Package: CNVPanelizer

Version: 1.18.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CNVPanelizer.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CNVPanelizer_1.18.0.tar.gz

StartedAt: 2020-04-15 03:07:08 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:10:34 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 206.4 seconds

RetCode: 0

Status:  OK

CheckDir: CNVPanelizer.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CNVPanelizer.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CNVPanelizer_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/CNVPanelizer.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘1.18.0’
* 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 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/CNVPanelizer.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL CNVPanelizer
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘CNVPanelizer’ ...
** using staged installation
** 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 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 (CNVPanelizer)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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("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, 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

Calculating Background for s1
Calculating Background for s2
Calculating Background for s3
Calculating Background for s4
Saving plot to '/tmp/RtmpKXC5ev/s1_plot.pdf'
Saving plot to '/tmp/RtmpKXC5ev/s2_plot.pdf'
Saving plot to '/tmp/RtmpKXC5ev/s3_plot.pdf'
Saving plot to '/tmp/RtmpKXC5ev/s4_plot.pdf'
Saving plot to '/tmp/RtmpKXC5ev/sample1.pdf'
Saving plot to '/tmp/RtmpKXC5ev/sample2.pdf'
Saving plot to '/tmp/RtmpKXC5ev/sample3.pdf'
Saving plot to '/tmp/RtmpKXC5ev/sample4.pdf'
Calculating Background for c:/somefile1.bam
Saving file to '/tmp/RtmpKXC5ev/samples.xlsx'
[1] "GENE 1:  0.166666666666667"
[1] "GENE 2:  0.356348322549899"


RUNIT TEST PROTOCOL -- Wed Apr 15 03:10:31 2020 
*********************************************** 
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 
 49.132   0.296  49.529 

name	user	system	elapsed
Background	0.340	0.004	0.347
BedToGenomicRanges	0	0	0
BootList	0.124	0.012	0.136
CNVPanelizerFromReadCounts	0	0	0
CNVPanelizerFromReadCountsHelper	0.004	0.000	0.000
CollectColumnFromAllReportTables	0	0	0
CombinedNormalizedCounts	0.028	0.000	0.029
IndexMultipleBams	0	0	0
NormalizedCounts	0.000	0.000	0.003
PlotBootstrapDistributions	4.036	0.032	4.071
ReadCountsFromBam	0	0	0
ReadXLSXToList	0	0	0
ReportTables	0.472	0.000	0.473
RunCNVPanelizerShiny	0	0	0
SelectReferenceSetByInterquartileRange	0	0	0
SelectReferenceSetByKmeans	0	0	0
SelectReferenceSetByPercentil	0	0	0
SelectReferenceSetFromReadCounts	0	0	0
StatusHeatmap	0	0	0
WriteListToXLSX	0	0	0