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BioC 3.6: CHECK report for Chicago on tokay1

This page was generated on 2017-08-16 13:35:26 -0400 (Wed, 16 Aug 2017).

Package 204/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Chicago 1.5.0
Mikhail Spivakov
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Chicago
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Chicago
Version: 1.5.0
Command: rm -rf Chicago.buildbin-libdir Chicago.Rcheck && mkdir Chicago.buildbin-libdir Chicago.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Chicago.buildbin-libdir Chicago_1.5.0.tar.gz >Chicago.Rcheck\00install.out 2>&1 && cp Chicago.Rcheck\00install.out Chicago-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Chicago.buildbin-libdir --install="check:Chicago-install.out" --force-multiarch --no-vignettes --timings Chicago_1.5.0.tar.gz
StartedAt: 2017-08-15 22:18:36 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:21:40 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 184.3 seconds
RetCode: 0
Status:  OK  
CheckDir: Chicago.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Chicago.buildbin-libdir Chicago.Rcheck && mkdir Chicago.buildbin-libdir Chicago.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Chicago.buildbin-libdir Chicago_1.5.0.tar.gz >Chicago.Rcheck\00install.out 2>&1 && cp Chicago.Rcheck\00install.out Chicago-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Chicago.buildbin-libdir --install="check:Chicago-install.out" --force-multiarch --no-vignettes --timings Chicago_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Chicago.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Chicago/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Chicago' version '1.5.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'Chicago' 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
* 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' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
normaliseOtherEnds 13.80   5.25   15.66
exportResults       9.25   0.39   10.12
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
normaliseOtherEnds 17.75   6.56   17.34
exportResults      11.50   0.40   12.16
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/Chicago.Rcheck/00check.log'
for details.


Chicago.Rcheck/00install.out:


install for i386

* installing *source* package 'Chicago' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'Chicago' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Chicago' as Chicago_1.5.0.zip
* DONE (Chicago)

Chicago.Rcheck/examples_i386/Chicago-Ex.timings:

nameusersystemelapsed
cdUnitTest0.050.000.05
chicagoData000
chicagoPipeline0.160.000.17
copyCD0.020.000.02
defaultSettings000
estimateBrownianComponent0.350.000.36
estimateDistFun0.050.000.05
estimateTechnicalNoise0.060.000.06
exportResults 9.25 0.3910.12
getPvals0.080.000.03
getScores0.030.000.04
getSkOnly0.280.000.28
mergeSamples0.080.000.08
modifySettings0.010.000.02
normaliseBaits0.550.000.54
normaliseOtherEnds13.80 5.2515.66
overlapFragWithFeatures0.070.000.11
peakEnrichment4Features1.310.341.66
plotBaits0.140.000.14
plotDistFun0.010.000.01
readAndMerge0.070.000.06
readSample0.060.000.07
setExperiment000

Chicago.Rcheck/examples_x64/Chicago-Ex.timings:

nameusersystemelapsed
cdUnitTest0.050.000.05
chicagoData000
chicagoPipeline0.170.000.17
copyCD0.000.010.02
defaultSettings000
estimateBrownianComponent0.560.020.58
estimateDistFun0.050.000.04
estimateTechnicalNoise0.080.000.08
exportResults11.50 0.4012.16
getPvals0.010.000.01
getScores0.060.020.08
getSkOnly0.380.010.39
mergeSamples0.250.020.25
modifySettings0.010.000.02
normaliseBaits0.100.000.08
normaliseOtherEnds17.75 6.5617.34
overlapFragWithFeatures0.080.000.07
peakEnrichment4Features1.190.051.24
plotBaits0.190.000.19
plotDistFun0.010.000.01
readAndMerge0.110.000.11
readSample1.000.271.25
setExperiment0.020.000.02