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CHECK report for BaalChIP on celaya2

This page was generated on 2019-10-16 12:58:44 -0400 (Wed, 16 Oct 2019).

Package 95/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BaalChIP 1.10.0
Ines de Santiago
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/BaalChIP
Branch: RELEASE_3_9
Last Commit: 8120f17
Last Changed Date: 2019-05-02 11:54:03 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BaalChIP
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BaalChIP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BaalChIP_1.10.0.tar.gz
StartedAt: 2019-10-16 00:40:49 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 01:00:29 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 1180.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BaalChIP.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BaalChIP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BaalChIP_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/BaalChIP.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BaalChIP/DESCRIPTION’ ... OK
* this is package ‘BaalChIP’ version ‘1.10.0’
* 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 198.1Mb
  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 ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BaalChIP/test’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BaalChIP/test’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BaalChIP/test’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BaalChIP/test’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BaalChIP/test’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BaalChIP/test’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BaalChIP/test’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/BaalChIP.Rcheck/00check.log’
for details.



Installation output

BaalChIP.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BaalChIP
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, 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 -- Wed Oct 16 01:00:21 2019 
*********************************************** 
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 
 13.095   1.212  14.514 

Example timings

BaalChIP.Rcheck/BaalChIP-Ex.timings

nameusersystemelapsed
BaalChIP.get0.1360.0110.147
BaalChIP.report0.0420.0070.050
adjustmentBaalPlot1.2420.0501.293
plotQC1.7980.0851.884
plotSimul0.2840.0170.301
summaryASB0.0030.0020.005
summaryQC0.0180.0040.021