Back to Multiple platform build/check report for BioC 3.8
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for Clomial on malbec1

This page was generated on 2019-04-16 11:50:24 -0400 (Tue, 16 Apr 2019).

Package 271/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Clomial 1.18.1
Habil Zare
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/Clomial
Branch: RELEASE_3_8
Last Commit: b45ab1e
Last Changed Date: 2019-01-04 13:03:57 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  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: Clomial
Version: 1.18.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Clomial.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Clomial_1.18.1.tar.gz
StartedAt: 2019-04-15 22:57:21 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:00:21 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 180.1 seconds
RetCode: 0
Status:  OK 
CheckDir: Clomial.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Clomial.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Clomial_1.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/Clomial.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Clomial/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Clomial’ version ‘1.18.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘Clomial’ 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
* 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 ... NOTE
Clomial: no visible global function definition for ‘runif’
Clomial.generate.data: no visible global function definition for
  ‘runif’
Clomial.generate.data: no visible global function definition for
  ‘rbinom’
Clomial.likelihood: no visible global function definition for ‘dbinom’
Phi: no visible global function definition for ‘dbinom’
choose.best: no visible global function definition for ‘tail’
compute.P.reparam : update.Wj: no visible global function definition
  for ‘optim’
compute.P.reparam : plot.obj: no visible global function definition for
  ‘plot’
compute.q: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  dbinom optim plot rbinom runif tail
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dbinom", "optim", "rbinom", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
choose.best        56.656  2.320  59.062
Clomial-package    22.428  0.788  23.287
Clomial            21.296  0.940  22.265
compute.bic        12.040  0.536  12.596
Clomial.likelihood  9.436  0.340   9.798
Clomial.iterate     8.920  0.372   9.324
compute.errors      6.840  0.252   7.107
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/Clomial.Rcheck/00check.log’
for details.



Installation output

Clomial.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL Clomial
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘Clomial’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Clomial)

Tests output


Example timings

Clomial.Rcheck/Clomial-Ex.timings

nameusersystemelapsed
Clomial-package22.428 0.78823.287
Clomial21.296 0.94022.265
Clomial.generate.data0.0320.0000.034
Clomial.iterate8.9200.3729.324
Clomial.likelihood9.4360.3409.798
Clomial10000.3520.0080.375
breastCancer0.0000.0000.002
choose.best56.656 2.32059.062
compute.bic12.040 0.53612.596
compute.errors6.8400.2527.107