| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:05:19 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 | ||||
|
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. |
| Package 587/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| epialleleR 1.2.0 (landing page) Oleksii Nikolaienko
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: epialleleR |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:epialleleR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings epialleleR_1.2.0.tar.gz |
| StartedAt: 2022-04-12 07:19:29 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 07:23:44 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 255.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: epialleleR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:epialleleR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings epialleleR_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/epialleleR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epialleleR/DESCRIPTION’ ... OK
* this is package ‘epialleleR’ version ‘1.2.0’
* 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
* checking installed package size ... NOTE
installed size is 11.1Mb
sub-directories of 1Mb or more:
extdata 1.7Mb
libs 9.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.14-bioc/R/library/epialleleR/libs/epialleleR.so’:
Found ‘__printf_chk’, possibly from ‘printf’ (C)
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘putchar’, possibly from ‘putchar’ (C)
Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Found ‘srand48’, possibly from ‘srand48’ (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. 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 9.863 0.363 10.334
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.14-bioc/meat/epialleleR.Rcheck/00check.log’
for details.
epialleleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL epialleleR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’ * installing *source* package ‘epialleleR’ ... ** using staged installation ** libs g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -c rcpp_char_to_context.cpp -o rcpp_char_to_context.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -c rcpp_cx_report.cpp -o rcpp_cx_report.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -c rcpp_fep.cpp -o rcpp_fep.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -c rcpp_get_base_freqs.cpp -o rcpp_get_base_freqs.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -c rcpp_get_xm_beta.cpp -o rcpp_get_xm_beta.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -c rcpp_match_target.cpp -o rcpp_match_target.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -c rcpp_read_bam.cpp -o rcpp_read_bam.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -c rcpp_threshold_reads.cpp -o rcpp_threshold_reads.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o epialleleR.so RcppExports.o rcpp_char_to_context.o rcpp_cx_report.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 /home/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.14-bioc/R/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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 BED file [0.081s]
Reading BAM file [0.010s]
Computing ECDFs for within- and out-of-context per-read beta values [0.074s]
Reading BED file [0.024s]
Reading BAM file [0.009s]
Computing ECDFs for within- and out-of-context per-read beta values [0.040s]
Reading BED file [0.020s]
Reading BAM file [0.008s]
Preparing amplicon report [0.023s]
Reading BED file [0.016s]
Reading BAM file [0.008s]
Thresholding reads [0.001s]
Preparing amplicon report [0.021s]
Writing the report [0.000s]
Reading BED file [0.016s]
Reading BAM file [0.008s]
Thresholding reads [0.000s]
Preparing amplicon report [0.019s]
Reading BAM file [0.027s]
Thresholding reads [0.001s]
Preparing cytosine report [0.030s]
Reading BAM file [0.029s]
Thresholding reads [0.002s]
Preparing cytosine report [0.031s]
Writing the report [0.002s]
Reading BAM file [0.029s]
Thresholding reads [0.001s]
Preparing cytosine report [0.031s]
Reading BED file [0.016s]
Reading VCF file [0.531s]
Reading BAM file [0.007s]
Extracting base frequences [0.055s]
Reading VCF file [0.205s]
Reading BAM file [0.008s]
Extracting base frequencesAlready preprocessed VCF supplied as an input. Options 'bed' and 'zero.based.bed' will have no effect.
Reading BAM file [0.038s]
Thresholding reads [0.002s]
Extracting base frequences [0.119s]
Writing the report [0.009s]
Reading BED file [0.019s]
Reading VCF file [0.611s]
Reading BAM file [0.008s]
Extracting base frequences [0.062s]
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 Apr 12 07:23:41 2022
***********************************************
Number of test functions: 6
Number of errors: 0
Number of failures: 0
1 Test Suite :
epialleleR RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
20.179 1.131 21.361
epialleleR.Rcheck/epialleleR-Ex.timings
| name | user | system | elapsed | |
| generateBedEcdf | 0.176 | 0.016 | 0.194 | |
| generateBedReport | 1.248 | 0.087 | 1.273 | |
| generateCytosineReport | 0.145 | 0.009 | 0.136 | |
| generateVcfReport | 9.863 | 0.363 | 10.334 | |
| preprocessBam | 0.026 | 0.004 | 0.030 | |