Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:20 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for clstutils on tokay2


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? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 335/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clstutils 1.42.0  (landing page)
Noah Hoffman
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/clstutils
git_branch: RELEASE_3_14
git_last_commit: d7008cc
git_last_commit_date: 2021-10-26 11:58:18 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: clstutils
Version: 1.42.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clstutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings clstutils_1.42.0.tar.gz
StartedAt: 2022-04-12 17:29:06 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 17:30:53 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 107.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: clstutils.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clstutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings clstutils_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/clstutils.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.42.0'
* 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 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
** 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-3.14-bioc/meat/clstutils.Rcheck/00check.log'
for details.



Installation output

clstutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/clstutils_1.42.0.tar.gz && rm -rf clstutils.buildbin-libdir && mkdir clstutils.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clstutils.buildbin-libdir clstutils_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL clstutils_1.42.0.zip && rm clstutils_1.42.0.tar.gz clstutils_1.42.0.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
 21 2330k   21  492k    0     0   733k      0  0:00:03 --:--:--  0:00:03  733k
 86 2330k   86 2027k    0     0  1213k      0  0:00:01  0:00:01 --:--:-- 1214k
100 2330k  100 2330k    0     0  1281k      0  0:00:01  0:00:01 --:--:-- 1282k

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_1.42.0.zip
* DONE (clstutils)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'clstutils' successfully unpacked and MD5 sums checked

Tests output

clstutils.Rcheck/tests_i386/runalltests.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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-3.14-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 -- Tue Apr 12 17:30:24 2022 
*********************************************** 
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 (0.01 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 (0.49 seconds)
test_placeMat01: (2 checks) ... OK (1.91 seconds)
test_placeMat02: (3 checks) ... OK (3.12 seconds)
test_placefile: (1 checks) ... OK (0 seconds)
test_treeDists01: (2 checks) ... OK (2.17 seconds)
--------------------------- 
Test file: unit/taxTools_test.R 
test_findOutliers01: (1 checks) ... OK (0.05 seconds)
test_findOutliers02: (3 checks) ... OK (0.06 seconds)
test_maxDists01: (2 checks) ... OK (0.05 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 (0.01 seconds)
> 
> #q(runLast=FALSE)
> 
> proc.time()
   user  system elapsed 
  13.04    0.62   17.51 

clstutils.Rcheck/tests_x64/runalltests.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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: closing unused connection 3 (unit_output/merged.distmat)
Warning in for (i in seq_len(n)) { :
  closing unused connection 4 (C:/Users/biocbuild/bbs-3.14-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 -- Tue Apr 12 17:30:43 2022 
*********************************************** 
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 (0.02 seconds)
--------------------------- 
Test file: unit/placeTools_test.R 
test_classifyPlacements01: (0 checks) ... OK (4.58 seconds)
test_distfile: (1 checks) ... OK (0 seconds)
test_edgeMap01: (2 checks) ... OK (0.47 seconds)
test_placeMat01: (2 checks) ... OK (2.04 seconds)
test_placeMat02: (3 checks) ... OK (2.94 seconds)
test_placefile: (1 checks) ... OK (0 seconds)
test_treeDists01: (2 checks) ... OK (2.2 seconds)
--------------------------- 
Test file: unit/taxTools_test.R 
test_findOutliers01: (1 checks) ... OK (0.04 seconds)
test_findOutliers02: (3 checks) ... OK (0.06 seconds)
test_maxDists01: (2 checks) ... OK (0.05 seconds)
test_maxDists02: (2 checks) ... OK (0.06 seconds)
test_maxDists03: (3 checks) ... OK (0.07 seconds)
test_refpkgContents: (2 checks) ... OK (0 seconds)
test_taxonomyFromRefpkg01: (24 checks) ... OK (0.01 seconds)
> 
> #q(runLast=FALSE)
> 
> proc.time()
   user  system elapsed 
  13.57    0.70   17.95 

Example timings

clstutils.Rcheck/examples_i386/clstutils-Ex.timings

nameusersystemelapsed
classifyPlacements4.030.114.53
clstutils-package0.020.000.02
findOutliers0.070.020.08
maxDists0.210.030.25
prettyTree0.180.020.19
refpkgContents0.000.000.09
seqdat000
seqs0.000.010.01
taxonomyFromRefpkg0.060.030.16
treeDists2.850.132.97

clstutils.Rcheck/examples_x64/clstutils-Ex.timings

nameusersystemelapsed
classifyPlacements3.520.133.77
clstutils-package0.010.000.01
findOutliers0.040.010.05
maxDists0.140.000.14
prettyTree0.150.000.16
refpkgContents0.000.000.08
seqdat0.010.000.02
seqs0.000.020.01
taxonomyFromRefpkg0.080.000.17
treeDists2.830.092.93