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This page was generated on 2024-05-13 11:32:13 -0400 (Mon, 13 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
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
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the Sconify package: - 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: 2024-05-13 02:22:04 -0400 (Mon, 13 May 2024) |
EndedAt: 2024-05-13 02:24:03 -0400 (Mon, 13 May 2024) |
EllapsedTime: 119.3 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_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/Sconify.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-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 Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Sconify/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Sconify’ version ‘1.25.0’ * 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 12.52 0.207 12.783 * 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-arm64/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: aarch64-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 50.587832 (50 iterations in 0.01 seconds) Iteration 100: error is 51.087018 (50 iterations in 0.02 seconds) Iteration 150: error is 50.493786 (50 iterations in 0.01 seconds) Iteration 200: error is 52.851110 (50 iterations in 0.02 seconds) Iteration 250: error is 51.892293 (50 iterations in 0.02 seconds) Iteration 300: error is 0.803279 (50 iterations in 0.01 seconds) Iteration 350: error is 0.181729 (50 iterations in 0.01 seconds) Iteration 400: error is 0.164405 (50 iterations in 0.01 seconds) Iteration 450: error is 0.162753 (50 iterations in 0.01 seconds) Iteration 500: error is 0.163602 (50 iterations in 0.01 seconds) Iteration 550: error is 0.163600 (50 iterations in 0.01 seconds) Iteration 600: error is 0.164333 (50 iterations in 0.01 seconds) Iteration 650: error is 0.165877 (50 iterations in 0.01 seconds) Iteration 700: error is 0.163859 (50 iterations in 0.01 seconds) Iteration 750: error is 0.163468 (50 iterations in 0.01 seconds) Iteration 800: error is 0.165301 (50 iterations in 0.01 seconds) Iteration 850: error is 0.165208 (50 iterations in 0.01 seconds) Iteration 900: error is 0.163560 (50 iterations in 0.01 seconds) Iteration 950: error is 0.164031 (50 iterations in 0.01 seconds) Iteration 1000: error is 0.164312 (50 iterations in 0.01 seconds) Fitting performed in 0.24 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 0.16 seconds (sparsity = 0.129120)! Learning embedding... Iteration 50: error is 65.122445 (50 iterations in 0.33 seconds) Iteration 100: error is 60.739117 (50 iterations in 0.25 seconds) Iteration 150: error is 60.364105 (50 iterations in 0.25 seconds) Iteration 200: error is 60.234669 (50 iterations in 0.26 seconds) Iteration 250: error is 60.167885 (50 iterations in 0.27 seconds) Iteration 300: error is 1.346141 (50 iterations in 0.21 seconds) Iteration 350: error is 1.238939 (50 iterations in 0.20 seconds) Iteration 400: error is 1.203969 (50 iterations in 0.20 seconds) Iteration 450: error is 1.191645 (50 iterations in 0.20 seconds) Iteration 500: error is 1.183453 (50 iterations in 0.20 seconds) Iteration 550: error is 1.178062 (50 iterations in 0.19 seconds) Iteration 600: error is 1.172907 (50 iterations in 0.20 seconds) Iteration 650: error is 1.169936 (50 iterations in 0.19 seconds) Iteration 700: error is 1.167424 (50 iterations in 0.19 seconds) Iteration 750: error is 1.164648 (50 iterations in 0.19 seconds) Iteration 800: error is 1.161688 (50 iterations in 0.19 seconds) Iteration 850: error is 1.158908 (50 iterations in 0.19 seconds) Iteration 900: error is 1.157121 (50 iterations in 0.19 seconds) Iteration 950: error is 1.155831 (50 iterations in 0.19 seconds) Iteration 1000: error is 1.153953 (50 iterations in 0.18 seconds) Fitting performed in 4.27 seconds. [ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ] > > proc.time() user system elapsed 21.435 0.706 22.430
Sconify.Rcheck/Sconify-Ex.timings
name | user | system | elapsed | |
FcsToTibble | 0.143 | 0.006 | 0.151 | |
Fnn | 0.372 | 0.872 | 1.266 | |
GetKnnDe | 0.115 | 0.005 | 0.122 | |
GetMarkerNames | 0.027 | 0.002 | 0.029 | |
ImputeTesting | 3.156 | 0.026 | 3.229 | |
MakeHist | 0.355 | 0.009 | 0.366 | |
MakeKnnList | 0.367 | 0.007 | 0.374 | |
MeaningOfLife | 0.001 | 0.001 | 0.000 | |
ParseMarkers | 0.280 | 0.031 | 0.319 | |
PostProcessing | 0.148 | 0.004 | 0.153 | |
ProcessMultipleFiles | 0.112 | 0.005 | 0.118 | |
QuantNormalizeElements | 0.215 | 0.002 | 0.217 | |
SconeValues | 12.520 | 0.207 | 12.783 | |
SplitFile | 0.080 | 0.002 | 0.082 | |
StringToNumbers | 0.000 | 0.000 | 0.001 | |
SubsampleAndTsne | 2.030 | 0.089 | 2.132 | |
TsneVis | 0.189 | 0.005 | 0.194 | |