CRAN Package Check Results for Maintainer ‘Robin Denz <robin.denz at rub.de>’

Last updated on 2026-08-03 21:53:01 CEST.

Package	OK	NOTE	ERROR
adjustedCurves	11	2
CareDensity	12	1
contsurvplot	12	1
simDAG	10		3

Package adjustedCurves

Current CRAN status: OK: 11, NOTE: 2

Version: 0.11.4
Check: Rd contents
Result: NOTE Rd files without \usage: ‘cif_aalen_johansen.Rd’ ‘cif_aiptw.Rd’ ‘cif_aiptw_pseudo.Rd’ ‘cif_direct.Rd’ ‘cif_direct_pseudo.Rd’ ‘cif_iptw.Rd’ ‘cif_iptw_pseudo.Rd’ ‘cif_matching.Rd’ ‘surv_aiptw.Rd’ ‘surv_aiptw_pseudo.Rd’ ‘surv_direct.Rd’ ‘surv_direct_pseudo.Rd’ ‘surv_emp_lik.Rd’ ‘surv_iptw_cox.Rd’ ‘surv_iptw_km.Rd’ ‘surv_iptw_pseudo.Rd’ ‘surv_iv_2SRIF.Rd’ ‘surv_km.Rd’ ‘surv_matching.Rd’ ‘surv_prox_aiptw.Rd’ ‘surv_prox_iptw.Rd’ ‘surv_strat_amato.Rd’ ‘surv_strat_cupples.Rd’ ‘surv_strat_nieto.Rd’ \arguments should not be documented without \usage. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.11.4
Check: for new files in some other directories
Result: NOTE Found the following files/directories: ‘~/tmp/scratch/Rtmp0QEZCR’ ‘~/tmp/scratch/Rtmp0aYVQ6’ ‘~/tmp/scratch/Rtmp0cYomu’ ‘~/tmp/scratch/Rtmp0lLkyk’ ‘~/tmp/scratch/Rtmp1eot7X’ ‘~/tmp/scratch/Rtmp1uOMko’ ‘~/tmp/scratch/Rtmp3AD90v’ ‘~/tmp/scratch/Rtmp3Z8lTg’ ‘~/tmp/scratch/Rtmp3c1u0t’ ‘~/tmp/scratch/Rtmp3e6dpx’ ‘~/tmp/scratch/Rtmp3hqcOf’ ‘~/tmp/scratch/Rtmp41z8YT’ ‘~/tmp/scratch/Rtmp42uRzR’ ‘~/tmp/scratch/Rtmp4G0DZJ’ ‘~/tmp/scratch/Rtmp4xszHq’ ‘~/tmp/scratch/Rtmp5QJW3A’ ‘~/tmp/scratch/Rtmp5fSuIg’ ‘~/tmp/scratch/Rtmp66dCKz’ ‘~/tmp/scratch/Rtmp6zdesU’ ‘~/tmp/scratch/Rtmp7MDuCG’ ‘~/tmp/scratch/Rtmp7XSQnT’ ‘~/tmp/scratch/Rtmp84qc8u’ ‘~/tmp/scratch/Rtmp8QVm71’ ‘~/tmp/scratch/Rtmp8Y8Zy8’ ‘~/tmp/scratch/Rtmp8dhDQD’ ‘~/tmp/scratch/Rtmp8kCOKy’ ‘~/tmp/scratch/Rtmp8pA2yj’ ‘~/tmp/scratch/Rtmp9176sk’ ‘~/tmp/scratch/Rtmp967dle’ ‘~/tmp/scratch/RtmpAZAAP3’ ‘~/tmp/scratch/RtmpAazZJ6’ ‘~/tmp/scratch/RtmpAiCiJ4’ ‘~/tmp/scratch/RtmpBYJDK7’ ‘~/tmp/scratch/RtmpDHzubd’ ‘~/tmp/scratch/RtmpE5DnhA’ ‘~/tmp/scratch/RtmpELXR9D’ ‘~/tmp/scratch/RtmpEUB7jA’ ‘~/tmp/scratch/RtmpEoeD91’ ‘~/tmp/scratch/RtmpEzFBpc’ ‘~/tmp/scratch/RtmpF7yUUr’ ‘~/tmp/scratch/RtmpFgQWZn’ ‘~/tmp/scratch/RtmpFtTIHm’ ‘~/tmp/scratch/RtmpG4vgBS’ ‘~/tmp/scratch/RtmpGI0u8m’ ‘~/tmp/scratch/RtmpGKDLB9’ ‘~/tmp/scratch/RtmpGNoXkv’ ‘~/tmp/scratch/RtmpGbKRNf’ ‘~/tmp/scratch/RtmpGg0fnQ’ ‘~/tmp/scratch/RtmpGixJxz’ ‘~/tmp/scratch/RtmpHYjYB2’ ‘~/tmp/scratch/RtmpHor3V8’ ‘~/tmp/scratch/RtmpI1d7yW’ ‘~/tmp/scratch/RtmpISuRWA’ ‘~/tmp/scratch/RtmpIrQqW6’ ‘~/tmp/scratch/RtmpJ1aAwn’ ‘~/tmp/scratch/RtmpJ2CRJa’ ‘~/tmp/scratch/RtmpJ8ZjbU’ ‘~/tmp/scratch/RtmpJ9Bd04’ ‘~/tmp/scratch/RtmpJWEgRb’ ‘~/tmp/scratch/RtmpJXrS6m’ ‘~/tmp/scratch/RtmpJjtxfB’ ‘~/tmp/scratch/RtmpKEwtAO’ ‘~/tmp/scratch/RtmpKJmEoR’ ‘~/tmp/scratch/RtmpKUdgSX’ ‘~/tmp/scratch/RtmpKV7aNt’ ‘~/tmp/scratch/RtmpL1bpL2’ ‘~/tmp/scratch/RtmpLNivLs’ ‘~/tmp/scratch/RtmpLTvJUz’ ‘~/tmp/scratch/RtmpLiokjS’ ‘~/tmp/scratch/RtmpMKW2Yy’ ‘~/tmp/scratch/RtmpMgBrmp’ ‘~/tmp/scratch/RtmpMmjj2U’ ‘~/tmp/scratch/RtmpNEkOvO’ ‘~/tmp/scratch/RtmpO5ZCcD’ ‘~/tmp/scratch/RtmpOAEJSD’ ‘~/tmp/scratch/RtmpOtvf6k’ ‘~/tmp/scratch/RtmpOy7ubi’ ‘~/tmp/scratch/RtmpQ8M0Lj’ ‘~/tmp/scratch/RtmpQiyalq’ ‘~/tmp/scratch/RtmpQjkP06’ ‘~/tmp/scratch/RtmpQmLzFK’ ‘~/tmp/scratch/RtmpR8qIM6’ ‘~/tmp/scratch/RtmpRSaZcF’ ‘~/tmp/scratch/RtmpRSg57L’ ‘~/tmp/scratch/RtmpSUGc9R’ ‘~/tmp/scratch/RtmpSocHYj’ ‘~/tmp/scratch/RtmpTdlYUk’ ‘~/tmp/scratch/RtmpV2L28J’ ‘~/tmp/scratch/RtmpVIbLD4’ ‘~/tmp/scratch/RtmpVVLMov’ ‘~/tmp/scratch/RtmpVfuGEU’ ‘~/tmp/scratch/RtmpVycpqy’ ‘~/tmp/scratch/RtmpW37YEJ’ ‘~/tmp/scratch/RtmpWD3QgH’ ‘~/tmp/scratch/RtmpXEvxcT’ ‘~/tmp/scratch/RtmpXFR6Vb’ ‘~/tmp/scratch/RtmpY0oO62’ ‘~/tmp/scratch/RtmpY3FMEr’ ‘~/tmp/scratch/RtmpYS6mM1’ ‘~/tmp/scratch/RtmpZ0r0jz’ ‘~/tmp/scratch/RtmpZeY4dw’ ‘~/tmp/scratch/RtmpZzuXBz’ ‘~/tmp/scratch/RtmpaCCJyo’ ‘~/tmp/scratch/RtmpaIglUQ’ ‘~/tmp/scratch/RtmpaK5r6u’ ‘~/tmp/scratch/RtmpaKeY1R’ ‘~/tmp/scratch/RtmpaOHSwH’ ‘~/tmp/scratch/RtmpaV0ciL’ ‘~/tmp/scratch/Rtmpbfg5f3’ ‘~/tmp/scratch/Rtmpbi7MG1’ ‘~/tmp/scratch/RtmpbwcUiU’ ‘~/tmp/scratch/RtmpcDo6XQ’ ‘~/tmp/scratch/RtmpcFYLYv’ ‘~/tmp/scratch/RtmpcGtNEy’ ‘~/tmp/scratch/Rtmpcm73Mo’ ‘~/tmp/scratch/Rtmpd60ovO’ ‘~/tmp/scratch/Rtmpd8p4j9’ ‘~/tmp/scratch/RtmpdIu9FE’ ‘~/tmp/scratch/RtmpdJVf3G’ ‘~/tmp/scratch/Rtmpdea5Ml’ ‘~/tmp/scratch/RtmpdhUEfo’ ‘~/tmp/scratch/Rtmpe6Nmeo’ ‘~/tmp/scratch/RtmpeExatI’ ‘~/tmp/scratch/RtmpeOrue4’ ‘~/tmp/scratch/RtmpercAOK’ ‘~/tmp/scratch/RtmpfThfF7’ ‘~/tmp/scratch/Rtmpg1EKXU’ ‘~/tmp/scratch/Rtmpg8U5qw’ ‘~/tmp/scratch/Rtmpg9DLpm’ ‘~/tmp/scratch/RtmpgdenvK’ ‘~/tmp/scratch/RtmpgurZUg’ ‘~/tmp/scratch/RtmpgwIG0K’ ‘~/tmp/scratch/Rtmph7VmUw’ ‘~/tmp/scratch/RtmphSbnC3’ ‘~/tmp/scratch/Rtmphz4LpL’ ‘~/tmp/scratch/Rtmpi8JG9R’ ‘~/tmp/scratch/RtmpjHaiuq’ ‘~/tmp/scratch/RtmpjXSWDW’ ‘~/tmp/scratch/RtmpjkNbhg’ ‘~/tmp/scratch/RtmpkLVbdx’ ‘~/tmp/scratch/RtmpkUKFJv’ ‘~/tmp/scratch/RtmpkYoS4O’ ‘~/tmp/scratch/Rtmpl927wA’ ‘~/tmp/scratch/RtmplFBHYG’ ‘~/tmp/scratch/RtmplkR3f6’ ‘~/tmp/scratch/Rtmploe9zT’ ‘~/tmp/scratch/RtmpmHCrOZ’ ‘~/tmp/scratch/Rtmpn6R33V’ ‘~/tmp/scratch/Rtmpn8OLv3’ ‘~/tmp/scratch/RtmpnWVGhj’ ‘~/tmp/scratch/Rtmpnk6mJ1’ ‘~/tmp/scratch/RtmpoJuoAm’ ‘~/tmp/scratch/RtmppCm1ac’ ‘~/tmp/scratch/RtmppJ36eX’ ‘~/tmp/scratch/RtmppVxqh1’ ‘~/tmp/scratch/RtmppYCdqg’ ‘~/tmp/scratch/Rtmpq17WZU’ ‘~/tmp/scratch/RtmpqXbfnR’ ‘~/tmp/scratch/RtmpqYTeGZ’ ‘~/tmp/scratch/RtmprBX6Ay’ ‘~/tmp/scratch/RtmprX2rSH’ ‘~/tmp/scratch/RtmprdmxBV’ ‘~/tmp/scratch/Rtmps177fE’ ‘~/tmp/scratch/RtmpsJGl7z’ ‘~/tmp/scratch/RtmptPpMrp’ ‘~/tmp/scratch/RtmptPybgU’ ‘~/tmp/scratch/Rtmptbx5qN’ ‘~/tmp/scratch/RtmpuDMKcr’ ‘~/tmp/scratch/RtmpuKAdOW’ ‘~/tmp/scratch/RtmpubPvG6’ ‘~/tmp/scratch/RtmpusOVAK’ ‘~/tmp/scratch/RtmpvCezoE’ ‘~/tmp/scratch/RtmpvX4C00’ ‘~/tmp/scratch/RtmpvcvoZY’ ‘~/tmp/scratch/Rtmpvjx8e0’ ‘~/tmp/scratch/RtmpvmKF7D’ ‘~/tmp/scratch/Rtmpvw80Dj’ ‘~/tmp/scratch/RtmpwNXMVY’ ‘~/tmp/scratch/RtmpwkC3ZI’ ‘~/tmp/scratch/Rtmpyacpvg’ ‘~/tmp/scratch/Rtmpyi6L0L’ ‘~/tmp/scratch/RtmpytWBgP’ ‘~/tmp/scratch/Rtmpz9cmdI’ ‘~/tmp/scratch/RtmpzHUyRG’ ‘~/tmp/scratch/RtmpzTWVCT’ ‘~/tmp/scratch/xvfb-run.068tLO’ ‘~/tmp/scratch/xvfb-run.0dAVOR’ ‘~/tmp/scratch/xvfb-run.122iol’ ‘~/tmp/scratch/xvfb-run.2UfTCj’ ‘~/tmp/scratch/xvfb-run.2ZScYR’ ‘~/tmp/scratch/xvfb-run.2wbbad’ ‘~/tmp/scratch/xvfb-run.40yWKQ’ ‘~/tmp/scratch/xvfb-run.42OJtd’ ‘~/tmp/scratch/xvfb-run.4S4pay’ ‘~/tmp/scratch/xvfb-run.4WuYuX’ ‘~/tmp/scratch/xvfb-run.5fWD9a’ ‘~/tmp/scratch/xvfb-run.69TkAi’ ‘~/tmp/scratch/xvfb-run.770Dsh’ ‘~/tmp/scratch/xvfb-run.8bjTj9’ ‘~/tmp/scratch/xvfb-run.93JwjE’ ‘~/tmp/scratch/xvfb-run.9qGR26’ ‘~/tmp/scratch/xvfb-run.ARFfLV’ ‘~/tmp/scratch/xvfb-run.EE1ex4’ ‘~/tmp/scratch/xvfb-run.FVgMtM’ ‘~/tmp/scratch/xvfb-run.GgtQJ9’ ‘~/tmp/scratch/xvfb-run.GszaPN’ ‘~/tmp/scratch/xvfb-run.HVZeVC’ ‘~/tmp/scratch/xvfb-run.Iuzc80’ ‘~/tmp/scratch/xvfb-run.JKpb40’ ‘~/tmp/scratch/xvfb-run.JYwdn0’ ‘~/tmp/scratch/xvfb-run.Jgvkd3’ ‘~/tmp/scratch/xvfb-run.Knuqk9’ ‘~/tmp/scratch/xvfb-run.Luqvh3’ ‘~/tmp/scratch/xvfb-run.OmMdbC’ ‘~/tmp/scratch/xvfb-run.PO7btS’ ‘~/tmp/scratch/xvfb-run.QA1hys’ ‘~/tmp/scratch/xvfb-run.QBrDGg’ ‘~/tmp/scratch/xvfb-run.REcu8U’ ‘~/tmp/scratch/xvfb-run.RuV5Q1’ ‘~/tmp/scratch/xvfb-run.SDzGP2’ ‘~/tmp/scratch/xvfb-run.UJPyE8’ ‘~/tmp/scratch/xvfb-run.V3ObiL’ ‘~/tmp/scratch/xvfb-run.Y4KUvw’ ‘~/tmp/scratch/xvfb-run.YbYO26’ ‘~/tmp/scratch/xvfb-run.ZedivF’ ‘~/tmp/scratch/xvfb-run.amOlZ6’ ‘~/tmp/scratch/xvfb-run.anBCIN’ ‘~/tmp/scratch/xvfb-run.bmOJLZ’ ‘~/tmp/scratch/xvfb-run.cuFYpn’ ‘~/tmp/scratch/xvfb-run.d8wsJ6’ ‘~/tmp/scratch/xvfb-run.e2oJVg’ ‘~/tmp/scratch/xvfb-run.f0buM3’ ‘~/tmp/scratch/xvfb-run.fO4kQT’ ‘~/tmp/scratch/xvfb-run.fW0Ikk’ ‘~/tmp/scratch/xvfb-run.fq1JO6’ ‘~/tmp/scratch/xvfb-run.hc3NlB’ ‘~/tmp/scratch/xvfb-run.hnsWNC’ ‘~/tmp/scratch/xvfb-run.iC9N06’ ‘~/tmp/scratch/xvfb-run.ji2kPi’ ‘~/tmp/scratch/xvfb-run.l4zAga’ ‘~/tmp/scratch/xvfb-run.lgJdCg’ ‘~/tmp/scratch/xvfb-run.lpQgOZ’ ‘~/tmp/scratch/xvfb-run.nGgehx’ ‘~/tmp/scratch/xvfb-run.nTsx5j’ ‘~/tmp/scratch/xvfb-run.oGy2RV’ ‘~/tmp/scratch/xvfb-run.pGFuUk’ ‘~/tmp/scratch/xvfb-run.pTT4ZH’ ‘~/tmp/scratch/xvfb-run.pzASNo’ ‘~/tmp/scratch/xvfb-run.q3D6Bu’ ‘~/tmp/scratch/xvfb-run.qAzsQc’ ‘~/tmp/scratch/xvfb-run.r6xNQc’ ‘~/tmp/scratch/xvfb-run.rSJ8mi’ ‘~/tmp/scratch/xvfb-run.rWYepD’ ‘~/tmp/scratch/xvfb-run.rl3Xrt’ ‘~/tmp/scratch/xvfb-run.sOamV8’ ‘~/tmp/scratch/xvfb-run.tA5geI’ ‘~/tmp/scratch/xvfb-run.tSdl3z’ ‘~/tmp/scratch/xvfb-run.teAiGl’ ‘~/tmp/scratch/xvfb-run.tmhZqO’ ‘~/tmp/scratch/xvfb-run.um6bQF’ ‘~/tmp/scratch/xvfb-run.v69uBT’ ‘~/tmp/scratch/xvfb-run.vv2Z67’ ‘~/tmp/scratch/xvfb-run.zZgA4d’ ‘~/tmp/scratch/xvfb-run.zbGQCa’ ‘~/tmp/scratch/xvfb-run.zbkp1V’ ‘~/tmp/scratch/xvfb-run.zpdy1c’ ‘~/tmp/scratch/xvfb-run.zr9dYA’ Flavor: r-devel-linux-x86_64-debian-gcc

