BioC 3.5: CHECK report for MODA on oaxaca

Package: MODA

Version: 1.1.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MODA_1.1.2.tar.gz

StartedAt: 2017-03-04 05:59:48 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 06:02:01 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 132.4 seconds

RetCode: 0

Status:  OK

CheckDir: MODA.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 MODA_1.1.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MODA.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MODA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MODA’ version ‘1.1.2’
* 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 ‘MODA’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
MIcondition: no visible binding for global variable ‘pwd’
WeightedModulePartitionSpectral: no visible binding for global variable
  ‘indicator’
Undefined global functions or variables:
  indicator pwd
* 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’ ... NOTE
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/MODA.Rcheck/00check.log’
for details.

* installing *source* package ‘MODA’ ...
** 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 (MODA)

name	user	system	elapsed
CompareAllNets	2.706	0.078	2.814
PartitionDensity	0.085	0.003	0.087
PartitionModularity	0.079	0.001	0.080
WeightedModulePartitionAmoutain	2.103	0.137	2.240
WeightedModulePartitionHierarchical	0.521	0.017	0.540
WeightedModulePartitionLouvain	0.186	0.006	0.192
WeightedModulePartitionSpectral	1.743	0.017	1.760
comparemodulestwonets	0.823	0.044	0.871
datExpr1	0.004	0.000	0.004
datExpr2	0.004	0.000	0.004