* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/lme4breeding.Rcheck’ * using R Under development (unstable) (2025-04-26 r88181) * 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 ‘lme4breeding/DESCRIPTION’ ... OK * this is package ‘lme4breeding’ version ‘1.0.60’ * 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 ‘lme4breeding’ 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 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 whether startup messages can be suppressed ... 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 ... [13s/13s] 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 ... [14s/14s] OK * checking examples with --run-donttest ... [25s/25s] ERROR Running examples in ‘lme4breeding-Ex.R’ failed The error most likely occurred in: > ### Name: DT_rice > ### Title: Rice lines dataset > ### Aliases: DT_rice GT_rice GTn_rice > ### Keywords: datasets > > ### ** Examples > > > data(DT_rice) > DT <- DT_rice > GT <- GT_rice > GTn <- GTn_rice > head(DT) HybID NSFTVID Flowering.time.at.Arkansas NSFTV_1 081215-A05 1 75.08333 NSFTV_3 081215-A06 3 89.50000 NSFTV_4 081215-A07 4 94.50000 NSFTV_5 081215-A08 5 87.50000 NSFTV_6 090414-A09 6 89.08333 NSFTV_7 090414-A10 7 105.00000 Flowering.time.at.Faridpur Flowering.time.at.Aberdeen NSFTV_1 64 81 NSFTV_3 66 83 NSFTV_4 67 93 NSFTV_5 70 108 NSFTV_6 73 101 NSFTV_7 NA 158 FT.ratio.of.Arkansas.Aberdeen FT.ratio.of.Faridpur.Aberdeen Culm.habit NSFTV_1 0.9269547 0.7901235 4.0 NSFTV_3 1.0783133 0.7951807 7.5 NSFTV_4 1.0161290 0.7204301 6.0 NSFTV_5 0.8101852 0.6481481 3.5 NSFTV_6 0.8820132 0.7227723 6.0 NSFTV_7 0.6645570 NA 3.0 Leaf.pubescence Flag.leaf.length Flag.leaf.width Awn.presence NSFTV_1 1 28.37500 1.2833333 0 NSFTV_3 0 39.00833 1.0000000 0 NSFTV_4 1 27.68333 1.5166667 0 NSFTV_5 1 30.41667 0.8916667 0 NSFTV_6 1 36.90833 1.7500000 0 NSFTV_7 1 36.99000 1.5500000 1 Panicle.number.per.plant Plant.height Panicle.length NSFTV_1 3.068053 110.9167 20.48182 NSFTV_3 4.051785 143.5000 26.83333 NSFTV_4 3.124565 128.0833 23.53333 NSFTV_5 3.697178 153.7500 28.96364 NSFTV_6 2.857428 148.3333 30.91667 NSFTV_7 2.859021 119.6000 24.62500 Primary.panicle.branch.number Seed.number.per.panicle NSFTV_1 9.272727 4.785975 NSFTV_3 9.166667 4.439706 NSFTV_4 8.666667 5.079709 NSFTV_5 6.363636 4.523960 NSFTV_6 11.166667 5.538646 NSFTV_7 13.333333 5.338019 Florets.per.panicle Panicle.fertility Seed.length Seed.width NSFTV_1 4.914658 0.879 8.064117 3.685183 NSFTV_3 4.727388 0.750 7.705383 2.951458 NSFTV_4 5.146437 0.935 8.237575 2.926367 NSFTV_5 4.730921 0.813 9.709375 2.382100 NSFTV_6 5.676468 0.871 7.118183 3.281892 NSFTV_7 5.435903 0.907 7.347255 2.528891 Seed.volume Seed.surface.area Brown.rice.seed.length NSFTV_1 2.587448 3.914120 5.794542 NSFTV_3 2.111145 3.658709 5.603658 NSFTV_4 2.154759 3.713856 6.120342 NSFTV_5 1.940221 3.700054 7.089883 NSFTV_6 2.202360 3.657370 5.136483 NSFTV_7 1.774465 3.474791 5.485345 Brown.rice.seed.width Brown.rice.surface.area Brown.rice.volume NSFTV_1 3.113958 3.511152 7.737358 NSFTV_3 2.566450 3.287373 5.105350 NSFTV_4 2.466983 3.334126 5.126958 NSFTV_5 2.044608 3.297792 4.085133 NSFTV_6 2.803858 3.284328 5.555183 NSFTV_7 2.188882 3.101569 3.591045 Seed.length.width.ratio Brown.rice.length.width.ratio Seed.color NSFTV_1 2.188 1.861 0 NSFTV_3 2.611 2.183 0 NSFTV_4 2.815 2.481 0 NSFTV_5 4.076 3.468 0 NSFTV_6 2.169 1.832 0 NSFTV_7 2.905 2.506 0 Pericarp.color Straighthead.suseptability Blast.resistance NSFTV_1 0 4.833333 8 NSFTV_3 0 7.831667 4 NSFTV_4 0 NA 3 NSFTV_5 0 8.333333 5 NSFTV_6 0 8.166667 3 NSFTV_7 0 8.585000 2 Amylose.content Alkali.spreading.value Protein.content NSFTV_1 15.61333 6.083333 8.45 NSFTV_3 23.26000 5.638889 9.20 NSFTV_4 23.12000 5.527778 8.00 NSFTV_5 19.32333 6.027778 9.60 NSFTV_6 23.24000 5.444444 8.50 NSFTV_7 20.18667 6.000000 11.75 Year07Flowering.time.at.Arkansas Year06Flowering.time.at.Arkansas NSFTV_1 73.0 77.16667 NSFTV_3 88.0 91.00000 NSFTV_4 105.5 83.50000 NSFTV_5 86.5 88.50000 NSFTV_6 85.5 92.66667 NSFTV_7 105.0 NA geno NSFTV_1 NSFTV_1 NSFTV_3 NSFTV_3 NSFTV_4 NSFTV_4 NSFTV_5 NSFTV_5 NSFTV_6 NSFTV_6 NSFTV_7 NSFTV_7 > M <- atcg1234(GT) Converting GBS or single-letter code to biallelic code | | | 0% | |= | 1% | |= | 2% | |== | 3% | |=== | 4% | |==== | 5% | |==== | 6% | |===== | 7% | |====== | 8% | |====== | 9% | |======= | 10% | |======== | 11% | |======== | 12% | |========= | 13% | |========== | 14% | |========== | 15% | |=========== | 16% | |============ | 17% | |============= | 18% | |============= | 19% | |============== | 20% | |=============== | 21% | |=============== | 22% | |================ | 23% | |================= | 24% | |================== | 25% | |================== | 26% | |=================== | 27% | |==================== | 28% | |==================== | 29% | |===================== | 30% | |====================== | 31% | |====================== | 32% | |======================= | 33% | |======================== | 34% | |======================== | 35% | |========================= | 36% | |========================== | 37% | |=========================== | 38% | |=========================== | 39% | |============================ | 40% | |============================= | 41% | |============================= | 42% | |============================== | 43% | |=============================== | 44% | |================================ | 45% | |================================ | 46% | |================================= | 47% | |================================== | 48% | |================================== | 49% | |=================================== | 50% | |==================================== | 51% | |==================================== | 52% | |===================================== | 53% | |====================================== | 54% | |====================================== | 55% | |======================================= | 56% | |======================================== | 57% | |========================================= | 58% | |========================================= | 59% | |========================================== | 60% | |=========================================== | 61% | |=========================================== | 62% | |============================================ | 63% | |============================================= | 