Multiple platform build/check report for BioC 3.6 - CHECK report for SpacePAC on veracruz1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SpacePAC_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/SpacePAC.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpacePAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpacePAC’ version ‘1.16.0’
* 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 ‘SpacePAC’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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: ‘iPAC’
  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
SpaceClust: no visible global function definition for ‘flush.console’
SpaceClust: no visible global function definition for ‘ppois’
create.Distance.Matrix: no visible global function definition for
  ‘dist’
create.Result.Matrix: no visible global function definition for
  ‘p.adjust’
get.Avg.Neighbor.Distance: no visible global function definition for
  ‘dist’
get.Local.Radius.Results: no visible global function definition for
  ‘sd’
make.3D.Sphere: no visible global function definition for ‘rgl.open’
make.3D.Sphere: no visible global function definition for ‘rgl.bg’
make.3D.Sphere: no visible global function definition for ‘plot3d’
make.3D.Sphere: no visible global function definition for ‘decorate3d’
make.3D.Sphere: no visible global function definition for ‘spheres3d’
Undefined global functions or variables:
  decorate3d dist flush.console p.adjust plot3d ppois rgl.bg rgl.open
  sd spheres3d
Consider adding
  importFrom("stats", "dist", "p.adjust", "ppois", "sd")
  importFrom("utils", "flush.console")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
SpaceClust 45.585  1.473  49.571
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/SpacePAC.Rcheck/00check.log’
for details.


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("SpacePAC")
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: 'gdata'

The following object is masked from 'package:stats':

    nobs

The following object is masked from 'package:utils':

    object.size

The following object is masked from 'package:base':

    startsWith


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:gdata':

    combine

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: 'S4Vectors'

The following objects are masked from 'package:gdata':

    first, first<-

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:gdata':

    trim


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Processing radius # 1 : radius length = 1.00 : Percentage complete 0.00 
Processing radius # 2 : radius length = 2.00 : Percentage complete 0.25 
Processing radius # 3 : radius length = 3.00 : Percentage complete 0.50 
Processing radius # 4 : radius length = 4.00 : Percentage complete 0.75 
Processing radius # 1 : radius length = 1.00 : Percentage complete 0.00 
Processing radius # 2 : radius length = 2.00 : Percentage complete 0.25 
Processing radius # 3 : radius length = 3.00 : Percentage complete 0.50 
Processing radius # 4 : radius length = 4.00 : Percentage complete 0.75 


RUNIT TEST PROTOCOL -- Thu Apr 12 09:52:45 2018 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SpacePAC RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 15.129   0.273  15.696

CHECK report for SpacePAC on veracruz1

Summary

Command output

Installation output

Tests output

Example timings

name	user	system	elapsed
SpaceClust	45.585	1.473	49.571
SpacePAC-package	0.000	0.001	0.001
make.3D.Sphere	0.001	0.000	0.001