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: 2017-10-18 01:29:21 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:34:27 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 306.0 seconds

RetCode: 0

Status:  OK

CheckDir: Pigengene.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Pigengene_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/Pigengene.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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  54.508  0.312  55.023
one.step.pigengene 51.408  0.228  51.666
module.heatmap     14.340  0.020  14.370
make.decision.tree 10.928  0.016  10.952
compact.tree       10.804  0.000  10.814
wgcna.one.step      7.876  0.000   7.878
compute.pigengene   6.244  0.016   6.261
learn.bn            5.600  0.144   5.738
* 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	54.508	0.312	55.023
aml	0.164	0.000	0.186
balance	0.376	0.004	0.378
calculate.beta	2.672	0.000	2.674
check.pigengene.input	0.040	0.000	0.043
compact.tree	10.804	0.000	10.814
compute.pigengene	6.244	0.016	6.261
dcor.matrix	0.184	0.000	0.186
draw.bn	0	0	0
eigengenes33	0.100	0.000	0.103
gene.mapping	1.336	0.056	1.439
get.fitted.leaf	0.556	0.008	0.565
get.genes	0.552	0.012	0.564
get.used.features	0.604	0.004	0.609
learn.bn	5.600	0.144	5.738
make.decision.tree	10.928	0.016	10.952
mds	0.1	0.0	0.1
module.heatmap	14.34	0.02	14.37
one.step.pigengene	51.408	0.228	51.666
pheatmap.type	0.220	0.000	0.221
pigengene	4.556	0.032	4.590
plot.pigengene	4.800	0.008	4.818
preds.at	0.628	0.008	0.636
project.eigen	4.500	0.016	4.519
pvalues.manova	0.024	0.000	0.021
wgcna.one.step	7.876	0.000	7.878