* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/heritEWAS.Rcheck’ * using R Under development (unstable) (2023-03-24 r84037) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2) GNU Fortran (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2) * running under: Fedora 34 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘heritEWAS/DESCRIPTION’ ... OK * this is package ‘heritEWAS’ version ‘0.2.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘heritEWAS’ can be installed ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... 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 ... OK * checking examples with --run-donttest ... ERROR Running examples in ‘heritEWAS-Ex.R’ failed The error most likely occurred in: > ### Name: ML_estimates > ### Title: Compute maximum likelihood estimates and Deltal > ### Aliases: ML_estimates > > ### ** Examples > > # Example data > str(ped) 'data.frame': 288 obs. of 8 variables: $ family: chr "aey" "aey" "aey" "aey" ... $ indiv : chr "aey001" "aey002" "aey003" "aey004" ... $ mother: chr NA "aey005" "aey002" "aey002" ... $ father: chr NA "aey006" "aey001" "aey001" ... $ sex : chr "M" "F" "F" "F" ... $ aff : num 0 0 0 0 0 0 0 1 0 0 ... $ age : num 28 41 70 12 18 13 49 40 15 32 ... $ typed : num 0 1 1 0 1 1 1 1 1 0 ... > str(M_values) num [1:1000, 1:128] -3.853 -2.325 -4.041 -0.741 -0.223 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:1000] "cg18584561" "cg01074083" "cg27639199" "cg26773954" ... ..$ : chr [1:128] "aey002" "aey003" "aey005" "aey006" ... > > # Calculate genotype probabilities > typed_genos <- genotype_combinations(ped) Family 1 (aey): Number of genotype combinations to check: 104 Family 2 (awz): Number of genotype combinations to check: 16 Family 3 (beu): Number of genotype combinations to check: 96 Family 4 (ety): Number of genotype combinations to check: 66 Family 5 (ibz): Number of genotype combinations to check: 192 Family 6 (kph): Number of genotype combinations to check: 64 Family 7 (ljd): Number of genotype combinations to check: 16 Family 8 (mps): Number of genotype combinations to check: 68 Family 9 (msn): Number of genotype combinations to check: 66 Family 10 (msp): Number of genotype combinations to check: 132 Family 11 (nmc): Number of genotype combinations to check: 7 Family 12 (nqc): Number of genotype combinations to check: 64 Family 13 (opq): Number of genotype combinations to check: 256 Family 14 (qor): Number of genotype combinations to check: 33 Family 15 (rpb): Number of genotype combinations to check: 68 Family 16 (rvn): Number of genotype combinations to check: 16 Family 17 (thv): Number of genotype combinations to check: 16 Family 18 (wkt): Number of genotype combinations to check: 104 Family 19 (yiu): Number of genotype combinations to check: 68 Family 20 (yvf): Number of genotype combinations to check: 192 > str(typed_genos) List of 20 $ aey:'data.frame': 36 obs. of 9 variables: ..