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CHECK report for TSCAN on celaya2

This page was generated on 2020-01-16 13:39:54 -0500 (Thu, 16 Jan 2020).

Package 1757/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TSCAN 1.25.0
Zhicheng Ji
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/TSCAN
Branch: master
Last Commit: 2e8d252
Last Changed Date: 2019-10-29 13:38:04 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: TSCAN
Version: 1.25.0
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_1.25.0.tar.gz
StartedAt: 2020-01-16 09:40:30 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 09:42:33 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 122.1 seconds
RetCode: 0
Status:  OK 
CheckDir: TSCAN.Rcheck
Warnings: 0

Command output

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### Running 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_1.25.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/TSCAN.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.25.0’
* 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 (user + system) or elapsed time > 5s
           user system elapsed
difftest 10.065   0.37  12.258
* 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-3.11-bioc/meat/TSCAN.Rcheck/00check.log’
for details.



Installation output

TSCAN.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TSCAN
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘TSCAN’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TSCAN)

Tests output


Example timings

TSCAN.Rcheck/TSCAN-Ex.timings

nameusersystemelapsed
TSCANorder2.2320.2662.498
TSCANui0.0000.0000.001
difftest10.065 0.37012.258
exprmclust1.9210.2192.140
orderscore1.9130.2222.135
plotmclust2.8130.3383.153
preprocess1.6410.1971.837
singlegeneplot2.4040.1412.578