Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-10-19 13:20:08 -0400 (Wed, 19 Oct 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
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 421/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
COTAN 1.0.0 (landing page) Galfrè Silvia Giulia
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: COTAN |
Version: 1.0.0 |
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings COTAN_1.0.0.tar.gz |
StartedAt: 2022-10-18 19:13:12 -0400 (Tue, 18 Oct 2022) |
EndedAt: 2022-10-18 19:16:23 -0400 (Tue, 18 Oct 2022) |
EllapsedTime: 191.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: COTAN.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings COTAN_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/COTAN.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-pc-linux-gnu (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 ‘1.0.0’ * 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 line endings in shell scripts ... 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 31.187 1.974 32.988 * 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 ‘/home/biocbuild/bbs-3.15-bioc/meat/COTAN.Rcheck/00check.log’ for details.
COTAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL COTAN ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’ * installing *source* package ‘COTAN’ ... ** using staged installation ** R ** data ** inst ** 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 4.2.1 (2022-06-23) -- "Funny-Looking Kid" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-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. > if(requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.209 0.031 0.225
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 4.2.1 (2022-06-23) -- "Funny-Looking Kid" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-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. > 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 rowname CTATTGATCAAA GCCGAGTAAGTC CACGCCGTCCCA TAAATACGTTAT GCGGAGCCTCCT 1119 Nnat 73.168400 43.104810 46.784146 18.684677 51.86938 1834 Tuba1a 30.128165 57.823526 36.613679 8.304301 54.92052 1787 Tmsb10 20.444112 14.718716 11.187513 16.608602 10.67899 917 Malat1 5.380029 10.513368 3.051140 31.141129 6.10228 51 Actb 11.836065 15.770052 9.153420 4.152151 13.73013 1788 Tmsb4x 2.152012 7.359358 26.443213 6.228226 3.05114 1841 Tubb5 11.836065 10.513368 13.221606 0.000000 9.15342 1460 Rpl32 2.152012 13.667379 8.136373 12.456452 6.10228 801 Hsp90ab1 5.380029 6.308021 6.102280 16.608602 6.10228 1837 Tubb2b 5.380029 10.513368 7.119327 2.076075 10.67899 757 H3f3b 7.532041 8.410695 6.102280 4.152151 7.62785 1838 Tubb3 5.380029 11.564705 2.034093 0.000000 13.73013 175 Atpif1 2.152012 6.308021 11.187513 4.152151 7.62785 782 Hnrnpa2b1 7.532041 9.462031 7.119327 4.152151 1.52557 939 Marcksl1 4.304024 6.308021 6.102280 0.000000 12.20456 [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 0.0241643297635311 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 45.139 5.515 47.130
COTAN.Rcheck/COTAN-Ex.timings
name | user | system | elapsed | |
add.row.to.meta | 0.102 | 0.004 | 0.106 | |
automatic.COTAN.object.creation | 31.187 | 1.974 | 32.988 | |
clean | 1.122 | 0.156 | 1.150 | |
cotan_analysis | 1.268 | 0.004 | 1.271 | |
drop.genes.cells | 0.090 | 0.004 | 0.095 | |
est.min.parameters | 0.085 | 0.004 | 0.089 | |
extract.coex | 0.09 | 0.00 | 0.09 | |
get.GDI | 0.102 | 0.000 | 0.103 | |
get.a | 0.09 | 0.00 | 0.09 | |
get.cell.number | 0.090 | 0.000 | 0.089 | |
get.cell.size | 0.086 | 0.000 | 0.086 | |
get.coex | 1.883 | 0.004 | 1.887 | |
get.constitutive.genes | 0.093 | 0.000 | 0.092 | |
get.expected.ct | 0.504 | 0.000 | 0.505 | |
get.gene.coexpression.space | 0.093 | 0.000 | 0.093 | |
get.genes | 0.086 | 0.000 | 0.087 | |
get.lambda | 0.09 | 0.00 | 0.09 | |
get.metadata | 0.09 | 0.00 | 0.09 | |
get.normdata | 0.132 | 0.004 | 0.136 | |
get.nu | 0.088 | 0.000 | 0.088 | |
get.observed.ct | 0.104 | 0.000 | 0.104 | |
get.pval | 0.090 | 0.004 | 0.094 | |
get.rawdata | 0.093 | 0.000 | 0.093 | |
get.subset | 0.082 | 0.000 | 0.082 | |
initRaw | 0.387 | 0.020 | 0.407 | |
mat2vec_rfast | 0.014 | 0.000 | 0.014 | |
plot_GDI | 0.230 | 0.028 | 0.258 | |
plot_general.heatmap | 0.822 | 0.020 | 0.842 | |
plot_heatmap | 0.498 | 0.008 | 0.505 | |
scCOTAN-class | 0.021 | 0.000 | 0.020 | |
vec2mat_rfast | 0.015 | 0.000 | 0.015 | |