Oleksii Nikolaienko
| Snapshot Date: 2024-10-27 02:55 -0400 (Sun, 27 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/epialleleR |
| git_branch: devel |
| git_last_commit: 30b1c2f |
| git_last_commit_date: 2024-10-26 12:52:48 -0400 (Sat, 26 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-10-28 11:48 -0400 (Mon, 28 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4501 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4761 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4504 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4535 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4483 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4491 |
| 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 652/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| epialleleR 1.13.5 (landing page) Oleksii Nikolaienko
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | 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. |
| Package: epialleleR |
| Version: 1.13.5 |
| 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_1.13.5.tar.gz |
| StartedAt: 2024-10-27 14:32:50 -0400 (Sun, 27 Oct 2024) |
| EndedAt: 2024-10-27 14:37:19 -0400 (Sun, 27 Oct 2024) |
| EllapsedTime: 268.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: epialleleR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.13.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/epialleleR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epialleleR/DESCRIPTION’ ... OK
* this is package ‘epialleleR’ version ‘1.13.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 15.0.0 (clang-1500.1.0.2.5)’
* 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 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 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-arm64/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 5.699 0.112 6.204
* 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-3.20-bioc/meat/epialleleR.Rcheck/00check.log’
for details.
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-arm64/Resources/library’ * installing *source* package ‘epialleleR’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++17 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rcpp_call_methylation.cpp -o rcpp_call_methylation.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rcpp_check_bam.cpp -o rcpp_check_bam.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rcpp_cx_report.cpp -o rcpp_cx_report.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rcpp_extract_patterns.cpp -o rcpp_extract_patterns.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rcpp_fep.cpp -o rcpp_fep.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rcpp_get_base_freqs.cpp -o rcpp_get_base_freqs.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rcpp_get_xm_beta.cpp -o rcpp_get_xm_beta.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rcpp_match_target.cpp -o rcpp_match_target.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rcpp_mhl_report.cpp -o rcpp_mhl_report.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rcpp_read_bam.cpp -o rcpp_read_bam.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rcpp_read_genome.cpp -o rcpp_read_genome.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rcpp_simulate_bam.cpp -o rcpp_simulate_bam.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rcpp_threshold_reads.cpp -o rcpp_threshold_reads.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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-arm64/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-arm64/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)
epialleleR.Rcheck/tests/runTests.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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.
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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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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 [0.031s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Making methylation calls [0.031s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Making methylation calls [0.031s]
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 [0.004s]
Preparing cytosine report [0.000s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.001s]
Preparing cytosine report [0.001s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.001s]
Preparing cytosine report [0.001s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.001s]
Preparing cytosine report [0.001s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.002s]
Preparing cytosine report [0.000s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.000s]
Preparing cytosine report [0.001s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.001s]
Preparing cytosine report [0.001s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.000s]
Preparing cytosine report [0.000s]
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, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.001s]
Preparing cytosine report [0.001s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.001s]
Preparing cytosine report [0.000s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.000s]
Preparing cytosine report [0.001s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.001s]
Preparing cytosine report [0.001s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.000s]
Preparing cytosine report [0.001s]
Reading BED file [0.025s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.003s]
Extracting methylation patterns [0.014s]
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
Reading BED file [0.003s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.002s]
Extracting methylation patterns [0.023s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.003s]
Extracting methylation patterns [0.011s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.003s]
Extracting methylation patterns [0.010s]
Reading BED file [0.003s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.003s]
Computing ECDFs for within- and out-of-context per-read beta values [0.003s]
Reading BED file [0.003s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.002s]
