Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:46 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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 2086/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
STdeconvolve 1.8.0 (landing page) Brendan Miller
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ||||||||
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. |
Package: STdeconvolve |
Version: 1.8.0 |
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_1.8.0.tar.gz |
StartedAt: 2024-05-07 01:18:15 -0400 (Tue, 07 May 2024) |
EndedAt: 2024-05-07 01:19:36 -0400 (Tue, 07 May 2024) |
EllapsedTime: 80.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: STdeconvolve.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/STdeconvolve.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-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 Ventura 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘STdeconvolve/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘STdeconvolve’ version ‘1.8.0’ * 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 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: alphaBool K perplexAdj Pixel.Groups rareCtsAdj Row.names value Var1 Var2 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 9.261 0.054 9.653 topGenes 1.226 0.078 5.076 optimalModel 1.033 0.058 7.060 * 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 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-3.19-bioc-mac-arm64/meat/STdeconvolve.Rcheck/00check.log’ for details.
STdeconvolve.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL STdeconvolve ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-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)
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: aarch64-apple-darwin20 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 13.778 0.265 14.055
STdeconvolve.Rcheck/STdeconvolve-Ex.timings
name | user | system | elapsed | |
cleanCounts | 0.251 | 0.013 | 0.264 | |
correlationPlot | 2.742 | 0.059 | 2.802 | |
fitLDA | 1.053 | 0.047 | 4.770 | |
getBetaTheta | 1.079 | 0.059 | 4.816 | |
getCorrMtx | 2.181 | 0.027 | 2.217 | |
getOverdispersedGenes | 0.615 | 0.051 | 0.668 | |
lsatPairs | 2.298 | 0.051 | 2.356 | |
optimalModel | 1.033 | 0.058 | 7.060 | |
perplexityPlot | 9.261 | 0.054 | 9.653 | |
preprocess | 0.615 | 0.050 | 0.664 | |
restrictCorpus | 0.441 | 0.127 | 0.574 | |
topGenes | 1.226 | 0.078 | 5.076 | |
vizAllTopics | 2.717 | 0.096 | 2.819 | |
vizGeneCounts | 0.696 | 0.045 | 0.742 | |
vizTopic | 2.463 | 0.068 | 2.536 | |