BioC 3.3: CHECK report for RTCA on morelia

Package: RTCA

Version: 1.23.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RTCA_1.23.0.tar.gz

StartedAt: 2016-04-21 07:12:22 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 07:12:56 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 34.5 seconds

RetCode: 0

Status:  OK

CheckDir: RTCA.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 RTCA_1.23.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/RTCA.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTCA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTCA’ version ‘1.23.0’
* 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 ‘RTCA’ can be installed ... [2s/2s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
myheatmap.2: no visible binding for global variable ‘dist’
myheatmap.2: no visible binding for global variable ‘hclust’
myheatmap.2: no visible global function definition for ‘median’
myheatmap.2: no visible global function definition for
  ‘order.dendrogram’
myheatmap.2: no visible global function definition for ‘as.dendrogram’
myheatmap.2: no visible global function definition for ‘reorder’
myheatmap.2: no visible global function definition for ‘image’
myheatmap.2: no visible global function definition for ‘axis’
myheatmap.2: no visible global function definition for ‘mtext’
myheatmap.2: no visible global function definition for ‘rect’
myheatmap.2: no visible global function definition for ‘text’
myheatmap.2: no visible global function definition for ‘plot.new’
myheatmap.2: no visible global function definition for ‘density’
myheatmap.2: no visible global function definition for ‘hist’
Undefined global functions or variables:
  as.dendrogram axis density dist hclust hist image median mtext
  order.dendrogram plot.new rect reorder text
Consider adding
  importFrom("graphics", "axis", "hist", "image", "mtext", "plot.new",
             "rect", "text")
  importFrom("stats", "as.dendrogram", "density", "dist", "hclust",
             "median", "order.dendrogram", "reorder")
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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/5s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘essentials.R’ [2s/2s]
 [3s/3s] 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/RTCA.Rcheck/00check.log’
for details.

* installing *source* package ‘RTCA’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘time’ from package ‘stats’ in package ‘RTCA’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘RTCA’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RTCA)

name	user	system	elapsed
RTCA-class	0.151	0.001	0.152
RTCAtimeline-class	0.002	0.000	0.002
alphaNames	0.004	0.000	0.005
combineRTCA	0.292	0.003	0.294
controlView	0.174	0.002	0.177
derivativeTransform	0.189	0.005	0.194
factor2numeric	0.001	0.001	0.002
interpolationTransform	0.336	0.011	0.347
nearestTimeIndex	0.238	0.009	0.248
parseRTCA	0.912	0.015	0.927
plateView	0.328	0.002	0.330
plotGridEffect	0.368	0.003	0.371
ratioTransform	0.142	0.002	0.144
rgrTransform	0.348	0.012	0.360
sliceRTCA	0.162	0.001	0.164
smoothTransform	0.275	0.004	0.279
spectramaxImport	0.016	0.003	0.019