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BioC 2.13: CHECK report for pint on zin1

This page was generated on 2014-04-05 09:47:51 -0700 (Sat, 05 Apr 2014).

Package 531/750HostnameOS / ArchBUILDCHECKBUILD BIN
pint 1.14.0
Olli-Pekka Huovilainen
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/pint
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: pint
Version: 1.14.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings pint_1.14.0.tar.gz
StartedAt: 2014-04-05 03:04:50 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 03:07:41 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 171.1 seconds
RetCode: 0
Status:  OK 
CheckDir: pint.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/pint.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pint/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pint’ version ‘1.14.0’
* 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 ‘pint’ can be installed ... [6s/6s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘Matrix’ ‘methods’ ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘pint/R/firstlib.R’:
  .onLoad calls:
    packageStartupMessage("\npint Copyright (C) 2008-2012 Olli-Pekka Huovilainen and Leo Lahti.\n\nThis program comes with ABSOLUTELY NO WARRANTY.\nThis is free software, and you are welcome to redistribute it\nunder the FreeBSD license.\nSee the licensing terms for details.\n")

See section ‘Good practice’ in '?.onAttach'.

findModel,GenomeModels: no visible binding for global variable ‘pIndex’
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘depsearch.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [110s/110s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
screen                    45.086  0.024  45.297
ChromosomeModels-class    40.146  0.044  40.406
plot                      10.741  0.008  10.781
GeneDependencyModel-class 10.509  0.000  10.523
* 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

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/pint.Rcheck/00check.log’
for details.

pint.Rcheck/00install.out:

* installing *source* package ‘pint’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘as.data.frame’ from package ‘base’ in package ‘pint’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pint)

pint.Rcheck/pint-Ex.timings:

nameusersystemelapsed
ChromosomeModels-class40.146 0.04440.406
GeneDependencyModel-class10.509 0.00010.523
fit.byname0.1240.0000.126
get.neighboring.probes0.0000.0000.001
get.neighs0.0040.0000.001
join.top.regions0.0040.0000.002
order.feature.info0.0000.0000.002
pint.data0.120.000.12
plot10.741 0.00810.781
screen45.086 0.02445.297
summarize.region.parameters0.0040.0000.003
window0.1560.0000.157
z.effect0.120.000.12