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This page was generated on 2024-02-18 02:29:04 -0500 (Sun, 18 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4424
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4400
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

Package 1658/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rCGH 1.33.0  (landing page)
Frederic Commo
Snapshot Date: 2024-02-16 14:10:20 -0500 (Fri, 16 Feb 2024)
git_url: https://git.bioconductor.org/packages/rCGH
git_branch: devel
git_last_commit: 77d8311
git_last_commit_date: 2023-10-24 10:44:17 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 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 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for rCGH on merida1


To the developers/maintainers of the rCGH package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: rCGH
Version: 1.33.0
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_1.33.0.tar.gz
StartedAt: 2024-02-17 09:04:39 -0500 (Sat, 17 Feb 2024)
EndedAt: 2024-02-17 09:19:51 -0500 (Sat, 17 Feb 2024)
EllapsedTime: 912.7 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_1.33.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/rCGH.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rCGH/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rCGH’ version ‘1.33.0’
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    rCGH 1.1.8 has been released as rCGH-1.2.2
  Cannot process chunk/lines:
    Cleaner version from 1.1.4.
  Cannot process chunk/lines:
    Should not give any warning due to functions masked by imported packages
  Cannot process chunk/lines:
    Not submitted!
  Cannot process chunk/lines:
    New bioconductor devel versioning after release cycle.
  Cannot process chunk/lines:
    The first and corresponding bioconductor release version is 1.0.0.
* 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 whether startup messages can be suppressed ... 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’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
byGeneTable  23.446  0.606  28.816
plotProfile  18.124  0.331  21.252
multiplot    17.390  0.420  20.160
rCGH-package 11.530  0.171  13.144
plotLOH      10.671  0.228  12.226
plotDensity  10.646  0.172  12.056
recenter     10.541  0.135  11.876
EMnormalize   9.934  0.284  12.756
view          9.725  0.125  11.627
adjustSignal  9.542  0.294  12.166
segmentCGH    9.469  0.109  11.089
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.19-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/4.4-x86_64/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) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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: 1.33.0
	This version may contain important changes.
	Use news(Version == '1.33.0', 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 -- Sat Feb 17 09:19:29 2024 
*********************************************** 
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 
 52.951   2.281  65.387 

Example timings

rCGH.Rcheck/rCGH-Ex.timings

nameusersystemelapsed
AllAccessors0.8180.0371.037
EMnormalize 9.934 0.28412.756
adjustSignal 9.542 0.29412.166
byGeneTable23.446 0.60628.816
hg180.0040.0050.012
hg190.0040.0040.010
hg380.0040.0040.009
multiplot17.39 0.4220.16
plotDensity10.646 0.17212.056
plotLOH10.671 0.22812.226
plotProfile18.124 0.33121.252
rCGH-Agilent-class0.0020.0010.004
rCGH-SNP6-class0.0010.0010.002
rCGH-class0.0010.0010.003
rCGH-cytoScan-class0.0010.0010.002
rCGH-generic-class0.0010.0010.002
rCGH-oncoScan-class0.0010.0000.001
rCGH-package11.530 0.17113.144
readAffyCytoScan0.5660.0150.654
readAffyOncoScan0.0290.0040.079
readAffySNP60.6050.0160.679
readAgilent0.7760.0200.898
readGeneric0.0150.0030.018
recenter10.541 0.13511.876
segmentCGH 9.469 0.10911.089
setInfo0.5970.0120.711
view 9.725 0.12511.627