* using log directory ‘/srv/hornik/tmp/CRAN/stUPscales.Rcheck’ * using R Under development (unstable) (2023-09-16 r85157) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 16.0.6 (13) GNU Fortran (Debian 13.2.0-3) 13.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘stUPscales/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘stUPscales’ version ‘1.0.3.5’ * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘J.A. Torres-Matallana ’ New submission Package was archived on CRAN Possibly misspelled words in DESCRIPTION: Agg (17:50) Spatio (3:8) disaggregation (12:33, 24:47) modularity (23:27) spatio (14:5, 19:5, 21:62, 22:53, 24:31) stUPscales (20:44) CRAN repository db overrides: X-CRAN-Comment: Archived on 2021-06-22 as requires archived package 'EmiStatR'. * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘stUPscales’ can be installed ... [10s/10s] OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [2s/2s] OK * checking whether the package can be loaded with stated dependencies ... [2s/2s] OK * checking whether the package can be unloaded cleanly ... [2s/2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK * checking whether the namespace can be unloaded cleanly ... [2s/2s] OK * checking loading without being on the library search path ... [2s/2s] OK * checking use of S3 registration ... 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 ... [12s/12s] NOTE Found if() conditions comparing class() to string: File ‘stUPscales/R/MC.setup.R’: if (i == indexVAR[2] | class(rng[[i]][1]) == "list") ... Use inherits() (or maybe is()) instead. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... 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 ... [1s/1s] OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [18s/23s] ERROR Running examples in ‘stUPscales-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: MC.analysis > ### Title: Analysis of the Monte Carlo simulation > ### Aliases: MC.analysis > ### Keywords: Monte Carlo simulation MC.analysis > > ### ** Examples > > ## the Monte Carlo simulation: MC.sim > library(EmiStatR) > > # library(xts) > # data(Esch_Sure2010) > # P <- IsReg(Esch_Sure2010, format = "%Y-%m-%d %H:%M:%S", tz = "CET") > # P1 <- P[[2]] > # P1 <- P1["2010-08",][1:55] > # P1 <- cbind.data.frame(time=index(P1), P1 = coredata(P1)) > > data(P1) > P1 <- P1[165:(110*2),] > plot(P1[,2], typ="l") > > library(stUPscales) > > setting_EmiStatR <- setup(id = "MC_sim1", + nsim = 4, # # use a larger number to have + # a proper confidence band of simulatios + seed = 123, + mcCores = 1, + ts.input = P1, + rng = rng <- list( + qs = 150, # [l/PE/d] + CODs = c(pdf = "nor", mu = 4.378, sigma = 0.751), # log[g/PE/d] + NH4s = c(pdf = "nor", mu = 1.473, sigma = 0.410), # log[g/PE/d] + qf = 0.04, # [l/s/ha] + CODf = 0, # [g/PE/d] + NH4f = 0, # [g/PE/d] + CODr = c(pdf = "nor", mu = 3.60, sigma = 1.45), # 71 log[mg/l] + NH4r = 1, # [mg/l] + nameCSO = "E1", # [-] + id = 1, # [-] + ns = "FBH Goesdorf", # [-] + nm = "Goesdorf", # [-] + nc = "Obersauer", # [-] + numc = 1, # [-] + use = "R/I", # [-] + Atotal = 36, # [ha] + Aimp = c(pdf = "uni", min = 4.5, max = 25), # [ha] + Cimp = c(pdf = "uni", min = 0.25, max = 0.95), # [-] + Cper = c(pdf = "uni", min = 0.05, max = 0.60), # [-] + tfS = 1, # [time steps] + pe = 650, # [PE] + Qd = 5, # [l/s] + Dd = 0.150, # [m] + Cd = 0.18, # [-] + V = 190, # [m3] + lev.ini = 0.10, # [m] + lev2vol = list(lev = c(.06, 1.10, 1.30, 3.30), # [m] + vol = c(0, 31, 45, 190)) # [m3] + ), + ar.model = ar.model <- list( + CODs = 0.5, + NH4s = 0.5, + CODr = 0.7), + var.model = var.model <- list( + inp = c("", ""), # c("CODs", "NH4s"), # c("", ""), + w = c(0.04778205, 0.02079010), + A = matrix(c(9.916452e-01, -8.755558e-05, + -0.003189094, 0.994553910), nrow=2, ncol=2), + C = matrix(c(0.009126591, 0.002237936, + 0.002237936, 0.001850941), nrow=2, ncol=2))) > > MC_setup <- MC.setup(setting_EmiStatR) > > sims <- MC.sim(x = MC_setup, EmiStatR.cores = 1) starting worker pid=3677617 on localhost:11019 at 21:16:34.767 discovered package(s): automatically exporting the following variables from the local environment: EmiStatR.cores, MC_setup, x explicitly exporting variables(s): obj1 explicitly exporting package(s): EmiStatR, stUPscales Loading required package: stUPscales Loading required package: mAr Loading required package: MASS Loading required package: lmom The legacy packages maptools, rgdal, and rgeos, underpinning the sp package, which was just loaded, will retire in October 2023. Please refer to R-spatial evolution reports for details, especially https://r-spatial.org/r/2023/05/15/evolution4.html. It may be desirable to make the sf package available; package maintainers should consider adding sf to Suggests:. The sp package is now running under evolution status 2 (status 2 uses the sf package in place of rgdal) Please note that 'maptools' will be retired during October 2023, plan transition at your earliest convenience (see https://r-spatial.org/r/2023/05/15/evolution4.html and earlier blogs for guidance);some functionality will be moved to 'sp'. Checking rgeos availability: FALSE loaded stUPscales and set parent environment numValues: 4, numResults: 0, stopped: TRUE [1] "1, 1 cores" [1] "done (used 1 of 32 cores)" [1] "2, 1 cores" [1] "3, 1 cores" [1] "4, 1 cores" [1] "done (used 1 of 32 cores)" got results for task 1 numValues: 4, numResults: 1, stopped: TRUE returning status FALSE got results for task 2 numValues: 4, numResults: 2, stopped: TRUE returning status FALSE got results for task 3 numValues: 4, numResults: 3, stopped: TRUE returning status FALSE got results for task 4 numValues: 4, numResults: 4, stopped: TRUE first call to combine function evaluating call object to combine results: fun(result.1, result.2, result.3, result.4) Warning in fun(result.1, result.2, result.3, result.4) : number of columns of result is not a multiple of vector length (arg 2) returning status TRUE [1] "End of 4 Monte-Carlo simulations." > > > ## Monte Carlo simulation analysis: MC.analysis > > # Deterministic simulation > # Definition of structure 1, E1: > > E1 <- list(id = 1, ns = "FBH Goesdorf", nm = "Goesdorf", nc = "Obersauer", numc = 1, + use = "R/I", Atotal = 36, Aimp = 25.2, Cimp = 0.80, Cper = 0.30, + tfS = 0, pe = 650, Qd = 5, + Dd = 0.150, Cd = 0.18, V = 190, lev.ini = 0.10, + lev2vol = list(lev = c(.06, 1.10, 1.30, 3.30), + vol = c(0, 31, 45, 190)) + ) > > # Defining deterministic input: > library(EmiStatR) > # data(P1) > > input.det <- input(spatial = 0, zero = 1e-5, + folder = system.file("shiny", package = "EmiStatR"), + cores = 1, + ww = list(qs = 150, CODs = 104, NH4s = 4.7), + inf = list(qf= 0.04, CODf = 0, NH4f = 0), + rw = list(CODr = 71, NH4r = 1, stat = "Dahl"), + P1 = P1, st = list(E1=E1), export = 0) > > # Invoking `EmiStatR` with the deterministic input: > sim.det <- EmiStatR(input.det) Error in tmpf[1:(11 + 2 + 2), 1] : incorrect number of dimensions Calls: EmiStatR -> EmiStatR Execution halted * checking PDF version of manual ... [4s/4s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 NOTEs