Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-29 12:05 -0400 (Mon, 29 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 Patched (2025-08-23 r88802) -- "Great Square Root" | 4833 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4621 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4566 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
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 1918/2334 | 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 | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
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: 2025-09-29 00:08:37 -0400 (Mon, 29 Sep 2025) |
EndedAt: 2025-09-29 00:10:47 -0400 (Mon, 29 Sep 2025) |
EllapsedTime: 129.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: Sconify.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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 (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed SconeValues 13.054 0.191 13.327 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Iteration 900: error is 1.149811 (50 iterations in 0.13 seconds) Iteration 950: error is 1.148487 (50 iterations in 0.13 seconds) Iteration 1000: error is 1.147395 (50 iterations in 0.11 seconds) Fitting performed in 2.72 seconds. [ FAIL 2 | WARN 4 | SKIP 0 | PASS 70 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test.post.processing.R:53:5'): Testing the output of the tSNE vis function ── TsneVis(...) has type 'object', not 'list'. ── Failure ('test.post.processing.R:60:5'): Testing the output of the make.hist function ── MakeHist(wand.final, 100, "IL7.fraction.cond.2", "fraction IL7") has type 'object', not 'list'. [ FAIL 2 | WARN 4 | SKIP 0 | PASS 70 ] Error: Test failures Execution halted * 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 ERROR See ‘/Users/biocbuild/bbs-3.22-bioc/meat/Sconify.Rcheck/00check.log’ for details.
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-x86_64/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.fail
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-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 0.01 seconds (sparsity = 0.970400)! Learning embedding... Iteration 50: error is 48.519500 (50 iterations in 0.01 seconds) Iteration 100: error is 51.300467 (50 iterations in 0.01 seconds) Iteration 150: error is 53.303677 (50 iterations in 0.01 seconds) Iteration 200: error is 50.918689 (50 iterations in 0.01 seconds) Iteration 250: error is 51.524025 (50 iterations in 0.01 seconds) Iteration 300: error is 1.414223 (50 iterations in 0.01 seconds) Iteration 350: error is 0.759576 (50 iterations in 0.01 seconds) Iteration 400: error is 0.297823 (50 iterations in 0.01 seconds) Iteration 450: error is 0.194307 (50 iterations in 0.01 seconds) Iteration 500: error is 0.187407 (50 iterations in 0.01 seconds) Iteration 550: error is 0.179162 (50 iterations in 0.01 seconds) Iteration 600: error is 0.173542 (50 iterations in 0.01 seconds) Iteration 650: error is 0.165531 (50 iterations in 0.01 seconds) Iteration 700: error is 0.165428 (50 iterations in 0.01 seconds) Iteration 750: error is 0.165784 (50 iterations in 0.01 seconds) Iteration 800: error is 0.164532 (50 iterations in 0.01 seconds) Iteration 850: error is 0.165501 (50 iterations in 0.01 seconds) Iteration 900: error is 0.165720 (50 iterations in 0.01 seconds) Iteration 950: error is 0.165608 (50 iterations in 0.01 seconds) Iteration 1000: error is 0.167167 (50 iterations in 0.01 seconds) Fitting performed in 0.16 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 0.13 seconds (sparsity = 0.129120)! Learning embedding... Iteration 50: error is 64.386893 (50 iterations in 0.23 seconds) Iteration 100: error is 60.703866 (50 iterations in 0.16 seconds) Iteration 150: error is 60.351178 (50 iterations in 0.15 seconds) Iteration 200: error is 60.222064 (50 iterations in 0.16 seconds) Iteration 250: error is 60.158373 (50 iterations in 0.17 seconds) Iteration 300: error is 1.336842 (50 iterations in 0.13 seconds) Iteration 350: error is 1.228546 (50 iterations in 0.12 seconds) Iteration 400: error is 1.198067 (50 iterations in 0.12 seconds) Iteration 450: error is 1.182071 (50 iterations in 0.12 seconds) Iteration 500: error is 1.173624 (50 iterations in 0.13 seconds) Iteration 550: error is 1.168681 (50 iterations in 0.14 seconds) Iteration 600: error is 1.164351 (50 iterations in 0.15 seconds) Iteration 650: error is 1.160853 (50 iterations in 0.12 seconds) Iteration 700: error is 1.157974 (50 iterations in 0.11 seconds) Iteration 750: error is 1.155606 (50 iterations in 0.11 seconds) Iteration 800: error is 1.153263 (50 iterations in 0.11 seconds) Iteration 850: error is 1.151365 (50 iterations in 0.11 seconds) Iteration 900: error is 1.149811 (50 iterations in 0.13 seconds) Iteration 950: error is 1.148487 (50 iterations in 0.13 seconds) Iteration 1000: error is 1.147395 (50 iterations in 0.11 seconds) Fitting performed in 2.72 seconds. [ FAIL 2 | WARN 4 | SKIP 0 | PASS 70 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test.post.processing.R:53:5'): Testing the output of the tSNE vis function ── TsneVis(...) has type 'object', not 'list'. ── Failure ('test.post.processing.R:60:5'): Testing the output of the make.hist function ── MakeHist(wand.final, 100, "IL7.fraction.cond.2", "fraction IL7") has type 'object', not 'list'. [ FAIL 2 | WARN 4 | SKIP 0 | PASS 70 ] Error: Test failures Execution halted
Sconify.Rcheck/Sconify-Ex.timings
name | user | system | elapsed | |
FcsToTibble | 0.125 | 0.006 | 0.132 | |
Fnn | 0.309 | 0.976 | 1.319 | |
GetKnnDe | 0.060 | 0.006 | 0.066 | |
GetMarkerNames | 0.028 | 0.003 | 0.031 | |
ImputeTesting | 3.583 | 0.027 | 3.627 | |
MakeHist | 0.636 | 0.011 | 0.651 | |
MakeKnnList | 0.288 | 0.036 | 0.324 | |
MeaningOfLife | 0.001 | 0.000 | 0.000 | |
ParseMarkers | 0.256 | 0.032 | 0.303 | |
PostProcessing | 0.077 | 0.002 | 0.080 | |
ProcessMultipleFiles | 0.122 | 0.007 | 0.129 | |
QuantNormalizeElements | 0.236 | 0.007 | 0.245 | |
SconeValues | 13.054 | 0.191 | 13.327 | |
SplitFile | 0.078 | 0.002 | 0.081 | |
StringToNumbers | 0 | 0 | 0 | |
SubsampleAndTsne | 1.479 | 0.059 | 1.559 | |
TsneVis | 0.345 | 0.008 | 0.355 | |