Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:39 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 62/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Anaquin 2.29.0 (landing page) Ted Wong
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the Anaquin package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Anaquin.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: Anaquin |
Version: 2.29.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Anaquin.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Anaquin_2.29.0.tar.gz |
StartedAt: 2024-08-26 20:28:31 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 20:29:39 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 67.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Anaquin.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Anaquin.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Anaquin_2.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Anaquin.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘Anaquin/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Anaquin’ version ‘2.29.0’ * 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 ‘Anaquin’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘ggplot2’ A package should be listed in only one of these fields. * 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘DESeq2’ All declared Imports should be used. * 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 ... NOTE prepare_Rd: plotConjoint.Rd:26-27: Dropping empty section \examples * 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘tPlotLOD.R’ Running ‘tPlotLinear.R’ Running ‘tPlotLogistic.R’ Running ‘tPlotROC.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/Anaquin.Rcheck/00check.log’ for details.
Anaquin.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Anaquin ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘Anaquin’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (Anaquin)
Anaquin.Rcheck/tests/tPlotLinear.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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. > # > # Copyright (C) 2016 - Garvan Institute of Medical Research > # > # Ted Wong, Bioinformatic Software Engineer at Garvan Institute > # > > library(RUnit) > library(Anaquin) Loading required package: ggplot2 > > .test.data <- function() + { + input <- c(15.1062, + 15.1062, + 966.797, + 241.699, + 30.2124, + 7734.38, + 483.398, + 30937.5, + 483.398, + 15.1062, + 483.398, + 241.699, + 60.4248, + 0.118017, + 7734.37, + 7734.38, + 120.85, + 1933.59, + 0.944138, + 120.85, + 7.5531, + 3.77655, + 3867.19, + 15468.8, + 1.88828, + 1933.59, + 120.85, + 3867.19, + 30.2124, + 0.472069, + 241.699, + 60.4248, + 0.944138, + 120.85, + 1.88828, + 60.4248, + 15468.8, + 60.4248, + 1933.59, + 1.88828, + 30.2124, + 0.944138, + 3867.19, + 15468.8, + 3867.19, + 30.2124, + 15.1062, + 1933.59, + 7.5531, + 0.472069, + 0.472069, + 0.236034, + 0.0590086, + 241.699, + 0.236034, + 0.472069, + 0.118017, + 120.85, + 0.118017, + 483.398, + 30937.5, + 7.5531, + 0.472069, + 483.398, + 7.5531, + 966.797, + 3.77655, + 30937.5, + 3.77655, + 3.77655, + 966.797, + 3.77655, + 0.236034, + 1.88828, + 0.0590086) + + o1 <- c(4.29354, + 6.41774, + 271.696, + 67.3212, + 3.1943, + 2628.81, + 245.034, + 14727.4, + 38.2906, + 8.41748, + 140.367, + 90.1342, + 5.03172, + 0.282232, + 2340.3, + 5418.16, + 124.648, + 157.443, + 0.437077, + 2.42797, + 3.88121, + NA, + 2010.24, + 7762.18, + 2.05478, + 526.579, + 29.9481, + 1369.19, + 9.21093, + 0.305795, + 50.4639, + 11.4579, + 0.291139, + 76.4986, + 3.2669, + 21.1347, + 8064.47, + 37.4146, + 438.561, + 0.38055, + 11.2435, + 0.88877, + 1491.72, + 4786.46, + 867.185, + 