64% | |============================================== | 65% | |============================================== | 66% | |=============================================== | 67% | |================================================ | 68% | |================================================ | 69% | |================================================= | 70% | |================================================== | 71% | |================================================== | 72% | |=================================================== | 73% | |==================================================== | 74% | |==================================================== | 75% | |===================================================== | 76% | |====================================================== | 77% | |======================================================= | 78% | |======================================================= | 79% | |======================================================== | 80% | |========================================================= | 81% | |========================================================= | 82% | |========================================================== | 83% | |=========================================================== | 84% | |============================================================ | 85% | |============================================================ | 86% | |============================================================= | 87% | |============================================================== | 88% | |============================================================== | 89% | |=============================================================== | 90% | |================================================================ | 91% | |================================================================ | 92% | |================================================================= | 93% | |================================================================== | 94% | |================================================================== | 95% | |=================================================================== | 96% | |==================================================================== | 97% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 100% Obtaining reference alleles | | | 0% | |= | 1% | |= | 2% | |== | 3% | |=== | 4% | |==== | 5% | |==== | 6% | |===== | 7% | |====== | 8% | |====== | 9% | |======= | 10% | |======== | 11% | |======== | 12% | |========= | 13% | |========== | 14% | |========== | 15% | |=========== | 16% | |============ | 17% | |============= | 18% | |============= | 19% | |============== | 20% | |=============== | 21% | |=============== | 22% | |================ | 23% | |================= | 24% | |================== | 25% | |================== | 26% | |=================== | 27% | |==================== | 28% | |==================== | 29% | |===================== | 30% | |====================== | 31% | |====================== | 32% | |======================= | 33% | |======================== | 34% | |======================== | 35% | |========================= | 36% | |========================== | 37% | |=========================== | 38% | |=========================== | 39% | |============================ | 40% | |============================= | 41% | |============================= | 42% | |============================== | 43% | |=============================== | 44% | |================================ | 45% | |================================ | 46% | |================================= | 47% | |================================== | 48% | |================================== | 49% | |=================================== | 50% | |==================================== | 51% | |==================================== | 52% | |===================================== | 53% | |====================================== | 54% | |====================================== | 55% | |======================================= | 56% | |======================================== | 57% | |========================================= | 58% | |========================================= | 59% | |========================================== | 60% | |=========================================== | 61% | |=========================================== | 62% | |============================================ | 63% | |============================================= | 64% | |============================================== | 65% | |============================================== | 66% | |=============================================== | 67% | |================================================ | 68% | |================================================ | 69% | |================================================= | 70% | |================================================== | 71% | |================================================== | 72% | |=================================================== | 73% | |==================================================== | 74% | |==================================================== | 75% | |===================================================== | 76% | |====================================================== | 77% | |======================================================= | 78% | |======================================================= | 79% | |======================================================== | 80% | |========================================================= | 81% | |========================================================= | 82% | |========================================================== | 83% | |=========================================================== | 84% | |============================================================ | 85% | |============================================================ | 86% | |============================================================= | 87% | |============================================================== | 88% | |============================================================== | 89% | |=============================================================== | 90% | |================================================================ | 91% | |================================================================ | 92% | |================================================================= | 