Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
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 1924/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Sconify 1.28.1 (landing page) Tyler J Burns
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | 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: 1.28.1 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Sconify_1.28.1.tar.gz |
StartedAt: 2025-10-16 03:22:33 -0400 (Thu, 16 Oct 2025) |
EndedAt: 2025-10-16 03:24:49 -0400 (Thu, 16 Oct 2025) |
EllapsedTime: 136.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Sconify.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Sconify_1.28.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-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 ‘1.28.1’ * 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 11.766 0.132 11.908 * 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-3.21-bioc/R/bin/R CMD INSTALL Sconify ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘Sconify’ ... ** this is package ‘Sconify’ version ‘1.28.1’ ** 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 52.604365 (50 iterations in 0.01 seconds) Iteration 100: error is 52.941963 (50 iterations in 0.01 seconds) Iteration 150: error is 54.547214 (50 iterations in 0.01 seconds) Iteration 200: error is 55.475063 (50 iterations in 0.01 seconds) Iteration 250: error is 52.546360 (50 iterations in 0.01 seconds) Iteration 300: error is 1.226017 (50 iterations in 0.01 seconds) Iteration 350: error is 0.729698 (50 iterations in 0.01 seconds) Iteration 400: error is 0.248717 (50 iterations in 0.01 seconds) Iteration 450: error is 0.217112 (50 iterations in 0.01 seconds) Iteration 500: error is 0.212353 (50 iterations in 0.01 seconds) Iteration 550: error is 0.210103 (50 iterations in 0.01 seconds) Iteration 600: error is 0.211386 (50 iterations in 0.01 seconds) Iteration 650: error is 0.212954 (50 iterations in 0.01 seconds) Iteration 700: error is 0.215807 (50 iterations in 0.01 seconds) Iteration 750: error is 0.217222 (50 iterations in 0.01 seconds) Iteration 800: error is 0.216356 (50 iterations in 0.01 seconds) Iteration 850: error is 0.215537 (50 iterations in 0.01 seconds) Iteration 900: error is 0.216193 (50 iterations in 0.01 seconds) Iteration 950: error is 0.216553 (50 iterations in 0.01 seconds) Iteration 1000: error is 0.215007 (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 66.983609 (50 iterations in 0.21 seconds) Iteration 100: error is 60.747735 (50 iterations in 0.16 seconds) Iteration 150: error is 60.313309 (50 iterations in 0.16 seconds) Iteration 200: error is 60.182912 (50 iterations in 0.17 seconds) Iteration 250: error is 60.124605 (50 iterations in 0.17 seconds) Iteration 300: error is 1.334607 (50 iterations in 0.14 seconds) Iteration 350: error is 1.231727 (50 iterations in 0.13 seconds) Iteration 400: error is 1.202211 (50 iterations in 0.14 seconds) Iteration 450: error is 1.187785 (50 iterations in 0.14 seconds) Iteration 500: error is 1.180237 (50 iterations in 0.14 seconds) Iteration 550: error is 1.176652 (50 iterations in 0.13 seconds) Iteration 600: error is 1.173632 (50 iterations in 0.14 seconds) Iteration 650: error is 1.171729 (50 iterations in 0.14 seconds) Iteration 700: error is 1.169637 (50 iterations in 0.14 seconds) Iteration 750: error is 1.168604 (50 iterations in 0.14 seconds) Iteration 800: error is 1.166284 (50 iterations in 0.14 seconds) Iteration 850: error is 1.164540 (50 iterations in 0.14 seconds) Iteration 900: error is 1.163144 (50 iterations in 0.14 seconds) Iteration 950: error is 1.161478 (50 iterations in 0.14 seconds) Iteration 1000: error is 1.159731 (50 iterations in 0.14 seconds) Fitting performed in 2.93 seconds. [ FAIL 0 | WARN 2 | SKIP 0 | PASS 72 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 72 ] > > proc.time() user system elapsed 18.426 0.439 18.857
Sconify.Rcheck/Sconify-Ex.timings
name | user | system | elapsed | |
FcsToTibble | 0.106 | 0.006 | 0.114 | |
Fnn | 0.309 | 1.091 | 1.400 | |
GetKnnDe | 0.076 | 0.009 | 0.085 | |
GetMarkerNames | 0.026 | 0.006 | 0.033 | |
ImputeTesting | 3.257 | 0.043 | 3.300 | |
MakeHist | 0.539 | 0.021 | 0.559 | |
MakeKnnList | 0.282 | 0.049 | 0.331 | |
MeaningOfLife | 0.000 | 0.000 | 0.001 | |
ParseMarkers | 0.236 | 0.015 | 0.251 | |
PostProcessing | 0.075 | 0.004 | 0.079 | |
ProcessMultipleFiles | 0.095 | 0.005 | 0.099 | |
QuantNormalizeElements | 0.163 | 0.001 | 0.164 | |
SconeValues | 11.766 | 0.132 | 11.908 | |
SplitFile | 0.071 | 0.002 | 0.073 | |
StringToNumbers | 0 | 0 | 0 | |
SubsampleAndTsne | 1.685 | 0.011 | 1.696 | |
TsneVis | 0.195 | 0.014 | 0.210 | |