanComparable,(TT))
| ^~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/preprocessor/cat.hpp:29:34: note: in definition of macro ‘BOOST_PP_CAT_I’
29 | # define BOOST_PP_CAT_I(a, b) a ## b
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/concept_def.hpp:23:12: note: in expansion of macro ‘BOOST_PP_CAT’
23 | struct BOOST_PP_CAT(name,Concept) \
| ^~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:241:3: note: in expansion of macro ‘BOOST_concept’
241 | BOOST_concept(LessThanComparable,(TT))
| ^~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/usage.hpp: In instantiation of ‘boost::concepts::usage_requirements<Model>::~usage_requirements() [with Model = boost::DefaultConstructible<int>]’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp:50:47: required from ‘static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::concepts::usage_requirements<boost::DefaultConstructible<int> >]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:137:5: required from ‘struct boost::DefaultConstructible<int>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:135:3: required from ‘struct boost::DefaultConstructibleConcept<int>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of ‘template<class Model> boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints<Model, (& Model::constraints)>*) [with Model = boost::DefaultConstructibleConcept<int>]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:42:5: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp:72:8: required from ‘struct boost::concepts::requirement_<void (*)(boost::DefaultConstructibleConcept<int>)>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/continuous_interval.hpp:45:9: required from ‘boost::icl::discrete_interval<DomainT, Compare>::discrete_interval(const DomainT&, const DomainT&, boost::icl::interval_bounds, boost::icl::discrete_interval<DomainT, Compare>*) [with DomainT = int; Compare = std::less]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/discrete_interval.hpp:120:16: required from ‘static boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::interval_type boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::construct(const domain_type&, const domain_type&, boost::icl::interval_bounds) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>; domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/concept/interval.hpp:254:52: required from ‘typename boost::enable_if<boost::icl::has_dynamic_bounds<Type>, Type>::type boost::icl::construct(const typename interval_traits<Type>::domain_type&, const typename interval_traits<Type>::domain_type&, interval_bounds) [with Type = discrete_interval<int, std::less>; typename boost::enable_if<has_dynamic_bounds<Type>, Type>::type = discrete_interval<int, std::less>; typename interval_traits<Type>::domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/interval.hpp:91:47: required from ‘static boost::icl::interval<DomainT, Compare>::interval_type boost::icl::interval<DomainT, Compare>::closed(const DomainT&, const DomainT&) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>]’
rcpp_read_bam.cpp:73:58: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/usage.hpp:20:48: warning: ‘this’ pointer is null [-Wnonnull]
20 | ~usage_requirements() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/usage.hpp:37:7: note: in a call to non-static member function ‘boost::DefaultConstructible<TT>::~DefaultConstructible() [with TT = int]’
37 | ~model()
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:137:5: note: in expansion of macro ‘BOOST_CONCEPT_USAGE’
137 | BOOST_CONCEPT_USAGE(DefaultConstructible) {
| ^~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/usage.hpp: In instantiation of ‘boost::concepts::usage_requirements<Model>::~usage_requirements() [with Model = boost::LessThanComparable<int>]’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp:50:47: required from ‘static void boost::concepts::requirement<boost::concepts::failed************ Model::************>::failed() [with Model = boost::concepts::usage_requirements<boost::LessThanComparable<int> >]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:243:5: required from ‘struct boost::LessThanComparable<int>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:241:3: required from ‘struct boost::LessThanComparableConcept<int>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:32:62: required by substitution of ‘template<class Model> boost::concepts::detail::yes boost::concepts::detail::has_constraints_(Model*, wrap_constraints<Model, (& Model::constraints)>*) [with Model = boost::LessThanComparableConcept<int>]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/has_constraints.hpp:42:5: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/detail/general.hpp:72:8: required from ‘struct boost::concepts::requirement_<void (*)(boost::LessThanComparableConcept<int>)>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/continuous_interval.hpp:46:9: required from ‘boost::icl::discrete_interval<DomainT, Compare>::discrete_interval(const DomainT&, const DomainT&, boost::icl::interval_bounds, boost::icl::discrete_interval<DomainT, Compare>*) [with DomainT = int; Compare = std::less]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/discrete_interval.hpp:120:16: required from ‘static boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::interval_type boost::icl::dynamic_interval_traits<boost::icl::discrete_interval<DomainT, Compare> >::construct(const domain_type&, const domain_type&, boost::icl::interval_bounds) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>; domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/concept/interval.hpp:254:52: required from ‘typename boost::enable_if<boost::icl::has_dynamic_bounds<Type>, Type>::type boost::icl::construct(const typename interval_traits<Type>::domain_type&, const typename interval_traits<Type>::domain_type&, interval_bounds) [with Type = discrete_interval<int, std::less>; typename boost::enable_if<has_dynamic_bounds<Type>, Type>::type = discrete_interval<int, std::less>; typename interval_traits<Type>::domain_type = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/icl/interval.hpp:91:47: required from ‘static boost::icl::interval<DomainT, Compare>::interval_type boost::icl::interval<DomainT, Compare>::closed(const DomainT&, const DomainT&) [with DomainT = int; Compare = std::less; interval_type = boost::icl::discrete_interval<int, std::less>]’
