Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-05-15 13:46:30 -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 459/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ctc 1.79.0  (landing page)
Antoine Lucas
Snapshot Date: 2024-05-13 14:05:07 -0400 (Mon, 13 May 2024)
git_url: https://git.bioconductor.org/packages/ctc
git_branch: devel
git_last_commit: 5a4349b
git_last_commit_date: 2024-04-30 10:10:59 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for ctc on kunpeng2


To the developers/maintainers of the ctc package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ctc.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: ctc
Version: 1.78.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:ctc.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings ctc_1.78.0.tar.gz
StartedAt: 2024-05-09 06:21:32 -0000 (Thu, 09 May 2024)
EndedAt: 2024-05-09 06:21:54 -0000 (Thu, 09 May 2024)
EllapsedTime: 22.0 seconds
RetCode: 0
Status:   OK  
CheckDir: ctc.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:ctc.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings ctc_1.78.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ctc.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 ‘ctc/DESCRIPTION’ ... OK
* this is package ‘ctc’ version ‘1.78.0’
* 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 ‘ctc’ 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.
Malformed Description field: should contain one or more complete sentences.
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘amap’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘amap’
  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 ... OK
* checking R code for possible problems ... NOTE
.First.lib: warning in .packages(all = TRUE): partial argument match of
  'all' to 'all.available'
.onLoad: warning in .packages(all = TRUE): partial argument match of
  'all' to 'all.available'
hclust2treeview: warning in .packages(all = TRUE): partial argument
  match of 'all' to 'all.available'
hclust2treeview: no visible global function definition for ‘hclust’
hclust2treeview: no visible global function definition for ‘dist’
r2atr: no visible global function definition for ‘write.table’
r2cdt: no visible global function definition for ‘write.table’
r2cluster: no visible global function definition for ‘write.table’
r2gtr: no visible global function definition for ‘write.table’
r2xcluster: no visible global function definition for ‘write.table’
read.eisen: no visible global function definition for ‘read.table’
xcluster2r: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  dist hclust read.table write.table
Consider adding
  importFrom("stats", "dist", "hclust")
  importFrom("utils", "read.table", "write.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 files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ctc.Rcheck/00check.log’
for details.


Installation output

ctc.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL ctc
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘ctc’ ...
** using staged installation
** R
** demo
** exec
** 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 (ctc)

Tests output


Example timings

ctc.Rcheck/ctc-Ex.timings

nameusersystemelapsed
hc2Newick0.0170.0040.021
hclust2treeview0.0170.0000.016
r2cluster0.0030.0000.003
r2gtr0.0070.0000.007
r2xcluster0.0090.0000.009
xcluster000
xcluster2r0.0030.0000.004