Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 1853/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Sconify 1.25.0 (landing page) Tyler J Burns
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.25.0 |
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_1.25.0.tar.gz |
StartedAt: 2024-06-10 09:40:26 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 09:45:02 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 275.4 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_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Sconify.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-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 Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Sconify/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Sconify’ version ‘1.25.0’ * 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 30.736 0.364 37.750 ImputeTesting 9.063 0.058 11.428 * 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/4.4-x86_64/Resources/library’ * installing *source* package ‘Sconify’ ... ** 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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 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 = 0.967400)! Learning embedding... Iteration 50: error is 54.182424 (50 iterations in 0.02 seconds) Iteration 100: error is 49.213650 (50 iterations in 0.02 seconds) Iteration 150: error is 53.357058 (50 iterations in 0.02 seconds) Iteration 200: error is 52.619021 (50 iterations in 0.02 seconds) Iteration 250: error is 49.157728 (50 iterations in 0.02 seconds) Iteration 300: error is 1.279819 (50 iterations in 0.01 seconds) Iteration 350: error is 0.688972 (50 iterations in 0.01 seconds) Iteration 400: error is 0.287308 (50 iterations in 0.01 seconds) Iteration 450: error is 0.209693 (50 iterations in 0.01 seconds) Iteration 500: error is 0.198163 (50 iterations in 0.01 seconds) Iteration 550: error is 0.200273 (50 iterations in 0.01 seconds) Iteration 600: error is 0.200744 (50 iterations in 0.01 seconds) Iteration 650: error is 0.198961 (50 iterations in 0.01 seconds) Iteration 700: error is 0.201158 (50 iterations in 0.01 seconds) Iteration 750: error is 0.199734 (50 iterations in 0.01 seconds) Iteration 800: error is 0.200078 (50 iterations in 0.01 seconds) Iteration 850: error is 0.200445 (50 iterations in 0.01 seconds) Iteration 900: error is 0.199806 (50 iterations in 0.01 seconds) Iteration 950: error is 0.201206 (50 iterations in 0.02 seconds) Iteration 1000: error is 0.200545 (50 iterations in 0.01 seconds) Fitting performed in 0.30 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 0.21 seconds (sparsity = 0.129120)! Learning embedding... Iteration 50: error is 65.427559 (50 iterations in 0.35 seconds) Iteration 100: error is 60.724882 (50 iterations in 0.26 seconds) Iteration 150: error is 60.321096 (50 iterations in 0.26 seconds) Iteration 200: error is 60.181057 (50 iterations in 0.28 seconds) Iteration 250: error is 60.120456 (50 iterations in 0.30 seconds) Iteration 300: error is 1.340939 (50 iterations in 0.22 seconds) Iteration 350: error is 1.232154 (50 iterations in 0.21 seconds) Iteration 400: error is 1.204105 (50 iterations in 0.21 seconds) Iteration 450: error is 1.191287 (50 iterations in 0.21 seconds) Iteration 500: error is 1.182420 (50 iterations in 0.22 seconds) Iteration 550: error is 1.175595 (50 iterations in 0.22 seconds) Iteration 600: error is 1.171390 (50 iterations in 0.23 seconds) Iteration 650: error is 1.167422 (50 iterations in 0.22 seconds) Iteration 700: error is 1.164883 (50 iterations in 0.22 seconds) Iteration 750: error is 1.163513 (50 iterations in 0.22 seconds) Iteration 800: error is 1.161508 (50 iterations in 0.22 seconds) Iteration 850: error is 1.158791 (50 iterations in 0.23 seconds) Iteration 900: error is 1.156413 (50 iterations in 0.23 seconds) Iteration 950: error is 1.154983 (50 iterations in 0.23 seconds) Iteration 1000: error is 1.152639 (50 iterations in 0.23 seconds) Fitting performed in 4.77 seconds. [ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ] > > proc.time() user system elapsed 47.269 1.080 57.341
Sconify.Rcheck/Sconify-Ex.timings
name | user | system | elapsed | |
FcsToTibble | 0.305 | 0.011 | 0.387 | |
Fnn | 0.999 | 2.778 | 4.637 | |
GetKnnDe | 0.118 | 0.020 | 0.184 | |
GetMarkerNames | 0.062 | 0.005 | 0.087 | |
ImputeTesting | 9.063 | 0.058 | 11.428 | |
MakeHist | 0.723 | 0.017 | 0.897 | |
MakeKnnList | 0.840 | 0.028 | 1.042 | |
MeaningOfLife | 0.000 | 0.000 | 0.001 | |
ParseMarkers | 0.562 | 0.040 | 0.739 | |
PostProcessing | 0.258 | 0.006 | 0.321 | |
ProcessMultipleFiles | 0.260 | 0.008 | 0.331 | |
QuantNormalizeElements | 0.529 | 0.005 | 0.644 | |
SconeValues | 30.736 | 0.364 | 37.750 | |
SplitFile | 0.200 | 0.004 | 0.249 | |
StringToNumbers | 0.000 | 0.001 | 0.001 | |
SubsampleAndTsne | 2.807 | 0.061 | 3.493 | |
TsneVis | 0.400 | 0.013 | 0.516 | |