rcpp_read_bam.cpp:73:58: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/usage.hpp:20:48: warning: ‘this’ pointer is null [-Wnonnull]
20 | ~usage_requirements() { ((Model*)0)->~Model(); }
| ~~~~~~~~~~~~~~~~~~~^~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept/usage.hpp:37:7: note: in a call to non-static member function ‘boost::LessThanComparable<TT>::~LessThanComparable() [with TT = int]’
37 | ~model()
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/concept_check.hpp:243:5: note: in expansion of macro ‘BOOST_CONCEPT_USAGE’
243 | BOOST_CONCEPT_USAGE(LessThanComparable) {
| ^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c rcpp_read_genome.cpp -o rcpp_read_genome.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c rcpp_simulate_bam.cpp -o rcpp_simulate_bam.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c rcpp_threshold_reads.cpp -o rcpp_threshold_reads.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o epialleleR.so RcppExports.o rcpp_call_methylation.o rcpp_check_bam.o rcpp_cx_report.o rcpp_extract_patterns.o rcpp_fep.o rcpp_get_base_freqs.o rcpp_get_xm_beta.o rcpp_match_target.o rcpp_mhl_report.o rcpp_read_bam.o rcpp_read_genome.o rcpp_simulate_bam.o rcpp_threshold_reads.o /home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-epialleleR/00new/epialleleR/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 (epialleleR)
epialleleR.Rcheck/tests/runTests.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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.
> BiocGenerics:::testPackage("epialleleR")
Reading reference genome file [0.001s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Making methylation calls [0.023s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Making methylation calls [0.022s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Making methylation calls [0.022s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Making methylation calls [E::hts_open_format] Failed to open file "" : No such file or directory
Making methylation calls [E::hts_open_format] Failed to open file "" : No such file or directory
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.023s]
Filtering reads [0.000s]
Preparing cytosine report [0.003s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.003s]
Filtering reads [0.000s]
Preparing cytosine report [0.003s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Filtering reads [0.000s]
Preparing cytosine report [0.003s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.004s]
Filtering reads [0.000s]
Preparing cytosine report [0.003s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.005s]
Filtering reads [0.000s]
Preparing cytosine report [0.003s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.005s]
Filtering reads [0.000s]
Preparing cytosine report [0.003s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.006s]
Filtering reads [0.000s]
Preparing cytosine report [0.003s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.005s]
Filtering reads [0.000s]
Preparing cytosine report [0.002s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.007s]
Filtering reads [0.000s]
Preparing cytosine report [0.005s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Filtering reads [0.000s]
Preparing cytosine report [0.004s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.006s]
Filtering reads [0.001s]
Preparing cytosine report [0.003s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.005s]
Filtering reads [0.001s]
Preparing cytosine report [0.004s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
Filtering reads [0.001s]
Preparing cytosine report [0.004s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
Filtering reads [0.001s]
Preparing cytosine report [0.004s]
Reading BED file [0.092s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Extracting methylation patterns [0.052s]
0E73D2923FF97A91 85C3CFCF53F38F39 47722D75C7003661 8F3533D5B9238A19 C462A3CE8FA64FB7 C0EE9CEA6CEC7F73 73AE34FF06880D91 6D35C6B11345E351 7DD1305C28282FD1 4BE66B4BE09A7811 A48A487216CAE720 805CAB957B75F967 767A775A6775A367 02ED1CF7380BBF18 83848B29B3F9FD70 50666447E6155378 6F6A105B958A9896 083090CE5977519F 68274DDFE647B18F 43CB3C445F0062E0 AA965D58EEF55912 7492C3D98A2727F7 8AA0019DE2F05F23 CA846BC7D9726E02 A6E7EF44DD4926C9 B6718A510AA8A248 EDCE055B659CEBA1 4CEC133797B05CF9 808D4B22BA22A539 F81B7EE769A4812F 3F58F3B81B25C7DE D4FBA5F32B459DF9 89FC3C8B5DA842BF 964484532C541975
Reading BED file [0.014s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Extracting methylation patterns [0.091s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Extracting methylation patterns [0.034s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Extracting methylation patterns [0.033s]
Reading BED file [0.012s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
