Back to Build/check report for BioC 3.15 experimental data
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This page was generated on 2022-10-18 14:50:14 -0400 (Tue, 18 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
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 systemPipeRdata on nebbiolo1


To the developers/maintainers of the systemPipeRdata package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 371/410HostnameOS / ArchINSTALLBUILDCHECK
systemPipeRdata 2.0.1  (landing page)
Thomas Girke
Snapshot Date: 2022-10-18 07:30:03 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/systemPipeRdata
git_branch: RELEASE_3_15
git_last_commit: 66644e7
git_last_commit_date: 2022-04-28 01:42:10 -0400 (Thu, 28 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: systemPipeRdata
Version: 2.0.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:systemPipeRdata.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings systemPipeRdata_2.0.1.tar.gz
StartedAt: 2022-10-18 11:46:37 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 11:47:48 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 70.3 seconds
RetCode: 0
Status:   OK  
CheckDir: systemPipeRdata.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:systemPipeRdata.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings systemPipeRdata_2.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-data-experiment/meat/systemPipeRdata.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 ‘systemPipeRdata/DESCRIPTION’ ... OK
* this is package ‘systemPipeRdata’ version ‘2.0.1’
* 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 ... NOTE
Found the following hidden files and directories:
  inst/extdata/param/.batchtools.conf.R
  inst/extdata/param/.batchtools.conf.R.sge
  inst/extdata/param/.batchtools.conf.R.torque
  inst/extdata/workflows/new/.batchtools.conf.R
  inst/rmarkdown/templates/systemPipeR_new/skeleton/.batchtools.conf.R
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘systemPipeRdata’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 264.6Mb
  sub-directories of 1Mb or more:
    extdata  264.4Mb
* 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
.subsetAnno: no visible global function definition for ‘%within%’
.subsetAnno: no visible global function definition for ‘relist’
.subsetAnno: no visible global function definition for ‘shift’
getSubsetReads: no visible binding for global variable ‘anno’
Undefined global functions or variables:
  %within% anno relist shift
Consider adding
  importFrom("utils", "relist")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-data-experiment/meat/systemPipeRdata.Rcheck/00check.log’
for details.



Installation output

systemPipeRdata.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL systemPipeRdata
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘systemPipeRdata’ ...
** using staged installation
** 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 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 (systemPipeRdata)

Tests output

systemPipeRdata.Rcheck/tests/runTests.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> BiocGenerics:::testPackage("systemPipeRdata")


RUNIT TEST PROTOCOL -- Tue Oct 18 11:47:45 2022 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
systemPipeRdata RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  2.248   0.107   2.338 

Example timings

systemPipeRdata.Rcheck/systemPipeRdata-Ex.timings

nameusersystemelapsed
availableWF0.0020.0000.001
genWorkenvir0.0040.0000.004
getSubsetReads000
pathList0.0030.0000.004