Frederic Commo
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/rCGH |
| Branch: RELEASE_3_9 |
| Last Commit: 9d50f3a |
| Last Changed Date: 2019-05-02 11:53:56 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:07:04 -0400 (Wed, 16 Oct 2019).
| Package 1326/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rCGH 1.14.0 Frederic Commo
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: rCGH |
| Version: 1.14.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rCGH.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rCGH_1.14.0.tar.gz |
| StartedAt: 2019-10-16 04:19:55 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:27:10 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 434.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rCGH.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rCGH.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rCGH_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/rCGH.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.14.0’
* 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 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 or elapsed time > 5s
user system elapsed
byGeneTable 15.938 0.445 16.577
multiplot 15.099 0.459 15.699
plotProfile 13.433 0.269 13.828
rCGH-package 10.487 0.310 11.052
plotLOH 9.887 0.248 10.226
recenter 9.572 0.206 9.898
plotDensity 9.006 0.205 9.340
segmentCGH 8.514 0.238 8.807
EMnormalize 8.449 0.281 8.826
view 8.454 0.204 8.709
adjustSignal 7.413 0.112 7.568
* 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-3.9-bioc/meat/rCGH.Rcheck/00check.log’
for details.
rCGH.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL rCGH ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)
rCGH.Rcheck/tests/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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("rCGH")
********************************************************
Current version: 1.14.0
This version may contain important changes.
Use news(Version == '1.14.0', 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 -- Wed Oct 16 04:27:03 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
31.028 1.366 32.765
rCGH.Rcheck/rCGH-Ex.timings
| name | user | system | elapsed | |
| AllAccessors | 1.315 | 0.000 | 1.330 | |
| EMnormalize | 8.449 | 0.281 | 8.826 | |
| adjustSignal | 7.413 | 0.112 | 7.568 | |
| byGeneTable | 15.938 | 0.445 | 16.577 | |
| hg18 | 0.000 | 0.003 | 0.003 | |
| hg19 | 0.003 | 0.000 | 0.002 | |
| hg38 | 0.002 | 0.000 | 0.003 | |
| multiplot | 15.099 | 0.459 | 15.699 | |
| plotDensity | 9.006 | 0.205 | 9.340 | |
| plotLOH | 9.887 | 0.248 | 10.226 | |
| plotProfile | 13.433 | 0.269 | 13.828 | |
| rCGH-Agilent-class | 0.002 | 0.000 | 0.001 | |
| rCGH-SNP6-class | 0.000 | 0.000 | 0.001 | |
| rCGH-class | 0.001 | 0.000 | 0.000 | |
| rCGH-cytoScan-class | 0.001 | 0.000 | 0.001 | |
| rCGH-generic-class | 0.000 | 0.000 | 0.001 | |
| rCGH-oncoScan-class | 0.001 | 0.000 | 0.000 | |
| rCGH-package | 10.487 | 0.310 | 11.052 | |
| readAffyCytoScan | 0.526 | 0.004 | 0.530 | |
| readAffyOncoScan | 0.026 | 0.000 | 0.047 | |
| readAffySNP6 | 0.473 | 0.008 | 0.497 | |
| readAgilent | 0.854 | 0.000 | 0.854 | |
| readGeneric | 0.012 | 0.000 | 0.025 | |
| recenter | 9.572 | 0.206 | 9.898 | |
| segmentCGH | 8.514 | 0.238 | 8.807 | |
| setInfo | 0.594 | 0.008 | 0.601 | |
| view | 8.454 | 0.204 | 8.709 | |