* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/clampSeg.Rcheck’ * using R Under development (unstable) (2025-11-16 r89026) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) * running under: Fedora Linux 40 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘clampSeg/DESCRIPTION’ ... OK * this is package ‘clampSeg’ version ‘1.2-0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘clampSeg’ can be installed ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [12s/12s] OK * checking Rd files ... 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 ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking examples with --run-donttest ... [30m/31m] ERROR Running examples in ‘clampSeg-Ex.R’ failed The error most likely occurred in: > ### Name: clampSeg-package > ### Title: Idealisation of Patch Clamp Recordings > ### Aliases: clampSeg-package clampSeg > ### Keywords: package nonparametric > > ### ** Examples > > ## idealisation of the gramicidin A recording given by gramA > # the used filter > filter <- lowpassFilter(type = "bessel", param = list(pole = 4L, cutoff = 1e3 / 1e4), + sr = 1e4) > > # the corresponding time points > time <- 9 + seq(along = gramA) / filter$sr > > # plot of the data as in (Pein et al., 2018, Figure 1 lower panel) > plot(time, gramA, pch = ".", col = "grey30", ylim = c(20, 50), + ylab = "Conductance in pS", xlab = "Time in s") > > ## No test: > # idealisations require Monte-Carlo simulations > # and therefore might last a few minutes, > # progress of the Monte-Carlo simulations is reported > # JSMURF assuming homogeneous noise > fit1 <- jsmurf(gramA, filter = filter, family = "jsmurfPS", + startTime = 9, messages = 100) 100 of 10000 simulations are completed. 200 of 10000 simulations are completed. 300 of 10000 simulations are completed. 400 of 10000 simulations are completed. 500 of 10000 simulations are completed. 600 of 10000 simulations are completed. 700 of 10000 simulations are completed. 800 of 10000 simulations are completed. 900 of 10000 simulations are completed. 1000 of 10000 simulations are completed. 1100 of 10000 simulations are completed. 1200 of 10000 simulations are completed. 1300 of 10000 simulations are completed. 1400 of 10000 simulations are completed. 1500 of 10000 simulations are completed. 1600 of 10000 simulations are completed. 1700 of 10000 simulations are completed. 1800 of 10000 simulations are completed. 1900 of 10000 simulations are completed. 2000 of 10000 simulations are completed. 2100 of 10000 simulations are completed. 2200 of 10000 simulations are completed. 2300 of 10000 simulations are completed. 2400 of 10000 simulations are 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of 10000 simulations are completed. 5000 of 10000 simulations are completed. 5100 of 10000 simulations are completed. 5200 of 10000 simulations are completed. 5300 of 10000 simulations are completed. 5400 of 10000 simulations are completed. 5500 of 10000 simulations are completed. 5600 of 10000 simulations are completed. 5700 of 10000 simulations are completed. 5800 of 10000 simulations are completed. 5900 of 10000 simulations are completed. 6000 of 10000 simulations are completed. 6100 of 10000 simulations are completed. 6200 of 10000 simulations are completed. 6300 of 10000 simulations are completed. 6400 of 10000 simulations are completed. 6500 of 10000 simulations are completed. 6600 of 10000 simulations are completed. 6700 of 10000 simulations are completed. 6800 of 10000 simulations are completed. 6900 of 10000 simulations are completed. 7000 of 10000 simulations are completed. 7100 of 10000 simulations are completed. 7200 of 10000 simulations are completed. 7300 of 10000 simulations are completed. 7400 of 10000 simulations are completed. 7500 of 10000 simulations are completed. 7600 of 10000 simulations are completed. 7700 of 10000 simulations are completed. 7800 of 10000 simulations are completed. 7900 of 10000 simulations are completed. 8000 of 10000 simulations are completed. 8100 of 10000 simulations are completed. 8200 of 10000 simulations are completed. 8300 of 10000 simulations are completed. 8400 of 10000 simulations are completed. 8500 of 10000 simulations are completed. 8600 of 10000 simulations are completed. 8700 of 10000 simulations are completed. 8800 of 10000 simulations are completed. 8900 of 10000 simulations are completed. 9000 of 10000 simulations are completed. 9100 of 10000 simulations are completed. 9200 of 10000 simulations are completed. 9300 of 10000 simulations are completed. 9400 of 10000 simulations are completed. 9500 of 10000 simulations are completed. 9600 of 10000 simulations are completed. 9700 of 10000 simulations are completed. 9800 of 10000 simulations are completed. 9900 of 10000 simulations are completed. 10000 of 10000 simulations are completed. > # JSMURF allowing heterogeneous noise > fit2 <- jsmurf(gramA, filter = filter, family = "hjsmurf", + startTime = 9, messages = 100) 100 of 10000 simulations are completed. 200 of 10000 simulations are completed. 300 of 10000 simulations are completed. 400 of 10000 simulations are completed. 500 of 10000 simulations are completed. 600 of 10000 simulations are completed. 700 of 10000 simulations are completed. 800 of 10000 simulations are completed. 900 of 10000 simulations are completed. 1000 of 10000 simulations are completed. 1100 of 10000 simulations are completed. 1200 of 10000 simulations are completed. 1300 of 10000 simulations are completed. 1400 of 10000 simulations are completed. 1500 of 10000 simulations are completed. 