Package: SSPA

Version: 2.22.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:SSPA.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings SSPA_2.22.1.tar.gz

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

EndedAt: 2019-04-16 03:16:44 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 40.7 seconds

RetCode: 0

Status:  OK

CheckDir: SSPA.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:SSPA.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings SSPA_2.22.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/SSPA.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 ‘SSPA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SSPA’ version ‘2.22.1’
* 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 ‘SSPA’ 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
Package in Depends field not imported from: ‘methods’
  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
Dn: no visible global function definition for ‘points’
Gnhat: no visible global function definition for ‘qnorm’
Gnhat : <anonymous>: no visible global function definition for ‘pnorm’
Hntilde: no visible global function definition for ‘dbinom’
deconvolution: no visible global function definition for ‘approx’
findroot: no visible global function definition for ‘curve’
findroot: no visible global function definition for ‘grid’
findroot: no visible global function definition for ‘abline’
picardplot: no visible global function definition for ‘points’
picardplot: no visible global function definition for ‘abline’
pilotData: no visible global function definition for ‘new’
qbitri: no visible global function definition for ‘runif’
rbitri: no visible global function definition for ‘runif’
regularization: no visible global function definition for ‘points’
regularization: no visible global function definition for ‘par’
sampleSize: no visible global function definition for ‘new’
simdat : <anonymous>: no visible global function definition for ‘rnorm’
simdat: no visible global function definition for ‘rnorm’
trimbin: no visible global function definition for ‘quantile’
trimbin: no visible global function definition for ‘hist’
trimbin: no visible global function definition for ‘ecdf’
df0,Distribution : <anonymous>: no visible global function definition
  for ‘dnorm’
df0,Distribution : <anonymous>: no visible global function definition
  for ‘dt’
df0,Distribution : <anonymous>: no visible global function definition
  for ‘df’
df0,Distribution : <anonymous>: no visible global function definition
  for ‘dchisq’
df1,Distribution : <anonymous>: no visible global function definition
  for ‘dnorm’
df1,Distribution : <anonymous>: no visible global function definition
  for ‘dt’
df1,Distribution : <anonymous>: no visible global function definition
  for ‘df’
df1,Distribution : <anonymous>: no visible global function definition
  for ‘dchisq’
pf0,Distribution : <anonymous>: no visible global function definition
  for ‘pnorm’
pf0,Distribution : <anonymous>: no visible global function definition
  for ‘pt’
pf0,Distribution : <anonymous>: no visible global function definition
  for ‘pf’
pf0,Distribution : <anonymous>: no visible global function definition
  for ‘pchisq’
pf1,Distribution : <anonymous>: no visible global function definition
  for ‘pnorm’
pf1,Distribution : <anonymous>: no visible global function definition
  for ‘pt’
pf1,Distribution : <anonymous>: no visible global function definition
  for ‘pf’
pf1,Distribution : <anonymous>: no visible global function definition
  for ‘pchisq’
plot,PilotData : <anonymous>: no visible global function definition for
  ‘panel.histogram’
plot,PilotData : <anonymous>: no visible global function definition for
  ‘panel.xyplot’
plot,PilotData : <anonymous>: no visible global function definition for
  ‘panel.abline’
plot,PilotData: no visible binding for global variable
  ‘prepanel.qqmathline’
plot,PilotData : <anonymous>: no visible global function definition for
  ‘panel.qqmathline’
plot,PilotData : <anonymous>: no visible global function definition for
  ‘panel.qqmath’
qf0,Distribution : <anonymous>: no visible global function definition
  for ‘qnorm’
qf0,Distribution : <anonymous>: no visible global function definition
  for ‘qt’
qf0,Distribution : <anonymous>: no visible global function definition
  for ‘qf’
qf0,Distribution : <anonymous>: no visible global function definition
  for ‘qchisq’
show,PilotData: no visible global function definition for ‘str’
show,SampleSize: no visible global function definition for ‘str’
Undefined global functions or variables:
  abline approx curve dbinom dchisq df dnorm dt ecdf grid hist new
  panel.abline panel.histogram panel.qqmath panel.qqmathline
  panel.xyplot par pchisq pf pnorm points prepanel.qqmathline pt qchisq
  qf qnorm qt quantile rnorm runif str
Consider adding
  importFrom("graphics", "abline", "curve", "grid", "hist", "par",
             "points")
  importFrom("methods", "new")
  importFrom("stats", "approx", "dbinom", "dchisq", "df", "dnorm", "dt",
             "ecdf", "pchisq", "pf", "pnorm", "pt", "qchisq", "qf",
             "qnorm", "qt", "quantile", "rnorm", "runif")
  importFrom("utils", "str")
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
sampleSize 5.86  0.108   5.976
* 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/SSPA.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL SSPA
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘SSPA’ ...
** 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 massdist.c -o massdist.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c nncg.c -o nncg.o
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o SSPA.so Rinit.o massdist.o nncg.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/SSPA/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 (SSPA)

name	user	system	elapsed
Nutrigenomics	0.044	0.008	0.053
dbitri	0.004	0.000	0.004
deepSAGE	0.040	0.000	0.037
pbitri	0.020	0.000	0.021
pilotData	0.244	0.000	0.246
qbitri	0.000	0.000	0.002
rbitri	0.004	0.000	0.002
sampleSize	5.860	0.108	5.976
simdat	0.040	0.004	0.042