Oleksii Nikolaienko
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/epialleleR |
| git_branch: devel |
| git_last_commit: e5fbf73 |
| git_last_commit_date: 2024-03-21 13:46:46 -0400 (Thu, 21 Mar 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:40:41 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 653/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| epialleleR 1.11.9 (landing page) Oleksii Nikolaienko
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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: 1.11.9 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:epialleleR.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings epialleleR_1.11.9.tar.gz |
| StartedAt: 2024-03-28 05:04:14 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 05:10:34 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 379.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: epialleleR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:epialleleR.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings epialleleR_1.11.9.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/epialleleR.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* 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 ‘1.11.9’
* 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 18.1Mb
sub-directories of 1Mb or more:
extdata 2.0Mb
libs 15.9Mb
* 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 ... 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 ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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 10.635 0.806 12.371
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/epialleleR.Rcheck/00check.log’
for details.
epialleleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL epialleleR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/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 Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 [0.000s]
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 [0.023s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Making methylation calls [0.023s]
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 [0.015s]
Preparing cytosine report [0.003s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.002s]
Preparing cytosine report [0.002s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.003s]
Preparing cytosine report [0.003s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.004s]
Preparing cytosine report [0.002s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.004s]
Preparing cytosine report [0.002s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.003s]
Preparing cytosine report [0.001s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.003s]
Preparing cytosine report [0.002s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.002s]
Preparing cytosine report [0.001s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.003s]
Preparing cytosine report [0.002s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.002s]
Preparing cytosine report [0.001s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.003s]
Preparing cytosine report [0.001s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.003s]
Preparing cytosine report [0.002s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.003s]
Preparing cytosine report [0.002s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.002s]
Preparing cytosine report [0.002s]
Reading BED file [0.103s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
Extracting methylation patterns [0.052s]
700E88C59B8E1291 B22EDF110D4CD739 6D4D1D09AB9D4E61 DA1077D00DF7FA19 17B1D84B18FB47B7 D714A221CF410F73 30218F712BC2A991 C9EEE0D0EBFA9351 69302B2426CFE5D1 74B906180284BA11 3273B3EA86C4B420 8C16271D77A41967 6642DACD2EC58167 A873BA36B5B83B18 3E4A11324C95C870 BBBF79130C835A78 BA0A985E39FD5296 2E6A8A06D6B9AD9F EF5F667956CDAF8F 422CDA98ABB039E0 A4AA47CFFA944A12 90F3A6744108FFF7 9CC2C54FE77AAB23 8FD6B1631290C102 0F65F42CE826C8C9 34BBE4124BC2A148 384C68B92CAE5FA1 64B576B1B1D896F9 2A4A928FEA52B739 9A20C36ED612622F 9C0F7503FCC4CBDE 14559975A2ADAFF9 46839668718DFDBF EF186AC3DE5AC175
Reading BED file [0.015s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
Extracting methylation patterns [0.075s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Extracting methylation patterns [0.050s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Extracting methylation patterns [0.051s]
Reading BED file [0.015s]
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 [0.022s]
Reading BED file [0.016s]
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 [0.050s]
Reading BED file [0.016s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
Preparing amplicon report [0.024s]
Reading BED file [0.016s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Thresholding reads [0.001s]
Preparing amplicon report [0.025s]
Writing the report [0.000s]
Reading BED file [0.016s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.005s]
Thresholding reads [0.001s]
Preparing amplicon report [0.025s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.015s]
Thresholding reads [0.003s]
Preparing cytosine report [0.023s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.019s]
Thresholding reads [0.002s]
Preparing cytosine report [0.023s]
Writing the report [0.003s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.014s]
Thresholding reads [0.002s]
Preparing cytosine report [0.023s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.003s]
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]
Preparing cytosine report [0.001s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.002s]
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 [0.003s]
Preparing cytosine report [0.001s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.002s]
Preparing cytosine report [0.001s]
Writing sample BAM [0.005s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.002s]
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]
Preparing cytosine report [0.001s]
Writing sample BAM [0.005s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.002s]
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]
Preparing cytosine report [0.001s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.015s]
Preparing lMHL report [0.063s]
Writing the report [0.004s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.015s]
Preparing lMHL report [0.050s]
Writing the report [0.004s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.014s]
Preparing lMHL report [0.061s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.014s]
Preparing cytosine report [0.023s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.014s]
Preparing lMHL report [0.062s]
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 [0.005s]
Preparing lMHL report [0.007s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.011s]
Preparing lMHL report [0.008s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Preparing cytosine report [0.005s]
Writing sample BAM [0.018s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.003s]
Preparing cytosine report [0.003s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.002s]
Preparing lMHL report [0.003s]
Reading BED file [0.016s]
Reading VCF file [2.412s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Extracting base frequences [0.080s]
Reading VCF file [0.260s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
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 [0.015s]
Thresholding reads [0.002s]
Extracting base frequences [0.202s]
Writing the report [0.011s]
Reading BED file [0.016s]
Reading VCF file [1.241s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.006s]
Extracting base frequences [0.080s]
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
Writing sample BAM [0.007s]
Checking BAM file: long-read, single-end, unsorted alignment detected
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, single-end, unsorted alignment detected
Reading reference genome file [0.000s]
Reading reference genome file [E::fai_build3_core] Failed to open the file /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/epialleleR/extdata/test
Reading reference genome file [E::fai_build3_core] Failed to open the file
Writing sample BAM [0.005s]
Writing sample BAM [0.006s]
Checking BAM file: Writing sample BAM Writing sample BAM [0.005s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.002s]
Preparing cytosine report [0.001s]
Writing sample BAM [0.058s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.003s]
Thresholding reads [0.000s]
Preparing cytosine report [0.001s]
Writing sample BAM [0.019s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.002s]
Preparing cytosine report [0.003s]
Writing sample BAM [0.019s]
Checking BAM file: short-read, 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: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.003s]
Preparing cytosine report [0.002s]
Writing sample BAM [0.007s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.003s]
Preparing cytosine report [0.002s]
RUNIT TEST PROTOCOL -- Thu Mar 28 05:10:30 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
28.270 1.257 31.551
epialleleR.Rcheck/epialleleR-Ex.timings
| name | user | system | elapsed | |
| callMethylation | 0.010 | 0.000 | 0.033 | |
| extractPatterns | 2.935 | 0.221 | 3.186 | |
| generateBedEcdf | 0.129 | 0.020 | 0.147 | |
| generateBedReport | 0.205 | 0.025 | 0.211 | |
| generateCytosineReport | 0.093 | 0.011 | 0.092 | |
| generateMhlReport | 0.196 | 0.013 | 0.188 | |
| generateVcfReport | 10.635 | 0.806 | 12.371 | |
| preprocessBam | 0.061 | 0.012 | 0.064 | |
| preprocessGenome | 0.002 | 0.000 | 0.002 | |
| simulateBam | 0.014 | 0.000 | 0.013 | |