1600 of 10000 simulations are completed. 1700 of 10000 simulations are completed. 1800 of 10000 simulations are completed. 1900 of 10000 simulations are completed. 2000 of 10000 simulations are completed. 2100 of 10000 simulations are completed. 2200 of 10000 simulations are completed. 2300 of 10000 simulations are completed. 2400 of 10000 simulations are completed. 2500 of 10000 simulations are completed. 2600 of 10000 simulations are completed. 2700 of 10000 simulations are completed. 2800 of 10000 simulations are completed. 2900 of 10000 simulations are completed. 3000 of 10000 simulations are completed. 3100 of 10000 simulations are completed. 3200 of 10000 simulations are completed. 3300 of 10000 simulations are completed. 3400 of 10000 simulations are completed. 3500 of 10000 simulations are completed. 3600 of 10000 simulations are completed. 3700 of 10000 simulations are completed. 3800 of 10000 simulations are completed. 3900 of 10000 simulations are completed. 4000 of 10000 simulations are completed. 4100 of 10000 simulations are completed. 4200 of 10000 simulations are completed. 4300 of 10000 simulations are completed. 4400 of 10000 simulations are completed. 4500 of 10000 simulations are completed. 4600 of 10000 simulations are completed. 4700 of 10000 simulations are completed. 4800 of 10000 simulations are completed. 4900 of 10000 simulations are completed. 5000 of 10000 simulations are completed. 5100 of 10000 simulations are completed. 5200 of 10000 simulations are completed. 5300 of 10000 simulations are completed. 5400 of 10000 simulations are completed. 5500 of 10000 simulations are completed. 5600 of 10000 simulations are completed. 5700 of 10000 simulations are completed. 5800 of 10000 simulations are completed. 5900 of 10000 simulations are completed. 6000 of 10000 simulations are completed. 6100 of 10000 simulations are completed. 6200 of 10000 simulations are completed. 6300 of 10000 simulations are completed. 6400 of 10000 simulations are completed. 6500 of 10000 simulations are completed. 6600 of 10000 simulations are completed. 6700 of 10000 simulations are completed. 6800 of 10000 simulations are completed. 6900 of 10000 simulations are completed. 7000 of 10000 simulations are completed. 7100 of 10000 simulations are completed. 7200 of 10000 simulations are completed. 7300 of 10000 simulations are completed. 7400 of 10000 simulations are completed. 7500 of 10000 simulations are completed. 7600 of 10000 simulations are completed. 7700 of 10000 simulations are completed. 7800 of 10000 simulations are completed. 7900 of 10000 simulations are completed. 8000 of 10000 simulations are completed. 8100 of 10000 simulations are completed. 8200 of 10000 simulations are completed. 8300 of 10000 simulations are completed. 8400 of 10000 simulations are completed. 8500 of 10000 simulations are completed. 8600 of 10000 simulations are completed. 8700 of 10000 simulations are completed. 8800 of 10000 simulations are completed. 8900 of 10000 simulations are completed. 9000 of 10000 simulations are completed. 9100 of 10000 simulations are completed. 9200 of 10000 simulations are completed. 9300 of 10000 simulations are completed. 9400 of 10000 simulations are completed. 9500 of 10000 simulations are completed. 9600 of 10000 simulations are completed. 9700 of 10000 simulations are completed. 9800 of 10000 simulations are completed. 9900 of 10000 simulations are completed. 10000 of 10000 simulations are completed. > # JULES assuming homogeneous noise > fit3 <- jules(gramA, filter = filter, startTime = 9, messages = 100) 100 of 10000 simulations are completed. 200 of 10000 simulations are completed. 300 of 10000 simulations are completed. 400 of 10000 simulations are completed. 500 of 10000 simulations are completed. 600 of 10000 simulations are completed. 700 of 10000 simulations are completed. 800 of 10000 simulations are completed. 900 of 10000 simulations are completed. 1000 of 10000 simulations are completed. 1100 of 10000 simulations are completed. 1200 of 10000 simulations are completed. 1300 of 10000 simulations are completed. 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of 10000 simulations are completed. 8800 of 10000 simulations are completed. 8900 of 10000 simulations are completed. 9000 of 10000 simulations are completed. 9100 of 10000 simulations are completed. 9200 of 10000 simulations are completed. 9300 of 10000 simulations are completed. 9400 of 10000 simulations are completed. 9500 of 10000 simulations are completed. 9600 of 10000 simulations are completed. 9700 of 10000 simulations are completed. 9800 of 10000 simulations are completed. 9900 of 10000 simulations are completed. 10000 of 10000 simulations are completed. > # HILDE assuming homogeneous noise > fit4 <- hilde(gramA, filter = filter, family = "jsmurfPS", method = "LR", + startTime = 9, messages = 10) 10 of 1000 simulations are completed. 20 of 1000 simulations are completed. 30 of 1000 simulations are completed. 40 of 1000 simulations are completed. 50 of 1000 simulations are completed. 60 of 1000 simulations are completed. 70 of 1000 simulations are completed. 80 of 1000 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OK * checking tests ... Running ‘testthat.R’ [202s/212s] [203s/213s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [26s/26s] OK * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 1 ERROR See ‘/data/blackswan/ripley/R/packages/tests-devel/clampSeg.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 36:14.75, 2070.43 + 26.35