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This page was generated on 2023-10-20 09:38:01 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 610/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBSeq 1.40.0  (landing page)
Ning Leng
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/EBSeq
git_branch: RELEASE_3_17
git_last_commit: 7d1d2a2
git_last_commit_date: 2023-04-25 10:27:13 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for EBSeq on kjohnson2


To the developers/maintainers of the EBSeq 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: EBSeq
Version: 1.40.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EBSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EBSeq_1.40.0.tar.gz
StartedAt: 2023-10-17 17:12:01 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 17:14:04 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 122.5 seconds
RetCode: 0
Status:   OK  
CheckDir: EBSeq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EBSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EBSeq_1.40.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/EBSeq.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 ‘EBSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EBSeq’ version ‘1.40.0’
* 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 ‘EBSeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
DenNHist: no visible global function definition for ‘hist’
DenNHist: no visible global function definition for ‘lines’
DenNHist: no visible global function definition for ‘dbeta’
DenNHist: no visible global function definition for ‘legend’
EBMultiTest : <anonymous>: no visible global function definition for
  ‘quantile’
EBMultiTest: no visible global function definition for ‘quantile’
EBMultiTest : <anonymous>: no visible binding for global variable ‘var’
EBMultiTest: no visible binding for global variable ‘var’
EBTest : <anonymous>: no visible global function definition for
  ‘quantile’
EBTest: no visible global function definition for ‘quantile’
EBTest: no visible binding for global variable ‘var’
GetDEResults: no visible binding for global variable ‘median’
LogN: no visible global function definition for ‘optim’
LogNMulti: no visible global function definition for ‘optim’
MedianNorm : <anonymous>: no visible global function definition for
  ‘median’
MedianNorm : <anonymous> : <anonymous>: no visible global function
  definition for ‘median’
PlotPattern: no visible global function definition for ‘par’
PlotPattern: no visible global function definition for ‘rainbow’
PlotPattern: no visible global function definition for ‘heatmap’
PlotPostVsRawFC: no visible global function definition for ‘par’
PlotPostVsRawFC: no visible global function definition for ‘abline’
PlotPostVsRawFC: no visible global function definition for ‘rect’
PolyFitPlot: no visible global function definition for ‘lm’
PolyFitPlot: no visible global function definition for ‘smoothScatter’
PolyFitPlot: no visible global function definition for ‘axis’
PolyFitPlot: no visible global function definition for ‘lines’
QQP: no visible global function definition for ‘rbeta’
QQP: no visible global function definition for ‘qqplot’
QQP: no visible global function definition for ‘lm’
QQP: no visible global function definition for ‘abline’
QuantileNorm : <anonymous>: no visible global function definition for
  ‘quantile’
beta.mom: no visible global function definition for ‘var’
Undefined global functions or variables:
  abline axis dbeta heatmap hist legend lines lm median optim par
  qqplot quantile rainbow rbeta rect smoothScatter var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "axis", "hist", "legend", "lines",
             "par", "rect", "smoothScatter")
  importFrom("stats", "dbeta", "heatmap", "lm", "median", "optim",
             "qqplot", "quantile", "rbeta", "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
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
GetMultiFC  4.172  0.044   5.403
EBMultiTest 4.016  0.039   6.003
GetMultiPP  4.003  0.041   5.852
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/EBSeq.Rcheck/00check.log’
for details.



Installation output

EBSeq.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘EBSeq’ ...
** using staged installation
** R
** data
** demo
** 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 (EBSeq)

Tests output


Example timings

EBSeq.Rcheck/EBSeq-Ex.timings

nameusersystemelapsed
DenNHist2.1900.0653.410
EBMultiTest4.0160.0396.003
EBSeq_NingLeng-package0.3840.0180.510
EBTest0.3720.0140.491
GeneMat0.0020.0010.003
GetDEResults0.3930.0130.518
GetMultiFC4.1720.0445.403
GetMultiPP4.0030.0415.852
GetNg0.0060.0010.014
GetNormalizedMat0.0060.0020.012
GetPP0.3830.0120.577
GetPPMat0.5080.0190.765
GetPatterns0.0010.0010.001
IsoList0.0020.0010.007
IsoMultiList0.0010.0010.005
Likefun0.0000.0010.001
LikefunMulti0.0000.0000.001
LogN000
LogNMulti0.0000.0000.001
MedianNorm0.0040.0020.010
MultiGeneMat0.0020.0010.002
PlotPattern0.0100.0010.018
PlotPostVsRawFC0.7040.0241.054
PolyFitPlot0.0100.0020.018
PostFC0.5190.0170.721
QQP1.7130.0422.539
QuantileNorm0.0040.0020.007
RankNorm0.0070.0020.010
beta.mom0.0000.0000.001
crit_fun0.5680.0170.849
f0000
f1000