$ p : num [1:36] 0.93458 0.00935 0.00467 0.00467 0.00234 ... ..$ aey002: num [1:36] 0 0 0 0 1 1 1 1 0 0 ... ..$ aey003: num [1:36] 0 1 0 0 0 0 1 1 0 0 ... ..$ aey005: num [1:36] 0 0 1 1 1 1 1 1 0 0 ... ..$ aey006: num [1:36] 0 0 0 0 0 0 0 0 0 0 ... ..$ aey007: num [1:36] 0 0 0 1 0 1 0 1 0 0 ... ..$ aey008: num [1:36] 0 0 0 0 0 0 0 0 1 1 ... ..$ aey009: num [1:36] 0 0 0 0 0 0 0 0 0 0 ... ..$ aey012: num [1:36] 0 0 0 0 0 0 0 0 0 1 ... $ awz:'data.frame': 13 obs. of 5 variables: ..$ p : num [1:13] 0.95714 0.00476 0.00476 0.00476 0.00952 ... ..$ awz002: int [1:13] 0 0 0 0 0 1 1 1 1 1 ... ..$ awz007: int [1:13] 0 0 0 0 1 0 0 0 0 1 ... ..$ awz011: int [1:13] 0 0 1 1 0 0 0 1 1 0 ... ..$ awz013: int [1:13] 0 1 0 1 0 0 1 0 1 0 ... $ beu:'data.frame': 35 obs. of 8 variables: ..$ p : num [1:35] 0.93925 0.00935 0.00467 0.00234 0.00234 ... ..$ beu001: num [1:35] 0 0 0 0 0 0 0 1 1 1 ... ..$ beu002: num [1:35] 0 0 0 0 0 0 0 0 0 0 ... ..$ beu003: num [1:35] 0 0 0 0 0 0 0 0 0 1 ... ..$ beu004: num [1:35] 0 0 0 0 0 0 0 0 1 0 ... ..$ beu006: num [1:35] 0 0 0 1 1 1 1 0 0 0 ... ..$ beu007: num [1:35] 0 0 1 0 0 1 1 0 0 0 ... ..$ beu010: num [1:35] 0 1 0 0 1 0 1 0 0 0 ... $ ety:'data.frame': 51 obs. of 8 variables: ..$ p : num [1:51] 0.940421 0.004673 0.001168 0.000876 0.000292 ... ..$ ety003: num [1:51] 0 0 0 0 0 0 0 0 0 0 ... ..$ ety004: num [1:51] 0 0 0 0 0 0 0 0 0 0 ... ..$ ety005: num [1:51] 0 0 0 0 0 0 0 1 1 1 ... ..$ ety006: num [1:51] 0 0 0 1 1 1 1 0 0 1 ... ..$ ety007: num [1:51] 0 0 1 0 0 1 1 0 1 0 ... ..$ ety011: num [1:51] 0 0 0 0 0 0 0 0 0 0 ... ..$ ety013: num [1:51] 0 1 0 0 1 0 1 0 0 0 ... $ ibz:'data.frame': 99 obs. of 9 variables: ..$ p : num [1:99] 0.943925 0.009346 0.009346 0.000876 0.000292 ... ..$ ibz003: num [1:99] 0 0 0 0 0 0 0 0 0 0 ... ..$ ibz004: num [1:99] 0 1 0 0 0 0 0 0 0 0 ... ..$ ibz006: num [1:99] 0 0 0 1 1 1 1 1 1 1 ... ..$ ibz007: num [1:99] 0 0 0 0 0 0 0 0 0 0 ... ..$ ibz008: num [1:99] 0 0 0 0 0 0 0 0 0 0 ... ..$ ibz009: num [1:99] 0 0 0 0 0 0 0 1 1 1 ... ..$ ibz011: num [1:99] 0 0 0 0 0 1 1 0 0 1 ... ..$ ibz016: num [1:99] 0 0 1 0 1 0 1 0 1 0 ... $ kph:'data.frame': 64 obs. of 7 variables: ..$ p : num [1:64] 0.94911 0.00506 0.00506 0.00506 0.00149 ... ..$ kph001: int [1:64] 0 0 0 0 0 0 0 0 0 0 ... ..$ kph003: int [1:64] 0 0 0 0 0 0 0 0 0 0 ... ..$ kph004: int [1:64] 0 0 0 0 0 0 0 0 1 1 ... ..$ kph005: int [1:64] 0 0 0 0 1 1 1 1 0 0 ... ..$ kph009: int [1:64] 0 0 1 1 0 0 1 1 0 0 ... ..$ kph011: int [1:64] 0 1 0 1 0 1 0 1 0 1 ... $ ljd:'data.frame': 13 obs. of 5 variables: ..$ p : num [1:13] 0.95714 0.00476 0.00476 0.00476 0.00238 ... ..$ ljd004: int [1:13] 0 0 0 0 0 0 0 0 1 1 ... ..$ ljd005: int [1:13] 0 0 0 0 1 1 1 1 0 1 ... ..$ ljd009: int [1:13] 0 0 1 1 0 0 1 1 0 0 ... ..$ ljd010: int [1:13] 0 1 0 1 0 1 0 1 0 0 ... $ mps:'data.frame': 68 obs. of 8 variables: ..$ p : num [1:68] 0.936186 0.009492 0.000438 0.000146 0.001606 ... ..