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CHECK report for SpacePAC on merida2

This page was generated on 2018-10-17 08:51:52 -0400 (Wed, 17 Oct 2018).

Package 1402/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpacePAC 1.18.3
Gregory Ryslik
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/SpacePAC
Branch: RELEASE_3_7
Last Commit: 3b691da
Last Changed Date: 2018-08-24 12:11:38 -0400 (Fri, 24 Aug 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SpacePAC
Version: 1.18.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SpacePAC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SpacePAC_1.18.3.tar.gz
StartedAt: 2018-10-17 00:11:32 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 00:14:45 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 192.7 seconds
RetCode: 0
Status:  OK 
CheckDir: SpacePAC.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SpacePAC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SpacePAC_1.18.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/SpacePAC.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 ‘SpacePAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpacePAC’ version ‘1.18.3’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
SpaceClust 69.04  2.208  73.302
* 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-3.7-bioc/meat/SpacePAC.Rcheck/00check.log’
for details.



Installation output

SpacePAC.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SpacePAC
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘SpacePAC’ ...
** R
** 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 (SpacePAC)

Tests output

SpacePAC.Rcheck/tests/runTests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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 -- Wed Oct 17 00:14:40 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 
 18.916   0.516  19.593 

Example timings

SpacePAC.Rcheck/SpacePAC-Ex.timings

nameusersystemelapsed
SpaceClust69.040 2.20873.302
SpacePAC-package0.0010.0010.001
make.3D.Sphere0.0020.0000.002