7.30535, + 2.78194, + 559.819, + 3.69124, + 0.523401, + 0.474327, + 0.929315, + 0.722466, + 111.985, + 1.1903, + 1.47662, + 0.285894, + 35.2424, + 0.700978, + 419.301, + 25760.2, + 2.5859, + 1.31373, + 24.5161, + 4.35937, + 457.339, + 2.59279, + 15205, + 0.64947, + 1.1555, + 261.917, + 0.252222, + 0.443106, + 0.376111, + 1.0948) + + o2 <- c(3.09828, + 8.68183, + 272.248, + 80.5532, + 3.17143, + 2813.75, + 252.489, + 15776.6, + 55.5334, + 7.92421, + 134.694, + 92.8906, + 8.70729, + 0.88829, + 2313.62, + 5647.12, + 121.991, + 157.827, + 0.411342, + 2.28061, + 2.82815, + 2.02179, + 2007.42, + 8399.07, + 1.32179, + 479.284, + 30.1469, + 1354.44, + 7.04809, + 0.688492, + 45.6092, + 16.2209, + 0.655503, + 64.66, + 2.49032, + 23.6616, + 8801.15, + 37.5889, + 402.614, + 0.792792, + 13.1838, + 1.30589, + 1546.73, + 5024.49, + 870.876, + 6.57147, + 3.05968, + 568.894, + 3.72397, + 0.650601, + NA, + 0.970407, + 0.902928, + 107.726, + NA, + 1.74165, + 0.15758, + 42.8825, + 0.632109, + 436.377, + 27119.4, + 4.50098, + 0.297246, + 18.5351, + 2.64522, + 490.524, + 1.45904, + 15831, + 0.729047, + 0.449076, + 277.903, + 2.34995, + 0.385306, + 0.864491, + 0.944744) + + o3 <- c(5.78108, + 8.41477, + 261.53, + 71.0515, + 2.22543, + 2554.46, + 235.358, + 14074.1, + 52.9666, + 5.93463, + 130.117, + 89.6172, + 13.3467, + 2.71212, + 2186.4, + 5142.73, + 122.094, + 202.948, + 3.26205, + 3.628, + 2.82539, + 1.14586, + 1921.63, + 7459.34, + 0.987163, + 469.363, + 27.2883, + 1303.06, + 10.1981, + 1.0284, + 44.2452, + 14.9583, + 1.95817, + 62.0998, + 4.66003, + 24.9048, + 7705.65, + 39.1692, + 377.697, + 1.70661, + 12.2224, + 2.68944, + 1432.93, + 4672.95, + 821.054, + 6.00481, + 2.91698, + 549.193, + 6.69091, + 2.97898, + 1.91727, + 3.08212, + 2.09839, + 113.618, + 2.05095, + 4.40774, + 1.82189, + 36.1417, + 4.30722, + 410.602, + 23843.5, + 6.58454, + 1.3233, + 22.6614, + 6.2324, + 443.329, + 1.81664, + 14447.8, + 2.18542, + 0.148822, + 237.506, + 2.7184, + 2.3283, + 2.68241, + 3.31801) + + return (data.frame(Input=input, Observed1=o1, Observed2=o2, Observed3=o3)) + } > > test.PlotLinear_1 <- function() + { + x <- .test.data() + r <- plotLinear(row.names(x), + log2(x$Input), + log2(x$Observed1)) + + checkEqualsNumeric(r$LOQ$model$breaks, 0.9170727) + } > > test.PlotLinear_2 <- function() + { + x <- .test.data() + r <- plotLinear(row.names(x), + log2(x$Input), + log2(x[,c(2:4)])) + + checkEqualsNumeric(r$LOQ$model$breaks, 1.917068888) + } > > test.PlotLinear_3 <- function() + { + x <- "15.1062, + 15.1062, + 241.699, + 0.472069, + 120.85, + 483.398, + 0.0590086, + 483.398, + 15.1062, + 241.699, + 60.4248, + 120.85, + 120.85, + 0.472069, + 0.118017, + 0.0590086, + 0.944138, + 0.118017, + 7.5531, + 3.77655, + 0.236034, + 60.4248, + 1.88828, + 241.699, + 0.118017, + 0.236034, + 0.472069, + 30.2124, + 241.699, + 60.4248, + 0.944138, + 0.944138, + 0.118017, + 1.88828, + 60.4248, + 60.4248, + 0.944138, + 1.88828, + 0.472069, + 0.944138, + 15.1062, + 7.5531, + 15.1062, + 0.472069, + 15.1062, + 60.4248, + 7.5531, + 30.2124, + 30.2124, + 0.0590086, + 0.236034, + 0.0590086, + 241.699, + 0.236034, + 30.2124, + 120.85, + 0.118017, + 120.85, + 1.88828, + 7.5531, + 30.2124, + 483.398, + 7.5531, + 966.797, + 3.77655, + 241.699, + 3.77655, + 3.77655, + 3.77655, + 0.236034, + 1.88828, + 0.0590086" + + y <- "2292.02, + 1728.11, + 33095.9, + 51.557, + 13616.2, + 54615.3, + 5.75489, + 60652.2, + 1205.27, + 30255, + 7645.25, + 11118.4, + 16529.2, + 48.5283, + 12.6669, + 8.29854, + 96.6785, + 14.3095, + 1151.03, + 481.086, + 22.5602, + 9128.84, + 203.783, + 24093.9, + 15.2307, + 22.7496, + 50.3159, + 4104.9, + 19207.5, + 6752.21, + 123.603, + 187.043, + 14.0419, + 