Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-08-08 13:19:51 -0400 (Mon, 08 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4362
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4180
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 nebbiolo1


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? 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 1657/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RIPAT 1.6.0  (landing page)
Min-Jeong Baek
Snapshot Date: 2022-08-07 13:55:12 -0400 (Sun, 07 Aug 2022)
git_url: https://git.bioconductor.org/packages/RIPAT
git_branch: RELEASE_3_15
git_last_commit: 68c07aa
git_last_commit_date: 2022-04-26 12:07:40 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RIPAT
Version: 1.6.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:RIPAT.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings RIPAT_1.6.0.tar.gz
StartedAt: 2022-08-07 21:43:01 -0400 (Sun, 07 Aug 2022)
EndedAt: 2022-08-07 21:44:17 -0400 (Sun, 07 Aug 2022)
EllapsedTime: 75.7 seconds
RetCode: 0
Status:   OK  
CheckDir: RIPAT.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:RIPAT.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings RIPAT_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/RIPAT.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RIPAT/DESCRIPTION’ ... OK
* this is package ‘RIPAT’ version ‘1.6.0’
* 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 11.647  0.768  12.416
makeData      6.181  0.248   7.736
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/RIPAT.Rcheck/00check.log’
for details.



Installation output

RIPAT.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL RIPAT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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
annoByCpG4.1550.1834.341
annoByGene1.5430.0511.595
annoByRepeat1.3260.0121.338
annoByVar0.8030.0280.830
blast_gene0.0590.0040.063
blast_obj0.0020.0000.002
cpg_exam_db0.0090.0000.009
drawingKaryo11.647 0.76812.416
gene_exam_db0.0350.0000.035
makeData6.1810.2487.736
makeDocument4.0570.1604.217
makeInputObj0.5060.0560.566
makeInputObj20.5460.0120.557
micro_exam_db0.0050.0000.004
repeat_exam_db0.0040.0040.007
tss_exam_db0.0240.0000.023
var_exam_db0.0680.0000.069