93% | |================================================================== | 94% | |================================================================== | 95% | |=================================================================== | 96% | |==================================================================== | 97% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 100% Checking for markers with more than 2 alleles. If found will be removed. | | | 0% | |= | 1% | |= | 2% | |== | 3% | |=== | 4% | |==== | 5% | |==== | 6% | |===== | 7% | |====== | 8% | |====== | 9% | |======= | 10% | |======== | 11% | |======== | 12% | |========= | 13% | |========== | 14% | |========== | 15% | |=========== | 16% | |============ | 17% | |============= | 18% | |============= | 19% | |============== | 20% | |=============== | 21% | |=============== | 22% | |================ | 23% | |================= | 24% | |================== | 25% | |================== | 26% | |=================== | 27% | |==================== | 28% | |==================== | 29% | |===================== | 30% | |====================== | 31% | |====================== | 32% | |======================= | 33% | |======================== | 34% | |======================== | 35% | |========================= | 36% | |========================== | 37% | |=========================== | 38% | |=========================== | 39% | |============================ | 40% | |============================= | 41% | |============================= | 42% | |============================== | 43% | |=============================== | 44% | |================================ | 45% | |================================ | 46% | |================================= | 47% | |================================== | 48% | |================================== | 49% | |=================================== | 50% | |==================================== | 51% | |==================================== | 52% | |===================================== | 53% | |====================================== | 54% | |====================================== | 55% | |======================================= | 56% | |======================================== | 57% | |========================================= | 58% | |========================================= | 59% | |========================================== | 60% | |=========================================== | 61% | |=========================================== | 62% | |============================================ | 63% | |============================================= | 64% | |============================================== | 65% | |============================================== | 66% | |=============================================== | 67% | |================================================ | 68% | |================================================ | 69% | |================================================= | 70% | |================================================== | 71% | |================================================== | 72% | |=================================================== | 73% | |==================================================== | 74% | |==================================================== | 75% | |===================================================== | 76% | |====================================================== | 77% | |======================================================= | 78% | |======================================================= | 79% | |======================================================== | 80% | |========================================================= | 81% | |========================================================= | 82% | |========================================================== | 83% | |=========================================================== | 84% | |============================================================ | 85% | |============================================================ | 86% | |============================================================= | 87% | |============================================================== | 88% | |============================================================== | 89% | |=============================================================== | 90% | |================================================================ | 91% | |================================================================ | 92% | |================================================================= | 93% | |================================================================== | 94% | |================================================================== | 95% | |=================================================================== | 96% | |==================================================================== | 97% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 100% Converting to numeric format | | | 0% | |= | 1% | |= | 2% | |== | 3% | |=== | 4% | |==== | 5% | |==== | 6% | |===== | 7% | |====== | 8% | |====== | 9% | |======= | 10% | |======== | 11% | |======== | 12% | |========= | 13% | |========== | 14% | |========== | 15% | |=========== | 16% | |============ | 17% | |============= | 18% | |============= | 19% | |============== | 20% | |=============== | 21% | |=============== | 22% | |================ | 23% | |================= | 24% | |================== | 25% | |================== | 26% | |=================== | 27% | |==================== | 28% | |==================== | 29% | |===================== | 30% | |====================== | 31% | |====================== | 32% | |======================= | 33% | |======================== | 34% | |======================== | 35% | |========================= | 36% | |========================== | 37% | |=========================== | 38% | |=========================== | 39% | |============================ | 40% | |============================= | 41% | |============================= | 42% | |============================== | 43% | |=============================== | 44% | |================================ | 45% | |================================ | 46% | |================================= | 47% | |================================== | 48% | |================================== | 49% | |=================================== | 50% | |==================================== | 