Package CareDensity

Current CRAN status: OK: 12, NOTE: 1

Version: 0.1.0
Check: for new files in some other directories
Result: NOTE Found the following files/directories: ‘~/tmp/scratch/Rtmp02XA4A’ ‘~/tmp/scratch/Rtmp0Ebvby’ ‘~/tmp/scratch/Rtmp0JbFde’ ‘~/tmp/scratch/Rtmp0K3CQV’ ‘~/tmp/scratch/Rtmp0ZKzLf’ ‘~/tmp/scratch/Rtmp13lDSH’ ‘~/tmp/scratch/Rtmp1DCPWB’ ‘~/tmp/scratch/Rtmp1GFOqr’ ‘~/tmp/scratch/Rtmp1PbJ2v’ ‘~/tmp/scratch/Rtmp1YvfQY’ ‘~/tmp/scratch/Rtmp1g1cgt’ ‘~/tmp/scratch/Rtmp1t9Zii’ ‘~/tmp/scratch/Rtmp24K4x5’ ‘~/tmp/scratch/Rtmp2Xh1pR’ ‘~/tmp/scratch/Rtmp38dYzq’ ‘~/tmp/scratch/Rtmp4w5aGD’ ‘~/tmp/scratch/Rtmp76hgDy’ ‘~/tmp/scratch/Rtmp7qLNPE’ ‘~/tmp/scratch/Rtmp85OA2K’ ‘~/tmp/scratch/Rtmp8BNihj’ ‘~/tmp/scratch/Rtmp8U5f6s’ ‘~/tmp/scratch/Rtmp8b5IuK’ ‘~/tmp/scratch/Rtmp8wFaWP’ ‘~/tmp/scratch/Rtmp9dP2SZ’ ‘~/tmp/scratch/RtmpAGLPxp’ ‘~/tmp/scratch/RtmpAUDzSV’ ‘~/tmp/scratch/RtmpAmLLto’ ‘~/tmp/scratch/RtmpAxmB5b’ ‘~/tmp/scratch/RtmpB0WrgK’ ‘~/tmp/scratch/RtmpBAjurk’ ‘~/tmp/scratch/RtmpBFhLzO’ ‘~/tmp/scratch/RtmpBbY3XJ’ ‘~/tmp/scratch/RtmpBfm429’ ‘~/tmp/scratch/RtmpBzY8zr’ ‘~/tmp/scratch/RtmpCNAHVP’ ‘~/tmp/scratch/RtmpCdF38d’ ‘~/tmp/scratch/RtmpCzEbVG’ ‘~/tmp/scratch/RtmpD8sABw’ ‘~/tmp/scratch/RtmpDhA9TF’ ‘~/tmp/scratch/RtmpDy3ERI’ ‘~/tmp/scratch/RtmpFHb0To’ ‘~/tmp/scratch/RtmpFLp2Cz’ ‘~/tmp/scratch/RtmpFlf9zU’ ‘~/tmp/scratch/RtmpG7iX3q’ ‘~/tmp/scratch/RtmpGeihXF’ ‘~/tmp/scratch/RtmpHe4gp0’ ‘~/tmp/scratch/RtmpHgtrLK’ ‘~/tmp/scratch/RtmpHjgQvL’ ‘~/tmp/scratch/RtmpHtOS3p’ ‘~/tmp/scratch/RtmpIS9h6h’ ‘~/tmp/scratch/RtmpIw8elC’ ‘~/tmp/scratch/RtmpK2ToKd’ ‘~/tmp/scratch/RtmpK2ymon’ ‘~/tmp/scratch/RtmpK7w8NW’ ‘~/tmp/scratch/RtmpKFuEY2’ ‘~/tmp/scratch/RtmpLMoSr1’ ‘~/tmp/scratch/RtmpMKItMi’ ‘~/tmp/scratch/RtmpMZUGIx’ ‘~/tmp/scratch/RtmpNwFbmS’ ‘~/tmp/scratch/RtmpOcg2u8’ ‘~/tmp/scratch/RtmpQ9GzEP’ ‘~/tmp/scratch/RtmpQ9RHzI’ ‘~/tmp/scratch/RtmpQz5kwz’ ‘~/tmp/scratch/RtmpRFq8Lb’ ‘~/tmp/scratch/RtmpRr4emH’ ‘~/tmp/scratch/RtmpS2qp2B’ ‘~/tmp/scratch/RtmpSZduZ4’ ‘~/tmp/scratch/RtmpStCotG’ ‘~/tmp/scratch/RtmpT7EXqu’ ‘~/tmp/scratch/RtmpTRISFL’ ‘~/tmp/scratch/RtmpTRYd0l’ ‘~/tmp/scratch/RtmpTxcPdV’ ‘~/tmp/scratch/RtmpU8ieN3’ ‘~/tmp/scratch/RtmpUvkdeq’ ‘~/tmp/scratch/RtmpVDCpQ0’ ‘~/tmp/scratch/RtmpWSEFT8’ ‘~/tmp/scratch/RtmpWXo3SS’ ‘~/tmp/scratch/RtmpWbGI7Z’ ‘~/tmp/scratch/RtmpWiDE5u’ ‘~/tmp/scratch/RtmpXMy2bt’ ‘~/tmp/scratch/RtmpYPWcJ6’ ‘~/tmp/scratch/RtmpZDvNlD’ ‘~/tmp/scratch/RtmpZNSu32’ ‘~/tmp/scratch/RtmpZUwNPf’ ‘~/tmp/scratch/RtmpbcC3Un’ ‘~/tmp/scratch/RtmpbfzwX7’ ‘~/tmp/scratch/Rtmpbyk79C’ ‘~/tmp/scratch/Rtmpc4LZDG’ ‘~/tmp/scratch/RtmpcF3y5O’ ‘~/tmp/scratch/RtmpcrFx1e’ ‘~/tmp/scratch/Rtmpd2SX4f’ ‘~/tmp/scratch/Rtmpdb2Gpo’ ‘~/tmp/scratch/Rtmpdcv6NJ’ ‘~/tmp/scratch/RtmpdgLawt’ ‘~/tmp/scratch/RtmpdkCr7x’ ‘~/tmp/scratch/RtmpeKcQpG’ ‘~/tmp/scratch/Rtmpf37kCC’ ‘~/tmp/scratch/Rtmpg2sXor’ ‘~/tmp/scratch/RtmpgPsXtQ’ ‘~/tmp/scratch/Rtmphdcvjl’ ‘~/tmp/scratch/Rtmpi9gGzX’ ‘~/tmp/scratch/RtmpioqCXa’ ‘~/tmp/scratch/RtmpixoygZ’ ‘~/tmp/scratch/RtmpkNq64z’ ‘~/tmp/scratch/RtmpkoO8c7’ ‘~/tmp/scratch/Rtmpl9cGp8’ ‘~/tmp/scratch/RtmplL8v3D’ ‘~/tmp/scratch/Rtmplaz1w8’ ‘~/tmp/scratch/RtmplcJWS2’ ‘~/tmp/scratch/Rtmpm0pyzy’ ‘~/tmp/scratch/Rtmpm6PZFh’ ‘~/tmp/scratch/RtmpnckfRx’ ‘~/tmp/scratch/Rtmpne2Tk1’ ‘~/tmp/scratch/RtmpoduQOQ’ ‘~/tmp/scratch/RtmpoowaHO’ ‘~/tmp/scratch/RtmppXLd8B’ ‘~/tmp/scratch/Rtmpq05B0O’ ‘~/tmp/scratch/Rtmpq0aSch’ ‘~/tmp/scratch/Rtmpq9C6gu’ ‘~/tmp/scratch/Rtmpq9xre6’ ‘~/tmp/scratch/RtmpqCH2yQ’ ‘~/tmp/scratch/RtmpqzB63f’ ‘~/tmp/scratch/Rtmpr4ntTP’ ‘~/tmp/scratch/RtmprB8ko8’ ‘~/tmp/scratch/RtmprhcXyZ’ ‘~/tmp/scratch/Rtmprza5HN’ ‘~/tmp/scratch/Rtmps5i2GX’ ‘~/tmp/scratch/RtmpsPIobP’ ‘~/tmp/scratch/RtmpsWZEkg’ ‘~/tmp/scratch/RtmpseMofd’ ‘~/tmp/scratch/RtmpsgxSps’ ‘~/tmp/scratch/RtmpvWU7Dm’ ‘~/tmp/scratch/Rtmpvdz1Mu’ ‘~/tmp/scratch/Rtmpw9zG3B’ ‘~/tmp/scratch/RtmpwgWBDx’ ‘~/tmp/scratch/RtmpxR5znK’ ‘~/tmp/scratch/RtmpxV69wp’ ‘~/tmp/scratch/RtmpyNef8b’ ‘~/tmp/scratch/Rtmpz3iVxx’ ‘~/tmp/scratch/Rtmpz7cqeJ’ ‘~/tmp/scratch/ccVpjGbA.s’ ‘~/tmp/scratch/xvfb-run.07DwOG’ ‘~/tmp/scratch/xvfb-run.09GlZ8’ ‘~/tmp/scratch/xvfb-run.0X6u0A’ ‘~/tmp/scratch/xvfb-run.1IVTwg’ ‘~/tmp/scratch/xvfb-run.1ftMju’ ‘~/tmp/scratch/xvfb-run.2laqnm’ ‘~/tmp/scratch/xvfb-run.2tehmz’ ‘~/tmp/scratch/xvfb-run.3paomi’ ‘~/tmp/scratch/xvfb-run.5xr43A’ ‘~/tmp/scratch/xvfb-run.6Btl5D’ ‘~/tmp/scratch/xvfb-run.8qpFTd’ ‘~/tmp/scratch/xvfb-run.A4nDXp’ ‘~/tmp/scratch/xvfb-run.ALcpkz’ ‘~/tmp/scratch/xvfb-run.AeJLon’ ‘~/tmp/scratch/xvfb-run.Aep1JR’ ‘~/tmp/scratch/xvfb-run.B9dfWA’ ‘~/tmp/scratch/xvfb-run.CkXVdD’ ‘~/tmp/scratch/xvfb-run.CpbjWv’ ‘~/tmp/scratch/xvfb-run.EoEA2H’ ‘~/tmp/scratch/xvfb-run.Ew3ffJ’ ‘~/tmp/scratch/xvfb-run.FI9fJl’ ‘~/tmp/scratch/xvfb-run.FtlcV2’ ‘~/tmp/scratch/xvfb-run.GO4sYJ’ ‘~/tmp/scratch/xvfb-run.IWPJyr’ ‘~/tmp/scratch/xvfb-run.JUf65M’ ‘~/tmp/scratch/xvfb-run.Kmjtd6’ ‘~/tmp/scratch/xvfb-run.LVI2ZD’ ‘~/tmp/scratch/xvfb-run.LnR9Tn’ ‘~/tmp/scratch/xvfb-run.NhiPpU’ ‘~/tmp/scratch/xvfb-run.NhrQGA’ ‘~/tmp/scratch/xvfb-run.P0UAxx’ ‘~/tmp/scratch/xvfb-run.PH3CCg’ ‘~/tmp/scratch/xvfb-run.PU5pZY’ ‘~/tmp/scratch/xvfb-run.QeLMbu’ ‘~/tmp/scratch/xvfb-run.RHKboF’ ‘~/tmp/scratch/xvfb-run.RSlr2b’ ‘~/tmp/scratch/xvfb-run.Rj7Sqi’ ‘~/tmp/scratch/xvfb-run.S2Gg6a’ ‘~/tmp/scratch/xvfb-run.SIcygT’ ‘~/tmp/scratch/xvfb-run.T2eL0L’ ‘~/tmp/scratch/xvfb-run.WA1Ajv’ ‘~/tmp/scratch/xvfb-run.WlU5Yl’ ‘~/tmp/scratch/xvfb-run.WrUmLy’ ‘~/tmp/scratch/xvfb-run.XetS1H’ ‘~/tmp/scratch/xvfb-run.a1BJO9’ ‘~/tmp/scratch/xvfb-run.gruYXX’ ‘~/tmp/scratch/xvfb-run.hlpT25’ ‘~/tmp/scratch/xvfb-run.jllDv1’ ‘~/tmp/scratch/xvfb-run.oha8dI’ ‘~/tmp/scratch/xvfb-run.pUFAKO’ ‘~/tmp/scratch/xvfb-run.q0lckk’ ‘~/tmp/scratch/xvfb-run.q58YkQ’ ‘~/tmp/scratch/xvfb-run.sNaXth’ ‘~/tmp/scratch/xvfb-run.tb8QvZ’ ‘~/tmp/scratch/xvfb-run.tkwq6A’ ‘~/tmp/scratch/xvfb-run.wOLs4P’ ‘~/tmp/scratch/xvfb-run.x2qXt3’ ‘~/tmp/scratch/xvfb-run.xCgdJ3’ ‘~/tmp/scratch/xvfb-run.xCy3Tl’ ‘~/tmp/scratch/xvfb-run.xkoC8U’ ‘~/tmp/scratch/xvfb-run.zLmljn’ ‘/dev/shm/sm_segment.gimli1.1001.b8d50000.0’ ‘/dev/shm/sm_segment.gimli1.1001.c3540000.0’ ‘~/.cache/pocl/uncached/tempfile_MgzrKA’ ‘~/.cache/pocl/uncached/tempfile_rNhcmC’ Flavor: r-devel-linux-x86_64-debian-gcc