263.462, + 3310.3, + 8270.03, + 119.862, + 280.256, + 1e-05, + 115.157, + 2042.86, + 1084.78, + 1773.62, + 54.5923, + 1733.97, + 6365.94, + 901.141, + 4224.51, + 3612.83, + 14.9924, + 29.9387, + 5.04516, + 30960.8, + 35.6649, + 3664.05, + 17094.3, + 13.5061, + 13986.2, + 248.781, + 918.314, + 3502.82, + 64966.4, + 860.103, + 3426.51, + 515.013, + 32569.1, + 609.002, + 427.186, + 677.121, + 25.5264, + 199.22, + 8.10828" + + z <- "R1_101, + R1_102, + R1_11, + R1_12, + R1_13, + R1_14, + R1_21, + R1_22, + R1_23, + R1_31, + R1_32, + R1_33, + R1_41, + R1_42, + R1_43, + R1_51, + R1_52, + R1_53, + R1_61, + R1_62, + R1_63, + R1_71, + R1_72, + R1_73, + R1_81, + R1_82, + R1_83, + R1_91, + R1_92, + R1_93, + R2_1, + R2_105, + R2_115, + R2_116, + R2_117, + R2_140, + R2_143, + R2_151, + R2_152, + R2_153, + R2_154, + R2_18, + R2_19, + R2_20, + R2_24, + R2_26, + R2_27, + R2_28, + R2_32, + R2_33, + R2_37, + R2_38, + R2_41, + R2_42, + R2_45, + R2_46, + R2_47, + R2_53, + R2_55, + R2_57, + R2_59, + R2_6, + R2_60, + R2_63, + R2_65, + R2_66, + R2_67, + R2_68, + R2_71, + R2_72, + R2_73, + R2_76" + + r <- plotLinear(unlist(strsplit(z, split=',')), + log2(as.numeric(unlist(strsplit(x, split=',')))), + log2(as.numeric(unlist(strsplit(y, split=',')))), + showLOQ=TRUE) + + checkEquals(NULL, r$LOQ) + } > > test.PlotLinear_4 <- function() + { + x <- "10.0708, + 5.0354, + 0.8886, + 14.2176, + 107.422, + 859.375, + 161.133, + 80.5664, + 1.7772, + 28.4352, + 5156.25, + 2578.12, + 483.398, + 3437.5, + 27500, + 53.7109, + 429.688, + 0.8886, + 14.2176, + 483.398, + 26.8555, + 214.844, + 3.5544, + 56.8704, + 0.0786781, + 0.0393391, + 454.963, + 7279.41, + 5156.25, + 2578.12, + 13.4277, + 107.422, + 966.797, + 966.797, + 0.629425, + 0.314713, + 120.85, + 0.4443, + 7.1088, + 2.5177, + 1.25885, + 227.482, + 3639.71, + 7734.38, + 7734.38, + 1.25885, + 0.629425, + 1289.06, + 644.531, + 60.4248, + 60.4248, + 3750, + 117.188, + 20.1416, + 10.0708, + 0.0143051, + 0.457764, + 120.85, + 120.85, + 30.2124, + 30.2124, + 80.5664, + 40.2832, + 0.269754, + 0.539507, + 1.07901, + 30.2124, + 30.2124, + 60.4248, + 2209.82, + 4419.64, + 8839.29, + 58.5938, + 1875, + 0.269754, + 0.539507, + 1.07901, + 15.1062, + 15.1062, + 0.134877, + 0.269754, + 0.539507, + 1933.59, + 1933.59, + 7734.38, + 7734.38, + 2578.12, + 1289.06, + 0.944138, + 20.1416, + 10.0708, + 1.67847, + 13.4277, + 1875, + 58.5938, + 0.839233, + 6.71387, + 0.0674384, + 0.134877, + 0.269754, + 0.0674384, + 0.134877, + 0.269754, + 0.0674384, + 0.134877, + 161.133, + 80.5664, + 0.0337192, + 0.134877, + 0.0314713, + 0.0629425, + 0.125885, + 0.25177, + 0.0168596, + 0.0674384, + 80.5664, + 40.2832, + 0.0168596, + 0.0337192, + 0.0674384, + 322.266, + 161.133, + 937.5, + 30000, + 0.4443, + 7.1088, + 0.134877, + 0.269754, + 0.4443, + 7.1088, + 29.2969, + 937.5, + 3.77655, + 937.5, + 30000, + 3.77655, + 0.114441, + 3.66211, + 28.4352, + 454.963, + 0.114441, + 3.66211, + 0.0157356, + 0.0314713, + 0.0629425, + 0.125885, + 0.0572205, + 1.83105, + 29.2969, + 937.5" + + y1 <- "0.837485, + 0.121353, + 0.0379273, + 0.768669, + 1.90631, + 0.744164, + 1.0572e-06, + 3.87601, + 8.51e-08, + 0.779118, + 214.214, + 1091.49, + 54.3986, + 380.045, + 0.15194, + 2.09719, + 17.9671, + 0.0795291, + 0.478201, + 3.56595, + 2.38232, + 15.8246, + 0.394103, + 0.895861, + 8.8e-09, + 0.0712489, + 35.6487, + 614.35, + 988.259, + 178.257, + 0.532468, + 3.26565, + 44.7566, + 41.5003, + 0.0639191, + NA, + 4.2057, + 4.25e-08, + 0.596072, + 0.232307, + 0.0675099, + 2.28788, + 423.966, + 3907.65, + 3567.12, + 0.111393, + 3.9771e-06, + 133.993, + 154.723, + 4.34212, + 0.996274, + 85.0451, + 4.61353, + 0.163091, + 0.379198, + NA, + 0.038774, + 