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 12:33:36 -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: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rCGH.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings rCGH_1.14.0.tar.gz |
| StartedAt: 2019-10-16 06:23:00 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:39:15 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 975.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rCGH.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rCGH.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings rCGH_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/rCGH.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'rCGH' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGcAUNG/R.INSTALL18047c594532/rCGH/man/adjustSignal.Rd:79: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGcAUNG/R.INSTALL18047c594532/rCGH/man/byGeneTable.Rd:36: file link 'select' in package 'AnnotationDbi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGcAUNG/R.INSTALL18047c594532/rCGH/man/segmentCGH.Rd:37: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGcAUNG/R.INSTALL18047c594532/rCGH/man/segmentCGH.Rd:69: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGcAUNG/R.INSTALL18047c594532/rCGH/man/view.Rd:9: file link 'shiny' in package 'shiny' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/rCGH.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
byGeneTable 17.61 0.28 17.98
multiplot 14.46 0.14 14.61
plotProfile 13.66 0.06 13.72
plotLOH 11.62 0.06 11.69
recenter 10.34 0.03 10.38
rCGH-package 9.91 0.03 9.94
EMnormalize 9.34 0.43 10.29
segmentCGH 9.61 0.00 9.61
plotDensity 9.57 0.00 9.56
view 8.75 0.02 8.76
adjustSignal 8.39 0.00 8.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
multiplot 17.36 0.01 17.37
byGeneTable 15.25 0.06 15.31
plotProfile 11.06 0.08 173.07
plotDensity 10.76 0.00 10.77
plotLOH 10.07 0.03 10.09
EMnormalize 9.75 0.14 9.89
rCGH-package 8.08 0.06 8.15
adjustSignal 7.49 0.00 7.50
view 7.03 0.14 7.17
recenter 6.45 0.05 34.78
segmentCGH 6.44 0.01 56.46
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/rCGH.Rcheck/00check.log'
for details.
rCGH.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/rCGH_1.14.0.tar.gz && rm -rf rCGH.buildbin-libdir && mkdir rCGH.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rCGH.buildbin-libdir rCGH_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL rCGH_1.14.0.zip && rm rCGH_1.14.0.tar.gz rCGH_1.14.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
61 3768k 61 2336k 0 0 6252k 0 --:--:-- --:--:-- --:--:-- 6347k
100 3768k 100 3768k 0 0 9752k 0 --:--:-- --:--:-- --:--:-- 9917k
install for i386
* 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
converting help for package 'rCGH'
finding HTML links ... done
AllAccessors html
EMnormalize html
adjustSignal html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGcAUNG/R.INSTALL18047c594532/rCGH/man/adjustSignal.Rd:79: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
agilentDB html
byGeneTable html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGcAUNG/R.INSTALL18047c594532/rCGH/man/byGeneTable.Rd:36: file link 'select' in package 'AnnotationDbi' does not exist and so has been treated as a topic
hg18 html
hg19 html
hg38 html
multiplot html
plotDensity html
plotLOH html
plotProfile html
rCGH-Agilent-class html
rCGH-SNP6-class html
rCGH-class html
rCGH-cytoScan-class html
rCGH-generic-class html
rCGH-oncoScan-class html
rCGH-package html
readAffyCytoScan html
readAffyOncoScan html
readAffySNP6 html
readAgilent html
readGeneric html
recenter html
segmentCGH html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGcAUNG/R.INSTALL18047c594532/rCGH/man/segmentCGH.Rd:37: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGcAUNG/R.INSTALL18047c594532/rCGH/man/segmentCGH.Rd:69: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
setInfo html
show-methods html
view html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGcAUNG/R.INSTALL18047c594532/rCGH/man/view.Rd:9: file link 'shiny' in package 'shiny' does not exist and so has been treated as a topic
** 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
install for x64
* installing *source* package 'rCGH' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rCGH' as rCGH_1.14.0.zip
* DONE (rCGH)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'rCGH' successfully unpacked and MD5 sums checked
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rCGH.Rcheck/tests_i386/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 06:38:09 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
20.54 1.45 31.09
|
rCGH.Rcheck/tests_x64/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-w64-mingw32/x64 (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 06:38:53 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
26.31 0.79 27.15
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rCGH.Rcheck/examples_i386/rCGH-Ex.timings
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rCGH.Rcheck/examples_x64/rCGH-Ex.timings
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