BioC 3.5: CHECK report for parglms on malbec2

Package: parglms

Version: 1.8.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings parglms_1.8.0.tar.gz

StartedAt: 2017-10-18 01:21:33 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:22:17 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 44.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: parglms.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings parglms_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/parglms.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘parglms/DESCRIPTION’ ... OK
* this is package ‘parglms’ version ‘1.8.0’
* 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 ‘parglms’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 loading without being on the library search path ... 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
.parglm: no visible binding for global variable ‘ind’
getX: no visible global function definition for ‘model.matrix’
getY: no visible global function definition for ‘model.response’
getY: no visible global function definition for ‘model.frame’
predict.parglm: no visible binding for global variable ‘z’
predict.parglm: no visible global function definition for ‘model.frame’
predict.parglm: no visible global function definition for
  ‘model.extract’
predict.parglm: no visible global function definition for
  ‘model.matrix’
Undefined global functions or variables:
  ind model.extract model.frame model.matrix model.response z
Consider adding
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "model.response")
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 files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘parglms.Rmd’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
parGLM-methods 5.104   0.04    5.23
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘parglms_unit_tests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/parglms.Rcheck/00check.log’
for details.

* installing *source* package ‘parglms’ ...
** R
** 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 (parglms)

name	user	system	elapsed
parGLM-methods	5.104	0.040	5.230
parglms-package	0.000	0.000	0.002