Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-05 12:05 -0400 (Fri, 05 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4618 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4565 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4544 |
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 1909/2322 | 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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Sconify_1.29.0.tar.gz |
StartedAt: 2025-09-05 03:55:44 -0400 (Fri, 05 Sep 2025) |
EndedAt: 2025-09-05 03:57:57 -0400 (Fri, 05 Sep 2025) |
EllapsedTime: 133.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Sconify.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Sconify_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Sconify.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * 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 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 ... 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed SconeValues 12.276 0.182 12.459 * 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: OK
Sconify.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Sconify ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 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(Sconify) > > test_check("Sconify") Read the 100 x 27 data matrix successfully! OpenMP is working. 1 threads. Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000 Computing input similarities... Building tree... Done in 0.01 seconds (sparsity = 0.967400)! Learning embedding... Iteration 50: error is 51.998104 (50 iterations in 0.01 seconds) Iteration 100: error is 52.283897 (50 iterations in 0.01 seconds) Iteration 150: error is 51.401491 (50 iterations in 0.01 seconds) Iteration 200: error is 53.097568 (50 iterations in 0.01 seconds) Iteration 250: error is 54.146485 (50 iterations in 0.01 seconds) Iteration 300: error is 1.311662 (50 iterations in 0.01 seconds) Iteration 350: error is 0.474460 (50 iterations in 0.01 seconds) Iteration 400: error is 0.207220 (50 iterations in 0.01 seconds) Iteration 450: error is 0.185355 (50 iterations in 0.01 seconds) Iteration 500: error is 0.179366 (50 iterations in 0.01 seconds) Iteration 550: error is 0.175746 (50 iterations in 0.01 seconds) Iteration 600: error is 0.175941 (50 iterations in 0.01 seconds) Iteration 650: error is 0.175111 (50 iterations in 0.01 seconds) Iteration 700: error is 0.173882 (50 iterations in 0.01 seconds) Iteration 750: error is 0.174175 (50 iterations in 0.01 seconds) Iteration 800: error is 0.174346 (50 iterations in 0.01 seconds) Iteration 850: error is 0.174877 (50 iterations in 0.01 seconds) Iteration 900: error is 0.173639 (50 iterations in 0.01 seconds) Iteration 950: error is 0.175058 (50 iterations in 0.01 seconds) Iteration 1000: error is 0.174023 (50 iterations in 0.01 seconds) Fitting performed in 0.17 seconds. Read the 1000 x 27 data matrix successfully! OpenMP is working. 1 threads. Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000 Computing input similarities... Building tree... Done in 0.12 seconds (sparsity = 0.129120)! Learning embedding... Iteration 50: error is 66.380147 (50 iterations in 0.28 seconds) Iteration 100: error is 60.695638 (50 iterations in 0.17 seconds) Iteration 150: error is 60.321465 (50 iterations in 0.16 seconds) Iteration 200: error is 60.187887 (50 iterations in 0.17 seconds) Iteration 250: error is 60.120934 (50 iterations in 0.17 seconds) Iteration 300: error is 1.328680 (50 iterations in 0.14 seconds) Iteration 350: error is 1.226639 (50 iterations in 0.14 seconds) Iteration 400: error is 1.196830 (50 iterations in 0.14 seconds) Iteration 450: error is 1.179636 (50 iterations in 0.14 seconds) Iteration 500: error is 1.171795 (50 iterations in 0.14 seconds) Iteration 550: error is 1.167925 (50 iterations in 0.14 seconds) Iteration 600: error is 1.164065 (50 iterations in 0.14 seconds) Iteration 650: error is 1.158916 (50 iterations in 0.14 seconds) Iteration 700: error is 1.156117 (50 iterations in 0.14 seconds) Iteration 750: error is 1.153829 (50 iterations in 0.14 seconds) Iteration 800: error is 1.150609 (50 iterations in 0.14 seconds) Iteration 850: error is 1.147521 (50 iterations in 0.14 seconds) Iteration 900: error is 1.145082 (50 iterations in 0.14 seconds) Iteration 950: error is 1.142951 (50 iterations in 0.14 seconds) Iteration 1000: error is 1.140493 (50 iterations in 0.14 seconds) Fitting performed in 3.04 seconds. [ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ] > > proc.time() user system elapsed 19.207 0.721 19.966
Sconify.Rcheck/Sconify-Ex.timings
name | user | system | elapsed | |
FcsToTibble | 0.132 | 0.002 | 0.134 | |
Fnn | 0.198 | 0.139 | 0.337 | |
GetKnnDe | 0.074 | 0.015 | 0.089 | |
GetMarkerNames | 0.025 | 0.020 | 0.044 | |
ImputeTesting | 3.258 | 0.106 | 3.364 | |
MakeHist | 0.295 | 0.005 | 0.300 | |
MakeKnnList | 0.290 | 0.006 | 0.296 | |
MeaningOfLife | 0 | 0 | 0 | |
ParseMarkers | 0.207 | 0.036 | 0.242 | |
PostProcessing | 0.077 | 0.013 | 0.091 | |
ProcessMultipleFiles | 0.104 | 0.005 | 0.110 | |
QuantNormalizeElements | 0.197 | 0.001 | 0.198 | |
SconeValues | 12.276 | 0.182 | 12.459 | |
SplitFile | 0.071 | 0.002 | 0.074 | |
StringToNumbers | 0.001 | 0.000 | 0.000 | |
SubsampleAndTsne | 1.805 | 0.003 | 1.809 | |
TsneVis | 0.169 | 0.003 | 0.173 | |