Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:53:30 -0400 (Wed, 17 Oct 2018).
Package 995/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
NGScopy 1.14.0 Xiaobei Zhao
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: NGScopy |
Version: 1.14.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NGScopy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NGScopy_1.14.0.tar.gz |
StartedAt: 2018-10-16 22:57:12 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 22:58:29 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 77.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: NGScopy.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NGScopy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NGScopy_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/NGScopy.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘NGScopy/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘NGScopy’ version ‘1.14.0’ * 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 ‘NGScopy’ can be installed ... OK * 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 ... NOTE .count_starts: no visible global function definition for ‘median’ .count_starts: no visible global function definition for ‘sd’ .help_segmtype: no visible global function definition for ‘help’ .make_windows : .unit: no visible global function definition for ‘median’ .make_windows : .unit: no visible global function definition for ‘sd’ .plot_out: no visible global function definition for ‘pdf’ .plot_out: no visible global function definition for ‘dev.off’ .unit_plot_out: no visible global function definition for ‘par’ read_regions: no visible global function definition for ‘read.table’ Undefined global functions or variables: dev.off help median par pdf read.table sd Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "par") importFrom("stats", "median", "sd") importFrom("utils", "help", "read.table") 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 ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... NOTE The following files look like leftovers/mistakes: ‘ngscopy-case1b-cmdline.out’ Please remove them from your package. * checking examples ... 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.7-bioc/meat/NGScopy.Rcheck/00check.log’ for details.
NGScopy.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL NGScopy ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘NGScopy’ ... ** 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 * DONE (NGScopy)
NGScopy.Rcheck/NGScopy-Ex.timings
name | user | system | elapsed | |
NGScopy-class | 0.973 | 0.025 | 1.035 | |
df.to.gr | 0.001 | 0.000 | 0.002 | |
help_segmtype | 0.001 | 0.000 | 0.001 | |
ngscopy_cmdline_example | 0.017 | 0.001 | 0.019 | |
ngscopy_unittest | 0.002 | 0.000 | 0.002 | |
parse_segmtype | 0.002 | 0.001 | 0.002 | |
read_regions | 0.010 | 0.001 | 0.011 | |