Noah Hoffman
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/clstutils |
| Branch: RELEASE_3_8 |
| Last Commit: 84f9bcf |
| Last Changed Date: 2018-10-30 11:41:47 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:21:33 -0400 (Sat, 13 Apr 2019).
| Package 275/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| clstutils 1.30.0 Noah Hoffman
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: clstutils |
| Version: 1.30.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clstutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings clstutils_1.30.0.tar.gz |
| StartedAt: 2019-04-13 01:17:23 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 01:19:50 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 147.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: clstutils.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clstutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings clstutils_1.30.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/clstutils.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clstutils/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'clstutils' version '1.30.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 whether package 'clstutils' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYthUPy/R.INSTALL14489842131/clstutils/man/classifyPlacements.Rd:31: file link 'classifyIter' in package 'clst' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/clstutils.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 : <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 include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runalltests.R'
OK
** running tests for arch 'x64' ...
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: 2 WARNINGs, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/clstutils.Rcheck/00check.log'
for details.
clstutils.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/clstutils_1.30.0.tar.gz && rm -rf clstutils.buildbin-libdir && mkdir clstutils.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clstutils.buildbin-libdir clstutils_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL clstutils_1.30.0.zip && rm clstutils_1.30.0.tar.gz clstutils_1.30.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2332k 100 2332k 0 0 30.0M 0 --:--:-- --:--:-- --:--:-- 31.6M
install for i386
* installing *source* package 'clstutils' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'clstutils'
finding HTML links ... done
classifyPlacements html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYthUPy/R.INSTALL14489842131/clstutils/man/classifyPlacements.Rd:31: file link 'classifyIter' in package 'clst' does not exist and so has been treated as a topic
clstutils-package html
finding level-2 HTML links ... done
findOutliers html
maxDists html
prettyTree html
refpkgContents html
seqdat html
seqs html
taxonomyFromRefpkg html
treeDists html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'clstutils' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clstutils' as clstutils_1.30.0.zip
* DONE (clstutils)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'clstutils' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
clstutils.Rcheck/tests_i386/runalltests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 if (!missing(definition) && is.null(definition)) { :
closing unused connection 3 (unit_output/merged.distmat)
done successfully.
Executing test function test_placefile ... done successfully.
Executing test function test_treeDists01 ... Warning in .set_row_names(nrows) :
closing unused connection 3 (C:/Users/biocbuild/bbs-3.8-bioc/R/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 -- Sat Apr 13 01:19:25 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 (0.02 seconds)
test_seqs: (1 checks) ... OK (0 seconds)
---------------------------
Test file: unit/placeTools_test.R
test_classifyPlacements01: (0 checks) ... OK (4.24 seconds)
test_distfile: (1 checks) ... OK (0 seconds)
test_edgeMap01: (2 checks) ... OK (0.67 seconds)
test_placeMat01: (2 checks) ... OK (2.44 seconds)
test_placeMat02: (3 checks) ... OK (2.9 seconds)
test_placefile: (1 checks) ... OK (0 seconds)
test_treeDists01: (2 checks) ... OK (2.22 seconds)
---------------------------
Test file: unit/taxTools_test.R
test_findOutliers01: (1 checks) ... OK (0.05 seconds)
test_findOutliers02: (3 checks) ... OK (0.05 seconds)
test_maxDists01: (2 checks) ... OK (0.03 seconds)
test_maxDists02: (2 checks) ... OK (0.05 seconds)
test_maxDists03: (3 checks) ... OK (0.03 seconds)
test_refpkgContents: (2 checks) ... OK (0 seconds)
test_taxonomyFromRefpkg01: (24 checks) ... OK (0.01 seconds)
>
> #q(runLast=FALSE)
>
> proc.time()
user system elapsed
12.62 0.85 16.87
|
clstutils.Rcheck/tests_x64/runalltests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 match.arg(method) :
closing unused connection 3 (unit_output/merged.distmat)
Warning: closing unused connection 4 (C:/Users/biocbuild/bbs-3.8-bioc/R/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 -- Sat Apr 13 01:19:45 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 (0.01 seconds)
test_seqs: (1 checks) ... OK (0 seconds)
---------------------------
Test file: unit/placeTools_test.R
test_classifyPlacements01: (0 checks) ... OK (4.49 seconds)
test_distfile: (1 checks) ... OK (0 seconds)
test_edgeMap01: (2 checks) ... OK (0.58 seconds)
test_placeMat01: (2 checks) ... OK (2.34 seconds)
test_placeMat02: (3 checks) ... OK (3.08 seconds)
test_placefile: (1 checks) ... OK (0 seconds)
test_treeDists01: (2 checks) ... OK (2.26 seconds)
---------------------------
Test file: unit/taxTools_test.R
test_findOutliers01: (1 checks) ... OK (0.03 seconds)
test_findOutliers02: (3 checks) ... OK (0.05 seconds)
test_maxDists01: (2 checks) ... OK (0.03 seconds)
test_maxDists02: (2 checks) ... OK (0.03 seconds)
test_maxDists03: (3 checks) ... OK (0.05 seconds)
test_refpkgContents: (2 checks) ... OK (0 seconds)
test_taxonomyFromRefpkg01: (24 checks) ... OK (0 seconds)
>
> #q(runLast=FALSE)
>
> proc.time()
user system elapsed
12.92 0.87 19.54
|
|
clstutils.Rcheck/examples_i386/clstutils-Ex.timings
|
clstutils.Rcheck/examples_x64/clstutils-Ex.timings
|