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This page was generated on 2024-06-18 17:57 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 1082/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iterClust 1.26.0  (landing page)
Hongxu Ding
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/iterClust
git_branch: RELEASE_3_19
git_last_commit: bbf9d2a
git_last_commit_date: 2024-04-30 11:01:29 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows 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 iterClust on nebbiolo1

To the developers/maintainers of the iterClust package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iterClust.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: iterClust
Version: 1.26.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:iterClust.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings iterClust_1.26.0.tar.gz
StartedAt: 2024-06-17 00:28:07 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 00:28:51 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 44.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: iterClust.Rcheck
Warnings: NA

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:iterClust.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings iterClust_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/iterClust.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘iterClust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iterClust’ version ‘1.26.0’
* 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 ‘iterClust’ 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
iterClust 14.211  0.052  14.264
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘introduction.rnw’ using Sweave
Warning in fun(libname, pkgname) :
  Package 'iterClust' is deprecated and will be removed from Bioconductor
  version 3.20
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Initialize iteration 1
Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...
Heterogenous cluster detected, iterClust proceeding...
Removing outlier samples...
Iteration 1 done, giving 5 clusters in total


Initialize iteration 2, for each cluster given by the previous iteration:
Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Heterogenous cluster detected, iterClust proceeding...
Removing outlier samples...
Iteration 2 done, giving 7 clusters in total


Initialize iteration 3, for each cluster given by the previous iteration:
Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

Feature selection...
Generating clustering schemes...
Evaluating each clustering scheme...

iterClust finished, giving 7 clusters in total

Error: processing vignette 'introduction.rnw' failed with diagnostics:
 chunk 10 (label = consensusclust) 
Error in library(ConsensusClusterPlus) : 
  there is no package called ‘ConsensusClusterPlus’

--- failed re-building ‘introduction.rnw’

SUMMARY: processing the following file failed:
  ‘introduction.rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/iterClust.Rcheck/00check.log’
for details.


Installation output

iterClust.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL iterClust
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘iterClust’ ...
** using staged installation
** R
** 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
Warning in fun(libname, pkgname) :
  Package 'iterClust' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'iterClust' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (iterClust)

Tests output


Example timings

iterClust.Rcheck/iterClust-Ex.timings

nameusersystemelapsed
clustEval0.0000.0000.001
clustHetero000
coreClust000
featureSelect0.0010.0000.000
iterClust14.211 0.05214.264
obsEval0.0010.0000.001
obsOutlier000