Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-30 12:08 -0400 (Sat, 30 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 1908/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Sconify 1.29.0 (landing page) Tyler J Burns
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the Sconify package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Sconify.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. |
Package: Sconify |
Version: 1.29.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Sconify.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Sconify_1.29.0.tar.gz |
StartedAt: 2025-08-29 21:35:37 -0400 (Fri, 29 Aug 2025) |
EndedAt: 2025-08-29 21:36:43 -0400 (Fri, 29 Aug 2025) |
EllapsedTime: 65.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Sconify.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Sconify.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Sconify_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Sconify.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Sconify/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Sconify’ version ‘1.29.0’ * 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 ‘Sconify’ 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 ... OK * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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: OK
Sconify.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Sconify ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘Sconify’ ... ** this is package ‘Sconify’ version ‘1.29.0’ ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Note: wrong number of arguments to '/' Note: wrong number of arguments to 'asinh' ** 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 (Sconify)
Sconify.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 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(Sconify) > > test_check("Sconify") Read the 100 x 27 data matrix successfully! Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000 Computing input similarities... Building tree... Done in 0.00 seconds (sparsity = 0.966000)! Learning embedding... Iteration 50: error is 52.953902 (50 iterations in 0.01 seconds) Iteration 100: error is 56.091405 (50 iterations in 0.01 seconds) Iteration 150: error is 55.259925 (50 iterations in 0.01 seconds) Iteration 200: error is 56.968425 (50 iterations in 0.01 seconds) Iteration 250: error is 57.482874 (50 iterations in 0.01 seconds) Iteration 300: error is 1.417019 (50 iterations in 0.00 seconds) Iteration 350: error is 0.825905 (50 iterations in 0.00 seconds) Iteration 400: error is 0.435366 (50 iterations in 0.00 seconds) Iteration 450: error is 0.265505 (50 iterations in 0.00 seconds) Iteration 500: error is 0.248570 (50 iterations in 0.00 seconds) Iteration 550: error is 0.243293 (50 iterations in 0.00 seconds) Iteration 600: error is 0.242573 (50 iterations in 0.00 seconds) Iteration 650: error is 0.240451 (50 iterations in 0.00 seconds) Iteration 700: error is 0.240805 (50 iterations in 0.00 seconds) Iteration 750: error is 0.239556 (50 iterations in 0.00 seconds) Iteration 800: error is 0.237444 (50 iterations in 0.00 seconds) Iteration 850: error is 0.239481 (50 iterations in 0.00 seconds) Iteration 900: error is 0.239622 (50 iterations in 0.00 seconds) Iteration 950: error is 0.239217 (50 iterations in 0.00 seconds) Iteration 1000: error is 0.238326 (50 iterations in 0.00 seconds) Fitting performed in 0.08 seconds. Read the 1000 x 27 data matrix successfully! Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000 Computing input similarities... Building tree... Done in 0.05 seconds (sparsity = 0.129120)! Learning embedding... Iteration 50: error is 64.803602 (50 iterations in 0.10 seconds) Iteration 100: error is 60.784714 (50 iterations in 0.08 seconds) Iteration 150: error is 60.354229 (50 iterations in 0.08 seconds) Iteration 200: error is 60.206910 (50 iterations in 0.08 seconds) Iteration 250: error is 60.136255 (50 iterations in 0.09 seconds) Iteration 300: error is 1.359249 (50 iterations in 0.07 seconds) Iteration 350: error is 1.246645 (50 iterations in 0.07 seconds) Iteration 400: error is 1.215027 (50 iterations in 0.06 seconds) Iteration 450: error is 1.204065 (50 iterations in 0.06 seconds) Iteration 500: error is 1.196291 (50 iterations in 0.06 seconds) Iteration 550: error is 1.188271 (50 iterations in 0.06 seconds) Iteration 600: error is 1.176747 (50 iterations in 0.06 seconds) Iteration 650: error is 1.169759 (50 iterations in 0.06 seconds) Iteration 700: error is 1.166133 (50 iterations in 0.06 seconds) Iteration 750: error is 1.163286 (50 iterations in 0.06 seconds) Iteration 800: error is 1.160754 (50 iterations in 0.06 seconds) Iteration 850: error is 1.158754 (50 iterations in 0.06 seconds) Iteration 900: error is 1.156805 (50 iterations in 0.06 seconds) Iteration 950: error is 1.155484 (50 iterations in 0.06 seconds) Iteration 1000: error is 1.154607 (50 iterations in 0.06 seconds) Fitting performed in 1.36 seconds. [ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ] > > proc.time() user system elapsed 6.639 0.337 6.992
Sconify.Rcheck/Sconify-Ex.timings
name | user | system | elapsed | |
FcsToTibble | 0.041 | 0.001 | 0.042 | |
Fnn | 0.117 | 0.282 | 0.407 | |
GetKnnDe | 0.039 | 0.002 | 0.041 | |
GetMarkerNames | 0.009 | 0.001 | 0.009 | |
ImputeTesting | 0.980 | 0.008 | 0.988 | |
MakeHist | 0.102 | 0.003 | 0.104 | |
MakeKnnList | 0.114 | 0.002 | 0.115 | |
MeaningOfLife | 0 | 0 | 0 | |
ParseMarkers | 0.091 | 0.010 | 0.100 | |
PostProcessing | 0.026 | 0.001 | 0.027 | |
ProcessMultipleFiles | 0.037 | 0.002 | 0.040 | |
QuantNormalizeElements | 0.066 | 0.001 | 0.067 | |
SconeValues | 3.845 | 0.101 | 3.952 | |
SplitFile | 0.023 | 0.001 | 0.024 | |
StringToNumbers | 0 | 0 | 0 | |
SubsampleAndTsne | 0.630 | 0.058 | 0.689 | |
TsneVis | 0.055 | 0.001 | 0.056 | |