Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:51 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 |
To the developers/maintainers of the Sconify package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1810/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Sconify 1.18.0 (landing page) Tyler J Burns
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: Sconify |
Version: 1.18.0 |
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Sconify.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings Sconify_1.18.0.tar.gz |
StartedAt: 2023-04-11 05:45:59 -0400 (Tue, 11 Apr 2023) |
EndedAt: 2023-04-11 05:47:49 -0400 (Tue, 11 Apr 2023) |
EllapsedTime: 109.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Sconify.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Sconify.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings Sconify_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/Sconify.Rcheck' * using R version 4.2.3 (2023-03-15 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'Sconify/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'Sconify' version '1.18.0' * 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 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 12.69 0.25 12.94 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... 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-3.16-bioc\R\bin\R.exe CMD INSTALL Sconify ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-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 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) 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 0.01 seconds (sparsity = 0.965200)! Learning embedding... Iteration 50: error is 51.130468 (50 iterations in 0.01 seconds) Iteration 100: error is 49.156345 (50 iterations in 0.01 seconds) Iteration 150: error is 54.071890 (50 iterations in 0.01 seconds) Iteration 200: error is 50.280857 (50 iterations in 0.01 seconds) Iteration 250: error is 52.042615 (50 iterations in 0.01 seconds) Iteration 300: error is 1.470239 (50 iterations in 0.01 seconds) Iteration 350: error is 0.917758 (50 iterations in 0.01 seconds) Iteration 400: error is 0.330321 (50 iterations in 0.01 seconds) Iteration 450: error is 0.195539 (50 iterations in 0.01 seconds) Iteration 500: error is 0.186928 (50 iterations in 0.01 seconds) Iteration 550: error is 0.181185 (50 iterations in 0.01 seconds) Iteration 600: error is 0.167810 (50 iterations in 0.01 seconds) Iteration 650: error is 0.166107 (50 iterations in 0.01 seconds) Iteration 700: error is 0.167468 (50 iterations in 0.01 seconds) Iteration 750: error is 0.167073 (50 iterations in 0.01 seconds) Iteration 800: error is 0.167694 (50 iterations in 0.01 seconds) Iteration 850: error is 0.157558 (50 iterations in 0.01 seconds) Iteration 900: error is 0.159973 (50 iterations in 0.01 seconds) Iteration 950: error is 0.162892 (50 iterations in 0.01 seconds) Iteration 1000: error is 0.163003 (50 iterations in 0.01 seconds) Fitting performed in 0.16 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 0.23 seconds (sparsity = 0.129120)! Learning embedding... Iteration 50: error is 64.759373 (50 iterations in 0.19 seconds) Iteration 100: error is 60.746741 (50 iterations in 0.17 seconds) Iteration 150: error is 60.347735 (50 iterations in 0.13 seconds) Iteration 200: error is 60.222986 (50 iterations in 0.16 seconds) Iteration 250: error is 60.151051 (50 iterations in 0.15 seconds) Iteration 300: error is 1.350560 (50 iterations in 0.13 seconds) Iteration 350: error is 1.236495 (50 iterations in 0.11 seconds) Iteration 400: error is 1.202827 (50 iterations in 0.11 seconds) Iteration 450: error is 1.189322 (50 iterations in 0.11 seconds) Iteration 500: error is 1.181125 (50 iterations in 0.14 seconds) Iteration 550: error is 1.175321 (50 iterations in 0.13 seconds) Iteration 600: error is 1.170875 (50 iterations in 0.11 seconds) Iteration 650: error is 1.165525 (50 iterations in 0.12 seconds) Iteration 700: error is 1.162565 (50 iterations in 0.11 seconds) Iteration 750: error is 1.158756 (50 iterations in 0.11 seconds) Iteration 800: error is 1.156004 (50 iterations in 0.11 seconds) Iteration 850: error is 1.153561 (50 iterations in 0.10 seconds) Iteration 900: error is 1.151807 (50 iterations in 0.11 seconds) Iteration 950: error is 1.151491 (50 iterations in 0.10 seconds) Iteration 1000: error is 1.151074 (50 iterations in 0.11 seconds) Fitting performed in 2.53 seconds. [ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ] > > proc.time() user system elapsed 19.04 0.78 19.78
Sconify.Rcheck/Sconify-Ex.timings
name | user | system | elapsed | |
FcsToTibble | 0.14 | 0.00 | 0.14 | |
Fnn | 0.61 | 0.65 | 1.27 | |
GetKnnDe | 0.06 | 0.00 | 0.07 | |
GetMarkerNames | 0.03 | 0.02 | 0.04 | |
ImputeTesting | 3.19 | 0.12 | 3.32 | |
MakeHist | 0.33 | 0.02 | 0.34 | |
MakeKnnList | 0.26 | 0.00 | 0.26 | |
MeaningOfLife | 0 | 0 | 0 | |
ParseMarkers | 0.24 | 0.06 | 0.49 | |
PostProcessing | 0.09 | 0.00 | 0.09 | |
ProcessMultipleFiles | 0.14 | 0.00 | 0.14 | |
QuantNormalizeElements | 0.41 | 0.00 | 0.41 | |
SconeValues | 12.69 | 0.25 | 12.94 | |
SplitFile | 0.09 | 0.00 | 0.09 | |
StringToNumbers | 0 | 0 | 0 | |
SubsampleAndTsne | 1.86 | 0.03 | 1.89 | |
TsneVis | 0.16 | 0.02 | 0.17 | |