Package contsurvplot

Current CRAN status: OK: 12, NOTE: 1

Version: 0.2.3
Check: for new files in some other directories
Result: NOTE Found the following files/directories: ‘~/tmp/scratch/Rtmp107UT2’ ‘~/tmp/scratch/Rtmp1MCpFa’ ‘~/tmp/scratch/Rtmp1XIKhv’ ‘~/tmp/scratch/Rtmp1b66fC’ ‘~/tmp/scratch/Rtmp2HCivd’ ‘~/tmp/scratch/Rtmp3Bcp59’ ‘~/tmp/scratch/Rtmp3DCBK4’ ‘~/tmp/scratch/Rtmp3bNMAS’ ‘~/tmp/scratch/Rtmp3er11B’ ‘~/tmp/scratch/Rtmp3p2gQI’ ‘~/tmp/scratch/Rtmp55qKXZ’ ‘~/tmp/scratch/Rtmp5PxYXX’ ‘~/tmp/scratch/Rtmp5TmacP’ ‘~/tmp/scratch/Rtmp5d2Ttr’ ‘~/tmp/scratch/Rtmp5j8CCV’ ‘~/tmp/scratch/Rtmp5rL0xf’ ‘~/tmp/scratch/Rtmp6WRinj’ ‘~/tmp/scratch/Rtmp6mSuNK’ ‘~/tmp/scratch/Rtmp6vHwHY’ ‘~/tmp/scratch/Rtmp6xWJKu’ ‘~/tmp/scratch/Rtmp6zcoEN’ ‘~/tmp/scratch/Rtmp7FbQDg’ ‘~/tmp/scratch/Rtmp7yVvCg’ ‘~/tmp/scratch/Rtmp8GKxcM’ ‘~/tmp/scratch/Rtmp8JXYLd’ ‘~/tmp/scratch/Rtmp8ZcrL2’ ‘~/tmp/scratch/Rtmp8cdzsD’ ‘~/tmp/scratch/Rtmp8uHPz3’ ‘~/tmp/scratch/Rtmp9KfXCd’ ‘~/tmp/scratch/Rtmp9YuYOF’ ‘~/tmp/scratch/Rtmp9gWZQ2’ ‘~/tmp/scratch/Rtmp9ggQsQ’ ‘~/tmp/scratch/RtmpARIjkL’ ‘~/tmp/scratch/RtmpARZXVZ’ ‘~/tmp/scratch/RtmpAutbtO’ 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Package simDAG

Current CRAN status: OK: 10, ERROR: 3

Version: 1.0.0
Check: examples
Result: ERROR Running examples in ‘simDAG-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: node_binomial > ### Title: Generate Data from a (Mixed) Binomial Regression Model > ### Aliases: node_binomial > > ### ** Examples > > library(simDAG) > > set.seed(5425) > > # define needed DAG > dag <- empty_dag() + + node("age", type="rnorm", mean=50, sd=4) + + node("sex", type="rbernoulli", p=0.5) + + node("smoking", type="binomial", parents=c("age", "sex"), + betas=c(1.1, 0.4), intercept=-2) > > # define the same DAG, but using a pretty formula > dag <- empty_dag() + + node("age", type="rnorm", mean=50, sd=4) + + node("sex", type="rbernoulli", p=0.5) + + node("smoking", type="binomial", + formula= ~ -2 + age*1.1 + sexTRUE*0.4) > > # simulate data from it > sim_dat <- sim_from_dag(dag=dag, n_sim=100) > > # returning only the estimated probability instead > dag <- empty_dag() + + node("age", type="rnorm", mean=50, sd=4) + + node("sex", type="rbernoulli", p=0.5) + + node("smoking", type="binomial", parents=c("age", "sex"), + betas=c(1.1, 0.4), intercept=-2, return_prob=TRUE) > > sim_dat <- sim_from_dag(dag=dag, n_sim=100) > > ## an example using a random effect > if (requireNamespace("simr")) { + + library(simr) + + dag_mixed <- empty_dag() + + node("School", type="rcategorical", probs=rep(0.1, 10), + labels=LETTERS[1:10]) + + node("Age", type="rnorm", mean=12, sd=2) + + node("Grade", type="binomial", formula= ~ -10 + Age*1.2 + (1|School), + var_corr=0.3) + + sim_dat <- sim_from_dag(dag=dag_mixed, n_sim=100) + } Loading required namespace: simr Loading required package: lme4 Loading required package: Matrix Attaching package: ‘simr’ The following object is masked from ‘package:lme4’: getData Error: An error occured when processing node 'Grade'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64

