* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/CopulaREMADA.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 ‘CopulaREMADA/DESCRIPTION’ ... OK * this is package ‘CopulaREMADA’ version ‘1.7.5’ * 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 ‘CopulaREMADA’ can be installed ... [26s/27s] OK * checking package 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 ... [35s/36s] 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 data for ASCII and uncompressed saves ... OK * checking examples ... [26s/27s] OK * checking examples with --run-donttest ... [30m/31m] ERROR Running examples in ‘CopulaREMADA-Ex.R’ failed The error most likely occurred in: > ### Name: imperfect.fivariateVineCopulaREMADA > ### Title: Maximum likelihood estimation of 5-variate 1-truncated D-vine > ### copula mixed models for meta-analysis of diagnostic accuracy studies > ### without a gold standard > ### Aliases: imperfect.fivevariateVineCopulaREMADA.norm.comprehensive > ### imperfect.fivevariateVineCopulaREMADA.beta.comprehensive > ### Keywords: maximum likelihood copula distribution > > ### ** Examples > > ## No test: > data(Pap) > attach(Pap) > > nq=15 > gl=gauss.quad.prob(nq,"uniform") > data(mgrid5d15) > mgrid=mgrid5d15 > > tau2par=tau2par.bvn > qcond=qcondbvn > > start=c(rep(0.6,5),rep(0.5,5),rep(0.01,4)) > est.norm=imperfect.fivevariateVineCopulaREMADA.norm.comprehensive(y11,y10,y01, + y00,gl,mgrid,qcond,tau2par,start) iteration = 0 Step: [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Parameter: [1] 0.4054651 0.4054651 0.4054651 0.4054651 0.4054651 -0.6931472 [7] -0.6931472 -0.6931472 -0.6931472 -0.6931472 0.0100000 0.0100000 [13] 0.0100000 0.0100000 Function Value [1] 9683.892 Gradient: [1] 52.58311 -48.44770 -121.38414 -217.75388 -157.70678 -130.75028 [7] -248.33611 -188.21917 -258.20060 -226.65604 -145.44384 -176.69115 [13] -40.28388 -287.41793 iteration = 1 Step: [1] -0.05258311 0.04844770 0.12138414 0.21775388 0.15770678 0.13075028 [7] 0.24833611 0.18821917 0.25820060 0.22665604 0.14544384 0.17669115 [13] 0.04028388 0.28741793 Parameter: [1] 0.35288200 0.45391280 0.52684925 0.62321899 0.56317188 -0.56239690 [7] -0.44481107 -0.50492801 -0.43494658 -0.46649114 0.15544384 0.18669115 [13] 0.05028388 0.29741793 Function Value [1] 9367.491 Gradient: [1] 29.404317 -29.904435 -67.631430 -104.038738 -54.415177 -89.369583 [7] -171.193602 -109.291481 -145.993505 -141.972532 -8.429855 13.206907 [13] -8.373259 -34.242457 iteration = 2 Step: [1] -0.077603251 0.080022736 0.178395186 0.267645944 0.130407625 [6] 0.242216900 0.464447751 0.290019142 0.385931813 0.380643889 [11] -0.006252725 -0.078645927 0.016565344 0.040924963 Parameter: [1] 0.27527874 0.53393554 0.70524443 0.89086494 0.69357951 -0.32018000 [7] 0.01963669 -0.21490887 -0.04901477 -0.08584726 0.14919112 0.10804522 [13] 0.06684923 0.33834289 Function Value [1] 9168.039 Gradient: [1] 11.6345509 -13.8681262 -35.3766427 -32.0297531 -21.9438807 -58.1252716 [7] -65.0287766 -44.7221228 -49.0883631 -64.5613072 -0.5512211 0.5910370 [13] -2.4387500 -8.7252447 iteration = 3 Step: [1] -0.053478275 0.061066399 0.148221537 0.157963997 0.091701312 [6] 0.233406341 0.311520954 0.204121813 0.240465695 0.286635473 [11] -0.011134997 -0.038535995 0.009111007 0.016379737 Parameter: [1] 0.22180047 0.59500194 0.85346597 1.04882893 0.78528082 -0.08677366 [7] 0.33115764 -0.01078705 0.19145093 0.20078822 0.13805612 0.06950923 [13] 0.07596023 0.35472263 Function Value [1] 9106.296 Gradient: [1] 7.652068 -8.988505 -22.248945 -16.975223 -11.135346 -33.552622 [7] -21.969461 -16.095681 -20.101290 -31.767102 1.979570 -3.918120 [13] -2.961098 -5.621569 