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BioC 3.5: CHECK report for Clonality on tokay2

This page was generated on 2017-08-16 13:20:51 -0400 (Wed, 16 Aug 2017).

Package 230/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Clonality 1.24.0
Irina Ostrovnaya
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/Clonality
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Clonality
Version: 1.24.0
Command: rm -rf Clonality.buildbin-libdir Clonality.Rcheck && mkdir Clonality.buildbin-libdir Clonality.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Clonality.buildbin-libdir Clonality_1.24.0.tar.gz >Clonality.Rcheck\00install.out 2>&1 && cp Clonality.Rcheck\00install.out Clonality-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=Clonality.buildbin-libdir --install="check:Clonality-install.out" --force-multiarch --no-vignettes --timings Clonality_1.24.0.tar.gz
StartedAt: 2017-08-15 22:44:56 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:49:22 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 266.5 seconds
RetCode: 0
Status:  OK  
CheckDir: Clonality.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Clonality.buildbin-libdir Clonality.Rcheck && mkdir Clonality.buildbin-libdir Clonality.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Clonality.buildbin-libdir Clonality_1.24.0.tar.gz >Clonality.Rcheck\00install.out 2>&1 && cp Clonality.Rcheck\00install.out Clonality-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=Clonality.buildbin-libdir --install="check:Clonality-install.out" --force-multiarch --no-vignettes --timings Clonality_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/Clonality.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 'Clonality/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Clonality' version '1.24.0'
* 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 'Clonality' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Foreign function call to a different package:
  .Fortran("fndcpt", ..., PACKAGE = "DNAcopy")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* 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
clonality.analysis  68.59   0.32   68.90
LRtesting3or4tumors 21.74   0.00   21.73
LOHclonality         7.15   0.01    7.17
ECMtesting           5.29   0.00    5.29
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
clonality.analysis  63.31   0.14   63.49
LRtesting3or4tumors 19.85   0.00   19.85
ECMtesting           8.08   0.00    8.07
LOHclonality         7.81   0.00    7.82
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/Clonality.Rcheck/00check.log'
for details.


Clonality.Rcheck/00install.out:


install for i386

* installing *source* package 'Clonality' ...
** 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 'Clonality' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Clonality' as Clonality_1.24.0.zip
* DONE (Clonality)

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

nameusersystemelapsed
ECMtesting5.290.005.29
LOHclonality7.150.017.17
LRtesting3or4tumors21.74 0.0021.73
SNVtest0.360.000.36
ave.adj.probes1.090.011.11
chromosomePlots000
clonality.analysis68.59 0.3268.90
genomewidePlots000
histogramPlot000
mutation.proba1.380.001.38
mutation.rem4.250.014.26
splitChromosomes0.030.000.03

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

nameusersystemelapsed
ECMtesting8.080.008.07
LOHclonality7.810.007.82
LRtesting3or4tumors19.85 0.0019.85
SNVtest0.370.010.39
ave.adj.probes1.270.001.26
chromosomePlots000
clonality.analysis63.31 0.1463.49
genomewidePlots000
histogramPlot000
mutation.proba0.880.020.89
mutation.rem2.780.002.78
splitChromosomes0.030.000.03