Version: 1.0.0
Check: tests
Result: ERROR Running ‘testthat.R’ [109s/172s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(simDAG) > library(testthat) > library(data.table) Attaching package: 'data.table' The following object is masked from 'package:base': %notin% > library(igraph) Attaching package: 'igraph' The following object is masked from 'package:testthat': compare The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union > library(ggdag) Attaching package: 'ggdag' The following object is masked from 'package:stats': filter > > data.table::setDTthreads(1) > > test_check("simDAG") Saving _problems/test_node_lmer-21.R Saving _problems/test_node_lmer-52.R Saving _problems/test_node_lmer-85.R Saving _problems/test_node_lmer-116.R Saving _problems/test_node_lmer-148.R Saving _problems/test_node_lmer-178.R Saving _problems/test_node_lmer-208.R Saving _problems/test_node_lmer-239.R Saving _problems/test_node_lmer-272.R Saving _problems/test_node_lmer-393.R Saving _problems/test_node_zeroinfl-114.R t = 1 node = sickness2 t = 1 node = sickness1 t = 2 node = sickness2 t = 2 node = sickness1 t = 3 node = sickness2 t = 3 node = sickness1 t = 4 node = sickness2 t = 4 node = sickness1 t = 5 node = sickness2 t = 5 node = sickness1 starting worker pid=2131454 on localhost:11940 at 11:10:14.921 starting worker pid=2131455 on localhost:11940 at 11:10:15.033 | | | 0%Loading required package: simDAG loaded simDAG and set parent environment Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% Loading required package: simDAG Loading required package: foreach Loading required package: rngtools loaded simDAG and set parent environment Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% Loading required package: foreach Loading required package: rngtools | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%starting worker pid=2132926 on localhost:11940 at 11:10:19.675 starting worker pid=2132925 on localhost:11940 at 11:10:19.725 Loading required package: simDAG Loading required package: simDAG loaded simDAG and set parent environment loaded simDAG and set parent environment Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% Loading required package: foreach Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% Loading required package: rngtools Loading required package: foreach Loading required package: rngtools starting worker pid=2135067 on localhost:11940 at 11:10:26.364 starting worker pid=2135066 on localhost:11940 at 11:10:26.483 Loading required package: simDAG loaded simDAG and set parent environment Loading required package: simDAG Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% Loading required package: foreach loaded simDAG and set parent environment Loading required package: rngtools Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% Loading required package: foreach Loading required package: rngtools starting worker pid=2137686 on localhost:11940 at 11:10:34.765 starting worker pid=2137687 on localhost:11940 at 11:10:34.854 | | | 0%Loading required package: simDAG loaded simDAG and set parent environment Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% Loading required package: foreach Loading required package: simDAG Loading required package: rngtools loaded simDAG and set parent environment Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% Loading required package: foreach Loading required package: rngtools | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%starting worker pid=2139536 on localhost:11940 at 11:10:40.308 starting worker pid=2139537 on localhost:11940 at 11:10:40.340 | | | 0%Loading required package: simDAG loaded simDAG and set parent environment Loading required package: simDAG Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% Loading required package: foreach loaded simDAG and set parent environment Loading required package: rngtools Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% Loading required package: foreach Loading required package: rngtools | |=================================== | 50% | |======================================================================| 100%starting worker pid=2140722 on localhost:11940 at 11:10:45.393 starting worker pid=2140721 on localhost:11940 at 11:10:45.520 | | | 0%Loading required package: simDAG Loading required package: simDAG loaded simDAG and set parent environment loaded simDAG and set parent environment Attaching package: ‘data.table’ Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% The following object is masked from ‘package:base’: %notin% Loading required package: foreach Loading required package: foreach Loading required package: rngtools Loading required package: rngtools | |=================================== | 50% | |======================================================================| 100%[ FAIL 11 | WARN 14 | SKIP 56 | PASS 1032 ] ══ Skipped tests (56) ══════════════════════════════════════════════════════════ • On CRAN (56): 'test_DAG.network_S3.r:4:1', 'test_DAG.network_S3.r:10:1', 'test_DAG.network_S3.r:18:1', 'test_DAG.network_S3.r:24:1', 'test_DAG.network_S3.r:32:1', 'test_DAG.network_S3.r:44:1', 'test_DAG.network_S3.r:50:1', 'test_DAG.network_S3.r:58:1', 'test_DAG.network_S3.r:64:1', 'test_DAG.network_S3.r:72:1', 'test_DAG.node_S3.r:4:1', 'test_DAG.node_S3.r:9:1', 'test_DAG.node_S3.r:14:1', 'test_DAG.node_S3.r:19:1', 'test_DAG.node_S3.r:24:1', 'test_DAG.node_S3.r:32:1', 'test_DAG.node_S3.r:37:1', 'test_DAG.node_S3.r:42:1', 'test_DAG.node_S3.r:47:1', 'test_DAG.node_S3.r:52:1', 'test_dag.r:14:1', 'test_dag.r:21:1', 'test_dag.r:34:1', 'test_dag.r:44:1', 'test_dag.r:51:1', 'test_dag.r:64:1', 'test_node.r:548:1', 'test_node_rsurv.r:99:3', 'test_plot.DAG.r:11:1', 'test_plot.DAG.r:15:1', 'test_plot.DAG.r:19:1', 'test_plot.DAG.r:23:1', 'test_plot.DAG.r:27:1', 'test_plot.DAG.r:31:1', 'test_plot.DAG.r:35:1', 'test_plot.DAG.r:40:1', 'test_plot.DAG.r:44:1', 'test_plot.DAG.r:52:1', 'test_plot.DAG.r:59:1', 'test_plot.DAG.r:64:1', 'test_plot.DAG.r:69:1', 'test_plot.DAG.r:100:1', 'test_plot.DAG.r:104:1', 'test_plot.DAG.r:108:1', 'test_plot.simDT.r:24:1', 'test_plot.simDT.r:28:1', 'test_plot.simDT.r:32:1', 'test_plot.simDT.r:36:1', 'test_plot.simDT.r:40:1', 'test_plot.simDT.r:48:1', 'test_plot.simDT.r:56:1', 'test_simDT_S3.r:11:1', 'test_simDT_S3.r:15:1', 'test_simDT_S3.r:20:1', 'test_simDT_S3.r:25:1', 'test_sim_discrete_event.r:693:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_node_lmer.r:21:3'): simple random effect ─────────────────────── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:21:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:52:3'): simple random effect in disrete-time simulation ── Error: An error occured when processing node 'Y' at time t = 1. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_discrete_time(...) at test_node_lmer.r:52:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:85:3'): simple random effect + categorical fixed effect ── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:85:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:116:3'): simple random effect + interaction effect ── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:116:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:148:3'): simple random effect + interaction effect of categorical vars ── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:148:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:178:3'): simple random effect + cubic terms ──────── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:178:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:208:3'): simple random effect + ONLY cubic terms ─── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:208:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:239:3'): multiple random effects ─────────────────── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=2, npar=2, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:239:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:272:3'): with random effects and random slopes ───── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=3, npar=3, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:272:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:393:3'): simple random effect with non-default link ── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:393:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_zeroinfl.r:114:3'): with random effects ─────────────────── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag, n_sim = 100) at test_node_zeroinfl.r:114:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) [ FAIL 11 | WARN 14 | SKIP 56 | PASS 1032 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘simDAG.Rmd’ using rmarkdown --- finished re-building ‘simDAG.Rmd’ --- re-building ‘v_cookbook.Rmd’ using rmarkdown Quitting from v_cookbook.Rmd:132-140 [unnamed-chunk-7] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error: ! An error occured when processing node 'Outcome'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) --- Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag, n_sim = 1000) 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'v_cookbook.Rmd' failed with diagnostics: An error occured when processing node 'Outcome'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) --- failed re-building ‘v_cookbook.Rmd’ --- re-building ‘v_covid_example.Rmd’ using rmarkdown --- finished re-building ‘v_covid_example.Rmd’ --- re-building ‘v_custom_nodes.Rmd’ using rmarkdown --- finished re-building ‘v_custom_nodes.Rmd’ --- re-building ‘v_sim_discrete_event.Rmd’ using rmarkdown --- finished re-building ‘v_sim_discrete_event.Rmd’ --- re-building ‘v_sim_discrete_time.Rmd’ using rmarkdown --- finished re-building ‘v_sim_discrete_time.Rmd’ --- re-building ‘v_sim_from_dag.Rmd’ using rmarkdown --- finished re-building ‘v_sim_from_dag.Rmd’ --- re-building ‘v_sim_networks.Rmd’ using rmarkdown --- finished re-building ‘v_sim_networks.Rmd’ --- re-building ‘v_using_formulas.Rmd’ using rmarkdown --- finished re-building ‘v_using_formulas.Rmd’ SUMMARY: processing the following file failed: ‘v_cookbook.Rmd’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64

Version: 1.0.0
Check: examples
Result: ERROR Running examples in 'simDAG-Ex.R' failed The error most likely occurred in: > ### Name: node_binomial > ### Title: Generate Data from a (Mixed) Binomial Regression Model > ### Aliases: node_binomial > > ### ** Examples > > library(simDAG) > > set.seed(5425) > > # define needed DAG > dag <- empty_dag() + + node("age", type="rnorm", mean=50, sd=4) + + node("sex", type="rbernoulli", p=0.5) + + node("smoking", type="binomial", parents=c("age", "sex"), + betas=c(1.1, 0.4), intercept=-2) > > # define the same DAG, but using a pretty formula > dag <- empty_dag() + + node("age", type="rnorm", mean=50, sd=4) + + node("sex", type="rbernoulli", p=0.5) + + node("smoking", type="binomial", + formula= ~ -2 + age*1.1 + sexTRUE*0.4) > > # simulate data from it > sim_dat <- sim_from_dag(dag=dag, n_sim=100) > > # returning only the estimated probability instead > dag <- empty_dag() + + node("age", type="rnorm", mean=50, sd=4) + + node("sex", type="rbernoulli", p=0.5) + + node("smoking", type="binomial", parents=c("age", "sex"), + betas=c(1.1, 0.4), intercept=-2, return_prob=TRUE) > > sim_dat <- sim_from_dag(dag=dag, n_sim=100) > > ## an example using a random effect > if (requireNamespace("simr")) { + + library(simr) + + dag_mixed <- empty_dag() + + node("School", type="rcategorical", probs=rep(0.1, 10), + labels=LETTERS[1:10]) + + node("Age", type="rnorm", mean=12, sd=2) + + node("Grade", type="binomial", formula= ~ -10 + Age*1.2 + (1|School), + var_corr=0.3) + + sim_dat <- sim_from_dag(dag=dag_mixed, n_sim=100) + } Loading required namespace: simr Loading required package: lme4 Loading required package: Matrix Attaching package: 'simr' The following object is masked from 'package:lme4': getData Error: An error occured when processing node 'Grade'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Execution halted Flavor: r-devel-windows-x86_64

