Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-22 11:05:40 -0500 (Sat, 22 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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 ctc on nebbiolo1


To the developers/maintainers of the ctc package:
- Please 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 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.

raw results

Package 428/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ctc 1.69.0  (landing page)
Antoine Lucas
Snapshot Date: 2022-01-21 13:55:18 -0500 (Fri, 21 Jan 2022)
git_url: https://git.bioconductor.org/packages/ctc
git_branch: master
git_last_commit: f7d625e
git_last_commit_date: 2021-10-26 11:45:37 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    NA    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ctc
Version: 1.69.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:ctc.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings ctc_1.69.0.tar.gz
StartedAt: 2022-01-21 18:49:31 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 18:49:46 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 15.0 seconds
RetCode: 0
Status:   OK  
CheckDir: ctc.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:ctc.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings ctc_1.69.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/ctc.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ctc/DESCRIPTION’ ... OK
* this is package ‘ctc’ version ‘1.69.0’
* 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 R 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 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 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/ctc.Rcheck/00check.log’
for details.



Installation output

ctc.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL ctc
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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
hc2Newick0.0150.0010.015
hclust2treeview0.0240.0150.039
r2cluster0.0030.0000.003
r2gtr0.0110.0000.011
r2xcluster0.0030.0000.003
xcluster0.0000.0000.001
xcluster2r0.0020.0000.003