3.21766, + 15.0352, + 1.38579, + 1.93683, + 9.35673, + 5.451, + 5e-08, + 0.0649624, + 0.384407, + 3.77595, + 7.44824, + 16.0071, + 270.303, + 3.494e-07, + 1671.87, + 6.812, + 325.095, + 3.935e-07, + 0.0616513, + 0.0305549, + 0.149523, + 0.726862, + 0.103768, + 1.596e-06, + 0.0463446, + 199.256, + 322.444, + 1093.72, + 1688.88, + 279.584, + 63.5678, + 0.110435, + 1.93013, + 0.374583, + 0.218183, + 1.74819, + 85.852, + 1.21e-08, + 0.377331, + 1.96912, + NA, + NA, + NA, + 0.130965, + 1.18e-08, + 2.91e-08, + NA, + NA, + 15.1834, + 9.38777, + NA, + 0.0799122, + 2.10385e-05, + NA, + 0.083846, + NA, + 0.0171778, + NA, + 3.35384, + 5.73421, + 5.8264e-06, + 6.246e-07, + 0.0200194, + 17.5116, + 11.0122, + 260.919, + 3964.2, + 0.100965, + 1.11491, + 0.0259428, + NA, + 0.288957, + 0.4821, + 1.20828, + 193.558, + 0.536125, + 187.495, + 7064.26, + 0.264505, + 0.0221402, + 0.396147, + 3.55531, + 73.5915, + NA, + NA, + 9.9647e-06, + 4.63e-08, + 4.7e-09, + 0.0237112, + 0.0392847, + 0.0456551, + 1.70831, + 91.1479" + + y2 <- "0.722778, + 0.733873, + 5.219e-07, + 0.604539, + 1.73717, + 1.1534, + 1.9165e-06, + 3.91994, + 4.754e-07, + 0.898643, + 207.593, + 1121.36, + 54.4085, + 373.338, + 0.169796, + 2.09949, + 16.8435, + 0.0616389, + 0.619896, + 3.89005, + 2.5968, + 16.6549, + 0.182859, + 0.948602, + 1.016e-07, + 0.0403375, + 39.1606, + 609.005, + 1008.73, + 157.116, + 0.234875, + 3.39922, + 42.6545, + 40.196, + 0.181165, + 2.847e-07, + 4.69883, + NA, + 0.189675, + 0.254871, + 0.391466, + 2.41451, + 426.951, + 3810.71, + 3577.81, + 0.0420185, + 4.103e-06, + 120.872, + 150.976, + 4.00902, + 1.09308, + 88.7421, + 4.36902, + 0.325112, + 0.487459, + 0.0794166, + 7.003e-07, + 3.75052, + 13.7295, + 1.36716, + 2.148, + 8.88517, + 5.73348, + 0.00058588, + 0.351373, + 0.329472, + 4.29572, + 7.05352, + 18.2358, + 266.712, + 3.379e-07, + 1650, + 6.13767, + 312.299, + NA, + 0.0414129, + NA, + 0.158325, + 1.03642, + 0.0698399, + 2.7166e-06, + 0.0904658, + 195.812, + 309.716, + 1161.1, + 1716.5, + 275.204, + 61.8612, + NA, + 1.05298, + 0.427896, + 3.555e-07, + 2.10418, + 80.0865, + 1.96e-08, + 0.512922, + 1.58903, + 6.00372e-05, + 0.0432046, + NA, + 2.8e-06, + 1e-10, + 0.0702308, + NA, + NA, + 15.5818, + 8.15287, + NA, + 0.089151, + 0.0283771, + 1.102e-07, + 1.27e-08, + 3.0816e-06, + NA, + 0.0412629, + 3.26266, + 7.27648, + NA, + NA, + NA, + 17.6655, + 10.9249, + 249.933, + 3641.64, + 0.0509423, + 0.640191, + 0.0444007, + 9.7502e-06, + 0.319625, + 0.436569, + 1.04639, + 191.152, + 0.279646, + 167.877, + 7014.58, + 0.392405, + 2.306e-07, + 0.334322, + 2.50338, + 65.9721, + 0.0358907, + 0.350269, + 3.09e-08, + 2.8e-09, + 0.0405143, + 9.942e-07, + NA, + 0.010433, + 1.02221, + 95.2976" + + y3 <- "0.490311, + 0.469879, + 0.16225, + 0.490533, + 2.13129, + 1.0798, + 2.2654e-06, + 4.24638, + 0.110956, + 0.62222, + 262.925, + 1096.04, + 48.0564, + 399.27, + 0.14716, + 3.38397, + 18.2888, + 3.547e-07, + 0.761565, + 4.13325, + 1.7191, + 17.8298, + 0.088615, + 1.34844, + NA, + NA, + 43.9125, + 605.221, + 1007.06, + 177.07, + 0.554892, + 3.52786, + 40.612, + 46.9536, + 2.0762e-06, + 0.0886553, + 4.04549, + 0.060803, + 0.413782, + 0.11363, + NA, + 2.72187, + 429.049, + 3861.91, + 3759.93, + 0.108981, + 3.9713e-06, + 121.845, + 146.047, + 4.52467, + 1.6103, + 93.0103, + 5.10038, + 0.51797, + 0.195218, + 2.26379e-05, + 0.0758392, + 3.94007, + 11.767, + 1.5896, + 2.04017, + 9.66727, + 6.0005, + 0.000148475, + 0.165744, + 0.127973, + 3.72053, + 6.65285, + 16.6536, + 279.149, + 2.128e-07, + 1707.2, + 7.94687, + 298.357, + NA, + 0.0357967, + NA, + 0.156696, + 0.911175, + NA, + 0.0614663, + 0.0476663, + 197.844, + 317.099, + 1223.97, + 1618.46, + 277.503, + 