BioC 3.4: CHECK report for Pigengene on malbec1

Package: Pigengene

Version: 1.0.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Pigengene_1.0.0.tar.gz

StartedAt: 2017-04-15 00:25:42 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:30:26 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 284.6 seconds

RetCode: 0

Status:  OK

CheckDir: Pigengene.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Pigengene_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/Pigengene.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.0.0’
* 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")

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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
one.step.pigengene 51.316  0.260  51.608
Pigengene-package  48.936  0.272  49.239
module.heatmap     15.408  0.020  15.441
make.decision.tree 10.840  0.036  10.885
compact.tree        9.740  0.016   9.762
wgcna.one.step      6.848  0.008   6.861
compute.pigengene   5.108  0.016   5.128
plot.pigengene      5.068  0.024   5.103
* 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-3.4-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	48.936	0.272	49.239
aml	0.116	0.000	0.115
balance	0.248	0.004	0.252
calculate.beta	0.200	0.000	0.197
check.pigengene.input	0.044	0.000	0.044
compact.tree	9.740	0.016	9.762
compute.pigengene	5.108	0.016	5.128
dcor.matrix	0.116	0.004	0.121
draw.bn	0.000	0.000	0.001
eigengenes33	0.368	0.000	0.368
gene.mapping	1.248	0.020	1.270
get.fitted.leaf	0.556	0.004	0.559
get.genes	0.588	0.004	0.592
get.used.features	0.580	0.004	0.586
learn.bn	4.820	0.072	4.897
make.decision.tree	10.840	0.036	10.885
mds	0.104	0.000	0.103
module.heatmap	15.408	0.020	15.441
one.step.pigengene	51.316	0.260	51.608
pheatmap.type	0.208	0.008	0.218
pigengene	4.912	0.052	4.967
plot.pigengene	5.068	0.024	5.103
preds.at	0.648	0.004	0.651
project.eigen	4.248	0.008	4.257
pvalues.manova	0.020	0.000	0.022
wgcna.one.step	6.848	0.008	6.861