iteration = 4 Step: [1] -0.05296791 0.06048046 0.14550897 0.14152948 0.08085472 0.22113376 [7] 0.24079296 0.15976929 0.19712400 0.25130885 -0.01808685 -0.02164878 [13] 0.01338421 0.01662666 Parameter: [1] 0.16883256 0.65548240 0.99897494 1.19035841 0.86613554 0.13436009 [7] 0.57195060 0.14898223 0.38857492 0.45209707 0.11996927 0.04786045 [13] 0.08934444 0.37134929 Function Value [1] 9083.444 Gradient: [1] 4.605958 -6.171758 -14.088444 -9.653432 -6.663375 -8.899415 [7] -4.572415 -1.185344 -6.832373 -13.173258 3.045525 -5.952201 [13] -3.010766 -5.825852 iteration = 5 Step: [1] -0.035403699 0.042769562 0.100061978 0.090146045 0.052607712 [6] 0.118851083 0.129812812 0.079152723 0.111819672 0.149317320 [11] -0.018851627 -0.003196877 0.012551957 0.016190322 Parameter: [1] 0.13342886 0.69825196 1.09903692 1.28050445 0.91874326 0.25321118 [7] 0.70176341 0.22813495 0.50039459 0.60141439 0.10111765 0.04466357 [13] 0.10189640 0.38753962 Function Value [1] 9078.071 Gradient: [1] 2.248871 -5.245107 -9.659050 -6.499185 -5.039035 -4.243828 3.074483 [8] 3.925945 -1.750308 -5.397096 2.196830 -5.728836 -1.658436 -7.728200 iteration = 6 Step: [1] -0.025677645 0.037839606 0.081133184 0.069055166 0.042094297 [6] 0.084460346 0.075275493 0.041157731 0.073592828 0.103639203 [11] -0.018502243 0.004390181 0.009649825 0.022826800 Parameter: [1] 0.10775122 0.73609157 1.18017010 1.34955962 0.96083755 0.33767152 [7] 0.77703891 0.26929269 0.57398742 0.70505359 0.08261540 0.04905375 [13] 0.11154622 0.41036642 Function Value [1] 9076.505 Gradient: [1] 1.8216269 -4.2979282 -7.1101276 -4.8295533 -3.8409635 0.6952505 [7] 8.3303039 6.4111773 0.4705253 -0.2313627 5.2691175 -5.9541308 [13] -0.9908326 -6.1106148 iteration = 7 Step: [1] -0.0127938415 0.0222975631 0.0432389947 0.0330896320 0.0215524662 [6] 0.0274194957 0.0073958669 -0.0004315621 0.0233309078 0.0358141280 [11] -0.0203411815 0.0116264238 0.0051339769 0.0170653189 Parameter: [1] 0.09495738 0.75838913 1.22340910 1.38264925 0.98239002 0.36509102 [7] 0.78443477 0.26886112 0.59731833 0.74086772 0.06227422 0.06068017 [13] 0.11668020 0.42743173 Function Value [1] 9075.752 Gradient: [1] 1.0277126 -3.9206134 -6.0985545 -4.0671370 -3.6981619 2.3317662 [7] 8.1263825 6.8455774 1.0461208 1.1430966 3.7961363 -4.7466492 [13] -0.3496989 -5.4925858 iteration = 8 Step: [1] -0.03139620 0.06765667 0.12314025 0.08741792 0.06197586 0.04567184 [7] -0.02789447 -0.04001445 0.03932681 0.06866410 -0.06427019 0.04285215 [13] 0.01200735 0.05721789 Parameter: [1] 0.063561182 0.826045803 1.346549351 1.470067172 1.044365877 [6] 0.410762858 0.756540304 0.228846672 0.636645137 0.809531815 [11] -0.001995965 0.103532327 0.128687547 0.484649626 Function Value [1] 9074.048 Gradient: [1] -0.56292993 -1.24189683 -4.01365531 -2.11741356 -3.61095128 4.05554238 [7] 0.14090983 7.64084689 1.16600677 3.22166488 1.12840462 -0.73119554 [13] 2.12407394 0.09283394 iteration = 9 Step: [1] -0.0129069807 0.0351045148 0.0676084015 0.0440369902 0.0371890344 [6] 0.0063519091 -0.0238762438 -0.0458417646 0.0090121074 0.0178268311 [11] -0.0356722250 0.0250296284 0.0005527647 0.0277424173 Parameter: [1] 0.05065420 0.86115032 1.41415775 1.51410416 1.08155491 0.41711477 [7] 0.73266406 0.18300491 0.64565724 0.82735865 -0.03766819 0.12856196 [13] 0.12924031 0.51239204 Function Value [1] 9073.382 Gradient: [1] -0.8087063 -0.3757123 -1.8315553 -0.9749665 -4.3085593 3.3287706 [7] -0.3523037 4.9442806 0.6696919 3.8631551 6.0997099 3.2764437 [13] 2.7434489 2.4088804 * 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/CopulaREMADA.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 34:09.84, 1946.86 + 57.58