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CHECK report for BaalChIP on tokay1

This page was generated on 2020-09-19 10:20:17 -0400 (Sat, 19 Sep 2020).

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 100/1912HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BaalChIP 1.15.0
Ines de Santiago
Snapshot Date: 2020-09-18 14:43:25 -0400 (Fri, 18 Sep 2020)
URL: https://git.bioconductor.org/packages/BaalChIP
Branch: master
Last Commit: 53476ef
Last Changed Date: 2020-04-27 15:01:46 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 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
riesling1 Windows Server 2019 Standard / x64  OK  OK  WARNINGS  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: BaalChIP
Version: 1.15.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BaalChIP.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BaalChIP_1.15.0.tar.gz
StartedAt: 2020-09-19 03:53:04 -0400 (Sat, 19 Sep 2020)
EndedAt: 2020-09-19 04:14:31 -0400 (Sat, 19 Sep 2020)
EllapsedTime: 1287.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BaalChIP.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BaalChIP.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BaalChIP_1.15.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BaalChIP.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BaalChIP/DESCRIPTION' ... OK
* this is package 'BaalChIP' version '1.15.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test', resetting
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BaalChIP/test', resetting
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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: 2 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/BaalChIP.Rcheck/00check.log'
for details.



Installation output

BaalChIP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BaalChIP_1.15.0.tar.gz && rm -rf BaalChIP.buildbin-libdir && mkdir BaalChIP.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BaalChIP.buildbin-libdir BaalChIP_1.15.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BaalChIP_1.15.0.zip && rm BaalChIP_1.15.0.tar.gz BaalChIP_1.15.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 69 44.3M   69 30.6M    0     0  77.9M      0 --:--:-- --:--:-- --:--:-- 78.6M
100 44.3M  100 44.3M    0     0  81.3M      0 --:--:-- --:--:-- --:--:-- 81.8M

install for i386

* 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
  converting help for package 'BaalChIP'
    finding HTML links ... done
    BaalChIP                                html  
    BaalChIP.get                            html  
    BaalChIP.report                         html  
    BaalChIP.run                            html  
    BaalObject                              html  
    ENCODEexample                           html  
    FAIREexample                            html  
    QCfilter                                html  
    UniqueMappability50bp_hg19              html  
    adjustmentBaalPlot                      html  
    alleleCounts                            html  
    blacklist_hg19                          html  
    filter1allele                           html  
    filterIntbias                           html  
    getASB                                  html  
    mergePerGroup                           html  
    pickrell2011cov1_hg19                   html  
    plotQC                                  html  
    plotSimul                               html  
    summaryASB                              html  
    summaryQC                               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

install for x64

* installing *source* package 'BaalChIP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BaalChIP' as BaalChIP_1.15.0.zip
* DONE (BaalChIP)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BaalChIP' successfully unpacked and MD5 sums checked

Tests output

BaalChIP.Rcheck/tests_i386/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: 'IRanges'

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

    windows


Attaching package: 'Biostrings'

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

    strsplit



RUNIT TEST PROTOCOL -- Sat Sep 19 04:14:09 2020 
*********************************************** 
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 
  10.78    0.78   11.54 

BaalChIP.Rcheck/tests_x64/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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.

> 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: 'IRanges'

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

    windows


Attaching package: 'Biostrings'

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

    strsplit



RUNIT TEST PROTOCOL -- Sat Sep 19 04:14:23 2020 
*********************************************** 
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 
  12.60    0.45   13.06 

Example timings

BaalChIP.Rcheck/examples_i386/BaalChIP-Ex.timings

nameusersystemelapsed
BaalChIP.get0.110.000.11
BaalChIP.report0.030.000.03
adjustmentBaalPlot0.630.000.62
plotQC0.790.000.80
plotSimul0.140.000.14
summaryASB000
summaryQC0.050.000.04

BaalChIP.Rcheck/examples_x64/BaalChIP-Ex.timings

nameusersystemelapsed
BaalChIP.get0.150.000.16
BaalChIP.report0.030.000.03
adjustmentBaalPlot1.080.021.09
plotQC0.930.000.94
plotSimul0.180.010.18
summaryASB000
summaryQC0.040.020.07