Multiple platform build/check report for BioC 3.9 - CHECK report for CNVPanelizer on merida2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CNVPanelizer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CNVPanelizer_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CNVPanelizer.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNVPanelizer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNVPanelizer’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CNVPanelizer’ 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
Unexported object imported by a ':::' call: ‘utils:::format.object_size’
  See the note in ?`:::` about the use of this operator.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/CNVPanelizer.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CNVPanelizer
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘CNVPanelizer’ ...
** R
** data
** 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
* DONE (CNVPanelizer)

Tests output


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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("CNVPanelizer")

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, colMeans, colSums, 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, rowMeans, rowSums,
    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

Calculating Background for s1
Calculating Background for s2
Calculating Background for s3
Calculating Background for s4
Saving plot to '/tmp/Rtmp4c4Fr3/s1_plot.pdf'
Saving plot to '/tmp/Rtmp4c4Fr3/s2_plot.pdf'
Saving plot to '/tmp/Rtmp4c4Fr3/s3_plot.pdf'
Saving plot to '/tmp/Rtmp4c4Fr3/s4_plot.pdf'
Saving plot to '/tmp/Rtmp4c4Fr3/sample1.pdf'
Saving plot to '/tmp/Rtmp4c4Fr3/sample2.pdf'
Saving plot to '/tmp/Rtmp4c4Fr3/sample3.pdf'
Saving plot to '/tmp/Rtmp4c4Fr3/sample4.pdf'
Calculating Background for c:/somefile1.bam
Saving file to '/tmp/Rtmp4c4Fr3/samples.xlsx'
Note: zip::zip() is deprecated, please use zip::zipr() instead
[1] "GENE 1:  0.125"
[1] "GENE 2:  0.330289129537908"


RUNIT TEST PROTOCOL -- Tue Apr  9 00:04:54 2019 
*********************************************** 
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CNVPanelizer RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 54.858   0.991  56.364

Example timings

name	user	system	elapsed
Background	0.338	0.043	0.383
BedToGenomicRanges	0.000	0.000	0.001
BootList	0.128	0.008	0.136
CNVPanelizerFromReadCounts	0.000	0.000	0.001
CNVPanelizerFromReadCountsHelper	0.001	0.000	0.001
CollectColumnFromAllReportTables	0.000	0.001	0.001
CombinedNormalizedCounts	0.029	0.005	0.034
IndexMultipleBams	0	0	0
NormalizedCounts	0.003	0.001	0.005
PlotBootstrapDistributions	4.433	0.124	4.592
ReadCountsFromBam	0.000	0.001	0.001
ReadXLSXToList	0	0	0
ReportTables	0.546	0.009	0.566
RunCNVPanelizerShiny	0.001	0.000	0.000
SelectReferenceSetByInterquartileRange	0.001	0.000	0.000
SelectReferenceSetByKmeans	0.000	0.000	0.001
SelectReferenceSetByPercentil	0	0	0
SelectReferenceSetFromReadCounts	0	0	0
StatusHeatmap	0.000	0.001	0.001
WriteListToXLSX	0	0	0

CHECK report for CNVPanelizer on merida2

Summary

Command output

Installation output

Tests output

Example timings