BioC 3.5: CHECK report for DaMiRseq on veracruz2

Package: DaMiRseq

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DaMiRseq_1.0.0.tar.gz

StartedAt: 2017-10-18 02:29:51 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:37:28 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 457.2 seconds

RetCode: 0

Status:  OK

CheckDir: DaMiRseq.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 DaMiRseq_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/DaMiRseq.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DaMiRseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DaMiRseq’ version ‘1.0.0’
* package encoding: UTF-8
* 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 ‘DaMiRseq’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
* 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
DaMiR.Allplot: warning in pheatmap(sampleDistMatrix,
  clustering_distance_rows = mydist, clustering_distance_cols = mydist,
  col = colors, breaks = seque, annotation_col = df): partial argument
  match of 'col' to 'color'
DaMiR.Clustplot: warning in pheatmap(count_data,
  clustering_distance_rows = d_r, clustering_distance_cols = d_c, scale
  = "row", col = colors, annotation_col = df): partial argument match
  of 'col' to 'color'
DaMiR.Allplot: no visible binding for global variable ‘X1’
DaMiR.Allplot: no visible binding for global variable ‘X2’
DaMiR.EnsembleLearning: no visible binding for global variable
  ‘Predictors’
DaMiR.EnsembleLearning: no visible binding for global variable
  ‘Accuracy’
DaMiR.MDSplot: no visible binding for global variable ‘X1’
DaMiR.MDSplot: no visible binding for global variable ‘X2’
Undefined global functions or variables:
  Accuracy Predictors X1 X2
* 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 ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
DaMiR.FSort            28.689  0.155  29.758
DaMiR.EnsembleLearning 14.581  0.085  15.029
DaMiR.Allplot           5.802  0.121   6.080
DaMiR.FSelect           4.675  0.283   5.093
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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-3.5-bioc/meat/DaMiRseq.Rcheck/00check.log’
for details.

* installing *source* package ‘DaMiRseq’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DaMiRseq)

name	user	system	elapsed
DaMiR.Allplot	5.802	0.121	6.080
DaMiR.Clustplot	0.973	0.011	1.011
DaMiR.EnsembleLearning	14.581	0.085	15.029
DaMiR.FBest	0.055	0.002	0.058
DaMiR.FReduct	0.019	0.002	0.023
DaMiR.FSelect	4.675	0.283	5.093
DaMiR.FSort	28.689	0.155	29.758
DaMiR.MDSplot	0.292	0.004	0.300
DaMiR.SV	0.770	0.052	0.839
DaMiR.SVadjust	0.112	0.011	0.127
DaMiR.corrplot	0.054	0.003	0.063
DaMiR.goldenDice	0.002	0.000	0.002