Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2022-03-18 11:08:18 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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 pipeFrame on riesling1


To the developers/maintainers of the pipeFrame package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pipeFrame.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 1431/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pipeFrame 1.11.0  (landing page)
Zheng Wei
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/pipeFrame
git_branch: master
git_last_commit: d377801
git_last_commit_date: 2021-10-26 12:51:30 -0400 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    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: pipeFrame
Version: 1.11.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:pipeFrame.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings pipeFrame_1.11.0.tar.gz
StartedAt: 2022-03-17 19:52:43 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 19:55:48 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 185.4 seconds
RetCode: 0
Status:   OK  
CheckDir: pipeFrame.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:pipeFrame.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings pipeFrame_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/pipeFrame.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pipeFrame/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pipeFrame' version '1.11.0'
* 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 whether package 'pipeFrame' 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 ... NOTE
Namespace in Imports field not imported from: 'rmarkdown'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
Step-class 5.42   1.33    6.88
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 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: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/pipeFrame.Rcheck/00check.log'
for details.



Installation output

pipeFrame.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL pipeFrame
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'pipeFrame' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pipeFrame'
    finding HTML links ... done
    Step-class                              html  
    Utils                                   html  
    getObjsInPipe                           html  
    graphMng                                html  
    ignoreCheck                             html  
    initPipeFrame                           html  
    loadConfig                              html  
    loadStep                                html  
    runWithFinishCheck                      html  
    setGenome                               html  
    setJobName                              html  
    setPipeName                             html  
    setRefDir                               html  
    setThreads                              html  
    setTmpDir                               html  
** 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 (pipeFrame)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'GreyListChIP' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'RiboDiPA' is missing or broken
 done

Tests output

pipeFrame.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(pipeFrame)
> 
> test_check("pipeFrame")
[1] "2022-03-17 19:55:35 EDT"
[1] "2022-03-17 19:55:35 EDT"
[1] "2022-03-17 19:55:35 EDT"
[1] "2022-03-17 19:55:35 EDT"
[1] "2022-03-17 19:55:35 EDT"
[1] "2022-03-17 19:55:35 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "D:\\biocbuild\\bbs-3.15-bioc\\meat\\pipeFrame.Rcheck\\tests\\testthat\\testJobName\\Step_01_pipe_OverlappedRandomRegion\\test.bed"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "D:\\biocbuild\\bbs-3.15-bioc\\meat\\pipeFrame.Rcheck\\tests\\testthat\\testJobName\\Step_00_pipe_RandomRegionOnGenome\\random.bed"
[1] "2022-03-17 19:55:36 EDT"
[1] "2022-03-17 19:55:36 EDT"
[1] "D:\\biocbuild\\bbs-3.15-bioc\\meat\\pipeFrame.Rcheck\\tests\\testthat\\testJobName\\Step_01_pipe_OverlappedRandomRegion\\test.bed"
[1] "2022-03-17 19:55:37 EDT"
[1] "2022-03-17 19:55:37 EDT"
[1] "2022-03-17 19:55:37 EDT"
[1] "2022-03-17 19:55:37 EDT"
[1] "2022-03-17 19:55:37 EDT"
[1] "2022-03-17 19:55:37 EDT"
[1] "2022-03-17 19:55:37 EDT"
[1] "2022-03-17 19:55:37 EDT"
[1] "2022-03-17 19:55:37 EDT"
[1] "2022-03-17 19:55:37 EDT"
[1] "2022-03-17 19:55:37 EDT"
[1] "2022-03-17 19:55:37 EDT"
[1] "2022-03-17 19:55:37 EDT"
[1] "2022-03-17 19:55:37 EDT"
[ FAIL 0 | WARN 46 | SKIP 0 | PASS 29 ]

[ FAIL 0 | WARN 46 | SKIP 0 | PASS 29 ]
> 
> proc.time()
   user  system elapsed 
  11.92    1.76   14.04 

Example timings

pipeFrame.Rcheck/pipeFrame-Ex.timings

nameusersystemelapsed
Step-class5.421.336.88
Utils000
getObjsInPipe000
graphMng0.060.010.08
ignoreCheck000
initPipeFrame000
loadConfig0.000.000.05
loadStep000
runWithFinishCheck000
setGenome000
setJobName000
setPipeName000
setRefDir000
setThreads000
setTmpDir000