BioC 3.5: CHECK report for Pigengene on malbec2

Package: Pigengene

Version: 1.2.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Pigengene_1.2.0.tar.gz

StartedAt: 2017-08-16 01:17:21 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:22:27 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 306.5 seconds

RetCode: 0

Status:  OK

CheckDir: Pigengene.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Pigengene_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/Pigengene.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pigengene/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pigengene’ version ‘1.2.0’
* 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 ‘Pigengene’ 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 ... NOTE
'library' or 'require' calls in package code:
  ‘AnnotationDbi’ ‘biomaRt’ ‘energy’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File ‘Pigengene/R/bn.calculation.R’:
  assignInNamespace("supported.clusters", fixArgs, "bnlearn")

check.pigengene.input: no visible global function definition for
  ‘setNames’
welch.pvalue: no visible global function definition for ‘as.formula’
welch.pvalue: no visible global function definition for ‘oneway.test’
Undefined global functions or variables:
  as.formula oneway.test setNames
Consider adding
  importFrom("stats", "as.formula", "oneway.test", "setNames")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
Pigengene-package  53.076  0.304  53.475
one.step.pigengene 52.728  0.252  53.016
module.heatmap     15.056  0.016  15.085
make.decision.tree 11.348  0.032  11.391
compact.tree       10.452  0.008  10.473
wgcna.one.step      7.816  0.004   7.825
compute.pigengene   6.104  0.024   6.135
plot.pigengene      5.284  0.044   5.332
learn.bn            5.200  0.112   5.319
* 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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/Pigengene.Rcheck/00check.log’
for details.

* installing *source* package ‘Pigengene’ ...
** 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 (Pigengene)

name	user	system	elapsed
Pigengene-package	53.076	0.304	53.475
aml	0.124	0.004	0.148
balance	0.252	0.004	0.257
calculate.beta	2.688	0.008	2.696
check.pigengene.input	0.044	0.000	0.043
compact.tree	10.452	0.008	10.473
compute.pigengene	6.104	0.024	6.135
dcor.matrix	0.212	0.008	0.235
draw.bn	0	0	0
eigengenes33	0.424	0.000	0.423
gene.mapping	1.300	0.044	1.382
get.fitted.leaf	0.648	0.000	0.652
get.genes	0.540	0.000	0.542
get.used.features	0.492	0.004	0.495
learn.bn	5.200	0.112	5.319
make.decision.tree	11.348	0.032	11.391
mds	0.100	0.000	0.102
module.heatmap	15.056	0.016	15.085
one.step.pigengene	52.728	0.252	53.016
pheatmap.type	0.216	0.000	0.216
pigengene	4.364	0.024	4.396
plot.pigengene	5.284	0.044	5.332
preds.at	0.620	0.016	0.638
project.eigen	4.068	0.008	4.081
pvalues.manova	0.024	0.000	0.023
wgcna.one.step	7.816	0.004	7.825