66.3776, + 0.072033, + 1.72695, + 0.216182, + 0.172833, + 1.6133, + 89.5909, + 2.87e-08, + 0.496378, + 1.83563, + 1.506e-07, + NA, + 0.137899, + NA, + NA, + NA, + 0.0146193, + 0.0325043, + 14.8062, + 7.7748, + 0.0247236, + NA, + 4.48882e-05, + NA, + 0.0305807, + 0.0408539, + 0.0168537, + NA, + 3.43573, + 7.86324, + NA, + NA, + 0.0196412, + 17.5211, + 11.9901, + 253.366, + 3609.29, + 9.812e-07, + 0.907263, + 0.0254687, + NA, + 0.208575, + 0.40283, + 0.836432, + 191.248, + 0.483889, + 197.458, + 6854.51, + 0.171308, + 4.1e-08, + 0.303812, + 1.92317, + 67.3608, + NA, + NA, + NA, + NA, + NA, + NA, + NA, + 0.0269071, + 2.66745, + 97.6445" + + z <- "R1_101_1, + R1_101_2, + R1_102_1, + R1_102_2, + R1_103_1, + R1_103_2, + R1_11_1, + R1_11_2, + R1_12_1, + R1_12_2, + R1_13_1, + R1_13_2, + R1_14_1, + R1_21_1, + R1_21_2, + R1_22_1, + R1_22_2, + R1_23_1, + R1_23_2, + R1_24_1, + R1_31_1, + R1_31_2, + R1_32_1, + R1_32_2, + R1_33_1, + R1_33_2, + R1_41_1, + R1_41_2, + R1_42_1, + R1_42_2, + R1_43_1, + R1_43_2, + R1_51_1, + R1_51_2, + R1_52_1, + R1_52_2, + R1_53_1, + R1_61_1, + R1_61_2, + R1_62_1, + R1_62_2, + R1_63_1, + R1_63_2, + R1_71_1, + R1_71_2, + R1_72_1, + R1_72_2, + R1_73_1, + R1_73_2, + R1_81_1, + R1_81_2, + R1_82_1, + R1_82_2, + R1_83_1, + R1_83_2, + R1_91_1, + R1_91_2, + R1_92_1, + R1_92_2, + R1_93_1, + R1_93_2, + R2_115_1, + R2_115_2, + R2_116_1, + R2_116_2, + R2_116_3, + R2_117_1, + R2_117_3, + R2_140_1, + R2_14_1, + R2_14_2, + R2_14_3, + R2_150_1, + R2_150_2, + R2_151_1, + R2_151_2, + R2_151_3, + R2_152_1, + R2_152_2, + R2_153_1, + R2_153_2, + R2_153_3, + R2_154_1, + R2_154_2, + R2_18_1, + R2_18_2, + R2_19_1, + R2_19_2, + R2_1_1, + R2_20_1, + R2_20_2, + R2_24_1, + R2_24_2, + R2_26_1, + R2_26_2, + R2_27_1, + R2_27_2, + R2_28_1, + R2_28_2, + R2_28_3, + R2_32_1, + R2_32_2, + R2_32_3, + R2_37_2, + R2_37_3, + R2_41_1, + R2_41_2, + R2_42_1, + R2_42_3, + R2_45_1, + R2_45_2, + R2_45_3, + R2_45_4, + R2_46_1, + R2_46_3, + R2_47_1, + R2_47_2, + R2_53_1, + R2_53_2, + R2_53_3, + R2_54_1, + R2_54_2, + R2_55_2, + R2_55_3, + R2_57_1, + R2_57_2, + R2_59_2, + R2_59_3, + R2_60_1, + R2_60_2, + R2_63_1, + R2_63_3, + R2_65_1, + R2_66_1, + R2_66_2, + R2_67_1, + R2_68_1, + R2_68_2, + R2_6_1, + R2_6_2, + R2_71_1, + R2_71_2, + R2_72_1, + R2_72_2, + R2_72_3, + R2_72_4, + R2_73_1, + R2_73_2, + R2_7_1, + R2_7_2" + + x <- log2(suppressWarnings(as.numeric(unlist(strsplit(x, split=','))))) + y1 <- log2(suppressWarnings(as.numeric(unlist(strsplit(y1, split=','))))) + y2 <- log2(suppressWarnings(as.numeric(unlist(strsplit(y2, split=','))))) + y3 <- log2(suppressWarnings(as.numeric(unlist(strsplit(y3, split=','))))) + z <- unlist(strsplit(z, split=',')) + + r <- plotLinear(c(z), + x, + data.frame(y1=y1, y2=y2, y3=y3), + showLOQ=TRUE, showSD=TRUE) + + checkEqualsNumeric(0.8296060465, r$LOQ$model$breaks) + } > > test.PlotLinear_1() [1] TRUE Warning messages: 1: The `<scale>` argument of `guides()` cannot be `FALSE`. Use "none" instead as of ggplot2 3.3.4. ℹ The deprecated feature was likely used in the Anaquin package. Please report the issue at <https://github.com/student-t/RAnaquin/issues>. 2: Use of `data$x` is discouraged. ℹ Use `x` instead. 3: Use of `data$y` is discouraged. ℹ Use `y` instead. 4: Use of `data$x` is discouraged. ℹ Use `x` instead. 5: Use of `data$y` is discouraged. ℹ Use `y` instead. 6: In geom_label(aes_string(x = "max(LOQ$breaks$k)", y = "min(y)"), : All aesthetics have length 1, but the data has 74 rows. ℹ Please consider using `annotate()` or provide this layer with data containing a single row. 7: The following aesthetics were dropped during statistical transformation: label. ℹ This can happen when ggplot fails to infer the correct grouping structure in the data. ℹ Did you forget to specify a `group` aesthetic or to convert a numerical variable into a factor? > test.PlotLinear_2() [1] TRUE Warning messages: 1: Use of `data$x` is discouraged. ℹ Use `x` instead. 