Multiple platform build/check report for BioC 3.6 - CHECK report for clstutils on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings clstutils_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/clstutils.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clstutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘clstutils’ version ‘1.26.0’
* 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 ‘clstutils’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘rjson’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘RSVGTipsDevice’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘ape’ ‘rjson’
  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 ... NOTE
Foreign function call to a different package:
  .Call("seq_root2tip", ..., PACKAGE = "ape")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
edgeMap: no visible global function definition for ‘fromJSON’
findOutliers: no visible global function definition for ‘quantile’
findOutliers: no visible binding for global variable ‘median’
maxDists: no visible binding for global variable ‘median’
placeData: no visible global function definition for ‘read.table’
prettyTree: no visible binding for global variable ‘par’
prettyTree: no visible global function definition for ‘plot’
prettyTree: no visible binding for global variable ‘.PlotPhyloEnv’
prettyTree: no visible binding for global variable ‘points’
prettyTree: no visible global function definition for ‘text’
prettyTree: no visible global function definition for ‘points’
prettyTree: no visible binding for global variable ‘legend’
refpkgContents: no visible global function definition for ‘fromJSON’
svgTree: no visible global function definition for ‘devSVGTips’
svgTree: no visible global function definition for ‘par’
svgTree: no visible global function definition for ‘plot’
svgTree: no visible binding for global variable ‘.PlotPhyloEnv’
svgTree : <anonymous>: no visible global function definition for
  ‘setSVGShapeToolTip’
svgTree : <anonymous>: no visible global function definition for
  ‘points’
svgTree: no visible global function definition for ‘dev.off’
svgTree2: no visible global function definition for ‘devSVGTips’
svgTree2: no visible global function definition for ‘par’
svgTree2: no visible global function definition for ‘plot’
svgTree2: no visible binding for global variable ‘.PlotPhyloEnv’
svgTree2: no visible global function definition for ‘dev.off’
taxonomyFromRefpkg: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  .PlotPhyloEnv dev.off devSVGTips fromJSON legend median par plot
  points quantile read.csv read.table setSVGShapeToolTip text
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "legend", "par", "plot", "points", "text")
  importFrom("stats", "median", "quantile")
  importFrom("utils", "read.csv", "read.table")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  tests/unit/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* 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
classifyPlacements 5.184  0.272    5.46
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runalltests.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: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/clstutils.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-pc-linux-gnu (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.

> library("RUnit")
> 
> options(warn=1)
> 
> dirs <- 'unit'
> 
> testFilePat <- ".*_test\\.R$"
> 
> allSuite <- defineTestSuite(name="allSuite",
+                             dirs=dirs,
+                             testFileRegexp=testFilePat,
+                             rngKind="default",
+                             rngNormalKind="default"
+                             )
> 
> testData <- runTestSuite(allSuite)
Loading required package: clst
Loading required package: rjson
Loading required package: ape


Executing test function test_seqdata  ...  done successfully.



Executing test function test_seqs  ...  done successfully.



Executing test function test_classifyPlacements01  ...   tax_id         tax_name   rank below above score match  min median  max   d
1  33958 Lactobacillaceae family   106    12  0.89     1 0.03   0.73 1.12 0.9
   at
1 860
 done successfully.



Executing test function test_distfile  ...  done successfully.



Executing test function test_edgeMap01  ...  done successfully.



Executing test function test_placeMat01  ...  done successfully.



Executing test function test_placeMat02  ... Warning in .Internal(gc(verbose, reset)) :
  closing unused connection 3 (unit_output/merged.distmat)
 done successfully.



Executing test function test_placefile  ... Warning in .Internal(gc(verbose, reset)) :
  closing unused connection 3 (/home/biocbuild/bbs-3.6-bioc/meat/clstutils.Rcheck/clstutils/extdata/merged.distmat.bz2)
 done successfully.



Executing test function test_treeDists01  ...  done successfully.



Executing test function test_findOutliers01  ...  done successfully.



Executing test function test_findOutliers02  ...  done successfully.



Executing test function test_maxDists01  ...  done successfully.



Executing test function test_maxDists02  ...  done successfully.



Executing test function test_maxDists03  ...  done successfully.



Executing test function test_refpkgContents  ...  done successfully.



Executing test function test_taxonomyFromRefpkg01  ...  done successfully.

> 
> printTextProtocol(testData, showDetails=TRUE)
RUNIT TEST PROTOCOL -- Wed Apr 11 22:20:42 2018 
*********************************************** 
Number of test functions: 16 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
allSuite - 16 test functions, 0 errors, 0 failures



Details 
*************************** 
Test Suite: allSuite 
Test function regexp: ^test.+ 
Test file regexp: .*_test\.R$ 
Involved directory: 
unit 
--------------------------- 
Test file: unit/data_test.R 
test_seqdata: (3 checks) ... OK (0.01 seconds)
test_seqs: (1 checks) ... OK (0 seconds)
--------------------------- 
Test file: unit/placeTools_test.R 
test_classifyPlacements01: (0 checks) ... OK (5.67 seconds)
test_distfile: (1 checks) ... OK (0 seconds)
test_edgeMap01: (2 checks) ... OK (0.47 seconds)
test_placeMat01: (2 checks) ... OK (2.52 seconds)
test_placeMat02: (3 checks) ... OK (4.66 seconds)
test_placefile: (1 checks) ... OK (0 seconds)
test_treeDists01: (2 checks) ... OK (2.73 seconds)
--------------------------- 
Test file: unit/taxTools_test.R 
test_findOutliers01: (1 checks) ... OK (0.03 seconds)
test_findOutliers02: (3 checks) ... OK (0.08 seconds)
test_maxDists01: (2 checks) ... OK (0.04 seconds)
test_maxDists02: (2 checks) ... OK (0.05 seconds)
test_maxDists03: (3 checks) ... OK (0.04 seconds)
test_refpkgContents: (2 checks) ... OK (0 seconds)
test_taxonomyFromRefpkg01: (24 checks) ... OK (0.03 seconds)
> 
> #q(runLast=FALSE)
> 
> proc.time()
   user  system elapsed 
 20.116   0.776  20.992

name	user	system	elapsed
classifyPlacements	5.184	0.272	5.460
clstutils-package	0.008	0.000	0.007
findOutliers	0.056	0.000	0.054
maxDists	0.652	0.004	0.658
prettyTree	0.072	0.000	0.069
refpkgContents	0.028	0.012	0.040
seqdat	0.004	0.000	0.002
seqs	0.000	0.004	0.005
taxonomyFromRefpkg	0.068	0.016	0.087
treeDists	3.428	0.180	3.612

CHECK report for clstutils on malbec1

Summary

Command output

Installation output

Tests output

Example timings