BioC 3.6: CHECK report for Pigengene on malbec1

Package: Pigengene

Version: 1.3.4

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Pigengene_1.3.4.tar.gz

StartedAt: 2017-08-16 01:23:39 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:28:41 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 302.1 seconds

RetCode: 0

Status:  OK

CheckDir: Pigengene.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Pigengene_1.3.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-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 ‘1.3.4’
* 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  52.716  0.312  53.071
one.step.pigengene 51.400  0.268  51.696
module.heatmap     14.292  0.008  14.309
make.decision.tree 11.156  0.072  11.239
compact.tree       10.280  0.008  10.295
wgcna.one.step      7.812  0.008   7.823
compute.pigengene   6.032  0.016   6.049
learn.bn            5.216  0.132   5.348
* 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-3.6-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	52.716	0.312	53.071
aml	0.124	0.000	0.126
balance	0.232	0.020	0.253
calculate.beta	2.672	0.008	2.681
check.pigengene.input	0.044	0.000	0.044
compact.tree	10.280	0.008	10.295
compute.pigengene	6.032	0.016	6.049
dcor.matrix	0.168	0.000	0.177
draw.bn	0.004	0.000	0.001
eigengenes33	0.412	0.004	0.417
gene.mapping	1.160	0.044	1.227
get.fitted.leaf	0.524	0.000	0.524
get.genes	0.508	0.000	0.508
get.used.features	0.480	0.008	0.488
learn.bn	5.216	0.132	5.348
make.decision.tree	11.156	0.072	11.239
mds	0.108	0.000	0.109
module.heatmap	14.292	0.008	14.309
one.step.pigengene	51.400	0.268	51.696
pheatmap.type	0.22	0.00	0.22
pigengene	4.860	0.064	4.928
plot.pigengene	4.944	0.004	4.953
preds.at	0.612	0.004	0.614
project.eigen	4.164	0.020	4.183
pvalues.manova	0.020	0.000	0.022
wgcna.one.step	7.812	0.008	7.823