2: Use of `data$y` is discouraged. ℹ Use `y` instead. 3: Use of `data$x` is discouraged. ℹ Use `x` instead. 4: Use of `data$y` is discouraged. ℹ Use `y` instead. 5: Use of `data$x` is discouraged. ℹ Use `x` instead. 6: Use of `data$ymin` is discouraged. ℹ Use `ymin` instead. 7: Use of `data$x` is discouraged. ℹ Use `x` instead. 8: Use of `data$ymax` is discouraged. ℹ Use `ymax` instead. 9: In geom_label(aes_string(x = "max(LOQ$breaks$k)", y = "min(y)"), : All aesthetics have length 1, but the data has 75 rows. ℹ Please consider using `annotate()` or provide this layer with data containing a single row. 10: The following aesthetics were dropped during statistical transformation: label. ℹ This can happen when ggplot fails to infer the correct grouping structure in the data. ℹ Did you forget to specify a `group` aesthetic or to convert a numerical variable into a factor? > test.PlotLinear_3() [1] TRUE Warning messages: 1: Use of `data$x` is discouraged. ℹ Use `x` instead. 2: Use of `data$y` is discouraged. ℹ Use `y` instead. 3: Use of `data$x` is discouraged. ℹ Use `x` instead. 4: Use of `data$y` is discouraged. ℹ Use `y` instead. 5: The following aesthetics were dropped during statistical transformation: label. ℹ This can happen when ggplot fails to infer the correct grouping structure in the data. ℹ Did you forget to specify a `group` aesthetic or to convert a numerical variable into a factor? > test.PlotLinear_4() [1] TRUE Warning messages: 1: Use of `data$x` is discouraged. ℹ Use `x` instead. 2: Use of `data$y` is discouraged. ℹ Use `y` instead. 3: Use of `data$x` is discouraged. ℹ Use `x` instead. 4: Use of `data$y` is discouraged. ℹ Use `y` instead. 5: Use of `data$x` is discouraged. ℹ Use `x` instead. 6: Use of `data$ymin` is discouraged. ℹ Use `ymin` instead. 7: Use of `data$x` is discouraged. ℹ Use `x` instead. 8: Use of `data$ymax` is discouraged. ℹ Use `ymax` instead. 9: In geom_label(aes_string(x = "max(LOQ$breaks$k)", y = "min(y)"), : All aesthetics have length 1, but the data has 135 rows. ℹ Please consider using `annotate()` or provide this layer with data containing a single row. 10: The following aesthetics were dropped during statistical transformation: label. ℹ This can happen when ggplot fails to infer the correct grouping structure in the data. ℹ Did you forget to specify a `group` aesthetic or to convert a numerical variable into a factor? > > proc.time() user system elapsed 7.791 0.376 8.156
Anaquin.Rcheck/tests/tPlotLOD.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # > # Copyright (C) 2016 - Garvan Institute of Medical Research > # > # Ted Wong, Bioinformatic Software Engineer at Garvan Institute > # > > library(RUnit) > library(Anaquin) Loading required package: ggplot2 > > test.PlotLOD_1 <- function() + { + data(UserGuideData_5.6.3) + data <- UserGuideData_5.6.3 + + xlab <- 'Average Counts' + ylab <- 'P-value' + title <- 'LODR Curves' + + r <- plotLOD(measured = data$Mean, + ratio = data$ExpLFC, + pval = data$Pval, + qval = data$Qval, + xlab = xlab, + ylab = ylab, + title = title, + FDR = 0.1) + + checkEquals(0, r[1,1]) + checkTrue(is.infinite(r[1,2])) + checkEquals(1, r[2,1]) + checkEqualsNumeric(3.617511181, r[2,2]) + checkEquals(2, r[3,1]) + checkEqualsNumeric(5.673070227, r[3,2]) + checkEquals(3, r[4,1]) + checkEqualsNumeric(2.584552757, r[4,2]) + checkEquals(4, r[5,1]) + checkEqualsNumeric(3.896317229, r[5,2]) + } > > test.PlotLOD_1() [1] "Threshold: 0.0330366" | | Ratio| LODR| |:--|-----:|--------:| |2 | 1| 3.617511| |3 | 2| 5.673070| |4 | 3| 2.584553| |5 | 4| 3.896317| [1] TRUE Warning messages: 1: Use of `limit$Ratio` is discouraged. ℹ Use `Ratio` instead. 2: In scale_y_log10() : log-10 transformation introduced infinite values. 3: Use of `limit$Ratio` is discouraged. ℹ Use `Ratio` instead. 4: In scale_y_log10() : log-10 transformation introduced infinite values. > > proc.time() user system elapsed 1.555 0.082 1.626
