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This page was generated on 2024-05-04 11:41:01 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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

Package 1775/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RIPAT 1.14.0  (landing page)
Min-Jeong Baek
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/RIPAT
git_branch: RELEASE_3_19
git_last_commit: f2a161d
git_last_commit_date: 2024-04-30 11:26:21 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for RIPAT on kunpeng2


To the developers/maintainers of the RIPAT package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: RIPAT
Version: 1.14.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:RIPAT.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings RIPAT_1.14.0.tar.gz
StartedAt: 2024-05-04 11:17:27 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 11:19:08 -0000 (Sat, 04 May 2024)
EllapsedTime: 101.2 seconds
RetCode: 0
Status:   OK  
CheckDir: RIPAT.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:RIPAT.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings RIPAT_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/RIPAT.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RIPAT/DESCRIPTION’ ... OK
* this is package ‘RIPAT’ version ‘1.14.0’
* 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 code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 15.358  0.832  16.297
makeData      7.435  0.259  10.174
annoByCpG     5.349  0.191   5.542
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.19-bioc/meat/RIPAT.Rcheck/00check.log’
for details.


Installation output

RIPAT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL RIPAT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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
Warning in fun(libname, pkgname) :
  Package 'RIPAT' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'RIPAT' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (RIPAT)

Tests output


Example timings

RIPAT.Rcheck/RIPAT-Ex.timings

nameusersystemelapsed
annoByCpG5.3490.1915.542
annoByGene2.1990.0322.235
annoByRepeat1.9270.0471.990
annoByVar1.0900.0561.155
blast_gene0.0730.0000.074
blast_obj0.0020.0000.002
cpg_exam_db0.0080.0000.008
drawingKaryo15.358 0.83216.297
gene_exam_db0.0310.0040.035
makeData 7.435 0.25910.174
makeDocument4.7200.1354.860
makeInputObj0.9080.0160.927
makeInputObj22.0680.0242.095
micro_exam_db0.0000.0040.005
repeat_exam_db0.0070.0000.007
tss_exam_db0.0210.0040.025
var_exam_db0.0700.0040.074