Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-03-01 11:38:52 -0500 (Fri, 01 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 648/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epialleleR 1.11.5  (landing page)
Oleksii Nikolaienko
Snapshot Date: 2024-02-28 14:00:14 -0500 (Wed, 28 Feb 2024)
git_url: https://git.bioconductor.org/packages/epialleleR
git_branch: devel
git_last_commit: 3efda21
git_last_commit_date: 2024-02-12 07:07:15 -0500 (Mon, 12 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for epialleleR on merida1


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.

raw results


Summary

Package: epialleleR
Version: 1.11.5
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:epialleleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings epialleleR_1.11.5.tar.gz
StartedAt: 2024-02-29 03:38:01 -0500 (Thu, 29 Feb 2024)
EndedAt: 2024-02-29 03:49:05 -0500 (Thu, 29 Feb 2024)
EllapsedTime: 664.0 seconds
RetCode: 0
Status:   OK  
CheckDir: epialleleR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:epialleleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings epialleleR_1.11.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/epialleleR.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epialleleR/DESCRIPTION’ ... OK
* this is package ‘epialleleR’ version ‘1.11.5’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... OK
  Not all R platforms support C++17
* checking installed package size ... OK
* 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 R 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 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 ... NOTE
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 ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/epialleleR/libs/epialleleR.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (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 17.465   0.49  20.913
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/epialleleR.Rcheck/00check.log’
for details.



Installation output

epialleleR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL epialleleR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘epialleleR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++17
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_call_methylation.cpp -o rcpp_call_methylation.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_check_bam.cpp -o rcpp_check_bam.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_cx_report.cpp -o rcpp_cx_report.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_extract_patterns.cpp -o rcpp_extract_patterns.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_fep.cpp -o rcpp_fep.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_get_base_freqs.cpp -o rcpp_get_base_freqs.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_get_xm_beta.cpp -o rcpp_get_xm_beta.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_match_target.cpp -o rcpp_match_target.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_mhl_report.cpp -o rcpp_mhl_report.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_read_bam.cpp -o rcpp_read_bam.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_read_genome.cpp -o rcpp_read_genome.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_simulate_bam.cpp -o rcpp_simulate_bam.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rcpp_threshold_reads.cpp -o rcpp_threshold_reads.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)

Tests output

epialleleR.Rcheck/tests/runTests.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("epialleleR")
Reading reference genome file [0.011s]
Making methylation calls [0.169s]
Making methylation calls [0.105s]
Making methylation calls [0.036s]
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: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.023s]
Preparing cytosine report [0.009s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.013s]
Preparing cytosine report [0.006s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Preparing cytosine report [0.006s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Preparing cytosine report [0.005s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.005s]
Preparing cytosine report [0.004s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.005s]
Preparing cytosine report [0.004s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.006s]
Preparing cytosine report [0.004s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.005s]
Preparing cytosine report [0.003s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
Preparing cytosine report [0.006s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Preparing cytosine report [0.005s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.005s]
Preparing cytosine report [0.004s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.005s]
Preparing cytosine report [0.004s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Preparing cytosine report [0.005s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.004s]
Preparing cytosine report [0.005s]
Reading BED file [0.144s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.009s]
Extracting methylation patterns [0.130s]
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
Reading BED file [0.037s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.011s]
Extracting methylation patterns [1.308s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.010s]
Extracting methylation patterns [0.126s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.011s]
Extracting methylation patterns [0.126s]
Reading BED file [0.036s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.015s]
Computing ECDFs for within- and out-of-context per-read beta values [0.046s]
Reading BED file [0.039s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.016s]
Computing ECDFs for within- and out-of-context per-read beta values [0.120s]
Reading BED file [0.040s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.013s]
Preparing amplicon report [0.054s]
Reading BED file [0.038s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.015s]
Thresholding reads [0.001s]
Preparing amplicon report [0.059s]
Writing the report [0.003s]
Reading BED file [0.034s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.015s]
Thresholding reads [0.001s]
Preparing amplicon report [0.059s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.030s]
Thresholding reads [0.002s]
Preparing cytosine report [0.053s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.033s]
Thresholding reads [0.002s]
Preparing cytosine report [0.056s]
Writing the report [0.005s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.039s]
Thresholding reads [0.002s]
Preparing cytosine report [0.056s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.012s]
Preparing cytosine report [0.004s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.021s]
Preparing lMHL report [0.091s]
Writing the report [0.013s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.022s]
Preparing lMHL report [0.090s]
Writing the report [0.009s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.021s]
Preparing lMHL report [0.093s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.021s]
Preparing cytosine report [0.053s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.010s]
Preparing lMHL report [0.010s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.009s]
Preparing lMHL report [0.009s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.011s]
Preparing cytosine report [0.008s]
Writing sample BAM [0.030s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.008s]
Preparing cytosine report [0.004s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.010s]
Preparing lMHL report [0.007s]
Reading BED file [0.031s]
Reading VCF file [1.395s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.008s]
Extracting base frequences [0.148s]
Reading VCF file [0.469s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.014s]
Extracting base frequences Already preprocessed VCF supplied as an input. Options 'bed' and 'zero.based.bed' will have no effect.
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.027s]
Thresholding reads [0.002s]
Extracting base frequences [1.659s]
Writing the report [0.024s]
Reading BED file [0.030s]
Reading VCF file [1.327s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.018s]
Extracting base frequences [0.137s]
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: Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.007s]
Checking BAM file: Checking BAM file: Checking BAM file: Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.006s]
Checking BAM file: Checking BAM file: Checking BAM file: Checking BAM file: paired-end, name-sorted alignment detected
Checking BAM file: single-end alignment detected
Reading reference genome file [0.001s]
Reading reference genome file [E::fai_build3_core] Failed to open the file /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/epialleleR/extdata/test
Reading reference genome file [E::fai_build3_core] Failed to open the file 
Writing sample BAM [0.007s]
Writing sample BAM [0.006s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.004s]
Preparing cytosine report [0.002s]
Writing sample BAM [0.117s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.006s]
Thresholding reads [0.000s]
Preparing cytosine report [0.003s]
Writing sample BAM [0.035s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.008s]
Preparing cytosine report [0.004s]
Writing sample BAM [0.030s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
Preparing cytosine report [0.004s]
Writing sample BAM [0.012s]
Reading reference genome file [0.002s]
Making methylation calls [0.030s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.004s]
Preparing cytosine report [0.003s]


RUNIT TEST PROTOCOL -- Thu Feb 29 03:48:49 2024 
*********************************************** 
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
epialleleR RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 43.029   2.666  53.567 

Example timings

epialleleR.Rcheck/epialleleR-Ex.timings

nameusersystemelapsed
callMethylation0.0230.0080.072
extractPatterns3.4660.2744.489
generateBedEcdf0.2430.0370.304
generateBedReport0.3510.0560.523
generateCytosineReport0.1710.0210.192
generateMhlReport0.3150.0260.361
generateVcfReport17.465 0.49020.913
preprocessBam0.0390.0050.041
preprocessGenome0.0090.0030.016
simulateBam0.0240.0070.036