Anaquin.Rcheck/tests/tPlotLogistic.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # > # Copyright (C) 2016 - Garvan Institute of Medical Research > # > # Ted Wong, Bioinformatic Software Engineer at Garvan Institute > # > > library(RUnit) > library(Anaquin) Loading required package: ggplot2 > > test.PlotLogistic_1 <- function() + { + data(UserGuideData_5.4.5.1) + x <- UserGuideData_5.4.5.1 + + r <- plotLogistic(row.names(x), + log2(x$Input), + x$Sn) + + # Expected fitted values by the sigmoid function + fitted <- c(0.505755856395065, + 0.222643528893781, + 0.010300016219899, + 0.648997187338457, + 0.92026304251071, + 0.928213869071803, + 0.924632245089082, + 0.914366418394931, + 0.0378973207098846, + 0.833752363429975, + 0.928358782240202, + 0.928345459227316, + 0.927911002760357, + 0.928353148175993, + 0.928363361215984, + 0.89836631575432, + 0.927796005796745, + 0.010300016219899, + 0.648997187338457, + 0.927911002760357, + 0.823993501178706, + 0.926214306703906, + 0.129043885951807, + 0.901398794826717, + 9.82865701336804e-05, + 2.59121362851877e-05, + 0.927855061830411, + 0.928361094753171, + 0.928358782240202, + 0.928345459227316, + 0.627066585253743, + 0.92026304251071, + 0.928244209392258, + 0.928244209392258, + 0.00533476431533362, + 0.00141231744552197, + 0.921893786460962, + 0.00273763028622125, + 0.352602355170263, + 0.0712810947952379, + 0.0199170597244443, + 0.926437613006538, + 0.928354231359681, + 0.928361365200111, + 0.928361365200111, + 0.0199170597244443, + 0.00533476431533362, + 0.928294923575079, + 0.928103273636578, + 0.904289792326221, + 0.904289792326221, + 0.928354751455318, + 0.921502218658016, + 0.760780539182587, + 0.505755856395065, + 3.70222949553412e-06, + 0.00289892966464432, + 0.921893786460962, + 0.921893786460962, + 0.843210863415579, + 0.843210863415579, + 0.0115580895205083, + 0.914366418394931, + 0.877413012253192, + 0.00105034244261124, + 0.00397177716642234, + 0.0148884100362838, + 0.843210863415579, + 0.843210863415579, + 0.904289792326221, + 0.0115580895205083, + 0.928339214782058, + 0.92835713602241, + 0.928361860492618, + 0.902862250061517, + 0.928330169636822, + 0.00105034244261124, + 0.00397177716642234, + 0.0148884100362838, + 0.671229716373391, + 0.671229716373391, + 0.000277119451357618, + 0.00105034244261124, + 0.00397177716642234, + 0.928332087966142, + 0.928332087966142, + 0.928361365200111, + 0.928361365200111, + 0.928345459227316, + 0.928294923575079, + 0.0115580895205083, + 0.760780539182587, + 0.505755856395065, + 0.0340966826710067, + 0.627066585253743, + 0.928330169636822, + 0.902862250061517, + 0.00923829474485884, + 0.328897268974982, + 7.30693701509513e-05, + 0.000277119451357618, + 0.00105034244261124, + 7.30693701509513e-05, + 0.000277119451357618, + 0.00105034244261124, + 5.65192799587101e-05, + 1.92634758951033e-05, + 7.30693701509513e-05, + 0.000277119451357618, + 3.09052920252929e-07, + 1.17234994662851e-06, + 4.44713748735444e-06, + 1.68695415881578e-05, + 0.924632245089082, + 0.914366418394931, + 1.92634758951033e-05, + 7.30693701509513e-05, + 0.000277119451357618, + 1.68695415881578e-05, + 6.39890691148908e-05, + 0.000242687866644135, + 0.000919934543895209, + 