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This page was generated on 2023-02-07 11:07:11 -0500 (Tue, 07 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for rCGH on merida1


To the developers/maintainers of the rCGH package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rCGH.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1600/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rCGH 1.29.0  (landing page)
Frederic Commo
Snapshot Date: 2023-02-06 14:00:21 -0500 (Mon, 06 Feb 2023)
git_url: https://git.bioconductor.org/packages/rCGH
git_branch: master
git_last_commit: f152ae6
git_last_commit_date: 2022-11-01 11:11:54 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: rCGH
Version: 1.29.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rCGH.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rCGH_1.29.0.tar.gz
StartedAt: 2023-02-07 05:29:44 -0500 (Tue, 07 Feb 2023)
EndedAt: 2023-02-07 05:44:20 -0500 (Tue, 07 Feb 2023)
EllapsedTime: 875.9 seconds
RetCode: 0
Status:   OK  
CheckDir: rCGH.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rCGH.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rCGH_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/rCGH.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rCGH/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rCGH’ version ‘1.29.0’
* 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 LazyData ... 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  19.063  0.210  24.828
multiplot    16.090  0.263  22.494
plotProfile  16.155  0.130  21.413
rCGH-package 10.911  0.100  13.772
EMnormalize  10.286  0.227  13.424
plotLOH      10.203  0.104  13.752
plotDensity  10.095  0.118  14.039
recenter     10.114  0.074  12.971
view          9.200  0.057  12.483
segmentCGH    8.993  0.049  11.502
adjustSignal  8.059  0.081  10.467
* 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-3.17-bioc/meat/rCGH.Rcheck/00check.log’
for details.



Installation output

rCGH.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rCGH
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/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) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 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: 1.29.0
	This version may contain important changes.
	Use news(Version == '1.29.0', 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 -- Tue Feb  7 05:44:05 2023 
*********************************************** 
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 
 45.908   1.450  62.710 

Example timings

rCGH.Rcheck/rCGH-Ex.timings

nameusersystemelapsed
AllAccessors0.9640.0251.256
EMnormalize10.286 0.22713.424
adjustSignal 8.059 0.08110.467
byGeneTable19.063 0.21024.828
hg180.0030.0010.004
hg190.0030.0010.007
hg380.0040.0010.004
multiplot16.090 0.26322.494
plotDensity10.095 0.11814.039
plotLOH10.203 0.10413.752
plotProfile16.155 0.13021.413
rCGH-Agilent-class0.0020.0010.002
rCGH-SNP6-class0.0000.0000.001
rCGH-class0.0010.0000.002
rCGH-cytoScan-class0.0010.0000.001
rCGH-generic-class0.0010.0010.001
rCGH-oncoScan-class0.0000.0000.001
rCGH-package10.911 0.10013.772
readAffyCytoScan0.5700.0130.723
readAffyOncoScan0.0280.0010.036
readAffySNP60.5290.0140.706
readAgilent0.8930.0161.164
readGeneric0.0140.0010.021
recenter10.114 0.07412.971
segmentCGH 8.993 0.04911.502
setInfo0.5900.0100.768
view 9.200 0.05712.483