Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:48:04 -0400 (Wed, 16 Oct 2019).
Package 113/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
BayesPeak 1.36.0 Jonathan Cairns
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: BayesPeak |
Version: 1.36.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BayesPeak.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BayesPeak_1.36.0.tar.gz |
StartedAt: 2019-10-16 00:45:59 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 00:49:42 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 222.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BayesPeak.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BayesPeak.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BayesPeak_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/BayesPeak.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BayesPeak/DESCRIPTION’ ... OK * this is package ‘BayesPeak’ version ‘1.36.0’ * 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 ‘BayesPeak’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.3Mb sub-directories of 1Mb or more: data 1.0Mb extdata 5.0Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘IRanges’ A package should be listed in only one of these fields. * 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 ... NOTE 'library' or 'require' call to ‘parallel’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered: identify.overfitdiag plot.PP plot.bed plot.job plot.overfitdiag See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE identify.overfitdiag: no visible global function definition for ‘identify’ plot.job: no visible global function definition for ‘plot’ plot.overfitdiag: no visible global function definition for ‘plot’ region.overfitdiag: no visible global function definition for ‘locator’ region.overfitdiag: no visible global function definition for ‘polygon’ Undefined global functions or variables: identify locator plot polygon Consider adding importFrom("graphics", "identify", "locator", "plot", "polygon") to your NAMESPACE file. * 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 ... NOTE S3 methods shown with full name in documentation object 'overfittingDiagnostics': ‘plot.overfitdiag’ ‘identify.overfitdiag’ S3 methods shown with full name in documentation object 'plot.PP': ‘plot.PP’ S3 methods shown with full name in documentation object 'plot.bed': ‘plot.bed’ S3 methods shown with full name in documentation object 'plot.job': ‘plot.job’ The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BayesPeak/libs/BayesPeak.so’: Found ‘___stdoutp’, 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed bayespeak 63.567 0.237 63.812 summarise.peaks 62.824 0.204 63.040 plot.job 6.030 0.234 6.290 * 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: 7 NOTEs See ‘/Users/biocbuild/bbs-3.9-bioc/meat/BayesPeak.Rcheck/00check.log’ for details.
BayesPeak.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BayesPeak ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘BayesPeak’ ... ** using staged installation ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c bayespeak.c -o bayespeak.o clang -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 BayesPeak.so bayespeak.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-BayesPeak/00new/BayesPeak/libs ** R ** data ** 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 (BayesPeak)
BayesPeak.Rcheck/BayesPeak-Ex.timings
name | user | system | elapsed | |
bayespeak | 63.567 | 0.237 | 63.812 | |
overfitting | 0.192 | 0.034 | 0.228 | |
plot.PP | 0.125 | 0.017 | 0.143 | |
plot.bed | 1.025 | 0.057 | 1.083 | |
plot.job | 6.030 | 0.234 | 6.290 | |
read.bed | 1.338 | 0.044 | 1.381 | |
summarise.peaks | 62.824 | 0.204 | 63.040 | |