Package: TSCAN

Version: 1.16.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings TSCAN_1.16.0.tar.gz

StartedAt: 2018-04-12 03:27:55 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:28:58 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 63.9 seconds

RetCode: 0

Status:  OK

CheckDir: TSCAN.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings TSCAN_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/TSCAN.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 ‘TSCAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TSCAN’ 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 ‘TSCAN’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
difftest : <anonymous>: no visible global function definition for
  ‘pchisq’
difftest: no visible global function definition for ‘p.adjust’
exprmclust: no visible global function definition for ‘prcomp’
exprmclust : <anonymous>: no visible global function definition for
  ‘lm’
exprmclust: no visible global function definition for ‘dist’
plotmclust: no visible binding for global variable ‘pca_dim_1’
plotmclust: no visible binding for global variable ‘pca_dim_2’
plotmclust: no visible binding for global variable ‘sample_name’
preprocess: no visible binding for global variable ‘sd’
preprocess: no visible global function definition for ‘hclust’
preprocess: no visible global function definition for ‘dist’
preprocess: no visible global function definition for ‘cutree’
preprocess: no visible global function definition for ‘aggregate’
singlegeneplot: no visible global function definition for
  ‘fitted.values’
singlegeneplot: no visible binding for global variable ‘predict’
Undefined global functions or variables:
  aggregate cutree dist fitted.values hclust lm p.adjust pca_dim_1
  pca_dim_2 pchisq prcomp predict sample_name sd
Consider adding
  importFrom("stats", "aggregate", "cutree", "dist", "fitted.values",
             "hclust", "lm", "p.adjust", "pchisq", "prcomp", "predict",
             "sd")
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
difftest 5.552  0.032   5.588
* 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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/TSCAN.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
TSCANorder	1.884	0.064	1.947
TSCANui	0	0	0
difftest	5.552	0.032	5.588
exprmclust	1.172	0.008	1.182
orderscore	1.168	0.028	1.196
plotmclust	2.056	0.020	2.079
preprocess	0.952	0.024	0.978
singlegeneplot	2.084	0.016	2.102