Package: TurboNorm

Version: 1.30.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:TurboNorm.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings TurboNorm_1.30.0.tar.gz

StartedAt: 2019-04-16 03:34:13 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:35:11 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 58.2 seconds

RetCode: 0

Status:  OK

CheckDir: TurboNorm.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:TurboNorm.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings TurboNorm_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/TurboNorm.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TurboNorm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TurboNorm’ version ‘1.30.0’
* 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 ‘TurboNorm’ 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 ... NOTE
Packages in Depends field not imported from:
  ‘convert’ ‘limma’ ‘marray’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
normalize.AffyBatch.pspline: no visible global function definition for
  ‘intensity<-’
pspline: no visible global function definition for ‘as’
pspline: no visible global function definition for ‘maRb<-’
pspline: no visible global function definition for ‘maGb<-’
pspline: no visible global function definition for ‘maA’
pspline: no visible global function definition for ‘maM’
pspline: no visible global function definition for ‘layout’
pspline: no visible global function definition for ‘maM<-’
pspline: no visible global function definition for ‘plot’
pspline: no visible global function definition for ‘lines’
turbotrend: no visible global function definition for ‘median’
Undefined global functions or variables:
  as intensity<- layout lines maA maGb<- maM maM<- maRb<- median plot
Consider adding
  importFrom("graphics", "layout", "lines", "plot")
  importFrom("methods", "as")
  importFrom("stats", "median")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
normalize.pspline 17.416  0.244  18.639
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/TurboNorm.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL TurboNorm
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘TurboNorm’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Rinit.c -o Rinit.o
Rinit.c:8:40: warning: missing braces around initializer [-Wmissing-braces]
 static const R_CMethodDef cMethods[] = {
                                        ^
Rinit.c:8:40: note: (near initialization for ‘cMethods’)
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c binners.c -o binners.o
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o TurboNorm.so Rinit.o binners.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/TurboNorm/libs
** 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 (TurboNorm)

name	user	system	elapsed
methylation	0.112	0.000	0.110
normalize.pspline	17.416	0.244	18.639
panel.pspline	2.148	0.028	2.186
pspline	1.840	0.000	1.845
turbotrend	0.424	0.000	0.423