5.0782655595262e-06, + 1.92634758951033e-05, + 7.30693701509513e-05, + 0.914366418394931, + 0.877413012253192, + 5.0782655595262e-06, + 1.92634758951033e-05, + 7.30693701509513e-05, + 0.927376994426196, + 0.924632245089082, + 0.928236933392859, + 0.928363390588447, + 0.00273763028622125, + 0.352602355170263, + 7.30693701509513e-05, + 0.000277119451357618, + 0.00105034244261124, + 0.00273763028622125, + 0.352602355170263, + 0.838521261207461, + 0.928236933392859, + 0.142553466244861, + 0.928236933392859, + 0.928363390588447, + 0.142553466244861, + 0.000202045715636617, + 0.135557087471656, + 0.833752363429975, + 0.927855061830411, + 0.000202045715636617, + 0.135557087471656, + 4.44713748735444e-06, + 1.68695415881578e-05, + 6.39890691148908e-05, + 0.000242687866644135, + 5.32713092910686e-05, + 0.0400403521055245, + 1.33872469655316e-06, + 5.0782655595262e-06, + 1.92634758951033e-05, + 0.838521261207461, + 0.928236933392859) + + checkEquals(r$LOA, 3.33) + #all(checkEqualsNumeric(fitted, r$fitted)) + } > > test.PlotLogistic_2 <- function() + { + data(UserGuideData_5.4.6.3) + x <- UserGuideData_5.4.6.3 + + checkException(plotLogistic(row.names(data), + log2(data$Input), + log2(data$Observed1))) + } > > test.PlotLogistic_1() [1] TRUE Warning messages: 1: The `<scale>` argument of `guides()` cannot be `FALSE`. Use "none" instead as of ggplot2 3.3.4. ℹ The deprecated feature was likely used in the Anaquin package. Please report the issue at <https://github.com/student-t/RAnaquin/issues>. 2: Use of `data$x` is discouraged. ℹ Use `x` instead. 3: Use of `data$y` is discouraged. ℹ Use `y` instead. 4: In geom_label(aes(x = min(data$x), y = max(data$y) - 0.1), label = label, : All aesthetics have length 1, but the data has 164 rows. ℹ Please consider using `annotate()` or provide this layer with data containing a single row. 5: Use of `data$x` is discouraged. ℹ Use `x` instead. 6: Use of `data$y` is discouraged. ℹ Use `y` instead. 7: In geom_label(aes(x = min(data$x), y = max(data$y) - 0.1), label = label, : All aesthetics have length 1, but the data has 164 rows. ℹ Please consider using `annotate()` or provide this layer with data containing a single row. > test.PlotLogistic_2() Error in data$Input : object of type 'closure' is not subsettable [1] TRUE > > proc.time() user system elapsed 2.442 0.138 2.569
Anaquin.Rcheck/tests/tPlotROC.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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. > # > # Copyright (C) 2016 - Garvan Institute of Medical Research > # > # Ted Wong, Bioinformatic Software Engineer at Garvan Institute > # > > library(RUnit) > library(Anaquin) Loading required package: ggplot2 > > test.PlotROC_1 <- function() + { + data(UserGuideData_5.6.3) + x <- UserGuideData_5.6.3 + x$label <- ifelse(abs(x$ExpLFC) <= 0, 'FP', 'TP') + + r <- plotROC(row.names(x), + 1-x$Pval, + abs(x$ExpLFC), + x$label, + refGroup=0) + + checkEquals(as.character(r$AUC[1,][1]), '4') + checkEqualsNumeric(r$AUC[1,]$AUC, 0.9062) + checkEquals(as.character(r$AUC[2,][1]), '3') + checkEqualsNumeric(r$AUC[2,]$AUC, 0.8939) + checkEquals(as.character(r$AUC[3,][1]), '2') + checkEqualsNumeric(r$AUC[3,]$AUC, 0.7955) + checkEquals(as.character(r$AUC[4,][1]), '1') + checkEqualsNumeric(r$AUC[4,]$AUC, 0.6713) + } > > test.PlotROC_1() | | AUC| |--:|------:| | 4| 0.9062| | 3| 0.8939| | 2| 0.7955| | 1| 0.6713| [1] TRUE > > proc.time() user system elapsed 1.354 0.084 1.428
Anaquin.Rcheck/Anaquin-Ex.timings
name | user | system | elapsed | |
plotLOD | 0.623 | 0.001 | 0.623 | |
plotLinear | 2.249 | 0.116 | 2.365 | |
plotLogistic | 1.143 | 0.008 | 1.151 | |
plotROC | 0.543 | 0.016 | 0.559 | |