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This page was generated on 2024-05-15 13:46:29 -0400 (Wed, 15 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4663
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
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

Package 360/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clstutils 1.53.0  (landing page)
Noah Hoffman
Snapshot Date: 2024-05-13 14:05:07 -0400 (Mon, 13 May 2024)
git_url: https://git.bioconductor.org/packages/clstutils
git_branch: devel
git_last_commit: 2ffb05f
git_last_commit_date: 2024-04-30 10:23:42 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for clstutils on kunpeng2


To the developers/maintainers of the clstutils package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: clstutils
Version: 1.52.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:clstutils.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings clstutils_1.52.0.tar.gz
StartedAt: 2024-05-09 05:54:40 -0000 (Thu, 09 May 2024)
EndedAt: 2024-05-09 05:55:43 -0000 (Thu, 09 May 2024)
EllapsedTime: 63.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: clstutils.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:clstutils.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings clstutils_1.52.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/clstutils.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clstutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘clstutils’ version ‘1.52.0’
* 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 ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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.
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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
classifyPlacements 5.055  0.147   5.215
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runalltests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/clstutils.Rcheck/00check.log’
for details.


Installation output

clstutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL clstutils
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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)

Tests output

clstutils.Rcheck/tests/runalltests.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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  ...  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 May  9 05:55:40 2024 
*********************************************** 
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 seconds)
test_seqs: (1 checks) ... OK (0 seconds)
--------------------------- 
Test file: unit/placeTools_test.R 
test_classifyPlacements01: (0 checks) ... OK (5.99 seconds)
test_distfile: (1 checks) ... OK (0 seconds)
test_edgeMap01: (2 checks) ... OK (0.6 seconds)
test_placeMat01: (2 checks) ... OK (2.53 seconds)
test_placeMat02: (3 checks) ... OK (3.89 seconds)
test_placefile: (1 checks) ... OK (0 seconds)
test_treeDists01: (2 checks) ... OK (3.31 seconds)
--------------------------- 
Test file: unit/taxTools_test.R 
test_findOutliers01: (1 checks) ... OK (0.04 seconds)
test_findOutliers02: (3 checks) ... OK (0.05 seconds)
test_maxDists01: (2 checks) ... OK (0.03 seconds)
test_maxDists02: (2 checks) ... OK (0.04 seconds)
test_maxDists03: (3 checks) ... OK (0.04 seconds)
test_refpkgContents: (2 checks) ... OK (0 seconds)
test_taxonomyFromRefpkg01: (24 checks) ... OK (0.02 seconds)
> 
> #q(runLast=FALSE)
> 
> proc.time()
   user  system elapsed 
 20.050   0.421  20.477 

Example timings

clstutils.Rcheck/clstutils-Ex.timings

nameusersystemelapsed
classifyPlacements5.0550.1475.215
clstutils-package0.0080.0000.009
findOutliers0.0390.0000.039
maxDists0.1570.0080.164
prettyTree0.1260.0000.126
refpkgContents0.0140.0140.022
seqdat0.0020.0000.002
seqs0.0060.0000.006
taxonomyFromRefpkg0.0410.0120.047
treeDists3.6630.0323.703