* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/TropFishR.Rcheck’ * using R Under development (unstable) (2023-11-23 r85618) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 13.2.1 20231011 (Red Hat 13.2.1-4) GNU Fortran (GCC) 13.2.1 20231011 (Red Hat 13.2.1-4) * running under: Fedora Linux 38 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘TropFishR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TropFishR’ version ‘1.6.3’ * 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 ‘TropFishR’ can be installed ... [11s/11s] OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking 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 ... [23s/23s] 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [11s/11s] OK * checking examples with --run-donttest ... [37s/37s] ERROR Running examples in ‘TropFishR-Ex.R’ failed The error most likely occurred in: > ### Name: ELEFAN > ### Title: ELEFAN > ### Aliases: ELEFAN > > ### ** Examples > > ## No test: > data(alba) > > ### Response Surface Analysis (varies Linf and K) ### > > # 'cross' method (used in FiSAT) > fit1 <- ELEFAN( + lfq = alba, method = "cross", + Linf_range = seq(from = 10, to = 20, length.out = 10), + K_range = exp(seq(from = log(0.1), to = log(2), length.out = 20)), + cross.date = alba$dates[3], cross.midLength = alba$midLengths[4], + contour = TRUE + ) Optimisation procuedure of ELEFAN is running. This will take some time. 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|======================================================================| 99% | |======================================================================| 100%> fit2$Rn_max; unlist(fit2$par) [1] 0.323 Linf K t_anchor C ts phiL 11.578947 1.710000 0.430000 0.000000 0.000000 2.360334 > plot(fit2); points(alba$dates[7], alba$midLengths[9], col=2, cex=2, lwd=2) > > > # 'optimise' method (default) > fit3 <- ELEFAN( + lfq = alba, method = "optimise", + Linf_range = seq(from = 10, to = 20, length.out = 10), + K_range = exp(seq(from = log(0.1), to = log(2), length.out = 20)), + contour = TRUE + ) Optimisation procuedure of ELEFAN is running. This will take some time. 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|==================================================================== | 96% | |==================================================================== | 97% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 99% | |======================================================================| 100%> fit3$Rn_max; unlist(fit3$par) [1] 0.324 Linf K t_anchor C ts phiL 11.1111111 1.0600000 0.8452627 0.0000000 0.0000000 2.1168208 > plot(fit3) > > > ### K-Scan (varies K, Linf is fixed) ### > > # 'cross' method > fit4 <- ELEFAN( + lfq = alba, method = "cross", + Linf_fix = 10, + K_range = round(exp(seq(from = log(0.1), to = log(2), length.out = 50)),2), + cross.date = alba$dates[3], cross.midLength = alba$midLengths[4] + ) Optimisation procuedure of ELEFAN is running. This will take some time. 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OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [365s/368s] 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/TropFishR.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 8:10.77, 467.41 + 19.83