pint 1.23.0
Olli-Pekka Huovilainen
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pint | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings pint_1.23.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/pint.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-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 ‘1.23.0’
* 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 ... 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 loading without being on the library search path ... 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
W.effects: no visible global function definition for ‘princomp’
W.effects: no visible global function definition for ‘cor’
calculate.arm: no visible global function definition for ‘as’
calculate.arm: no visible global function definition for ‘new’
calculate.arm.sparse: no visible global function definition for ‘new’
calculate.chr: no visible global function definition for ‘new’
calculate.chr.sparse: no visible global function definition for ‘new’
calculate.genome: no visible global function definition for ‘new’
calculate.genome.sparse: no visible global function definition for
‘new’
imputation: no visible global function definition for ‘rnorm’
imputation: no visible global function definition for ‘sd’
join.top.regions: no visible global function definition for ‘quantile’
plot.ChromosomeModels: no visible global function definition for ‘par’
plot.ChromosomeModels: no visible global function definition for
‘abline’
plot.ChromosomeModels: no visible global function definition for
‘points’
plot.ChromosomeModels: no visible global function definition for ‘text’
plot.ChromosomeModels: no visible global function definition for
‘lines’
plot.GeneDependencyModel: no visible global function definition for
‘gray’
plot.GeneDependencyModel: no visible global function definition for
‘par’
plot.GeneDependencyModel: no visible global function definition for
‘layout’
plot.GeneDependencyModel: no visible global function definition for
‘barplot’
plot.GeneDependencyModel: no visible global function definition for
‘legend’
plot.GeneDependencyModel: no visible global function definition for
‘mtext’
plot.GenomeModels: no visible global function definition for ‘par’
plot.GenomeModels: no visible global function definition for ‘abline’
plot.GenomeModels: no visible global function definition for ‘points’
plot.GenomeModels: no visible global function definition for ‘text’
plot.GenomeModels: no visible global function definition for ‘lines’
plot.GenomeModels: no visible global function definition for ‘axis’
summarize.region.parameters: no visible global function definition for
‘na.omit’
summarize.region.parameters: no visible global function definition for
‘cor’
z.effects: no visible global function definition for ‘princomp’
coerce,GeneDependencyModel-DependencyModel: no visible global function
definition for ‘new’
coerce<-,GeneDependencyModel-DependencyModel: no visible global
function definition for ‘slot<-’
coerce<-,GeneDependencyModel-DependencyModel: no visible global
function definition for ‘slot’
getPArm,ChromosomeModels: no visible global function definition for
‘new’
getQArm,ChromosomeModels: no visible global function definition for
‘new’
Undefined global functions or variables:
abline as axis barplot cor gray layout legend lines mtext na.omit new
par points princomp quantile rnorm sd slot slot<- text
Consider adding
importFrom("grDevices", "gray")
importFrom("graphics", "abline", "axis", "barplot", "layout", "legend",
"lines", "mtext", "par", "points", "text")
importFrom("methods", "as", "new", "slot", "slot<-")
importFrom("stats", "cor", "na.omit", "princomp", "quantile", "rnorm",
"sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 sizes of PDF files under ‘inst/doc’ ... 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
screen 31.940 0.028 32.068
ChromosomeModels-class 28.632 0.028 28.694
GeneDependencyModel-class 7.780 0.000 7.830
plot 7.728 0.000 7.735
* 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
‘/home/biocbuild/bbs-3.4-bioc/meat/pint.Rcheck/00check.log’
for details.
* 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)