Package: TSCAN

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TSCAN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TSCAN_1.20.0.tar.gz

StartedAt: 2019-04-16 03:15:52 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:17:26 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 93.3 seconds

RetCode: 0

Status:  OK

CheckDir: TSCAN.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TSCAN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TSCAN_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/TSCAN.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.20.0’
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
difftest 8.861  0.139   9.142
* 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-3.8-bioc/meat/TSCAN.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TSCAN
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘TSCAN’ ...
** R
** data
** inst
** byte-compile and prepare 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	2.827	0.116	2.978
TSCANui	0	0	0
difftest	8.861	0.139	9.142
exprmclust	2.844	0.074	4.029
orderscore	2.535	0.090	2.842
plotmclust	3.003	0.110	3.137
preprocess	2.537	0.072	3.067
singlegeneplot	3.154	0.054	4.385