| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:40:39 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 647/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| epialleleR 1.10.0 (landing page) Oleksii Nikolaienko
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: epialleleR |
| Version: 1.10.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:epialleleR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings epialleleR_1.10.0.tar.gz |
| StartedAt: 2023-11-02 10:15:49 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 10:22:38 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 408.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: epialleleR.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:epialleleR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings epialleleR_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/epialleleR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epialleleR/DESCRIPTION’ ... OK
* this is package ‘epialleleR’ version ‘1.10.0’
* 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++ (GCC) 10.3.1’
* checking C++ specification ... OK
Not all R platforms support C++17
* checking installed package size ... NOTE
installed size is 17.1Mb
sub-directories of 1Mb or more:
extdata 1.9Mb
libs 14.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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 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 ... 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 ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.3.1/site-library/epialleleR/libs/epialleleR.so’:
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘sprintf’, possibly from ‘sprintf’ (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 10.951 1.42 14.907
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/epialleleR.Rcheck/00check.log’
for details.
epialleleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL epialleleR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘epialleleR’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++17 g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rcpp_call_methylation.cpp -o rcpp_call_methylation.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rcpp_check_bam.cpp -o rcpp_check_bam.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rcpp_cx_report.cpp -o rcpp_cx_report.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rcpp_extract_patterns.cpp -o rcpp_extract_patterns.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rcpp_fep.cpp -o rcpp_fep.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rcpp_get_base_freqs.cpp -o rcpp_get_base_freqs.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rcpp_get_xm_beta.cpp -o rcpp_get_xm_beta.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rcpp_match_target.cpp -o rcpp_match_target.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rcpp_mhl_report.cpp -o rcpp_mhl_report.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rcpp_read_bam.cpp -o rcpp_read_bam.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rcpp_read_genome.cpp -o rcpp_read_genome.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rcpp_simulate_bam.cpp -o rcpp_simulate_bam.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rcpp_threshold_reads.cpp -o rcpp_threshold_reads.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/R/R-4.3.1/lib -lR installing to /home/biocbuild/R/R-4.3.1/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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]
Making methylation calls [0.023s]
Making methylation calls [0.023s]
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 [0.162s]
Preparing cytosine report [0.003s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.003s]
Preparing cytosine report [0.003s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.003s]
Preparing cytosine report [0.003s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.003s]
Preparing cytosine report [0.003s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.003s]
Preparing cytosine report [0.002s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.003s]
Preparing cytosine report [0.002s]
Reading BED file [0.078s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Extracting methylation patterns [0.053s]
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
Reading BED file [0.017s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Extracting methylation patterns [0.068s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Extracting methylation patterns [0.053s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Extracting methylation patterns [0.053s]
Reading BED file [0.015s]
Checking BAM file: 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 [0.021s]
Reading BED file [0.016s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Computing ECDFs for within- and out-of-context per-read beta values [0.048s]
Reading BED file [0.016s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Preparing amplicon report [0.026s]
Reading BED file [0.017s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
Thresholding reads [0.000s]
Preparing amplicon report [0.026s]
Writing the report [0.001s]
Reading BED file [0.017s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
Thresholding reads [0.004s]
Preparing amplicon report [0.027s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.014s]
Thresholding reads [0.002s]
Preparing cytosine report [0.033s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.015s]
Thresholding reads [0.002s]
Preparing cytosine report [0.033s]
Writing the report [0.003s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.015s]
Thresholding reads [0.002s]
Preparing cytosine report [0.033s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.003s]
Preparing cytosine report [0.001s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.015s]
Preparing lMHL report [0.058s]
Writing the report [0.005s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.014s]
Already preprocessed BAM supplied as an input. Explicitly set 'preprocessBam' options will have no effect.
Preparing lMHL report [0.058s]
Writing the report [0.005s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.015s]
Preparing lMHL report [0.058s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.014s]
Preparing cytosine report [0.033s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
Preparing lMHL report [0.005s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Preparing lMHL report [0.006s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Preparing cytosine report [0.004s]
Writing sample BAM [0.019s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.003s]
Preparing cytosine report [0.003s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.003s]
Preparing lMHL report [0.004s]
Reading BED file [0.019s]
Reading VCF file [1.612s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Extracting base frequences [0.078s]
Reading VCF file [0.258s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
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 [0.015s]
Thresholding reads [0.003s]
Extracting base frequences [0.209s]
Writing the report [0.010s]
Reading BED file [0.018s]
Reading VCF file [1.237s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Extracting base frequences [0.083s]
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 [0.003s]
Checking BAM file: Checking BAM file: Checking BAM file: Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.003s]
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 [0.005s]
Reading reference genome file [E::fai_build3_core] Failed to open the file /home/biocbuild/R/R-4.3.1/site-library/epialleleR/extdata/test
Reading reference genome file [E::fai_build3_core] Failed to open the file
Writing sample BAM [0.005s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.002s]
Preparing cytosine report [0.001s]
Writing sample BAM [0.111s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.002s]
Thresholding reads [0.000s]
Preparing cytosine report [0.002s]
Writing sample BAM [0.018s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.003s]
Preparing cytosine report [0.003s]
Writing sample BAM [0.019s]
Checking BAM file: paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.002s]
Preparing cytosine report [0.002s]
Writing sample BAM [0.008s]
Reading reference genome file [0.000s]
Making methylation calls [0.021s]
Checking BAM file: single-end alignment detected
Reading single-end BAM file [0.002s]
Preparing cytosine report [0.001s]
RUNIT TEST PROTOCOL -- Thu Nov 2 10:22:35 2023
***********************************************
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
27.405 2.417 34.182
epialleleR.Rcheck/epialleleR-Ex.timings
| name | user | system | elapsed | |
| callMethylation | 0.010 | 0.001 | 0.039 | |
| extractPatterns | 2.592 | 0.829 | 3.479 | |
| generateBedEcdf | 0.128 | 0.036 | 0.166 | |
| generateBedReport | 0.215 | 0.032 | 0.242 | |
| generateCytosineReport | 0.121 | 0.007 | 0.114 | |
| generateMhlReport | 0.226 | 0.008 | 0.212 | |
| generateVcfReport | 10.951 | 1.420 | 14.907 | |
| preprocessBam | 0.028 | 0.000 | 0.021 | |
| preprocessGenome | 0.002 | 0.000 | 0.003 | |
| simulateBam | 0.038 | 0.000 | 0.038 | |