Version: 1.0.0
Check: tests
Result: ERROR Running 'testthat.R' [107s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(simDAG) > library(testthat) > library(data.table) Attaching package: 'data.table' The following object is masked from 'package:base': %notin% > library(igraph) Attaching package: 'igraph' The following object is masked from 'package:testthat': compare The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union > library(ggdag) Attaching package: 'ggdag' The following object is masked from 'package:stats': filter > > data.table::setDTthreads(1) > > test_check("simDAG") Saving _problems/test_node_lmer-21.R Saving _problems/test_node_lmer-52.R Saving _problems/test_node_lmer-85.R Saving _problems/test_node_lmer-116.R Saving _problems/test_node_lmer-148.R Saving _problems/test_node_lmer-178.R Saving _problems/test_node_lmer-208.R Saving _problems/test_node_lmer-239.R Saving _problems/test_node_lmer-272.R Saving _problems/test_node_lmer-393.R Saving _problems/test_node_zeroinfl-114.R t = 1 node = sickness2 t = 1 node = sickness1 t = 2 node = sickness2 t = 2 node = sickness1 t = 3 node = sickness2 t = 3 node = sickness1 t = 4 node = sickness2 t = 4 node = sickness1 t = 5 node = sickness2 t = 5 node = sickness1 starting worker pid=92912 on localhost:11980 at 14:19:46.342 starting worker pid=63184 on localhost:11980 at 14:19:46.346 | | | 0%Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%starting worker pid=113416 on localhost:11980 at 14:19:48.903 starting worker pid=20020 on localhost:11980 at 14:19:48.919 Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools starting worker pid=48672 on localhost:11980 at 14:19:52.240 starting worker pid=97304 on localhost:11980 at 14:19:52.270 Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools starting worker pid=35724 on localhost:11980 at 14:19:55.939 starting worker pid=74396 on localhost:11980 at 14:19:55.955 | | | 0%Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%starting worker pid=48228 on localhost:11980 at 14:19:59.114 starting worker pid=90800 on localhost:11980 at 14:19:59.173 | | | 0%Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools | |=================================== | 50% | |======================================================================| 100%starting worker pid=112076 on localhost:11980 at 14:20:01.888 starting worker pid=103252 on localhost:11980 at 14:20:01.909 | | | 0%Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools | |=================================== | 50% | |======================================================================| 100%[ FAIL 11 | WARN 14 | SKIP 56 | PASS 1032 ] ══ Skipped tests (56) ══════════════════════════════════════════════════════════ • On CRAN (56): 'test_DAG.network_S3.r:4:1', 'test_DAG.network_S3.r:10:1', 'test_DAG.network_S3.r:18:1', 'test_DAG.network_S3.r:24:1', 'test_DAG.network_S3.r:32:1', 'test_DAG.network_S3.r:44:1', 'test_DAG.network_S3.r:50:1', 'test_DAG.network_S3.r:58:1', 'test_DAG.network_S3.r:64:1', 'test_DAG.network_S3.r:72:1', 'test_DAG.node_S3.r:4:1', 'test_DAG.node_S3.r:9:1', 'test_DAG.node_S3.r:14:1', 'test_DAG.node_S3.r:19:1', 'test_DAG.node_S3.r:24:1', 'test_DAG.node_S3.r:32:1', 'test_DAG.node_S3.r:37:1', 'test_DAG.node_S3.r:42:1', 'test_DAG.node_S3.r:47:1', 'test_DAG.node_S3.r:52:1', 'test_dag.r:14:1', 'test_dag.r:21:1', 'test_dag.r:34:1', 'test_dag.r:44:1', 'test_dag.r:51:1', 'test_dag.r:64:1', 'test_node.r:548:1', 'test_node_rsurv.r:99:3', 'test_plot.DAG.r:11:1', 'test_plot.DAG.r:15:1', 'test_plot.DAG.r:19:1', 'test_plot.DAG.r:23:1', 'test_plot.DAG.r:27:1', 'test_plot.DAG.r:31:1', 'test_plot.DAG.r:35:1', 'test_plot.DAG.r:40:1', 'test_plot.DAG.r:44:1', 'test_plot.DAG.r:52:1', 'test_plot.DAG.r:59:1', 'test_plot.DAG.r:64:1', 'test_plot.DAG.r:69:1', 'test_plot.DAG.r:100:1', 'test_plot.DAG.r:104:1', 'test_plot.DAG.r:108:1', 'test_plot.simDT.r:24:1', 'test_plot.simDT.r:28:1', 'test_plot.simDT.r:32:1', 'test_plot.simDT.r:36:1', 'test_plot.simDT.r:40:1', 'test_plot.simDT.r:48:1', 'test_plot.simDT.r:56:1', 'test_simDT_S3.r:11:1', 'test_simDT_S3.r:15:1', 'test_simDT_S3.r:20:1', 'test_simDT_S3.r:25:1', 'test_sim_discrete_event.r:693:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_node_lmer.r:21:3'): simple random effect ─────────────────────── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:21:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:52:3'): simple random effect in disrete-time simulation ── Error: An error occured when processing node 'Y' at time t = 1. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_discrete_time(...) at test_node_lmer.r:52:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:85:3'): simple random effect + categorical fixed effect ── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:85:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:116:3'): simple random effect + interaction effect ── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:116:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:148:3'): simple random effect + interaction effect of categorical vars ── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:148:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:178:3'): simple random effect + cubic terms ──────── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:178:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:208:3'): simple random effect + ONLY cubic terms ─── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:208:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:239:3'): multiple random effects ─────────────────── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=2, npar=2, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:239:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:272:3'): with random effects and random slopes ───── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=3, npar=3, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:272:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:393:3'): simple random effect with non-default link ── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:393:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_zeroinfl.r:114:3'): with random effects ─────────────────── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag, n_sim = 100) at test_node_zeroinfl.r:114:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) [ FAIL 11 | WARN 14 | SKIP 56 | PASS 1032 ] Error: ! Test failures. Execution halted Flavor: r-devel-windows-x86_64

Version: 1.0.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'simDAG.Rmd' using rmarkdown --- finished re-building 'simDAG.Rmd' --- re-building 'v_cookbook.Rmd' using rmarkdown Quitting from v_cookbook.Rmd:132-140 [unnamed-chunk-7] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error: ! An error occured when processing node 'Outcome'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) --- Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag, n_sim = 1000) 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'v_cookbook.Rmd' failed with diagnostics: An error occured when processing node 'Outcome'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) --- failed re-building 'v_cookbook.Rmd' --- re-building 'v_covid_example.Rmd' using rmarkdown --- finished re-building 'v_covid_example.Rmd' --- re-building 'v_custom_nodes.Rmd' using rmarkdown --- finished re-building 'v_custom_nodes.Rmd' --- re-building 'v_sim_discrete_event.Rmd' using rmarkdown --- finished re-building 'v_sim_discrete_event.Rmd' --- re-building 'v_sim_discrete_time.Rmd' using rmarkdown --- finished re-building 'v_sim_discrete_time.Rmd' --- re-building 'v_sim_from_dag.Rmd' using rmarkdown --- finished re-building 'v_sim_from_dag.Rmd' --- re-building 'v_sim_networks.Rmd' using rmarkdown --- finished re-building 'v_sim_networks.Rmd' --- re-building 'v_using_formulas.Rmd' using rmarkdown --- finished re-building 'v_using_formulas.Rmd' SUMMARY: processing the following file failed: 'v_cookbook.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-devel-windows-x86_64

