Frederic Commo
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/rCGH |
| Branch: RELEASE_3_6 |
| Last Commit: 7a08b43 |
| Last Changed Date: 2017-12-27 06:56:31 -0400 (Wed, 27 Dec 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:26:33 -0400 (Thu, 12 Apr 2018).
| Package 1134/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rCGH 1.8.1 Frederic Commo
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: rCGH |
| Version: 1.8.1 |
| Command: rm -rf rCGH.buildbin-libdir rCGH.Rcheck && mkdir rCGH.buildbin-libdir rCGH.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rCGH.buildbin-libdir rCGH_1.8.1.tar.gz >rCGH.Rcheck\00install.out 2>&1 && cp rCGH.Rcheck\00install.out rCGH-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=rCGH.buildbin-libdir --install="check:rCGH-install.out" --force-multiarch --no-vignettes --timings rCGH_1.8.1.tar.gz |
| StartedAt: 2018-04-12 02:31:01 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 02:41:45 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 644.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rCGH.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### rm -rf rCGH.buildbin-libdir rCGH.Rcheck && mkdir rCGH.buildbin-libdir rCGH.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rCGH.buildbin-libdir rCGH_1.8.1.tar.gz >rCGH.Rcheck\00install.out 2>&1 && cp rCGH.Rcheck\00install.out rCGH-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=rCGH.buildbin-libdir --install="check:rCGH-install.out" --force-multiarch --no-vignettes --timings rCGH_1.8.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/rCGH.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.8.1'
* 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-3.6-bioc/tmpdir/RtmpohbIF5/R.INSTALL3a441cbad86/rCGH/man/adjustSignal.Rd:79: missing file link 'mclapply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpohbIF5/R.INSTALL3a441cbad86/rCGH/man/byGeneTable.Rd:36: missing file link 'select'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpohbIF5/R.INSTALL3a441cbad86/rCGH/man/segmentCGH.Rd:37: missing file link 'mclapply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpohbIF5/R.INSTALL3a441cbad86/rCGH/man/segmentCGH.Rd:69: missing file link 'mclapply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpohbIF5/R.INSTALL3a441cbad86/rCGH/man/view.Rd:9: missing file link 'shiny'
See 'C:/Users/biocbuild/bbs-3.6-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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
multiplot 15.16 0.30 15.45
byGeneTable 14.25 0.28 15.63
plotProfile 12.25 0.25 12.50
rCGH-package 9.53 0.15 9.69
plotLOH 9.03 0.17 9.20
plotDensity 8.86 0.17 9.03
recenter 8.55 0.14 8.69
EMnormalize 8.25 0.22 8.47
view 7.66 0.19 7.85
segmentCGH 7.47 0.15 7.62
adjustSignal 6.32 0.17 6.50
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
byGeneTable 16.95 0.30 17.25
multiplot 14.75 0.22 14.97
plotProfile 12.79 0.16 12.94
recenter 9.90 0.18 10.09
rCGH-package 9.68 0.23 9.92
EMnormalize 9.37 0.17 9.65
plotLOH 8.90 0.19 9.09
plotDensity 8.83 0.21 9.05
view 8.23 0.14 8.38
segmentCGH 7.85 0.17 8.02
adjustSignal 7.22 0.17 7.39
* 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, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/rCGH.Rcheck/00check.log'
for details.
rCGH.Rcheck/00install.out
install for i386
* installing *source* package 'rCGH' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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-3.6-bioc/tmpdir/RtmpohbIF5/R.INSTALL3a441cbad86/rCGH/man/adjustSignal.Rd:79: missing file link 'mclapply'
agilentDB html
byGeneTable html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpohbIF5/R.INSTALL3a441cbad86/rCGH/man/byGeneTable.Rd:36: missing file link 'select'
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-3.6-bioc/tmpdir/RtmpohbIF5/R.INSTALL3a441cbad86/rCGH/man/segmentCGH.Rd:37: missing file link 'mclapply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpohbIF5/R.INSTALL3a441cbad86/rCGH/man/segmentCGH.Rd:69: missing file link 'mclapply'
setInfo html
show-methods html
view html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpohbIF5/R.INSTALL3a441cbad86/rCGH/man/view.Rd:9: missing file link 'shiny'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'rCGH' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rCGH' as rCGH_1.8.1.zip
* DONE (rCGH)
In R CMD INSTALL
In R CMD INSTALL
|
rCGH.Rcheck/tests_i386/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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: 1.8.1
This version may contain important changes.
Use news(Version == '1.8.1', 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 = 2
Group parameters:
Grp 1:
prop: 0.502, mean: -0.042, Sd: 0.138, peak height: 1.457
Grp 2:
prop: 0.498, mean: 0.872, Sd: 0.138, peak height: 1.443
Correction value: -0.042
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 -- Thu Apr 12 02:41:06 2018
***********************************************
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
28.37 1.01 29.56
|
rCGH.Rcheck/tests_x64/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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: 1.8.1
This version may contain important changes.
Use news(Version == '1.8.1', 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 = 2
Group parameters:
Grp 1:
prop: 0.502, mean: -0.042, Sd: 0.138, peak height: 1.457
Grp 2:
prop: 0.498, mean: 0.872, Sd: 0.138, peak height: 1.443
Correction value: -0.042
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 -- Thu Apr 12 02:41:40 2018
***********************************************
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
32.85 0.81 33.84
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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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