Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2022-01-14 13:08:29 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 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

CHECK results for RIPAT on machv2


To the developers/maintainers of the RIPAT package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RIPAT.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 1612/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RIPAT 1.4.0  (landing page)
Min-Jeong Baek
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/RIPAT
git_branch: RELEASE_3_14
git_last_commit: 8b46270
git_last_commit_date: 2021-10-26 13:02:01 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RIPAT
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RIPAT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RIPAT_1.4.0.tar.gz
StartedAt: 2022-01-13 17:15:10 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 17:17:06 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 116.1 seconds
RetCode: 0
Status:   OK  
CheckDir: RIPAT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RIPAT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RIPAT_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/RIPAT.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RIPAT/DESCRIPTION’ ... OK
* this is package ‘RIPAT’ version ‘1.4.0’
* 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 ‘RIPAT’ 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
annoByCpG: no visible global function definition for ‘hist’
annoByCpG: no visible binding for global variable ‘Range’
annoByCpG: no visible binding for global variable ‘Freq’
annoByCpG: no visible binding for global variable ‘Group’
annoByGene: no visible global function definition for ‘hist’
annoByGene: no visible binding for global variable ‘Range’
annoByGene: no visible binding for global variable ‘Freq’
annoByGene: no visible binding for global variable ‘Group’
annoByRepeat: no visible global function definition for ‘hist’
annoByRepeat: no visible binding for global variable ‘all_dist_dup_m’
annoByRepeat: no visible binding for global variable ‘Range’
annoByRepeat: no visible binding for global variable ‘Freq’
annoByRepeat: no visible binding for global variable ‘Group’
annoByVar: no visible global function definition for ‘hist’
annoByVar: no visible binding for global variable ‘Range’
annoByVar: no visible binding for global variable ‘Freq’
annoByVar: no visible binding for global variable ‘Group’
makeDocument : <anonymous>: no visible global function definition for
  ‘hist’
makeDocument: no visible binding for global variable ‘group’
makeDocument: no visible binding for global variable ‘type’
makeDocument: no visible binding for global variable ‘convert_p’
makeDocument: no visible global function definition for ‘par’
Undefined global functions or variables:
  Freq Group Range all_dist_dup_m convert_p group hist par type
Consider adding
  importFrom("graphics", "hist", "par")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
drawingKaryo 14.904  0.537  15.457
makeData     10.194  0.169  11.471
annoByCpG     6.281  0.314   6.611
makeDocument  5.916  0.414   6.379
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/RIPAT.Rcheck/00check.log’
for details.



Installation output

RIPAT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RIPAT
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘RIPAT’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RIPAT)

Tests output


Example timings

RIPAT.Rcheck/RIPAT-Ex.timings

nameusersystemelapsed
annoByCpG6.2810.3146.611
annoByGene2.4390.0582.498
annoByRepeat2.1970.0382.241
annoByVar1.2300.0271.259
blast_gene0.0710.0010.072
blast_obj0.0010.0010.003
cpg_exam_db0.0100.0010.011
drawingKaryo14.904 0.53715.457
gene_exam_db0.0510.0030.054
makeData10.194 0.16911.471
makeDocument5.9160.4146.379
makeInputObj1.0000.0401.042
makeInputObj20.9990.0311.031
micro_exam_db0.0040.0010.006
repeat_exam_db0.0090.0010.011
tss_exam_db0.0340.0020.036
var_exam_db0.1120.0020.114