Version: 1.0.0
Check: tests
Result: ERROR Running ‘testthat.R’ [104s/156s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(simDAG) > library(testthat) > library(data.table) Attaching package: 'data.table' The following object is masked from 'package:base': %notin% > library(igraph) Attaching package: 'igraph' The following object is masked from 'package:testthat': compare The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union > library(ggdag) Attaching package: 'ggdag' The following object is masked from 'package:stats': filter > > data.table::setDTthreads(1) > > test_check("simDAG") Saving _problems/test_node_lmer-21.R Saving _problems/test_node_lmer-52.R Saving _problems/test_node_lmer-85.R Saving _problems/test_node_lmer-116.R Saving _problems/test_node_lmer-148.R Saving _problems/test_node_lmer-178.R Saving _problems/test_node_lmer-208.R Saving _problems/test_node_lmer-239.R Saving _problems/test_node_lmer-272.R Saving _problems/test_node_lmer-393.R Saving _problems/test_node_zeroinfl-114.R t = 1 node = sickness2 t = 1 node = sickness1 t = 2 node = sickness2 t = 2 node = sickness1 t = 3 node = sickness2 t = 3 node = sickness1 t = 4 node = sickness2 t = 4 node = sickness1 t = 5 node = sickness2 t = 5 node = sickness1 starting worker pid=809398 on localhost:11861 at 22:19:42.653 starting worker pid=809399 on localhost:11861 at 22:19:42.776 | | | 0%Loading required package: simDAG loaded simDAG and set parent environment Loading required package: simDAG Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% Loading required package: foreach Loading required package: rngtools loaded simDAG and set parent environment Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% Loading required package: foreach Loading required package: rngtools | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%starting worker pid=810305 on localhost:11861 at 22:19:46.870 starting worker pid=810306 on localhost:11861 at 22:19:46.909 Loading required package: simDAG Loading required package: simDAG loaded simDAG and set parent environment loaded simDAG and set parent environment Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% Loading required package: foreach Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% Loading required package: foreach Loading required package: rngtools Loading required package: rngtools starting worker pid=811892 on localhost:11861 at 22:19:52.741 starting worker pid=811893 on localhost:11861 at 22:19:52.786 Loading required package: simDAG loaded simDAG and set parent environment Loading required package: simDAG Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% loaded simDAG and set parent environment Loading required package: foreach Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% Loading required package: foreach Loading required package: rngtools Loading required package: rngtools starting worker pid=814237 on localhost:11861 at 22:19:59.779 starting worker pid=814238 on localhost:11861 at 22:19:59.813 | | | 0%Loading required package: simDAG loaded simDAG and set parent environment Loading required package: simDAG loaded simDAG and set parent environment Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% Loading required package: foreach Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% Loading required package: rngtools Loading required package: foreach Loading required package: rngtools | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%starting worker pid=815944 on localhost:11861 at 22:20:05.327 starting worker pid=815943 on localhost:11861 at 22:20:05.362 | | | 0%Loading required package: simDAG loaded simDAG and set parent environment Loading required package: simDAG Attaching package: ‘data.table’ loaded simDAG and set parent environment The following object is masked from ‘package:base’: %notin% Loading required package: foreach Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% Loading required package: rngtools Loading required package: foreach Loading required package: rngtools | |=================================== | 50% | |======================================================================| 100%starting worker pid=817347 on localhost:11861 at 22:20:09.876 starting worker pid=817348 on localhost:11861 at 22:20:09.964 | | | 0%Loading required package: simDAG loaded simDAG and set parent environment Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% Loading required package: foreach Loading required package: simDAG Loading required package: rngtools loaded simDAG and set parent environment Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% Loading required package: foreach Loading required package: rngtools | |=================================== | 50% | |======================================================================| 100%[ FAIL 11 | WARN 14 | SKIP 56 | PASS 1032 ] ══ Skipped tests (56) ══════════════════════════════════════════════════════════ • On CRAN (56): 'test_DAG.network_S3.r:4:1', 'test_DAG.network_S3.r:10:1', 'test_DAG.network_S3.r:18:1', 'test_DAG.network_S3.r:24:1', 'test_DAG.network_S3.r:32:1', 'test_DAG.network_S3.r:44:1', 'test_DAG.network_S3.r:50:1', 'test_DAG.network_S3.r:58:1', 'test_DAG.network_S3.r:64:1', 'test_DAG.network_S3.r:72:1', 'test_DAG.node_S3.r:4:1', 'test_DAG.node_S3.r:9:1', 'test_DAG.node_S3.r:14:1', 'test_DAG.node_S3.r:19:1', 'test_DAG.node_S3.r:24:1', 'test_DAG.node_S3.r:32:1', 'test_DAG.node_S3.r:37:1', 'test_DAG.node_S3.r:42:1', 'test_DAG.node_S3.r:47:1', 'test_DAG.node_S3.r:52:1', 'test_dag.r:14:1', 'test_dag.r:21:1', 'test_dag.r:34:1', 'test_dag.r:44:1', 'test_dag.r:51:1', 'test_dag.r:64:1', 'test_node.r:548:1', 'test_node_rsurv.r:99:3', 'test_plot.DAG.r:11:1', 'test_plot.DAG.r:15:1', 'test_plot.DAG.r:19:1', 'test_plot.DAG.r:23:1', 'test_plot.DAG.r:27:1', 'test_plot.DAG.r:31:1', 'test_plot.DAG.r:35:1', 'test_plot.DAG.r:40:1', 'test_plot.DAG.r:44:1', 'test_plot.DAG.r:52:1', 'test_plot.DAG.r:59:1', 'test_plot.DAG.r:64:1', 'test_plot.DAG.r:69:1', 'test_plot.DAG.r:100:1', 'test_plot.DAG.r:104:1', 'test_plot.DAG.r:108:1', 'test_plot.simDT.r:24:1', 'test_plot.simDT.r:28:1', 'test_plot.simDT.r:32:1', 'test_plot.simDT.r:36:1', 'test_plot.simDT.r:40:1', 'test_plot.simDT.r:48:1', 'test_plot.simDT.r:56:1', 'test_simDT_S3.r:11:1', 'test_simDT_S3.r:15:1', 'test_simDT_S3.r:20:1', 'test_simDT_S3.r:25:1', 'test_sim_discrete_event.r:693:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_node_lmer.r:21:3'): simple random effect ─────────────────────── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:21:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:52:3'): simple random effect in disrete-time simulation ── Error: An error occured when processing node 'Y' at time t = 1. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_discrete_time(...) at test_node_lmer.r:52:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:85:3'): simple random effect + categorical fixed effect ── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:85:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:116:3'): simple random effect + interaction effect ── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:116:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:148:3'): simple random effect + interaction effect of categorical vars ── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:148:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:178:3'): simple random effect + cubic terms ──────── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:178:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:208:3'): simple random effect + ONLY cubic terms ─── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:208:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:239:3'): multiple random effects ─────────────────── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=2, npar=2, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:239:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:272:3'): with random effects and random slopes ───── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=3, npar=3, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:272:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:393:3'): simple random effect with non-default link ── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:393:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_zeroinfl.r:114:3'): with random effects ─────────────────── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag, n_sim = 100) at test_node_zeroinfl.r:114:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) [ FAIL 11 | WARN 14 | SKIP 56 | PASS 1032 ] Error: ! Test failures. Execution halted Flavor: r-patched-linux-x86_64