BioC 3.5: CHECK report for clst on malbec2

Package: clst

Version: 1.24.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings clst_1.24.0.tar.gz

StartedAt: 2017-10-17 22:04:52 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 22:05:24 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 32.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: clst.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 clst_1.24.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/clst.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 ‘clst/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘clst’ version ‘1.24.0’
* 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 ‘clst’ 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 ... NOTE
Foreign function call to a different package:
  .C("ROC", ..., PACKAGE = "ROC")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
findPMMI: no visible binding for global variable ‘median’
findPMMI: no visible global function definition for ‘quantile’
getTally: no visible binding for global variable ‘median’
scaleDistPlot: no visible global function definition for ‘cmdscale’
simpleROC: no visible global function definition for ‘new’
template: no visible global function definition for ‘str’
Undefined global functions or variables:
  cmdscale median new quantile str
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "cmdscale", "median", "quantile")
  importFrom("utils", "str")
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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  tests/unit/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* 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
scaleDistPlot 6.156  0.028    6.19
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runalltests.R’
 OK
* 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/clst.Rcheck/00check.log’
for details.

* installing *source* package ‘clst’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (clst)

name	user	system	elapsed
actino	0.016	0.000	0.015
bvseqs	0.000	0.004	0.001
classify	0.476	0.000	0.492
clst-package	0.084	0.000	0.085
findThreshold	0.036	0.000	0.037
plotDistances	0.18	0.00	0.18
printClst	0.004	0.000	0.002
scaleDistPlot	6.156	0.028	6.190
strep	0.000	0.000	0.001