Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-17 11:37:53 -0400 (Fri, 17 May 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" | 4663 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4398 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4425 |
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 1847/2230 | 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 | see weekly results here | ||||||||||||
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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Sconify.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Sconify_1.25.0.tar.gz |
StartedAt: 2024-05-16 04:59:43 -0400 (Thu, 16 May 2024) |
EndedAt: 2024-05-16 05:01:47 -0400 (Thu, 16 May 2024) |
EllapsedTime: 124.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Sconify.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Sconify.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Sconify_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/Sconify.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * 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 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 15.9 0.39 16.3 * 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: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Sconify ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 0.02 seconds (sparsity = 0.968600)! Learning embedding... Iteration 50: error is 54.159619 (50 iterations in 0.01 seconds) Iteration 100: error is 52.852716 (50 iterations in 0.01 seconds) Iteration 150: error is 51.265046 (50 iterations in 0.02 seconds) Iteration 200: error is 53.228294 (50 iterations in 0.01 seconds) Iteration 250: error is 54.580903 (50 iterations in 0.01 seconds) Iteration 300: error is 1.199900 (50 iterations in 0.01 seconds) Iteration 350: error is 0.333266 (50 iterations in 0.01 seconds) Iteration 400: error is 0.223244 (50 iterations in 0.01 seconds) Iteration 450: error is 0.222522 (50 iterations in 0.01 seconds) Iteration 500: error is 0.218826 (50 iterations in 0.01 seconds) Iteration 550: error is 0.218162 (50 iterations in 0.01 seconds) Iteration 600: error is 0.220909 (50 iterations in 0.01 seconds) Iteration 650: error is 0.222884 (50 iterations in 0.01 seconds) Iteration 700: error is 0.222903 (50 iterations in 0.01 seconds) Iteration 750: error is 0.223680 (50 iterations in 0.01 seconds) Iteration 800: error is 0.220684 (50 iterations in 0.01 seconds) Iteration 850: error is 0.220798 (50 iterations in 0.01 seconds) Iteration 900: error is 0.221753 (50 iterations in 0.01 seconds) Iteration 950: error is 0.222034 (50 iterations in 0.01 seconds) Iteration 1000: error is 0.221649 (50 iterations in 0.01 seconds) Fitting performed in 0.18 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 0.18 seconds (sparsity = 0.129120)! Learning embedding... Iteration 50: error is 65.675848 (50 iterations in 0.34 seconds) Iteration 100: error is 60.761423 (50 iterations in 0.24 seconds) Iteration 150: error is 60.343831 (50 iterations in 0.18 seconds) Iteration 200: error is 60.210177 (50 iterations in 0.16 seconds) Iteration 250: error is 60.157230 (50 iterations in 0.17 seconds) Iteration 300: error is 1.336406 (50 iterations in 0.14 seconds) Iteration 350: error is 1.226238 (50 iterations in 0.15 seconds) Iteration 400: error is 1.195763 (50 iterations in 0.11 seconds) Iteration 450: error is 1.184217 (50 iterations in 0.11 seconds) Iteration 500: error is 1.174449 (50 iterations in 0.11 seconds) Iteration 550: error is 1.167777 (50 iterations in 0.11 seconds) Iteration 600: error is 1.163764 (50 iterations in 0.11 seconds) Iteration 650: error is 1.159963 (50 iterations in 0.11 seconds) Iteration 700: error is 1.156359 (50 iterations in 0.12 seconds) Iteration 750: error is 1.153106 (50 iterations in 0.11 seconds) Iteration 800: error is 1.151136 (50 iterations in 0.11 seconds) Iteration 850: error is 1.148869 (50 iterations in 0.11 seconds) Iteration 900: error is 1.147638 (50 iterations in 0.11 seconds) Iteration 950: error is 1.146841 (50 iterations in 0.11 seconds) Iteration 1000: error is 1.145198 (50 iterations in 0.11 seconds) Fitting performed in 2.82 seconds. [ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ] > > proc.time() user system elapsed 23.28 1.01 24.34
Sconify.Rcheck/Sconify-Ex.timings
name | user | system | elapsed | |
FcsToTibble | 0.13 | 0.02 | 0.14 | |
Fnn | 0.50 | 0.51 | 1.01 | |
GetKnnDe | 0.07 | 0.00 | 0.06 | |
GetMarkerNames | 0.03 | 0.00 | 0.03 | |
ImputeTesting | 4.68 | 0.06 | 4.75 | |
MakeHist | 0.46 | 0.02 | 0.47 | |
MakeKnnList | 0.39 | 0.00 | 0.39 | |
MeaningOfLife | 0 | 0 | 0 | |
ParseMarkers | 0.34 | 0.05 | 0.55 | |
PostProcessing | 0.17 | 0.00 | 0.17 | |
ProcessMultipleFiles | 0.13 | 0.00 | 0.16 | |
QuantNormalizeElements | 0.19 | 0.01 | 0.20 | |
SconeValues | 15.90 | 0.39 | 16.30 | |
SplitFile | 0.13 | 0.00 | 0.12 | |
StringToNumbers | 0 | 0 | 0 | |
SubsampleAndTsne | 1.78 | 0.05 | 1.83 | |
TsneVis | 0.17 | 0.00 | 0.17 | |