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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1366/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MultiDataSet 1.34.0  (landing page)
Xavier Escribà Montagut
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/MultiDataSet
git_branch: RELEASE_3_20
git_last_commit: a1217b2
git_last_commit_date: 2024-10-29 10:10:29 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for MultiDataSet on merida1

To the developers/maintainers of the MultiDataSet package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MultiDataSet.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: MultiDataSet
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MultiDataSet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MultiDataSet_1.34.0.tar.gz
StartedAt: 2024-12-20 06:40:49 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 06:46:43 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 354.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MultiDataSet.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MultiDataSet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MultiDataSet_1.34.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MultiDataSet.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MultiDataSet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MultiDataSet’ version ‘1.34.0’
* 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 ‘MultiDataSet’ 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    o Add function to add matrices to MDS.
  Cannot process chunk/lines:
    o Add vignettes published in scientific article.
  Cannot process chunk/lines:
    o Remove non-critical dependencies.
  Cannot process chunk/lines:
    o Add wrappers for two functions to integrate omic data: mcia (from omicade4 package) and iClusterPlus.
  Cannot process chunk/lines:
    o Add advanced subsetting by phenotype and feature.
  Cannot process chunk/lines:
    BUG FIXES
  Cannot process chunk/lines:
    o Solve subsetting issues when sampleNames is different from ID column. 
* 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
Unexported objects imported by ':::' calls:
  ‘Biobase:::assayDataEnvLock’ ‘Biobase:::assayDataStorageMode’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
downloadGEO : <anonymous>: no visible global function definition for
  ‘methylationSet’
lambdaClayton: no visible global function definition for ‘qnorm’
lambdaClayton: no visible global function definition for ‘qchisq’
qq_plot: no visible global function definition for ‘qbeta’
Undefined global functions or variables:
  methylationSet qbeta qchisq qnorm
Consider adding
  importFrom("stats", "qbeta", "qchisq", "qnorm")
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 ... WARNING
Codoc mismatches from Rd file 'ResultSet-class.Rd':
\S4method{getAssociation}{ResultSet}
  Code: function(object, rid = 1, coef = 2, contrast = NULL, fNames =
                 NULL, robust = FALSE, ...)
  Docs: function(object, rid = 1, coef = 2, contrast = NULL, fNames =
                 NULL, ...)
  Argument names in code not in docs:
    robust
  Mismatches in argument names:
    Position: 6 Code: robust Docs: ...

* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
add_methy 24.008  1.455  26.476
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/MultiDataSet.Rcheck/00check.log’
for details.


Installation output

MultiDataSet.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MultiDataSet
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘MultiDataSet’ ...
** using staged installation
Warning in .write_description(db, file.path(outDir, "DESCRIPTION")) :
  Unknown encoding with non-ASCII data: converting to ASCII
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
in method for ‘add_methy’ with signature ‘"MultiDataSet","GenomicRatioSet"’: no definition for class “GenomicRatioSet”
** 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 (MultiDataSet)

Tests output


Example timings

MultiDataSet.Rcheck/MultiDataSet-Ex.timings

nameusersystemelapsed
MultiDataSet-class0.0010.0020.003
ResultSet-class0.0020.0010.003
add_eset0.1930.0240.218
add_genexp0.2760.0370.315
add_methy24.008 1.45526.476
add_rnaseq-methods0.1570.0020.177
add_rse0.4250.0180.488
add_se0.0840.0020.095
add_snps0.1160.0050.129
add_table0.0190.0010.021
chrNumToChar0.0010.0010.001
commonIds0.2670.0330.317
commonSamples0.2920.0400.342
getAssociation-methods0.0500.0440.097
lambdaClayton0.0020.0010.003
opt-methods0.0030.0020.005
qq_plot0.8920.1711.116
rowRangesElements0.2090.0280.249
volcano_plot0.4030.0620.505