Computing ECDFs for within- and out-of-context per-read beta values [0.010s]
Reading BED file [0.012s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.007s]
Computing ECDFs for within- and out-of-context per-read beta values [0.009s]
Reading BED file [0.011s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
Thresholding reads [0.000s]
Preparing amplicon report [0.019s]
Reading BED file [0.011s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
Filtering reads [0.000s]
Preparing amplicon report [0.019s]
Reading BED file [0.012s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Filtering and thresholding reads [0.001s]
Preparing amplicon report [0.019s]
Writing the report [0.001s]
Reading BED file [0.011s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
Filtering and thresholding reads [0.000s]
Preparing amplicon report [0.020s]
Reading BED file [0.011s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
Skipping filtering/thresholding [0.000s]
Preparing amplicon report [0.020s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
Filtering and thresholding reads [0.000s]
Preparing cytosine report [0.005s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Thresholding reads [0.000s]
Preparing cytosine report [0.004s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
Filtering reads [0.000s]
Preparing cytosine report [0.004s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Skipping filtering/thresholding [0.000s]
Preparing cytosine report [0.004s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.016s]
Filtering and thresholding reads [0.002s]
Preparing cytosine report [0.016s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.017s]
Filtering and thresholding reads [0.003s]
Preparing cytosine report [0.021s]
Writing the report [0.003s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.016s]
Filtering and thresholding reads [0.001s]
Preparing cytosine report [0.016s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.003s]
Skipping filtering/thresholding [0.000s]
Preparing cytosine report [0.001s]
Writing sample BAM [0.004s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.002s]
Skipping filtering/thresholding [0.001s]
Preparing cytosine report [0.000s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.001s]
Skipping filtering/thresholding [0.000s]
Preparing cytosine report [0.000s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.002s]
Skipping filtering/thresholding [0.001s]
Preparing cytosine report [0.000s]
Writing sample BAM [0.004s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.002s]
Skipping filtering/thresholding [0.000s]
Preparing cytosine report [0.000s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.002s]
Skipping filtering/thresholding [0.000s]
Preparing cytosine report [0.000s]
Writing sample BAM [0.004s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.002s]
Skipping filtering/thresholding [0.000s]
Preparing cytosine report [0.000s]
Writing sample BAM [0.003s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.002s]
Skipping filtering/thresholding [0.000s]
Preparing cytosine report [0.001s]
Writing sample BAM [0.003s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.002s]
Skipping filtering/thresholding [0.000s]
Preparing cytosine report [0.000s]
Writing sample BAM [0.003s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.002s]
Skipping filtering/thresholding [0.000s]
Preparing cytosine report [0.001s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.017s]
Preparing lMHL report [0.027s]
Writing the report [0.004s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.016s]
Preparing lMHL report [0.026s]
Writing the report [0.004s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.017s]
Preparing lMHL report [0.026s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.018s]
Skipping filtering/thresholding [0.000s]
Preparing cytosine report [0.016s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.018s]
Preparing lMHL report [0.026s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Preparing lMHL report [0.005s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Preparing lMHL report [0.005s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
Preparing lMHL report [0.006s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Preparing lMHL report [0.006s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Preparing lMHL report [0.005s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Preparing lMHL report [0.005s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Preparing lMHL report [0.005s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
Preparing lMHL report [0.005s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
Preparing lMHL report [0.006s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Skipping filtering/thresholding [0.000s]
Preparing cytosine report [0.004s]
Writing sample BAM [0.017s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.002s]
Filtering reads [0.000s]
Preparing cytosine report [0.012s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.002s]
Preparing lMHL report [0.003s]
Loading required namespace: VariantAnnotation
Loading required namespace: GenomeInfoDb
Reading BED file [0.011s]
Reading VCF file [0.614s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Filtering reads [0.000s]
Extracting base frequences [0.058s]
Reading VCF file [0.185s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Filtering reads [0.000s]
Extracting base frequences Already preprocessed VCF supplied as an input. Options 'bed' and 'zero.based.bed' will have no effect.
