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This page was generated on 2023-10-20 09:38:08 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1519/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pickgene 1.72.0  (landing page)
Brian S. Yandell
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/pickgene
git_branch: RELEASE_3_17
git_last_commit: 7709d0a
git_last_commit_date: 2023-04-25 09:39:42 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for pickgene on kjohnson2


To the developers/maintainers of the pickgene package:
- 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: pickgene
Version: 1.72.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pickgene.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pickgene_1.72.0.tar.gz
StartedAt: 2023-10-18 14:48:35 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 14:49:23 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 48.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: pickgene.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pickgene.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pickgene_1.72.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/pickgene.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pickgene/DESCRIPTION’ ... OK
* this is package ‘pickgene’ version ‘1.72.0’
* 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 ‘pickgene’ can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'oddsplot(exp(data[[x]]), ': unused argument (chip = "") 
See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/pickgene.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
do.oddsplot: warning in em.ggb(data[[conditions[1]]],
  data[[conditions[2]]], theta, theta[1:3], print = TRUE): partial
  argument match of 'print' to 'printit'
pickgene.poly: warning in pickgene.two(y[, i], intensity, geneid =
  geneID, singlelevel = singlelevel, npick = npickgene, ylab =
  ylabs[i], ...): partial argument match of 'npick' to 'npickgene'
lod.plot: possible error in oddsplot(exp(data[[x]]), exp(data[[y]]),
  theta, col = col, xlab = xlab, ylab = ylab, chip = ""): unused
  argument (chip = "")
nloglik: no visible binding for global variable ‘.fit.xx’
nloglik: no visible binding for global variable ‘.fit.yy’
nploglik: no visible binding for global variable ‘.fit.xx’
nploglik: no visible binding for global variable ‘.fit.yy’
nploglik: no visible binding for global variable ‘.fit.zz’
s.check1: no visible global function definition for ‘lod’
s.marg: no visible binding for global variable ‘x’
shrinkplot: no visible global function definition for ‘s.fits’
shrinkplot: no visible binding for global variable ‘lims’
Undefined global functions or variables:
  .fit.xx .fit.yy .fit.zz lims lod s.fits x
* checking Rd files ... NOTE
prepare_Rd: Simulation.pickgene.Rd:8: Dropping empty section \keyword
prepare_Rd: Simulation.pickgene.Rd:5-6: Dropping empty section \usage
prepare_Rd: Simulation.pickgene.Rd:7: Dropping empty section \details
* 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 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 in ‘inst/doc’ ... 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/pickgene.Rcheck/00check.log’
for details.



Installation output

pickgene.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pickgene
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘pickgene’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Note: possible error in 'oddsplot(exp(data[[x]]), ': unused argument (chip = "") 
** 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 (pickgene)

Tests output


Example timings

pickgene.Rcheck/pickgene-Ex.timings

nameusersystemelapsed
Simulation.pickgene1.0630.0611.708
em.ggb000
model.pickgene0.0110.0010.020
oddsplot000
pickgene0.0000.0010.000
robustscale000