##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Anaquin.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Anaquin_2.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Anaquin.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Anaquin/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Anaquin’ version ‘2.30.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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 sizes of PDF files under ‘inst/doc’ ... 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/Anaquin.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Anaquin
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
  6.389   0.223   6.618 

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
  1.347   0.128   1.474 

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
  2.040   0.145   2.186 

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
  1.185   0.130   1.313