Package: Pigengene

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Pigengene_1.6.0.tar.gz

StartedAt: 2018-10-16 23:15:18 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:22:23 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 425.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Pigengene.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Pigengene_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/Pigengene.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.6.0’
* 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 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.
':::' call which should be '::': ‘C50:::as.party.C5.0’
  See the note in ?`:::` about the use of this operator.
* 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 ... WARNING
Missing link or links in documentation object 'Pigengene-package.Rd':
  ‘[WGCNA]{WGCNA-package}’

Missing link or links in documentation object 'calculate.beta.Rd':
  ‘[WGCNA]{WGCNA-package}’

Missing link or links in documentation object 'compute.pigengene.Rd':
  ‘[WGCNA]{WGCNA-package}’

Missing link or links in documentation object 'learn.bn.Rd':
  ‘[WGCNA]{WGCNA-package}’

Missing link or links in documentation object 'one.step.pigengene.Rd':
  ‘[WGCNA]{WGCNA-package}’

Missing link or links in documentation object 'wgcna.one.step.Rd':
  ‘[WGCNA]{WGCNA-package}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
Pigengene-package  71.459  4.066  75.783
one.step.pigengene 68.690  4.000  72.574
module.heatmap     25.309  1.960  27.635
make.decision.tree 17.729  1.606  19.482
compact.tree       16.554  1.727  18.348
plot.pigengene      8.538  0.852   9.340
compute.pigengene   8.101  0.623   8.723
wgcna.one.step      8.415  0.111   8.542
pigengene           7.092  0.739   7.894
project.eigen       6.822  0.735   7.540
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/Pigengene.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Pigengene
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘Pigengene’ ...
** R
** data
** inst
** byte-compile and prepare 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	71.459	4.066	75.783
aml	0.351	0.020	0.365
balance	0.782	0.170	0.960
calculate.beta	2.993	0.102	3.123
check.nas	0.067	0.010	0.077
check.pigengene.input	0.065	0.009	0.075
compact.tree	16.554	1.727	18.348
compute.pigengene	8.101	0.623	8.723
dcor.matrix	0.184	0.050	0.237
draw.bn	0.001	0.000	0.001
eigengenes33	0.133	0.004	0.139
gene.mapping	1.386	0.125	1.516
get.fitted.leaf	0.966	0.067	1.027
get.genes	0.790	0.061	0.842
get.used.features	0.856	0.067	0.919
learn.bn	4.586	0.135	4.714
make.decision.tree	17.729	1.606	19.482
mds	0.137	0.010	0.149
module.heatmap	25.309	1.960	27.635
one.step.pigengene	68.690	4.000	72.574
pheatmap.type	0.648	0.020	0.668
pigengene	7.092	0.739	7.894
plot.pigengene	8.538	0.852	9.340
preds.at	0.966	0.082	1.042
project.eigen	6.822	0.735	7.540
pvalues.manova	0.123	0.017	0.134
wgcna.one.step	8.415	0.111	8.542