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CHECK report for BaalChIP on malbec1

This page was generated on 2021-01-24 11:49:18 -0500 (Sun, 24 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE BaalChIP PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 105/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BaalChIP 1.16.0
Ines de Santiago
Snapshot Date: 2021-01-23 14:40:16 -0500 (Sat, 23 Jan 2021)
URL: https://git.bioconductor.org/packages/BaalChIP
Branch: RELEASE_3_12
Last Commit: c466b6c
Last Changed Date: 2020-10-27 11:17:44 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: BaalChIP
Version: 1.16.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BaalChIP.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BaalChIP_1.16.0.tar.gz
StartedAt: 2021-01-23 23:31:13 -0500 (Sat, 23 Jan 2021)
EndedAt: 2021-01-23 23:46:43 -0500 (Sat, 23 Jan 2021)
EllapsedTime: 929.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BaalChIP.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BaalChIP.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BaalChIP_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BaalChIP.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BaalChIP/DESCRIPTION’ ... OK
* this is package ‘BaalChIP’ version ‘1.16.0’
* 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 ‘BaalChIP’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 198.2Mb
  sub-directories of 1Mb or more:
    data   95.8Mb
    test  101.9Mb
* 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
applyBayes: no visible binding for global variable ‘SNP_id’
plot.filt.barplot: no visible binding for global variable ‘cellname’
plot.filt.barplot: no visible binding for global variable ‘value’
plot.filt.barplot: no visible binding for global variable ‘variable’
plot.filt.boxplot: no visible binding for global variable ‘variable’
plot.filt.boxplot: no visible binding for global variable ‘value’
plot.filt.boxplot: no visible binding for global variable ‘coltype’
plot.filt.pie: no visible binding for global variable ‘variable’
plot.filt.pie: no visible binding for global variable ‘value.mean’
plot.simul: no visible binding for global variable ‘readslen’
plot.simul: no visible binding for global variable ‘perc_right’
plotadjustment: no visible binding for global variable ‘value’
plotadjustment: no visible binding for global variable ‘variable’
Undefined global functions or variables:
  SNP_id cellname coltype perc_right readslen value value.mean variable
* 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 ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test’, resetting
* 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/BaalChIP.Rcheck/00check.log’
for details.



Installation output

BaalChIP.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BaalChIP
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘BaalChIP’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (BaalChIP)

Tests output

BaalChIP.Rcheck/tests/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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("BaalChIP")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit



RUNIT TEST PROTOCOL -- Sat Jan 23 23:46:38 2021 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BaalChIP 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 
 12.416   0.272  13.060 

Example timings

BaalChIP.Rcheck/BaalChIP-Ex.timings

nameusersystemelapsed
BaalChIP.get0.1280.0000.128
BaalChIP.report0.0240.0000.026
adjustmentBaalPlot0.8320.0000.832
plotQC1.2520.0121.427
plotSimul0.2200.0320.255
summaryASB0.0040.0000.004
summaryQC0.0800.0000.081