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CHECK report for rCGH on celaya2

This page was generated on 2019-04-09 13:14:27 -0400 (Tue, 09 Apr 2019).

Package 1300/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rCGH 1.13.0
Frederic Commo
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/rCGH
Branch: master
Last Commit: cbec512
Last Changed Date: 2018-10-30 11:54:34 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK 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 [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: rCGH
Version: 1.13.0
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_1.13.0.tar.gz
StartedAt: 2019-04-09 04:47:53 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:56:27 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 513.2 seconds
RetCode: 0
Status:  OK 
CheckDir: rCGH.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /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_1.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/rCGH.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.13.0’
* 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 ... 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 ... 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’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
byGeneTable  16.749  0.610  17.360
multiplot    15.119  0.589  15.778
plotProfile  14.122  0.378  14.584
rCGH-package 10.325  0.173  10.500
EMnormalize   9.639  0.426  10.070
recenter      8.932  0.120   9.058
plotLOH       8.817  0.181   9.023
plotDensity   8.527  0.198   8.728
segmentCGH    8.355  0.091   8.448
view          8.090  0.097   8.187
adjustSignal  7.626  0.185   7.811
* 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: OK


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/3.6/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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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("rCGH")

	********************************************************
	Current version: 1.13.0
	This version may contain important changes.
	Use news(Version == '1.13.0', 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.
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 -- Tue Apr  9 04:56:17 2019 
*********************************************** 
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 
 36.851   2.664  39.469 

Example timings

rCGH.Rcheck/rCGH-Ex.timings

nameusersystemelapsed
AllAccessors1.1350.0811.220
EMnormalize 9.639 0.42610.070
adjustSignal7.6260.1857.811
byGeneTable16.749 0.61017.360
hg180.0040.0020.006
hg190.0050.0030.007
hg380.0060.0030.008
multiplot15.119 0.58915.778
plotDensity8.5270.1988.728
plotLOH8.8170.1819.023
plotProfile14.122 0.37814.584
rCGH-Agilent-class0.0010.0000.001
rCGH-SNP6-class0.0010.0000.001
rCGH-class0.0010.0000.002
rCGH-cytoScan-class0.0010.0000.001
rCGH-generic-class0.0010.0010.001
rCGH-oncoScan-class0.0010.0000.001
rCGH-package10.325 0.17310.500
readAffyCytoScan0.6050.0110.616
readAffyOncoScan0.1770.0540.231
readAffySNP60.4870.0120.501
readAgilent0.9840.0341.018
readGeneric0.0160.0010.019
recenter8.9320.1209.058
segmentCGH8.3550.0918.448
setInfo0.5870.0080.594
view8.0900.0978.187