Package: splineTimeR

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:splineTimeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings splineTimeR_1.8.0.tar.gz

StartedAt: 2018-10-17 00:14:01 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:16:48 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 167.8 seconds

RetCode: 0

Status:  OK

CheckDir: splineTimeR.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:splineTimeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings splineTimeR_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/splineTimeR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘splineTimeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘splineTimeR’ version ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Biobase’ ‘igraph’ ‘limma’ ‘GSEABase’ ‘gtools’ ‘splines’ ‘GeneNet’
  ‘longitudinal’ ‘FIs’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘splineTimeR’ 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
networkProperties: no visible global function definition for ‘is’
networkProperties: no visible global function definition for ‘data’
networkProperties: no visible binding for global variable ‘FIs’
networkProperties: no visible global function definition for ‘pdf’
networkProperties: no visible global function definition for ‘par’
networkProperties: no visible global function definition for ‘plot’
networkProperties: no visible global function definition for ‘ecdf’
networkProperties: no visible global function definition for ‘hist’
networkProperties: no visible global function definition for ‘dev.off’
networkProperties: no visible global function definition for ‘lm’
networkProperties: no visible global function definition for ‘abline’
networkProperties: no visible global function definition for ‘legend’
networkProperties: no visible global function definition for ‘axis’
pathEnrich: no visible global function definition for ‘is’
pathEnrich: no visible global function definition for ‘p.adjust’
pathEnrich: no visible global function definition for ‘write.table’
splineDiffExprs: no visible global function definition for ‘is’
splineDiffExprs: no visible global function definition for
  ‘model.matrix’
splineNetRecon: no visible global function definition for ‘is’
splinePlot: no visible global function definition for ‘is’
splinePlot: no visible global function definition for ‘model.matrix’
splinePlot: no visible global function definition for ‘predict’
splinePlot: no visible global function definition for ‘pdf’
splinePlot: no visible global function definition for ‘plot’
splinePlot: no visible global function definition for ‘points’
splinePlot: no visible global function definition for ‘legend’
splinePlot: no visible global function definition for ‘lines’
splinePlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  FIs abline axis data dev.off ecdf hist is legend lines lm
  model.matrix p.adjust par pdf plot points predict write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "hist", "legend", "lines",
             "par", "plot", "points")
  importFrom("methods", "is")
  importFrom("stats", "ecdf", "lm", "model.matrix", "p.adjust",
             "predict")
  importFrom("utils", "data", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
networkProperties 28.882  1.738  31.168
splineNetRecon    25.216  1.917  27.595
* 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-3.7-bioc/meat/splineTimeR.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 splineTimeR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘splineTimeR’ ...
** 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 (splineTimeR)

name	user	system	elapsed
TCsimData	0.036	0.006	0.046
networkProperties	28.882	1.738	31.168
pathEnrich	0.286	0.016	0.305
splineDiffExprs	0.073	0.014	0.088
splineNetRecon	25.216	1.917	27.595
splinePlot	0.058	0.008	0.068