Computing ECDFs for within- and out-of-context per-read beta values [0.003s]
Reading BED file [0.002s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.002s]
Preparing amplicon report [0.004s]
Reading BED file [0.003s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.003s]
Thresholding reads [0.000s]
Preparing amplicon report [0.004s]
Writing the report [0.001s]
Reading BED file [0.006s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.002s]
Thresholding reads [0.000s]
Preparing amplicon report [0.005s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.007s]
Thresholding reads [0.001s]
Preparing cytosine report [0.013s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.007s]
Thresholding reads [0.001s]
Preparing cytosine report [0.013s]
Writing the report [0.001s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.007s]
Thresholding reads [0.002s]
Preparing cytosine report [0.013s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.001s]
Preparing cytosine report [0.000s]
Writing sample BAM [0.001s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.000s]
Preparing cytosine report [0.001s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.001s]
Preparing cytosine report [0.000s]
Writing sample BAM [0.001s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.000s]
Preparing cytosine report [0.001s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.000s]
Preparing cytosine report [0.000s]
Writing sample BAM [0.001s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.000s]
Preparing cytosine report [0.000s]
Writing sample BAM [0.001s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.001s]
Preparing cytosine report [0.000s]
Writing sample BAM [0.000s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.000s]
Preparing cytosine report [0.000s]
Writing sample BAM [0.001s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.000s]
Preparing cytosine report [0.001s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.007s]
Preparing lMHL report [0.020s]
Writing the report [0.001s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.007s]
Preparing lMHL report [0.020s]
Writing the report [0.002s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.007s]
Preparing lMHL report [0.019s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.007s]
Preparing cytosine report [0.013s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.008s]
Preparing lMHL report [0.019s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.002s]
Preparing lMHL report [0.005s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.003s]
Preparing lMHL report [0.005s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.002s]
Preparing lMHL report [0.005s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.003s]
Preparing cytosine report [0.004s]
Writing sample BAM [0.005s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.000s]
Preparing cytosine report [0.001s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.000s]
Preparing lMHL report [0.001s]
Loading required namespace: VariantAnnotation
Reading BED file [0.003s]
Reading VCF file [0.327s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.002s]
Extracting base frequences [0.013s]
Reading VCF file [0.048s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.002s]
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 [0.007s]
Thresholding reads [0.001s]
Extracting base frequences [0.039s]
Writing the report [0.004s]
Reading BED file [0.003s]
Reading VCF file [0.324s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.002s]
Extracting base frequences [0.019s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.003s]
Extracting methylation patterns [0.013s]
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 [0.002s]
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 [0.001s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Writing sample BAM [0.002s]
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 /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/epialleleR/extdata/test
Reading reference genome file [E::fai_build3_core] Failed to open the file
Writing sample BAM [0.001s]
Writing sample BAM [0.001s]
Checking BAM file: Writing sample BAM Writing sample BAM [0.001s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.001s]
Preparing cytosine report [0.001s]
Writing sample BAM [0.012s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.001s]
Thresholding reads [0.000s]
Preparing cytosine report [0.001s]
Writing sample BAM [0.005s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.001s]
Preparing cytosine report [0.001s]
Writing sample BAM [0.006s]
Checking BAM file: short-read, paired-end, name-sorted alignment detected
Reading paired-end BAM file [0.001s]
Preparing cytosine report [0.000s]
Writing sample BAM [0.002s]
Reading reference genome file [0.000s]
Making methylation calls [0.025s]
Checking BAM file: short-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.001s]
Preparing cytosine report [0.000s]
Writing sample BAM [0.001s]
Checking BAM file: long-read, single-end, unsorted alignment detected
Reading single-end BAM file [0.001s]
Preparing cytosine report [0.001s]
RUNIT TEST PROTOCOL -- Sun Oct 27 14:37:16 2024
***********************************************
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 message:
In ggplot2::scale_y_continuous(transform = trans, limits = marginal.limits, :
composition(log-10,reverse) transformation introduced infinite values.
>
> proc.time()
user system elapsed
7.821 0.257 9.130
epialleleR.Rcheck/epialleleR-Ex.timings
| name | user | system | elapsed | |
| callMethylation | 0.004 | 0.002 | 0.035 | |
| extractPatterns | 0.444 | 0.022 | 0.465 | |
| generateBedEcdf | 0.044 | 0.002 | 0.044 | |
| generateBedReport | 0.062 | 0.002 | 0.059 | |
| generateCytosineReport | 0.051 | 0.001 | 0.047 | |
| generateMhlReport | 0.087 | 0.003 | 0.081 | |
| generateVcfReport | 5.699 | 0.112 | 6.204 | |
| plotPatterns | 0.296 | 0.003 | 0.298 | |
| preprocessBam | 0.020 | 0.003 | 0.020 | |
| preprocessGenome | 0.001 | 0.000 | 0.001 | |
| simulateBam | 0.002 | 0.001 | 0.003 | |