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CHECK report for rCGH on merida1

This page was generated on 2021-05-05 12:15:09 -0400 (Wed, 05 May 2021).

To the developers/maintainers of the rCGH package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1468/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rCGH 1.20.0  (landing page)
Frederic Commo
Snapshot Date: 2021-05-04 14:50:13 -0400 (Tue, 04 May 2021)
URL: https://git.bioconductor.org/packages/rCGH
Branch: RELEASE_3_12
Last Commit: 35225d2
Last Changed Date: 2020-10-27 11:06:33 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: rCGH
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rCGH.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rCGH_1.20.0.tar.gz
StartedAt: 2021-05-05 05:53:41 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 06:01:35 -0400 (Wed, 05 May 2021)
EllapsedTime: 474.0 seconds
RetCode: 0
Status:   OK  
CheckDir: rCGH.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rCGH.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rCGH_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/rCGH.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rCGH/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rCGH’ version ‘1.20.0’
* 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 ‘rCGH’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      2.8Mb
    extdata   1.2Mb
* 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
byGeneTable  13.292  0.206  13.538
multiplot    10.422  0.252  10.694
plotProfile   9.844  0.105  10.089
rCGH-package  7.690  0.101   7.809
EMnormalize   7.518  0.094   7.626
segmentCGH    7.538  0.070   7.918
recenter      7.011  0.072   7.222
plotDensity   6.956  0.071   7.042
view          6.696  0.043   6.758
plotLOH       6.327  0.105   6.447
adjustSignal  5.588  0.040   5.636
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/rCGH.Rcheck/00check.log’
for details.



Installation output

rCGH.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rCGH
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘rCGH’ ...
** 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 (rCGH)

Tests output

rCGH.Rcheck/tests/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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("rCGH")

	********************************************************
	Current version: 1.20.0
	This version may contain important changes.
	Use news(Version == '1.20.0', package = 'rCGH').
	********************************************************

SNP probes will be used.
Reading information...
Reading values...
Adding presettings...
Genome build: hg19
Log2Ratios QCs:
	dLRs: 0.162
	MAD: 0.128

Scaling...
Signal filtering...
Modeling allelic Difference...
Computing LRR segmentation using UndoSD: 0.179
Merging segments shorter than 10Kb.
Number of segments: 25
Merging peaks closer than 0.1 ...
Gaussian mixture estimation:
n.peaks =  3

Group parameters:
Grp 1:
prop: 0.504,	mean: -0.061,	Sd: 0.149,	peak height: 1.344
Grp 2:
prop: 0.481,	mean: 0.861,	Sd: 0.149,	peak height: 1.284
Grp 3:
prop: 0.015,	mean: 2.04,	Sd: 0.149,	peak height: 0.041

Correction value:  -0.061
Use plotDensity() to visualize the LRR densities.
  403 genes were dropped because they have exons located on both strands
  of the same reference sequence or on more than one reference sequence,
  so cannot be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a
  GRangesList object, or use suppressMessages() to suppress this message.
Creating byGene table...
SNP probes will be used.
Reading information...
Reading values...
Adding presettings...
Genome build: hg19
SNP probes will be used.
Reading information...
Reading values...
Adding presettings...
Genome build: hg19


RUNIT TEST PROTOCOL -- Wed May  5 06:01:26 2021 
*********************************************** 
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
rCGH RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 30.646   1.013  33.550 

Example timings

rCGH.Rcheck/rCGH-Ex.timings

nameusersystemelapsed
AllAccessors0.6410.0170.661
EMnormalize7.5180.0947.626
adjustSignal5.5880.0405.636
byGeneTable13.292 0.20613.538
hg180.0020.0010.004
hg190.0040.0030.006
hg380.0020.0010.003
multiplot10.422 0.25210.694
plotDensity6.9560.0717.042
plotLOH6.3270.1056.447
plotProfile 9.844 0.10510.089
rCGH-Agilent-class0.0020.0000.002
rCGH-SNP6-class0.0010.0000.002
rCGH-class0.0010.0010.001
rCGH-cytoScan-class0.0010.0010.001
rCGH-generic-class0.0000.0000.001
rCGH-oncoScan-class0.0010.0000.001
rCGH-package7.6900.1017.809
readAffyCytoScan0.4410.0060.449
readAffyOncoScan0.0210.0010.022
readAffySNP60.5680.0090.625
readAgilent0.5610.0110.600
readGeneric0.0110.0010.013
recenter7.0110.0727.222
segmentCGH7.5380.0707.918
setInfo0.5580.0180.579
view6.6960.0436.758