Back to Multiple platform build/check report for BioC 3.17:   simplified   long
ABCD[E]FGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-02-07 11:06:47 -0500 (Tue, 07 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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

CHECK results for epialleleR on merida1


To the developers/maintainers of the epialleleR package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 607/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epialleleR 1.7.0  (landing page)
Oleksii Nikolaienko
Snapshot Date: 2023-02-06 14:00:21 -0500 (Mon, 06 Feb 2023)
git_url: https://git.bioconductor.org/packages/epialleleR
git_branch: master
git_last_commit: 11ca088
git_last_commit_date: 2022-11-01 11:24:58 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: epialleleR
Version: 1.7.0
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_1.7.0.tar.gz
StartedAt: 2023-02-07 01:08:05 -0500 (Tue, 07 Feb 2023)
EndedAt: 2023-02-07 01:19:28 -0500 (Tue, 07 Feb 2023)
EllapsedTime: 683.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: epialleleR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/epialleleR.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epialleleR/DESCRIPTION’ ... OK
* this is package ‘epialleleR’ version ‘1.7.0’
* 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: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
* used SDK: ‘’
* 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 ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library/epialleleR/libs/epialleleR.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___sprintf_chk’, possibly from ‘sprintf’ (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 17.347  0.314  23.008
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-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/4.3/Resources/library’
* installing *source* package ‘epialleleR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
using C++17
using SDK: ‘’
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c rcpp_cx_report.cpp -o rcpp_cx_report.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c rcpp_extract_patterns.cpp -o rcpp_extract_patterns.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c rcpp_fep.cpp -o rcpp_fep.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c rcpp_get_base_freqs.cpp -o rcpp_get_base_freqs.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c rcpp_get_xm_beta.cpp -o rcpp_get_xm_beta.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c rcpp_match_target.cpp -o rcpp_match_target.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c rcpp_read_bam.cpp -o rcpp_read_bam.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c rcpp_threshold_reads.cpp -o rcpp_threshold_reads.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o epialleleR.so RcppExports.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_read_bam.o rcpp_threshold_reads.o /Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3/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) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 BED file [0.178s]
Reading BAM file [0.039s]
Extracting methylation patterns [0.138s]
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
Reading BED file [0.132s]
Reading BAM file [0.016s]
Extracting methylation patterns [0.165s]
Reading BAM file [0.026s]
Extracting methylation patterns [0.111s]
Reading BAM file [0.019s]
Extracting methylation patterns [0.116s]
Reading BED file [0.032s]
Reading BAM file [0.008s]
Computing ECDFs for within- and out-of-context per-read beta values [0.047s]
Reading BED file [0.039s]
Reading BAM file [0.008s]
Computing ECDFs for within- and out-of-context per-read beta values [0.030s]
Reading BED file [0.042s]
Reading BAM file [0.013s]
Preparing amplicon report [0.069s]
Reading BED file [0.041s]
Reading BAM file [0.015s]
Thresholding reads [0.000s]
Preparing amplicon report [0.061s]
Writing the report [0.002s]
Reading BED file [0.038s]
Reading BAM file [0.013s]
Thresholding reads [0.000s]
Preparing amplicon report [0.058s]
Reading BAM file [0.032s]
Thresholding reads [0.002s]
Preparing cytosine report [0.076s]
Reading BAM file [0.032s]
Thresholding reads [0.001s]
Preparing cytosine report [0.073s]
Writing the report [0.006s]
Reading BAM file [0.035s]
Thresholding reads [0.002s]
Preparing cytosine report [0.210s]
Reading BED file [0.035s]
Reading VCF file [1.632s]
Reading BAM file [0.008s]
Extracting base frequences [0.152s]
Reading VCF file [0.537s]
Reading BAM file [0.027s]
Extracting base frequencesAlready preprocessed VCF supplied as an input. Options 'bed' and 'zero.based.bed' will have no effect.
Reading BAM file [0.053s]
Thresholding reads [0.002s]
Extracting base frequences [0.292s]
Writing the report [0.032s]
Reading BED file [0.042s]
Reading VCF file [1.428s]
Reading BAM file [0.029s]
Extracting base frequences [0.153s]
Already preprocessed BAM supplied as an input. Options 'min.mapq', 'min.baseq', 'skip.duplicates' and 'nthreads' will have no effect.

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit



RUNIT TEST PROTOCOL -- Tue Feb  7 01:19:13 2023 
*********************************************** 
Number of test functions: 7 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
epialleleR RUnit Tests - 7 test functions, 0 errors, 0 failures
Number of test functions: 7 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 39.292   1.516  53.214 

Example timings

epialleleR.Rcheck/epialleleR-Ex.timings

nameusersystemelapsed
extractPatterns2.3350.1723.261
generateBedEcdf0.2810.0340.415
generateBedReport0.3540.0190.492
generateCytosineReport0.1840.0120.253
generateVcfReport17.347 0.31423.008
preprocessBam0.0320.0030.069