pint 1.26.0
Olli-Pekka Huovilainen
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/pint | | Branch: RELEASE_3_5 | | Last Commit: b86cffb | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf pint.buildbin-libdir pint.Rcheck && mkdir pint.buildbin-libdir pint.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pint.buildbin-libdir pint_1.26.0.tar.gz >pint.Rcheck\00install.out 2>&1 && cp pint.Rcheck\00install.out pint-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=pint.buildbin-libdir --install="check:pint-install.out" --force-multiarch --no-vignettes --timings pint_1.26.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/pint.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pint/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pint' version '1.26.0'
* 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 '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
* 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 ... 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 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
screen 25.61 0.01 25.63
ChromosomeModels-class 22.69 0.05 22.74
plot 6.60 0.00 6.59
GeneDependencyModel-class 6.17 0.03 6.20
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
ChromosomeModels-class 30.69 0.03 30.75
screen 29.20 0.03 29.24
plot 7.75 0.00 7.75
GeneDependencyModel-class 7.64 0.00 7.69
* 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/pint.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'pint' ...
** 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 'pint' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pint' as pint_1.26.0.zip
* DONE (pint)