Package: clstutils

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:clstutils.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings clstutils_1.32.0.tar.gz

StartedAt: 2019-10-16 01:32:26 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:34:10 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 103.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: clstutils.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:clstutils.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings clstutils_1.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/clstutils.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.32.0’
* 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 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 : : no visible global function definition for
  ‘setSVGShapeToolTip’
svgTree : : 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, .NOTPARALLEL See section ‘Writing portable
packages’ in the ‘Writing R Extensions’ manual.
* checking include directives in Makefiles ... 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
classifyPlacements 6.626  0.372   7.023
treeDists          6.487  0.364   6.855
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/clstutils.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL clstutils
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘clstutils’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (clstutils)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.

> 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  ...  done successfully.



Executing test function test_placefile  ...  done successfully.



Executing test function test_treeDists01  ... Warning in for (i in seq_len(n)) { :
  closing unused connection 3 (unit_output/merged.distmat)
Warning in for (i in seq_len(n)) { :
  closing unused connection 4 (/Library/Frameworks/R.framework/Versions/3.6/Resources/library/clstutils/extdata/merged.distmat.bz2)
 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 Oct 16 01:34:02 2019 
*********************************************** 
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 (0.04 seconds)
test_seqs: (1 checks) ... OK (0.01 seconds)
--------------------------- 
Test file: unit/placeTools_test.R 
test_classifyPlacements01: (0 checks) ... OK (9.17 seconds)
test_distfile: (1 checks) ... OK (0 seconds)
test_edgeMap01: (2 checks) ... OK (1.53 seconds)
test_placeMat01: (2 checks) ... OK (4.58 seconds)
test_placeMat02: (3 checks) ... OK (5.84 seconds)
test_placefile: (1 checks) ... OK (0 seconds)
test_treeDists01: (2 checks) ... OK (4.81 seconds)
--------------------------- 
Test file: unit/taxTools_test.R 
test_findOutliers01: (1 checks) ... OK (0.04 seconds)
test_findOutliers02: (3 checks) ... OK (0.14 seconds)
test_maxDists01: (2 checks) ... OK (0.05 seconds)
test_maxDists02: (2 checks) ... OK (0.05 seconds)
test_maxDists03: (3 checks) ... OK (0.07 seconds)
test_refpkgContents: (2 checks) ... OK (0 seconds)
test_taxonomyFromRefpkg01: (24 checks) ... OK (0.03 seconds)
> 
> #q(runLast=FALSE)
> 
> proc.time()
   user  system elapsed 
 30.043   2.428  32.624 

name	user	system	elapsed
classifyPlacements	6.626	0.372	7.023
clstutils-package	0.018	0.001	0.019
findOutliers	0.062	0.014	0.078
maxDists	0.301	0.055	0.362
prettyTree	0.085	0.006	0.091
refpkgContents	0.024	0.021	0.045
seqdat	0.003	0.002	0.006
seqs	0.005	0.004	0.010
taxonomyFromRefpkg	0.075	0.025	0.102
treeDists	6.487	0.364	6.855