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CHECK report for Clonality on malbec1

This page was generated on 2020-04-15 12:06:09 -0400 (Wed, 15 Apr 2020).

Package 302/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Clonality 1.34.0
Irina Ostrovnaya
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/Clonality
Branch: RELEASE_3_10
Last Commit: 681c6d1
Last Changed Date: 2019-10-29 13:08:18 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 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
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Clonality
Version: 1.34.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:Clonality.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings Clonality_1.34.0.tar.gz
StartedAt: 2020-04-15 00:56:20 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:59:17 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 177.4 seconds
RetCode: 0
Status:  OK 
CheckDir: Clonality.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:Clonality.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings Clonality_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/Clonality.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Clonality/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Clonality’ version ‘1.34.0’
* 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 ‘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
* 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 ... 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 ... NOTE
get.mutation.frequencies: no visible binding for global variable
  ‘freqdata’
Undefined global functions or variables:
  freqdata
* 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 ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
clonality.analysis  68.452  0.064  68.661
LRtesting3or4tumors 37.488  0.012  37.580
LOHclonality         9.252  0.000   9.266
ECMtesting           8.788  0.000   8.810
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/Clonality.Rcheck/00check.log’
for details.



Installation output

Clonality.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL Clonality
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘Clonality’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘Clonality.Rnw’ 
** 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 (Clonality)

Tests output


Example timings

Clonality.Rcheck/Clonality-Ex.timings

nameusersystemelapsed
ECMtesting8.7880.0008.810
LOHclonality9.2520.0009.266
LRtesting3or4tumors37.488 0.01237.580
SNVtest3.0960.0723.172
SNVtest20.6080.0000.608
ave.adj.probes2.1160.0122.131
chromosomePlots000
clonality.analysis68.452 0.06468.661
create.mutation.matrix1.7360.0241.764
genomewidePlots0.0000.0000.001
get.mutation.frequencies1.6560.0441.703
histogramPlot000
mutation.proba1.5480.0081.556
mutation.rem2.5120.0162.528
splitChromosomes0.0080.0000.006