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.017s]
Filtering and thresholding reads [0.002s]
Extracting base frequences [0.169s]
Writing the report [0.007s]
Reading BED file [0.011s]
Reading VCF file [0.649s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Filtering reads [0.000s]
Extracting base frequences [0.078s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Extracting methylation patterns [0.044s]
84 patterns supplied
46 unique
7 most frequent unique patterns were selected for plotting using 10 beta value bins:
[0,0.1) [0.1,0.2) [0.2,0.3) [0.3,0.4) [0.4,0.5) [0.5,0.6) [0.6,0.7) [0.7,0.8) [0.8,0.9) [0.9,1]
2 1 1 0 0 0 0 1 0 2
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Already preprocessed BAM supplied as an input. Explicitly set 'preprocessBam' options will have no effect.
Already preprocessed BAM supplied as an input. Explicitly set 'preprocessBam' options will have no effect.
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Checking BAM file: Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.003s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Checking BAM file: Checking BAM file: Checking BAM file: Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.003s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.006s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Writing sample BAM [0.006s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading BED file [0.011s]
Reading paired-end BAM file [0.010s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.008s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.009s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading single-end BAM file [0.011s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading single-end BAM file [0.011s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.011s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.011s]
Checking BAM file: Checking BAM file: Checking BAM file: Checking BAM file: short-read, paired-end, name-sorted alignment detected
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading single-end BAM file [0.004s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading reference genome file [0.001s]
Reading reference genome file [E::fai_build3_core] Failed to open the file /home/biocbuild/bbs-3.23-bioc/R/site-library/epialleleR/extdata/test
Reading reference genome file [E::fai_build3_core] Failed to open the file
Writing sample BAM [0.004s]
Writing sample BAM [0.004s]
Checking BAM file: Writing sample BAM Writing sample BAM [0.003s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.002s]
Filtering reads [0.000s]
Preparing cytosine report [0.000s]
Writing sample BAM [0.038s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.003s]
Filtering and thresholding reads [0.000s]
Preparing cytosine report [0.001s]
Writing sample BAM [0.016s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.003s]
Filtering reads [0.000s]
Preparing cytosine report [0.002s]
Writing sample BAM [0.016s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.007s]
Filtering reads [0.000s]
Preparing cytosine report [0.001s]
Writing sample BAM [0.008s]
Reading reference genome file [0.001s]
Making methylation calls [0.021s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.003s]
Filtering reads [0.000s]
Preparing cytosine report [0.001s]
Writing sample BAM [0.007s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.003s]
Filtering reads [0.000s]
Preparing cytosine report [0.002s]
RUNIT TEST PROTOCOL -- Wed Apr 29 23:51:18 2026
***********************************************
Number of test functions: 12
Number of errors: 0
Number of failures: 0
1 Test Suite :
epialleleR RUnit Tests - 12 test functions, 0 errors, 0 failures
Number of test functions: 12
Number of errors: 0
Number of failures: 0
Warning messages:
1: In ggplot2::scale_y_continuous(transform = trans, limits = marginal.limits, :
composition(log-10,reverse) transformation introduced infinite values.
2: Supplied endness is different from detected!
3: Supplied endness is different from detected!
4: Supplied endness is different from detected!
>
> proc.time()
user system elapsed
28.185 1.354 30.006
epialleleR.Rcheck/epialleleR-Ex.timings
| name | user | system | elapsed | |
| callMethylation | 0.009 | 0.003 | 0.029 | |
| extractPatterns | 3.535 | 0.080 | 3.505 | |
| generateBedEcdf | 0.115 | 0.001 | 0.116 | |
| generateBedReport | 3.518 | 0.015 | 3.269 | |
| generateCytosineReport | 1.367 | 0.013 | 1.284 | |
| generateMhlReport | 0.388 | 0.015 | 0.337 | |
| generateVcfReport | 18.090 | 1.364 | 19.776 | |
| plotPatterns | 2.045 | 0.132 | 2.101 | |
| preprocessBam | 0.179 | 0.016 | 0.186 | |
| preprocessGenome | 0.002 | 0.001 | 0.002 | |
| simulateBam | 0.010 | 0.002 | 0.012 | |