BioC 3.4: CHECK report for fastLiquidAssociation on zin1

Package: fastLiquidAssociation

Version: 1.9.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings fastLiquidAssociation_1.9.0.tar.gz

StartedAt: 2016-09-20 06:18:17 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 06:20:13 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 116.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: fastLiquidAssociation.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings fastLiquidAssociation_1.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/fastLiquidAssociation.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 ‘fastLiquidAssociation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fastLiquidAssociation’ version ‘1.9.0’
* 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 ‘fastLiquidAssociation’ 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 ... WARNING
'::' or ':::' import not declared from: ‘doParallel’
':::' call which should be '::': ‘doParallel:::stopImplicitCluster’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
jobsplit: no visible global function definition for ‘head’
wrapper: no visible global function definition for ‘head’
wrapper: no visible global function definition for ‘na.omit’
mass.CNM,matrix-data.frame: no visible global function definition for
  ‘head’
Undefined global functions or variables:
  head na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "head")
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 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
fastLiquidAssociation-package 1.276  0.112  17.032
fastboots.GLA-methods         0.680  0.136  14.372
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/fastLiquidAssociation.Rcheck/00check.log’
for details.

* installing *source* package ‘fastLiquidAssociation’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (fastLiquidAssociation)

name	user	system	elapsed
fastLiquidAssociation-package	1.276	0.112	17.032
fastMLA-methods	0.696	0.224	0.403
fastboots.GLA-methods	0.680	0.136	14.372
mass.CNM-methods	0.628	0.076	0.684