BioC 3.1: CHECK report for RNAinteract on morelia

Package: RNAinteract

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RNAinteract_1.16.0.tar.gz

StartedAt: 2015-10-09 05:45:23 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:48:32 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 188.7 seconds

RetCode: 0

Status:  OK

CheckDir: RNAinteract.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 RNAinteract_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/RNAinteract.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAinteract/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RNAinteract’ version ‘1.16.0’
* 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 ‘RNAinteract’ can be installed ... [17s/17s] 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
Namespace in Imports field not imported from: ‘ICS’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘Biobase’ ‘abind’ ‘locfit’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bindscreens: no visible global function definition for ‘abind’
createCellHTSFromFiles: no visible binding for global variable
  ‘assayDataNew’
normalizePlateEffect: no visible global function definition for
  ‘locfit’
normalizePlateEffect: no visible binding for global variable
  ‘locfit.robust’
* 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 ... [11s/11s] OK
* 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-3.1-bioc/meat/RNAinteract.Rcheck/00check.log’
for details.

* installing *source* package ‘RNAinteract’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (RNAinteract)

name	user	system	elapsed
RNAinteract-class	0.003	0.001	0.004
bindsamples	0.160	0.023	0.184
computePI	0.022	0.003	0.026
computePValues	0.176	0.008	0.183
embedPCA	0.016	0.001	0.017
estimateMainEffect	0.834	0.047	0.881
getData	0.136	0.002	0.139
getMain	0.008	0.002	0.009
getReplicateData	0.006	0.001	0.007
getSampleNames	0.005	0.000	0.006
getScale	0.004	0.001	0.003
grid.sgiHeatmap	0.095	0.009	0.104
normalizeMainEffectQuery	0.080	0.004	0.084
normalizeMainEffectTemplate	0.060	0.001	0.060
normalizePlateEffect	1.725	0.335	2.061
plotDoublePerturbation	0.072	0.009	0.082
plotHeatmap	0.057	0.017	0.074
reportAnnotation	0.025	0.005	0.030
sgi	0.008	0.000	0.008
sgisubset	0.013	0.000	0.014
startReport	0.020	0.002	0.022
summarizeSamples	0.08	0.00	0.08