51% | |==================================== | 52% | |===================================== | 53% | |====================================== | 54% | |====================================== | 55% | |======================================= | 56% | |======================================== | 57% | |========================================= | 58% | |========================================= | 59% | |========================================== | 60% | |=========================================== | 61% | |=========================================== | 62% | |============================================ | 63% | |============================================= | 64% | |============================================== | 65% | |============================================== | 66% | |=============================================== | 67% | |================================================ | 68% | |================================================ | 69% | |================================================= | 70% | |================================================== | 71% | |================================================== | 72% | |=================================================== | 73% | |==================================================== | 74% | |==================================================== | 75% | |===================================================== | 76% | |====================================================== | 77% | |======================================================= | 78% | |======================================================= | 79% | |======================================================== | 80% | |========================================================= | 81% | |========================================================= | 82% | |========================================================== | 83% | |=========================================================== | 84% | |============================================================ | 85% | |============================================================ | 86% | |============================================================= | 87% | |============================================================== | 88% | |============================================================== | 89% | |=============================================================== | 90% | |================================================================ | 91% | |================================================================ | 92% | |================================================================= | 93% | |================================================================== | 94% | |================================================================== | 95% | |=================================================================== | 96% | |==================================================================== | 97% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 100% Calculating minor allele frequency (MAF) | | | 0% | |= | 1% | |= | 2% | |== | 3% | |=== | 4% | |==== | 5% | |==== | 6% | |===== | 7% | |====== | 8% | |====== | 9% | |======= | 10% | |======== | 11% | |======== | 12% | |========= | 13% | |========== | 14% | |========== | 15% | |=========== | 16% | |============ | 17% | |============= | 18% | |============= | 19% | |============== | 20% | |=============== | 21% | |=============== | 22% | |================ | 23% | |================= | 24% | |================== | 25% | |================== | 26% | |=================== | 27% | |==================== | 28% | |==================== | 29% | |===================== | 30% | |====================== | 31% | |====================== | 32% | |======================= | 33% | |======================== | 34% | |======================== | 35% | |========================= | 36% | |========================== | 37% | |=========================== | 38% | |=========================== | 39% | |============================ | 40% | |============================= | 41% | |============================= | 42% | |============================== | 43% | |=============================== | 44% | |================================ | 45% | |================================ | 46% | |================================= | 47% | |================================== | 48% | |================================== | 49% | |=================================== | 50% | |==================================== | 51% | |==================================== | 52% | |===================================== | 53% | |====================================== | 54% | |====================================== | 55% | |======================================= | 56% | |======================================== | 57% | |========================================= | 58% | |========================================= | 59% | |========================================== | 60% | |=========================================== | 61% | |=========================================== | 62% | |============================================ | 63% | |============================================= | 64% | |============================================== | 65% | |============================================== | 66% | |=============================================== | 67% | |================================================ | 68% | |================================================ | 69% | |================================================= | 70% | |================================================== | 71% | |================================================== | 72% | |=================================================== | 73% | |==================================================== | 74% | |==================================================== | 75% | |===================================================== | 76% | |====================================================== | 77% | |======================================================= | 78% | |======================================================= | 79% | |======================================================== | 80% | |========================================================= | 81% | |========================================================= | 82% | |========================================================== | 83% | |=========================================================== | 