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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1179/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mdqc 1.68.0  (landing page)
Gabriela Cohen-Freue
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/mdqc
git_branch: RELEASE_3_20
git_last_commit: 53ca0da
git_last_commit_date: 2024-10-29 09:28:38 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for mdqc on lconway

To the developers/maintainers of the mdqc package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mdqc.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: mdqc
Version: 1.68.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mdqc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mdqc_1.68.0.tar.gz
StartedAt: 2024-11-19 23:43:46 -0500 (Tue, 19 Nov 2024)
EndedAt: 2024-11-19 23:47:52 -0500 (Tue, 19 Nov 2024)
EllapsedTime: 246.1 seconds
RetCode: 0
Status:   OK  
CheckDir: mdqc.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mdqc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mdqc_1.68.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/mdqc.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘mdqc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mdqc’ version ‘1.68.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘mdqc’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Tbsb: no visible global function definition for ‘pchisq’
Tbsc: no visible global function definition for ‘qchisq’
ksiint: no visible global function definition for ‘pgamma’
mdqc: no visible global function definition for ‘as.dist’
mdqc: no visible global function definition for ‘mahalanobis’
mySm: no visible global function definition for ‘var’
mySm: no visible global function definition for ‘mahalanobis’
plot.mdqc: no visible global function definition for ‘par’
plot.mdqc: no visible global function definition for ‘abline’
plot.mdqc: no visible global function definition for ‘qchisq’
plot.mdqc: no visible global function definition for ‘points’
plot.mdqc: no visible global function definition for ‘text’
print.mdqc: no visible global function definition for ‘qchisq’
summary.mdqc: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  abline as.dist mahalanobis par pchisq pgamma points qchisq text var
Consider adding
  importFrom("graphics", "abline", "par", "points", "text")
  importFrom("stats", "as.dist", "mahalanobis", "pchisq", "pgamma",
             "qchisq", "var")
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 ... 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 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/mdqc.Rcheck/00check.log’
for details.


Installation output

mdqc.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘mdqc’ ...
** using staged installation
** R
** data
** 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 (mdqc)

Tests output


Example timings

mdqc.Rcheck/mdqc-Ex.timings

nameusersystemelapsed
allQC0.0100.0040.014
mdqc1.1410.0161.159
plot.mdqc0.2680.0040.273
prcomp.robust0.1890.0060.197