Noah Hoffman
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/clstutils |
| git_branch: RELEASE_3_13 |
| git_last_commit: 97804e0 |
| git_last_commit_date: 2021-10-07 13:28:13 -0400 (Thu, 07 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:00 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the clstutils package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/clstutils.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 327/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| clstutils 1.40.1 (landing page) Noah Hoffman
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: clstutils |
| Version: 1.40.1 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clstutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings clstutils_1.40.1.tar.gz |
| StartedAt: 2021-10-14 21:11:21 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 21:13:16 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 114.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: clstutils.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clstutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings clstutils_1.40.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/clstutils.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.40.1'
* 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 whether package 'clstutils' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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.
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'
prettyTree: no visible binding for global variable '.PlotPhyloEnv'
refpkgContents: no visible global function definition for 'fromJSON'
Undefined global functions or variables:
.PlotPhyloEnv fromJSON
* 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 LazyData ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
classifyPlacements 3.37 0.09 5.68
** 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: 1 WARNING, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/clstutils.Rcheck/00check.log'
for details.
clstutils.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/clstutils_1.40.1.tar.gz && rm -rf clstutils.buildbin-libdir && mkdir clstutils.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clstutils.buildbin-libdir clstutils_1.40.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL clstutils_1.40.1.zip && rm clstutils_1.40.1.tar.gz clstutils_1.40.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
34 2330k 34 804k 0 0 1383k 0 0:00:01 --:--:-- 0:00:01 1383k
100 2330k 100 2330k 0 0 2008k 0 0:00:01 0:00:01 --:--:-- 2009k
install for i386
* 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
converting help for package 'clstutils'
finding HTML links ... done
classifyPlacements html
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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'clstutils' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clstutils' as clstutils_1.40.1.zip
* DONE (clstutils)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'clstutils' successfully unpacked and MD5 sums checked
|
clstutils.Rcheck/tests_i386/runalltests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 for (i in seq_len(n)) { :
closing unused connection 3 (unit_output/merged.distmat)
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 (C:/Users/biocbuild/bbs-3.13-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 -- Thu Oct 14 21:12:44 2021
***********************************************
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 (5.64 seconds)
test_distfile: (1 checks) ... OK (0 seconds)
test_edgeMap01: (2 checks) ... OK (0.42 seconds)
test_placeMat01: (2 checks) ... OK (2.72 seconds)
test_placeMat02: (3 checks) ... OK (4.09 seconds)
test_placefile: (1 checks) ... OK (0 seconds)
test_treeDists01: (2 checks) ... OK (2.13 seconds)
---------------------------
Test file: unit/taxTools_test.R
test_findOutliers01: (1 checks) ... OK (0.06 seconds)
test_findOutliers02: (3 checks) ... OK (0.05 seconds)
test_maxDists01: (2 checks) ... OK (0.06 seconds)
test_maxDists02: (2 checks) ... OK (0.05 seconds)
test_maxDists03: (3 checks) ... OK (0.06 seconds)
test_refpkgContents: (2 checks) ... OK (0 seconds)
test_taxonomyFromRefpkg01: (24 checks) ... OK (0.01 seconds)
>
> #q(runLast=FALSE)
>
> proc.time()
user system elapsed
16.31 0.59 20.84
|
clstutils.Rcheck/tests_x64/runalltests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 ... Warning in for (i in seq_len(n)) { :
closing unused connection 3 (unit_output/merged.distmat)
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 (C:/Users/biocbuild/bbs-3.13-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 -- Thu Oct 14 21:13:03 2021
***********************************************
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 (0.02 seconds)
---------------------------
Test file: unit/placeTools_test.R
test_classifyPlacements01: (0 checks) ... OK (4.34 seconds)
test_distfile: (1 checks) ... OK (0 seconds)
test_edgeMap01: (2 checks) ... OK (0.42 seconds)
test_placeMat01: (2 checks) ... OK (1.86 seconds)
test_placeMat02: (3 checks) ... OK (2.49 seconds)
test_placefile: (1 checks) ... OK (0 seconds)
test_treeDists01: (2 checks) ... OK (2.01 seconds)
---------------------------
Test file: unit/taxTools_test.R
test_findOutliers01: (1 checks) ... OK (0.06 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 (0.06 seconds)
test_refpkgContents: (2 checks) ... OK (0 seconds)
test_taxonomyFromRefpkg01: (24 checks) ... OK (0.02 seconds)
>
> #q(runLast=FALSE)
>
> proc.time()
user system elapsed
12.07 0.87 18.32
|
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clstutils.Rcheck/examples_i386/clstutils-Ex.timings
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clstutils.Rcheck/examples_x64/clstutils-Ex.timings
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