84% | |============================================================ | 85% | |============================================================ | 86% | |============================================================= | 87% | |============================================================== | 88% | |============================================================== | 89% | |=============================================================== | 90% | |================================================================ | 91% | |================================================================ | 92% | |================================================================= | 93% | |================================================================== | 94% | |================================================================== | 95% | |=================================================================== | 96% | |==================================================================== | 97% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 100% Imputing missing data with mode | | | 0% | |= | 1% | |= | 2% | |== | 3% | |=== | 4% | |==== | 5% | |==== | 6% | |===== | 7% | |====== | 8% | |====== | 9% | |======= | 10% | |======== | 11% | |======== | 12% | |========= | 13% | |========== | 14% | |========== | 15% | |=========== | 16% | |============ | 17% | |============= | 18% | |============= | 19% | |============== | 20% | |=============== | 21% | |=============== | 22% | |================ | 23% | |================= | 24% | |================== | 25% | |================== | 26% | |=================== | 27% | |==================== | 28% | |==================== | 29% | |===================== | 30% | |====================== | 31% | |====================== | 32% | |======================= | 33% | |======================== | 34% | |======================== | 35% | |========================= | 36% | |========================== | 37% | |=========================== | 38% | |=========================== | 39% | |============================ | 40% | |============================= | 41% | |============================= | 42% | |============================== | 43% | |=============================== | 44% | |================================ | 45% | |================================ | 46% | |================================= | 47% | |================================== | 48% | |================================== | 49% | |=================================== | 50% | |==================================== | 51% | |==================================== | 52% | |===================================== | 53% | |====================================== | 54% | |====================================== | 55% | |======================================= | 56% | |======================================== | 57% | |========================================= | 58% | |========================================= | 59% | |========================================== | 60% | |=========================================== | 61% | |=========================================== | 62% | |============================================ | 63% | |============================================= | 64% | |============================================== | 65% | |============================================== | 66% | |=============================================== | 67% | |================================================ | 68% | |================================================ | 69% | |================================================= | 70% | |================================================== | 71% | |================================================== | 72% | |=================================================== | 73% | |==================================================== | 74% | |==================================================== | 75% | |===================================================== | 76% | |====================================================== | 77% | |======================================================= | 78% | |======================================================= | 79% | |======================================================== | 80% | |========================================================= | 81% | |========================================================= | 82% | |========================================================== | 83% | |=========================================================== | 84% | |============================================================ | 85% | |============================================================ | 86% | |============================================================= | 87% | |============================================================== | 88% | |============================================================== | 89% | |=============================================================== | 90% | |================================================================ | 91% | |================================================================ | 92% | |================================================================= | 93% | |================================================================== | 94% | |================================================================== | 95% | |=================================================================== | 96% | |==================================================================== | 97% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 100% > > ## No test: > > ### univariate model > A <- A.mat(M$M) > A <- A + diag(1e-4, ncol(A), ncol(A)) > mix <- lmebreed(Protein.content ~ (1|geno), + relmat = list(geno=A), + data=DT) * Cholesky decomposition finished. * Relfactors (relmat) applied to Z * Optimizing ... * Done!! > vc <- VarCorr(mix); print(vc,comp=c("Variance")) Groups Name Variance geno (Intercept) 0.020938 Residual 0.835914 > > ### multi-trait model > DT2 <- stackTrait(data=DT, traits = colnames(DT)[3:12])$long Error in reshapeLong(data, idvar = idvar, timevar = timevar, varying = varying, : 'idvar' must uniquely identify records Calls: stackTrait -> reshape -> reshapeLong Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [29s/29s] 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/lme4breeding.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 2:36.73, 132.19 + 23.71