BioC 3.3: CHECK report for genotypeeval on morelia

Package: genotypeeval

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genotypeeval_1.1.0.tar.gz

StartedAt: 2016-04-21 03:05:29 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 03:10:05 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 276.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: genotypeeval.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genotypeeval_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/genotypeeval.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genotypeeval/DESCRIPTION’ ... OK
* this is package ‘genotypeeval’ version ‘1.1.0’
* 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 ‘genotypeeval’ can be installed ... [22s/22s] WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘genotypeeval’
See ‘/Users/biocbuild/bbs-3.3-bioc/meat/genotypeeval.Rcheck/00install.out’ for details.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ReadVCFDataChunk: no visible global function definition for
  ‘read.table’
getCoefs: no visible global function definition for ‘constrOptim’
Undefined global functions or variables:
  constrOptim read.table
Consider adding
  importFrom("stats", "constrOptim")
  importFrom("utils", "read.table")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [51s/51s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
getPlots         5.918  0.201   6.155
ReadVCFDataChunk 5.385  0.365   5.769
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [18s/18s]
 [18s/18s] 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/genotypeeval.Rcheck/00check.log’
for details.

* installing *source* package ‘genotypeeval’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘genotypeeval’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘genotypeeval’
* DONE (genotypeeval)

name	user	system	elapsed
GoldDataFromGRanges	0.069	0.000	0.069
GoldDataParam	0.001	0.000	0.001
ReadGoldData	0.633	0.032	0.687
ReadVCFData	3.461	0.158	3.633
ReadVCFDataChunk	5.385	0.365	5.769
VCFEvaluate	4.487	0.229	4.756
VCFQAParam	0.002	0.000	0.002
didSamplePass	4.194	0.212	4.434
didSamplePassOverall	3.241	0.182	3.433
getName	3.665	0.181	3.858
getPlots	5.918	0.201	6.155
getResults	4.500	0.205	4.754
getVR	2.779	0.198	3.059