Package: Pigengene

Version: 1.4.20

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Pigengene_1.4.20.tar.gz

StartedAt: 2018-04-12 01:49:04 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:54:11 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 307.4 seconds

RetCode: 0

Status:  OK

CheckDir: Pigengene.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Pigengene_1.4.20.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/Pigengene.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.20’
* 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.
Unexported object imported by a ':::' call: ‘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 ... 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  55.060  0.576  55.685
one.step.pigengene 53.500  0.464  54.013
module.heatmap     14.352  0.020  14.384
compact.tree       11.440  0.020  11.469
make.decision.tree 11.156  0.044  11.212
wgcna.one.step      7.220  0.008   7.229
compute.pigengene   6.888  0.016   6.909
learn.bn            5.472  0.176   5.658
plot.pigengene      5.096  0.040   5.140
* 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-3.6-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	55.060	0.576	55.685
aml	0.136	0.004	0.141
balance	0.316	0.032	0.348
calculate.beta	2.756	0.028	2.788
check.nas	0.048	0.000	0.045
check.pigengene.input	0.036	0.008	0.045
compact.tree	11.440	0.020	11.469
compute.pigengene	6.888	0.016	6.909
dcor.matrix	0.200	0.004	0.218
draw.bn	0	0	0
eigengenes33	0.1	0.0	0.1
gene.mapping	1.260	0.052	1.349
get.fitted.leaf	0.552	0.000	0.555
get.genes	0.544	0.004	0.546
get.used.features	0.556	0.012	0.568
learn.bn	5.472	0.176	5.658
make.decision.tree	11.156	0.044	11.212
mds	0.108	0.000	0.109
module.heatmap	14.352	0.020	14.384
one.step.pigengene	53.500	0.464	54.013
pheatmap.type	0.220	0.004	0.223
pigengene	4.684	0.124	4.810
plot.pigengene	5.096	0.040	5.140
preds.at	0.8	0.0	0.8
project.eigen	4.524	0.032	4.561
pvalues.manova	0.024	0.000	0.022
wgcna.one.step	7.220	0.008	7.229