Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-04 11:39:54 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 1871/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Sconify 1.23.0 (landing page) Tyler J Burns
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.23.0 |
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_1.23.0.tar.gz |
StartedAt: 2024-03-02 10:18:57 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 10:23:38 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 281.3 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_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Sconify.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Sconify/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Sconify’ version ‘1.23.0’ * 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 R 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 29.490 0.473 38.254 ImputeTesting 8.295 0.094 11.179 * 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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 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 = 0.965800)! Learning embedding... Iteration 50: error is 51.398469 (50 iterations in 0.02 seconds) Iteration 100: error is 54.190019 (50 iterations in 0.02 seconds) Iteration 150: error is 50.497187 (50 iterations in 0.02 seconds) Iteration 200: error is 55.682498 (50 iterations in 0.02 seconds) Iteration 250: error is 51.448790 (50 iterations in 0.02 seconds) Iteration 300: error is 1.733243 (50 iterations in 0.02 seconds) Iteration 350: error is 1.309429 (50 iterations in 0.01 seconds) Iteration 400: error is 0.576201 (50 iterations in 0.01 seconds) Iteration 450: error is 0.271077 (50 iterations in 0.02 seconds) Iteration 500: error is 0.192515 (50 iterations in 0.02 seconds) Iteration 550: error is 0.183041 (50 iterations in 0.02 seconds) Iteration 600: error is 0.166105 (50 iterations in 0.01 seconds) Iteration 650: error is 0.162620 (50 iterations in 0.01 seconds) Iteration 700: error is 0.161709 (50 iterations in 0.01 seconds) Iteration 750: error is 0.162079 (50 iterations in 0.01 seconds) Iteration 800: error is 0.161310 (50 iterations in 0.01 seconds) Iteration 850: error is 0.162055 (50 iterations in 0.01 seconds) Iteration 900: error is 0.161646 (50 iterations in 0.01 seconds) Iteration 950: error is 0.158425 (50 iterations in 0.01 seconds) Iteration 1000: error is 0.158666 (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 64.997583 (50 iterations in 0.35 seconds) Iteration 100: error is 60.646493 (50 iterations in 0.26 seconds) Iteration 150: error is 60.288654 (50 iterations in 0.27 seconds) Iteration 200: error is 60.173554 (50 iterations in 0.29 seconds) Iteration 250: error is 60.115803 (50 iterations in 0.30 seconds) Iteration 300: error is 1.336176 (50 iterations in 0.22 seconds) Iteration 350: error is 1.236525 (50 iterations in 0.21 seconds) Iteration 400: error is 1.205487 (50 iterations in 0.22 seconds) Iteration 450: error is 1.190461 (50 iterations in 0.22 seconds) Iteration 500: error is 1.181442 (50 iterations in 0.23 seconds) Iteration 550: error is 1.173868 (50 iterations in 0.23 seconds) Iteration 600: error is 1.166482 (50 iterations in 0.22 seconds) Iteration 650: error is 1.162250 (50 iterations in 0.23 seconds) Iteration 700: error is 1.159280 (50 iterations in 0.23 seconds) Iteration 750: error is 1.155892 (50 iterations in 0.23 seconds) Iteration 800: error is 1.154275 (50 iterations in 0.23 seconds) Iteration 850: error is 1.152366 (50 iterations in 0.22 seconds) Iteration 900: error is 1.150352 (50 iterations in 0.22 seconds) Iteration 950: error is 1.148222 (50 iterations in 0.22 seconds) Iteration 1000: error is 1.146398 (50 iterations in 0.21 seconds) Fitting performed in 4.83 seconds. [ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ] > > proc.time() user system elapsed 44.809 1.197 56.882
Sconify.Rcheck/Sconify-Ex.timings
name | user | system | elapsed | |
FcsToTibble | 0.282 | 0.011 | 0.379 | |
Fnn | 0.964 | 2.889 | 4.981 | |
GetKnnDe | 0.117 | 0.019 | 0.177 | |
GetMarkerNames | 0.057 | 0.005 | 0.081 | |
ImputeTesting | 8.295 | 0.094 | 11.179 | |
MakeHist | 0.681 | 0.019 | 0.907 | |
MakeKnnList | 0.790 | 0.030 | 1.062 | |
MeaningOfLife | 0.001 | 0.000 | 0.004 | |
ParseMarkers | 0.527 | 0.049 | 0.826 | |
PostProcessing | 0.186 | 0.004 | 0.237 | |
ProcessMultipleFiles | 0.238 | 0.009 | 0.313 | |
QuantNormalizeElements | 0.521 | 0.010 | 0.683 | |
SconeValues | 29.490 | 0.473 | 38.254 | |
SplitFile | 0.175 | 0.006 | 0.223 | |
StringToNumbers | 0.000 | 0.001 | 0.001 | |
SubsampleAndTsne | 2.782 | 0.097 | 3.655 | |
TsneVis | 0.370 | 0.011 | 0.484 | |