BioC 3.6: CHECK report for dexus on malbec1

Package: dexus

Version: 1.17.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings dexus_1.17.0.tar.gz

StartedAt: 2017-08-15 22:37:31 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:38:13 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 42.5 seconds

RetCode: 0

Status:  OK

CheckDir: dexus.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings dexus_1.17.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/dexus.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dexus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dexus’ version ‘1.17.0’
* 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 ‘dexus’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘DESeq’ ‘parallel’ ‘statmod’ ‘stats’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘BiocGenerics’
  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
dexss : <anonymous>: no visible global function definition for ‘hist’
dexss: no visible global function definition for ‘runif’
dexss: no visible global function definition for ‘new’
dexus : <anonymous>: no visible global function definition for ‘hist’
dexus: no visible global function definition for ‘runif’
dexus: no visible global function definition for ‘new’
dexus.parallel: no visible global function definition for ‘mclapply’
dexus.parallel: no visible global function definition for ‘new’
getSizeNB: no visible global function definition for ‘var’
initialize.clusters.kmeans: no visible global function definition for
  ‘kmeans’
initialize.clusters.kmeans: no visible global function definition for
  ‘median’
initialize.clusters.kmeans: no visible global function definition for
  ‘rnorm’
initialize.clusters.quantiles: no visible global function definition
  for ‘rnorm’
initialize.clusters.quantiles: no visible global function definition
  for ‘quantile’
initialize.clusters.quantiles : <anonymous>: no visible global function
  definition for ‘rnorm’
nbinomTestForMatrices : <anonymous>: no visible global function
  definition for ‘dnbinom’
normalize.rle : <anonymous>: no visible global function definition for
  ‘median’
normalize.uq : <anonymous>: no visible global function definition for
  ‘quantile’
testMulticlass : <anonymous>: no visible global function definition for
  ‘deviance’
testMulticlass : <anonymous>: no visible global function definition for
  ‘pchisq’
INIThreshold<-,DEXUSResult: no visible global function definition for
  ‘slot<-’
[,DEXUSResult-character: no visible global function definition for
  ‘new’
[,DEXUSResult-logical: no visible global function definition for ‘new’
[,DEXUSResult-numeric: no visible global function definition for ‘new’
plot,DEXUSResult-missing: no visible global function definition for
  ‘par’
plot,DEXUSResult-missing: no visible global function definition for
  ‘colorRampPalette’
plot,DEXUSResult-missing: no visible global function definition for
  ‘image’
plot,DEXUSResult-missing: no visible global function definition for
  ‘rect’
plot,DEXUSResult-missing: no visible global function definition for
  ‘points’
plot,DEXUSResult-missing: no visible global function definition for
  ‘axis’
Undefined global functions or variables:
  axis colorRampPalette deviance dnbinom hist image kmeans mclapply
  median new par pchisq points quantile rect rnorm runif slot<- var
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "hist", "image", "par", "points",
             "rect")
  importFrom("methods", "new", "slot<-")
  importFrom("stats", "deviance", "dnbinom", "kmeans", "median",
             "pchisq", "quantile", "rnorm", "runif", "var")
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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/dexus.Rcheck/00check.log’
for details.

* installing *source* package ‘dexus’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c dexus.cpp -o dexus.o
dexus.cpp: In function ‘SEXPREC* dexus_impl(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, int*, SEXP, SEXP, SEXP)’:
dexus.cpp:193:15: warning: unused variable ‘DEFAULT_R’ [-Wunused-variable]
  const double DEFAULT_R = 20; // R value used when re-setting clusters
               ^
dexus.cpp: In function ‘SEXPREC* dexss_impl(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, int*, SEXP, SEXP, SEXP)’:
dexus.cpp:575:15: warning: unused variable ‘DEFAULT_R’ [-Wunused-variable]
  const double DEFAULT_R = 20; // R value used when re-setting clusters
               ^
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o dexus.so dexus.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/dexus.Rcheck/dexus/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (dexus)

name	user	system	elapsed
DEXUSResult-class	0.000	0.000	0.002
DEXUSResult-subset	1.632	0.072	1.705
INI	1.036	0.076	1.111
INIThreshold-set	0.824	0.052	0.878
accessors	0.724	0.056	0.780
dexss	1.148	0.060	1.211
dexus	0.696	0.044	0.745
dexus.parallel	0.692	0.060	0.755
getSizeNB	0	0	0
normalizeData	0.920	0.076	0.996
plot	1.036	0.048	1.083
sort	0.916	0.044	0.962