Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:27 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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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 1795/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Sconify 1.19.0 (landing page) Tyler J Burns
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: Sconify |
Version: 1.19.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings Sconify_1.19.0.tar.gz |
StartedAt: 2023-02-07 14:59:16 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 15:02:30 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 193.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Sconify.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings Sconify_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Sconify.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘Sconify/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Sconify’ version ‘1.19.0’ * 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 17.604 0.035 17.643 ImputeTesting 5.534 0.056 6.794 * 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 ... ‘DataQuality.Rmd’ using ‘UTF-8’... OK ‘FindingIdealK.Rmd’ using ‘UTF-8’... OK ‘Step1.PreProcessing.Rmd’ using ‘UTF-8’... OK ‘Step2.TheSconeWorkflow.Rmd’ using ‘UTF-8’... OK ‘Step3.PostProcessing.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
Sconify.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Sconify ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (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 = 0.967800)! Learning embedding... Iteration 50: error is 51.419346 (50 iterations in 0.02 seconds) Iteration 100: error is 50.938392 (50 iterations in 0.02 seconds) Iteration 150: error is 53.894807 (50 iterations in 0.02 seconds) Iteration 200: error is 52.857783 (50 iterations in 0.02 seconds) Iteration 250: error is 54.056583 (50 iterations in 0.02 seconds) Iteration 300: error is 1.283556 (50 iterations in 0.02 seconds) Iteration 350: error is 0.732542 (50 iterations in 0.02 seconds) Iteration 400: error is 0.330171 (50 iterations in 0.01 seconds) Iteration 450: error is 0.214007 (50 iterations in 0.01 seconds) Iteration 500: error is 0.191046 (50 iterations in 0.01 seconds) Iteration 550: error is 0.181450 (50 iterations in 0.01 seconds) Iteration 600: error is 0.182610 (50 iterations in 0.01 seconds) Iteration 650: error is 0.180755 (50 iterations in 0.01 seconds) Iteration 700: error is 0.181740 (50 iterations in 0.01 seconds) Iteration 750: error is 0.182973 (50 iterations in 0.01 seconds) Iteration 800: error is 0.183341 (50 iterations in 0.01 seconds) Iteration 850: error is 0.183316 (50 iterations in 0.01 seconds) Iteration 900: error is 0.183922 (50 iterations in 0.01 seconds) Iteration 950: error is 0.185288 (50 iterations in 0.01 seconds) Iteration 1000: error is 0.184499 (50 iterations in 0.01 seconds) Fitting performed in 0.27 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 0.19 seconds (sparsity = 0.129120)! Learning embedding... Iteration 50: error is 66.996077 (50 iterations in 0.42 seconds) Iteration 100: error is 60.693906 (50 iterations in 0.28 seconds) Iteration 150: error is 60.285151 (50 iterations in 0.27 seconds) Iteration 200: error is 60.168073 (50 iterations in 0.28 seconds) Iteration 250: error is 60.133288 (50 iterations in 0.29 seconds) Iteration 300: error is 1.346037 (50 iterations in 0.25 seconds) Iteration 350: error is 1.232800 (50 iterations in 0.24 seconds) Iteration 400: error is 1.203524 (50 iterations in 0.24 seconds) Iteration 450: error is 1.192074 (50 iterations in 0.25 seconds) Iteration 500: error is 1.184037 (50 iterations in 0.24 seconds) Iteration 550: error is 1.178741 (50 iterations in 0.24 seconds) Iteration 600: error is 1.176020 (50 iterations in 0.24 seconds) Iteration 650: error is 1.173029 (50 iterations in 0.24 seconds) Iteration 700: error is 1.170700 (50 iterations in 0.24 seconds) Iteration 750: error is 1.168049 (50 iterations in 0.24 seconds) Iteration 800: error is 1.166709 (50 iterations in 0.24 seconds) Iteration 850: error is 1.165144 (50 iterations in 0.24 seconds) Iteration 900: error is 1.163502 (50 iterations in 0.23 seconds) Iteration 950: error is 1.162371 (50 iterations in 0.24 seconds) Iteration 1000: error is 1.161014 (50 iterations in 0.24 seconds) Fitting performed in 5.16 seconds. [ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ] > > proc.time() user system elapsed 31.112 0.265 31.434
Sconify.Rcheck/Sconify-Ex.timings
name | user | system | elapsed | |
FcsToTibble | 0.194 | 0.009 | 0.295 | |
Fnn | 0.354 | 0.343 | 0.753 | |
GetKnnDe | 0.103 | 0.000 | 0.103 | |
GetMarkerNames | 0.032 | 0.000 | 0.032 | |
ImputeTesting | 5.534 | 0.056 | 6.794 | |
MakeHist | 0.387 | 0.004 | 0.414 | |
MakeKnnList | 0.648 | 0.000 | 0.650 | |
MeaningOfLife | 0 | 0 | 0 | |
ParseMarkers | 0.307 | 0.010 | 0.354 | |
PostProcessing | 0.153 | 0.004 | 0.157 | |
ProcessMultipleFiles | 0.199 | 0.000 | 0.202 | |
QuantNormalizeElements | 0.633 | 0.000 | 0.633 | |
SconeValues | 17.604 | 0.035 | 17.643 | |
SplitFile | 0.142 | 0.000 | 0.141 | |
StringToNumbers | 0.001 | 0.000 | 0.000 | |
SubsampleAndTsne | 3.065 | 0.012 | 3.079 | |
TsneVis | 0.218 | 0.004 | 0.221 | |