BioC 3.5: CHECK report for Pigengene on oaxaca

Package: Pigengene

Version: 1.1.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Pigengene_1.1.2.tar.gz

StartedAt: 2017-03-04 07:07:27 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 07:16:09 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 522.3 seconds

RetCode: 0

Status:  OK

CheckDir: Pigengene.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Pigengene_1.1.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Pigengene.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.1.2’
* 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")

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
Consider adding
  importFrom("stats", "as.formula", "oneway.test")
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
module.heatmap     151.920 13.872 161.620
one.step.pigengene  66.267  3.188  69.829
Pigengene-package   63.989  2.807  66.994
compact.tree        14.793  1.659  17.203
make.decision.tree  13.650  1.433  15.098
plot.pigengene       9.477  0.738  10.269
compute.pigengene    7.198  0.658   7.876
project.eigen        7.061  0.645   7.730
pigengene            6.442  0.661   7.111
wgcna.one.step       6.636  0.060   6.701
learn.bn             6.014  0.076   6.091
* 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
  ‘/Users/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	63.989	2.807	66.994
aml	0.147	0.006	0.180
balance	0.969	0.195	1.165
calculate.beta	0.495	0.016	0.512
check.pigengene.input	0.045	0.006	0.050
compact.tree	14.793	1.659	17.203
compute.pigengene	7.198	0.658	7.876
dcor.matrix	0.185	0.052	0.256
draw.bn	0.001	0.001	0.000
eigengenes33	0.123	0.003	0.128
gene.mapping	2.036	0.087	2.180
get.fitted.leaf	0.700	0.036	0.737
get.genes	0.782	0.044	0.826
get.used.features	0.788	0.035	0.825
learn.bn	6.014	0.076	6.091
make.decision.tree	13.650	1.433	15.098
mds	0.140	0.007	0.147
module.heatmap	151.920	13.872	161.620
one.step.pigengene	66.267	3.188	69.829
pheatmap.type	0.298	0.004	0.302
pigengene	6.442	0.661	7.111
plot.pigengene	9.477	0.738	10.269
preds.at	0.951	0.058	1.010
project.eigen	7.061	0.645	7.730
pvalues.manova	0.038	0.002	0.040
wgcna.one.step	6.636	0.060	6.701