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This page was generated on 2023-10-20 09:38:13 -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 2025/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
STdeconvolve 1.4.0  (landing page)
Brendan Miller
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/STdeconvolve
git_branch: RELEASE_3_17
git_last_commit: 0f0d821
git_last_commit_date: 2023-04-25 11:37:59 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for STdeconvolve on kjohnson2


To the developers/maintainers of the STdeconvolve 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: STdeconvolve
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:STdeconvolve.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings STdeconvolve_1.4.0.tar.gz
StartedAt: 2023-10-19 04:57:31 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 05:05:18 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 467.3 seconds
RetCode: 0
Status:   OK  
CheckDir: STdeconvolve.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:STdeconvolve.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings STdeconvolve_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/STdeconvolve.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 ‘STdeconvolve/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘STdeconvolve’ version ‘1.4.0’
* package encoding: UTF-8
* 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 ‘STdeconvolve’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
correlationPlot: no visible binding for global variable ‘Var1’
correlationPlot: no visible binding for global variable ‘Var2’
correlationPlot: no visible binding for global variable ‘value’
fitLDA: no visible binding for global variable ‘rareCtsAdj’
fitLDA: no visible binding for global variable ‘K’
fitLDA: no visible binding for global variable ‘perplexAdj’
fitLDA: no visible binding for global variable ‘alphaBool’
perplexityPlot: no visible binding for global variable ‘rareCtsAdj’
perplexityPlot: no visible binding for global variable ‘K’
perplexityPlot: no visible binding for global variable ‘perplexAdj’
perplexityPlot: no visible binding for global variable ‘alphaBool’
vizAllTopics: no visible binding for global variable ‘x’
vizAllTopics: no visible binding for global variable ‘y’
vizAllTopics: no visible binding for global variable ‘Row.names’
vizAllTopics: no visible binding for global variable ‘Pixel.Groups’
vizGeneCounts: no visible binding for global variable ‘x’
vizGeneCounts: no visible binding for global variable ‘y’
vizTopic: no visible binding for global variable ‘x’
vizTopic: no visible binding for global variable ‘y’
Undefined global functions or variables:
  K Pixel.Groups Row.names Var1 Var2 alphaBool perplexAdj rareCtsAdj
  value x y
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
perplexityPlot  24.153  0.253  42.969
correlationPlot  8.371  0.237  15.561
vizAllTopics     8.009  0.397  17.449
vizTopic         7.204  0.301  15.759
lsatPairs        6.573  0.133  11.662
getCorrMtx       6.255  0.130  11.018
topGenes         3.730  0.824  36.881
fitLDA           4.031  0.139  27.683
getBetaTheta     3.690  0.147  26.924
optimalModel     3.580  0.161  54.317
preprocess       2.726  0.114   5.250
vizGeneCounts    2.406  0.167   5.502
restrictCorpus   2.038  0.470   6.896
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/STdeconvolve.Rcheck/00check.log’
for details.



Installation output

STdeconvolve.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘STdeconvolve’ ...
** 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 (STdeconvolve)

Tests output

STdeconvolve.Rcheck/tests/testthat.Rout

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(STdeconvolve)
> 
> test_check("STdeconvolve")
A 260x232 simple triplet matrix.
A 260x10 simple triplet matrix.
now fitting LDA model with K = 2 
now fitting LDA model with K = 3 
now fitting LDA model with K = 4 
now fitting LDA model with K = 5 
computing perplexity for LDA model with K = 2 
computing perplexity for LDA model with K = 3 
computing perplexity for LDA model with K = 4 
computing perplexity for LDA model with K = 5 
initial: [1e+02 - 3] [1e+03 - 3] [1e+04 - 2] done
initial: [1e+02 - 3] [1e+03 - 2] [1e+04 - 2] done
initial: [1e+02 - 4] [1e+03 - 4] [1e+04 - 3] done
initial: [1e+02 - 4] [1e+03 - 4] [1e+04 - 4] done
initial: [1e+02 - 4] [1e+03 - 4] [1e+04 - 4] done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 26 ]
> 
> proc.time()
   user  system elapsed 
 37.546   1.262  74.438 

Example timings

STdeconvolve.Rcheck/STdeconvolve-Ex.timings

nameusersystemelapsed
cleanCounts1.3360.0532.464
correlationPlot 8.371 0.23715.561
fitLDA 4.031 0.13927.683
getBetaTheta 3.690 0.14726.924
getCorrMtx 6.255 0.13011.018
getOverdispersedGenes2.4440.1004.458
lsatPairs 6.573 0.13311.662
optimalModel 3.580 0.16154.317
perplexityPlot24.153 0.25342.969
preprocess2.7260.1145.250
restrictCorpus2.0380.4706.896
topGenes 3.730 0.82436.881
vizAllTopics 8.009 0.39717.449
vizGeneCounts2.4060.1675.502
vizTopic 7.204 0.30115.759