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This page was generated on 2023-03-20 11:05:08 -0400 (Mon, 20 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4516
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4295
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4324
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 MultiDataSet on nebbiolo2


To the developers/maintainers of the MultiDataSet package:
- Please 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 How and When does the builder pull? When will my changes propagate? 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 1299/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MultiDataSet 1.26.0  (landing page)
Xavier Escribà Montagut
Snapshot Date: 2023-03-17 14:00:04 -0400 (Fri, 17 Mar 2023)
git_url: https://git.bioconductor.org/packages/MultiDataSet
git_branch: RELEASE_3_16
git_last_commit: a83a80a
git_last_commit_date: 2022-11-01 11:13:37 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: MultiDataSet
Version: 1.26.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:MultiDataSet.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings MultiDataSet_1.26.0.tar.gz
StartedAt: 2023-03-17 22:18:21 -0400 (Fri, 17 Mar 2023)
EndedAt: 2023-03-17 22:21:22 -0400 (Fri, 17 Mar 2023)
EllapsedTime: 181.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MultiDataSet.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:MultiDataSet.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings MultiDataSet_1.26.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/MultiDataSet.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘MultiDataSet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MultiDataSet’ 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 ‘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 ... 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
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 documentation object 'ResultSet':
\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 15.623   1.14  16.763
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘MultiDataSet.Rmd’ using ‘UTF-8’... OK
  ‘MultiDataSet_Extending_Proteome.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/MultiDataSet.Rcheck/00check.log’
for details.



Installation output

MultiDataSet.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL MultiDataSet
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/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-class0.0010.0000.001
ResultSet-class0.0020.0000.002
add_eset0.0800.0040.083
add_genexp0.1020.0080.110
add_methy15.623 1.14016.763
add_rnaseq-methods0.0840.0200.103
add_rse0.2290.0320.261
add_se0.0290.0120.040
add_snps0.0470.0040.052
add_table0.0040.0040.008
chrNumToChar000
commonIds0.0950.0160.112
commonSamples0.1220.0120.134
getAssociation-methods0.0180.0080.025
lambdaClayton0.0010.0000.002
opt-methods0.0010.0000.001
qq_plot0.2860.0590.346
rowRangesElements0.0870.0070.096
volcano_plot0.1250.0480.173