Back to Multiple platform build/check report for BioC 3.20:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 371/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clusterStab 1.77.0  (landing page)
James W. MacDonald
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/clusterStab
git_branch: devel
git_last_commit: c30003b
git_last_commit_date: 2024-04-30 10:14:18 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for clusterStab on palomino4

To the developers/maintainers of the clusterStab package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/clusterStab.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.

raw results


Summary

Package: clusterStab
Version: 1.77.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:clusterStab.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings clusterStab_1.77.0.tar.gz
StartedAt: 2024-06-10 01:03:11 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 01:04:03 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 52.7 seconds
RetCode: 0
Status:   OK  
CheckDir: clusterStab.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:clusterStab.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings clusterStab_1.77.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/clusterStab.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'clusterStab/DESCRIPTION' ... OK
* this is package 'clusterStab' version '1.77.0'
* 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 'clusterStab' 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 dependencies in R code ... NOTE
'library' or 'require' call to 'Biobase' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'stats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Biobase' 'methods'
  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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'clusterStab/R/zzz.R':
  .First.lib calls:
    require(Biobase)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

do.benhur: warning in matrix(placeone, nr = m.dim, nc = m.dim): partial
  argument match of 'nr' to 'nrow'
do.benhur: warning in matrix(placeone, nr = m.dim, nc = m.dim): partial
  argument match of 'nc' to 'ncol'
do.benhur: warning in matrix(placeone, nr = m.dim, nc = m.dim, byrow =
  TRUE): partial argument match of 'nr' to 'nrow'
do.benhur: warning in matrix(placeone, nr = m.dim, nc = m.dim, byrow =
  TRUE): partial argument match of 'nc' to 'ncol'
do.benhur: warning in matrix(placetwo, nr = m.dim, nc = m.dim): partial
  argument match of 'nr' to 'nrow'
do.benhur: warning in matrix(placetwo, nr = m.dim, nc = m.dim): partial
  argument match of 'nc' to 'ncol'
do.benhur: warning in matrix(placetwo, nr = m.dim, nc = m.dim, byrow =
  TRUE): partial argument match of 'nr' to 'nrow'
do.benhur: warning in matrix(placetwo, nr = m.dim, nc = m.dim, byrow =
  TRUE): partial argument match of 'nc' to 'ncol'
show,ClusterComp: warning in matrix(paste(round(object@percent, 0),
  "%", sep = ""), nr = 1): partial argument match of 'nr' to 'nrow'
.First.lib: no visible global function definition for 'addVigs2WinMenu'
do.benhur: no visible global function definition for 'hclust'
do.benhur: no visible global function definition for 'cutree'
do.benhur: no visible global function definition for 'new'
do.clusterComp: no visible global function definition for 'hclust'
do.clusterComp: no visible global function definition for 'cutree'
do.clusterComp: no visible global function definition for 'new'
makeDist: no visible global function definition for 'as.dist'
makeDist: no visible global function definition for 'cor'
makeDist: no visible global function definition for 'dist'
benhur,ExpressionSet: no visible global function definition for 'exprs'
clusterComp,ExpressionSet: no visible global function definition for
  'exprs'
ecdf,BenHur: no visible global function definition for 'par'
ecdf,BenHur: no visible global function definition for 'legend'
hist,BenHur: no visible global function definition for 'par'
Undefined global functions or variables:
  addVigs2WinMenu as.dist cor cutree dist exprs hclust legend new par
Consider adding
  importFrom("graphics", "legend", "par")
  importFrom("methods", "new")
  importFrom("stats", "as.dist", "cor", "cutree", "dist", "hclust")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 sizes of PDF files under 'inst/doc' ... 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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/clusterStab.Rcheck/00check.log'
for details.


Installation output

clusterStab.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL clusterStab
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'clusterStab' ...
** using staged installation
** R
** 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 (clusterStab)

Tests output


Example timings

clusterStab.Rcheck/clusterStab-Ex.timings

nameusersystemelapsed
benhur0.250.110.37
clusterComp0.110.000.11