BioC 3.5: CHECK report for Pigengene on veracruz2

Package: Pigengene

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Pigengene_1.2.0.tar.gz

StartedAt: 2017-10-18 07:18:02 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 07:24:43 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 401.2 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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Pigengene.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.2.0’
* 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 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
Pigengene-package  63.725  2.745  68.462
one.step.pigengene 60.858  2.795  65.664
module.heatmap     25.369  1.508  28.721
make.decision.tree 15.456  0.980  16.964
compact.tree       14.840  0.902  16.181
compute.pigengene   9.149  0.581  10.005
plot.pigengene      8.595  0.647   9.571
project.eigen       6.870  0.618   7.752
wgcna.one.step      7.362  0.106   7.717
pigengene           5.892  0.561   6.688
learn.bn            5.710  0.096   6.116
* 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	63.725	2.745	68.462
aml	0.160	0.006	0.169
balance	0.945	0.144	1.111
calculate.beta	2.605	0.034	2.696
check.pigengene.input	0.045	0.005	0.050
compact.tree	14.840	0.902	16.181
compute.pigengene	9.149	0.581	10.005
dcor.matrix	0.224	0.045	0.280
draw.bn	0.001	0.000	0.001
eigengenes33	0.131	0.003	0.138
gene.mapping	1.866	0.108	2.022
get.fitted.leaf	0.898	0.056	0.975
get.genes	0.846	0.052	0.916
get.used.features	0.792	0.047	0.945
learn.bn	5.710	0.096	6.116
make.decision.tree	15.456	0.980	16.964
mds	0.140	0.007	0.153
module.heatmap	25.369	1.508	28.721
one.step.pigengene	60.858	2.795	65.664
pheatmap.type	0.230	0.005	0.243
pigengene	5.892	0.561	6.688
plot.pigengene	8.595	0.647	9.571
preds.at	0.952	0.073	1.050
project.eigen	6.870	0.618	7.752
pvalues.manova	0.031	0.001	0.033
wgcna.one.step	7.362	0.106	7.717