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This page was generated on 2023-12-02 11:35:45 -0500 (Sat, 02 Dec 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4685
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4420
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4439
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 1368/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
multiSight 1.10.0  (landing page)
Florian Jeanneret
Snapshot Date: 2023-12-01 14:05:06 -0500 (Fri, 01 Dec 2023)
git_url: https://git.bioconductor.org/packages/multiSight
git_branch: RELEASE_3_18
git_last_commit: b9ae929
git_last_commit_date: 2023-10-24 11:32:57 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for multiSight on nebbiolo2


To the developers/maintainers of the multiSight package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/multiSight.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: multiSight
Version: 1.10.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:multiSight.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings multiSight_1.10.0.tar.gz
StartedAt: 2023-12-01 23:49:31 -0500 (Fri, 01 Dec 2023)
EndedAt: 2023-12-01 23:56:19 -0500 (Fri, 01 Dec 2023)
EllapsedTime: 407.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: multiSight.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:multiSight.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings multiSight_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/multiSight.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘multiSight/DESCRIPTION’ ... OK
* this is package ‘multiSight’ version ‘1.10.0’
* package encoding: UTF-8
* 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 ‘multiSight’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'multiSight' is deprecated and will be removed from
See ‘/home/biocbuild/bbs-3.18-bioc/meat/multiSight.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  CeCILL + file LICENSE
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘ggnewscale’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
mod_understand_server: no visible global function definition for
  ‘keytypes’
Undefined global functions or variables:
  keytypes
* 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 data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘multiSight-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: buildFeatTable
> ### Title: Models util function
> ### Aliases: buildFeatTable
> 
> ### ** Examples
> 
> data("omic2", package = "multiSight")
> splitData <- splitDatatoTrainTest(omic2, 0.8)
> data.train <- splitData$data.train
> data.test <- splitData$data.test
> 
> #diabloRes <- runSPLSDA(data.train)
> data("diabloRes", package = "multiSight")
> diabloModels <- diabloRes$model #sPLS-DA model using all omics.
> diabloFeats <- diabloRes$biosignature #selected features for each omic.
> diabloFeatTable <- buildFeatTable(diabloFeats[[1]], 
+   omic2[[1]], 
+   omic2$Y)
Error in xtfrm.data.frame(x) : cannot xtfrm data frames
Calls: buildFeatTable ... lapply -> FUN -> as.vector -> xtfrm -> xtfrm.data.frame
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘multiSight.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/multiSight.Rcheck/00check.log’
for details.


Installation output

multiSight.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL multiSight
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘multiSight’ ...
** using staged installation
** R
** data
** 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: Package 'multiSight' is deprecated and will be removed from
  Bioconductor version 3.19
** testing if installed package can be loaded from final location
Warning: Package 'multiSight' is deprecated and will be removed from
  Bioconductor version 3.19
** testing if installed package keeps a record of temporary installation path
* DONE (multiSight)

Tests output

multiSight.Rcheck/tests/testthat.Rout


R version 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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(testthat)
> # library(multiSight)
> 
> # test_check("multiSight")
> 
> proc.time()
   user  system elapsed 
  0.308   0.044   0.342 

Example timings

multiSight.Rcheck/multiSight-Ex.timings

nameusersystemelapsed
assessPerformance_Biosigner0.0900.0080.098
assessPerformance_Diablo0.0260.0000.026