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This page was generated on 2024-06-18 17:58 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 2086/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
STdeconvolve 1.8.0  (landing page)
Brendan Miller
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/STdeconvolve
git_branch: RELEASE_3_19
git_last_commit: 80525cd
git_last_commit_date: 2024-04-30 11:42:24 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for STdeconvolve on nebbiolo1

To the developers/maintainers of the STdeconvolve package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/STdeconvolve.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: STdeconvolve
Version: 1.8.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:STdeconvolve.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings STdeconvolve_1.8.0.tar.gz
StartedAt: 2024-06-17 04:23:30 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 04:27:54 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 264.6 seconds
RetCode: 0
Status:   OK  
CheckDir: STdeconvolve.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:STdeconvolve.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings STdeconvolve_1.8.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/STdeconvolve.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘STdeconvolve/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘STdeconvolve’ version ‘1.8.0’
* 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 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 loading without being on the library search path ... 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  17.236  0.249  17.484
correlationPlot  6.176  0.191   6.368
vizAllTopics     5.996  0.296   6.292
vizTopic         5.220  0.272   5.491
getBetaTheta     3.050  0.222  11.292
fitLDA           3.016  0.228  11.206
optimalModel     3.000  0.159  17.110
topGenes         2.876  0.188  10.990
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/STdeconvolve.Rcheck/00check.log’
for details.


Installation output

STdeconvolve.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL STdeconvolve
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 28.348   1.136  29.472 

Example timings

STdeconvolve.Rcheck/STdeconvolve-Ex.timings

nameusersystemelapsed
cleanCounts0.7040.0590.763
correlationPlot6.1760.1916.368
fitLDA 3.016 0.22811.206
getBetaTheta 3.050 0.22211.292
getCorrMtx4.5340.2034.737
getOverdispersedGenes1.6390.1091.749
lsatPairs4.7020.1444.846
optimalModel 3.000 0.15917.110
perplexityPlot17.236 0.24917.484
preprocess1.6890.1361.825
restrictCorpus1.2660.4481.714
topGenes 2.876 0.18810.990
vizAllTopics5.9960.2966.292
vizGeneCounts1.4520.1641.616
vizTopic5.2200.2725.491