BioC 3.5: CHECK report for Pigengene on toluca2

Package: Pigengene

Version: 1.1.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Pigengene_1.1.10.tar.gz

StartedAt: 2017-04-23 08:00:20 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 08:07:28 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 427.9 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_1.1.10.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 r72187)
* 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 ‘1.1.10’
* 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  73.949  2.936  79.017
one.step.pigengene 66.857  2.921  70.669
module.heatmap     27.981  2.077  30.892
compact.tree       16.744  1.812  18.846
make.decision.tree 16.630  1.562  18.423
plot.pigengene      9.747  0.735  10.643
compute.pigengene   7.897  0.718   8.726
project.eigen       7.418  0.653   8.189
pigengene           6.690  0.693   7.464
wgcna.one.step      7.104  0.073   7.228
learn.bn            6.132  0.071   6.221
* 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	73.949	2.936	79.017
aml	0.163	0.007	0.175
balance	0.885	0.182	1.105
calculate.beta	0.653	0.028	0.761
check.pigengene.input	0.058	0.009	0.077
compact.tree	16.744	1.812	18.846
compute.pigengene	7.897	0.718	8.726
dcor.matrix	0.196	0.044	0.244
draw.bn	0.001	0.000	0.001
eigengenes33	0.144	0.003	0.149
gene.mapping	2.269	0.108	2.380
get.fitted.leaf	0.798	0.052	0.849
get.genes	0.767	0.039	0.806
get.used.features	0.793	0.050	0.842
learn.bn	6.132	0.071	6.221
make.decision.tree	16.630	1.562	18.423
mds	0.151	0.008	0.161
module.heatmap	27.981	2.077	30.892
one.step.pigengene	66.857	2.921	70.669
pheatmap.type	0.309	0.005	0.326
pigengene	6.690	0.693	7.464
plot.pigengene	9.747	0.735	10.643
preds.at	1.038	0.063	1.184
project.eigen	7.418	0.653	8.189
pvalues.manova	0.034	0.002	0.035
wgcna.one.step	7.104	0.073	7.228