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 11:06:04 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
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 COTAN package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/COTAN.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 425/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
COTAN 1.2.0 (landing page) Galfrè Silvia Giulia
| 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: COTAN |
Version: 1.2.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:COTAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings COTAN_1.2.0.tar.gz |
StartedAt: 2023-04-10 19:37:44 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 19:40:44 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 179.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: COTAN.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:COTAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings COTAN_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/COTAN.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘COTAN/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘COTAN’ version ‘1.2.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘COTAN’ 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 data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed automatic.COTAN.object.creation 29.773 0.924 30.936 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ...6c6 < NULL --- > All Done! 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.16-bioc/meat/COTAN.Rcheck/00check.log’ for details.
COTAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL COTAN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘COTAN’ ... ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading ** 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 (COTAN)
COTAN.Rcheck/tests/spelling.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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. > if(requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.185 0.067 0.242
COTAN.Rcheck/tests/spelling.Rout.save
R version 3.4.1 (2017-06-30) -- "Single Candle" Copyright (C) 2017 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (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. > if(requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) All Done! > > proc.time() user system elapsed 0.372 0.039 0.408
COTAN.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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. > Sys.setenv(R_TESTS="") > library(testthat) > library(COTAN) > test_check("COTAN") [1] "Initializing S4 object" [1] "Initializing S4 object" [1] "Start estimation mu with linear method" [1] 2000 815 [1] "Start PCA" [1] "starting hclust" [1] "cotan analysis" [1] "mu estimator creation" [1] "save effective constitutive genes" [1] "start a minimization" [1] "Next gene: Trim2 number 1810" [1] "Final trance!" [1] "a min: -0.08001708984375 | a max 24.5703125 | negative a %: 2.4" [1] "coex dataframe creation" [1] "creation of observed yes/yes contingency table" [1] "mu estimator creation" [1] "expected contingency tables creation" [1] "The distance between estimated n of zeros and observed number of zero is 0.0241643297635317 over 2000" [1] "Done" [1] "coex estimation" [1] "Cleaning RAM" [1] "0610009D07Rik" "0610010F05Rik" "1110001J03Rik" "1110004F10Rik" [5] "1110008F13Rik" "1110038B12Rik" "1500011B03Rik" "1500012F01Rik" [9] "1700020I14Rik" "1700021F05Rik" "1700025G04Rik" "1810022K09Rik" [13] "1810037I17Rik" "2010107E04Rik" "2010107G23Rik" "2210016L21Rik" [17] "2310036O22Rik" "2410002F23Rik" "2410006H16Rik" "2410015M20Rik" [21] "2410066E13Rik" "2610017I09Rik" "2610203C20Rik" "2700029M09Rik" [25] "2700060E02Rik" "2700094K13Rik" "2810004N23Rik" "2810008D09Rik" [29] "2810428I15Rik" "2900011O08Rik" "4833420G17Rik" "4833439L19Rik" [33] "4921524J17Rik" "4930506M07Rik" "4931428F04Rik" "6330403K07Rik" [37] "9130024F11Rik" "9330159F19Rik" "A030009H04Rik" "Aamp" [41] "Abcf1" "Abr" "Abracl" "Acat1" [45] "Acat2" "Acbd5" "Acbd6" "Acin1" [49] "Aco2" "Acot7" "Actb" "Actl6b" [53] "Actr10" "Actr1a" "Actr2" "Actr3" [57] "Adam10" "Add1" "Add2" "Adh5" [61] "Adprh" "Adss" "Aes" "Aff4" [65] "Aggf1" "Agrn" "Ahi1" "Ahsa1" [69] "Ahsa2" "Aimp1" "Akap8" "Akap8l" [73] "Akap9" "Akirin2" "Akr1a1" "Akt3" [77] "Aldoa" "Aldoc" "Alg2" "Amer2" [81] "Anapc11" "Anapc13" "Anapc16" "Anapc5" [85] "Ank2" "Ank3" "Ankra2" "Ankrd10" [89] "Ankrd11" "Ankrd12" "Ankrd32" "Anp32a" [93] "Anp32b" "Anp32e" "Ap1m1" "Ap1s1" [97] "Ap2m1" "Ap2s1" "Ap3b2" "Apba2" [1] "Get p-values on a set of genes on columns on a set of genes on rows" [1] "Using function S" [1] "function to generate S " [1] "function to generate GDI dataframe" [1] "Using S" [1] "function to generate S " [ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ] > > proc.time() user system elapsed 39.595 3.742 40.627
COTAN.Rcheck/COTAN-Ex.timings
name | user | system | elapsed | |
add.row.to.meta | 0.102 | 0.008 | 0.109 | |
automatic.COTAN.object.creation | 29.773 | 0.924 | 30.936 | |
clean | 2.301 | 0.041 | 2.352 | |
cotan_analysis | 1.173 | 0.043 | 1.223 | |
drop.genes.cells | 0.076 | 0.006 | 0.083 | |
est.min.parameters | 0.084 | 0.004 | 0.089 | |
extract.coex | 0.079 | 0.003 | 0.087 | |
get.GDI | 0.091 | 0.006 | 0.098 | |
get.a | 0.075 | 0.006 | 0.081 | |
get.cell.number | 0.081 | 0.004 | 0.085 | |
get.cell.size | 0.084 | 0.008 | 0.096 | |
get.coex | 1.404 | 0.013 | 1.552 | |
get.constitutive.genes | 0.109 | 0.007 | 0.119 | |
get.expected.ct | 0.447 | 0.007 | 0.456 | |
get.gene.coexpression.space | 0.088 | 0.004 | 0.093 | |
get.genes | 0.075 | 0.005 | 0.079 | |
get.lambda | 0.085 | 0.005 | 0.091 | |
get.metadata | 0.091 | 0.004 | 0.099 | |
get.normdata | 0.129 | 0.006 | 0.135 | |
get.nu | 0.083 | 0.005 | 0.090 | |
get.observed.ct | 0.092 | 0.005 | 0.099 | |
get.pval | 0.072 | 0.004 | 0.076 | |
get.rawdata | 0.075 | 0.005 | 0.082 | |
get.subset | 0.075 | 0.005 | 0.080 | |
initRaw | 0.446 | 0.011 | 0.464 | |
mat2vec_rfast | 0.001 | 0.000 | 0.000 | |
plot_GDI | 0.223 | 0.004 | 0.229 | |
plot_general.heatmap | 0.755 | 0.053 | 0.821 | |
plot_heatmap | 0.426 | 0.008 | 0.434 | |
scCOTAN-class | 0.008 | 0.002 | 0.010 | |
vec2mat_rfast | 0 | 0 | 0 | |