$ mps001: num [1:68] 0 0 0 0 0 0 0 0 0 0 ... ..$ mps003: num [1:68] 0 0 0 0 0 0 0 0 0 0 ... ..$ mps005: num [1:68] 0 0 0 0 0 0 0 0 1 1 ... ..$ mps006: num [1:68] 0 0 0 0 1 1 1 1 0 0 ... ..$ mps008: num [1:68] 0 0 0 0 0 0 0 0 0 0 ... ..$ mps011: num [1:68] 0 0 1 1 0 0 1 1 0 0 ... ..$ mps016: num [1:68] 0 1 0 1 0 1 0 1 0 1 ... $ msn:'data.frame': 50 obs. of 8 variables: ..$ p : num [1:50] 0.936332 0.00993 0.000876 0.000876 0.000292 ... ..$ msn001: num [1:50] 0 0 0 0 0 0 0 0 0 0 ... ..$ msn003: num [1:50] 0 0 0 0 0 0 0 0 0 0 ... ..$ msn005: num [1:50] 0 0 0 0 0 0 1 1 1 1 ... ..$ msn007: num [1:50] 0 0 1 1 1 1 0 0 1 1 ... ..$ msn010: num [1:50] 0 1 0 0 1 1 0 1 0 0 ... ..$ msn011: num [1:50] 0 0 0 0 0 0 0 0 0 0 ... ..$ msn013: num [1:50] 0 0 0 1 0 1 0 0 0 1 ... $ msp:'data.frame': 132 obs. of 9 variables: ..$ p : num [1:132] 0.931732 0.000365 0.000365 0.000365 0.001825 ... ..$ msp001: num [1:132] 0 0 0 0 0 0 0 0 0 0 ... ..$ msp004: num [1:132] 0 0 0 0 0 0 0 0 0 0 ... ..$ msp008: num [1:132] 0 0 0 0 0 0 0 0 0 0 ... ..$ msp009: num [1:132] 0 0 0 0 0 0 0 0 1 1 ... ..$ msp010: num [1:132] 0 0 0 0 1 1 1 1 0 0 ... ..$ msp011: num [1:132] 0 0 0 0 0 0 0 0 0 0 ... ..$ msp013: int [1:132] 0 0 1 1 0 0 1 1 0 0 ... ..$ msp014: int [1:132] 0 1 0 1 0 1 0 1 0 1 ... $ nmc:'data.frame': 6 obs. of 5 variables: ..$ p : num [1:6] 0.94286 0.00952 0.00952 0.00952 0.00952 ... ..$ nmc001: num [1:6] 0 0 1 0 1 0 ..$ nmc002: num [1:6] 0 1 1 0 0 0 ..$ nmc003: num [1:6] 0 0 0 1 1 0 ..$ nmc010: num [1:6] 0 0 0 0 0 1 $ nqc:'data.frame': 49 obs. of 7 variables: ..$ p : num [1:49] 0.94217 0.00292 0.00292 0.00292 0.00292 ... ..$ nqc004: int [1:49] 0 0 0 0 0 0 0 0 0 0 ... ..$ nqc005: int [1:49] 0 0 0 0 0 0 0 0 0 1 ... ..$ nqc008: int [1:49] 0 0 0 0 0 0 0 0 1 0 ... ..$ nqc009: int [1:49] 0 0 0 0 1 1 1 1 0 0 ... ..$ nqc012: int [1:49] 0 0 1 1 0 0 1 1 0 0 ... ..$ nqc013: int [1:49] 0 1 0 1 0 1 0 1 0 0 ... $ opq:'data.frame': 151 obs. of 9 variables: ..$ p : num [1:151] 0.93925 0.00117 0.00117 0.00117 0.00117 ... ..$ opq002: int [1:151] 0 0 0 0 0 0 0 0 0 0 ... ..$ opq004: int [1:151] 0 0 0 0 0 0 0 0 0 0 ... ..$ opq005: int [1:151] 0 0 0 0 0 0 0 0 0 0 ... ..$ opq008: int [1:151] 0 0 0 0 0 0 0 0 0 0 ... ..$ opq011: int [1:151] 0 0 0 0 0 0 0 0 1 1 ... ..$ opq013: int [1:151] 0 0 0 0 1 1 1 1 0 0 ... ..$ opq014: int [1:151] 0 0 1 1 0 0 1 1 0 0 ... ..$ opq015: int [1:151] 0 1 0 1 0 1 0 1 0 1 ... $ qor:'data.frame': 26 obs. of 7 variables: ..$ p : num [1:26] 0.92775 0.00573 0.00573 0.00573 0.00573 ... ..$ qor002: num [1:26] 0 0 0 0 0 0 0 0 0 0 ... ..$ qor005: num [1:26] 0 0 0 0 0 0 0 0 1 1 ... ..$ qor010: num [1:26] 0 0 0 0 1 1 1 1 0 0 ... ..$ qor011: num [1:26] 0 0 0 0 0 0 0 0 0 0 ... ..$ qor014: num [1:26] 0 0 1 1 0 0 1 1 0 0 ... ..$ qor017: num [1:26] 0 1 0 1 0 1 0 1 0 1 ... $ rpb:'data.frame': 44 obs. of 8 variables: ..$ p : num [1:44] 0.945238 0.000595 0.000595 0.000595 0.000595 ... ..$ rpb001: num [1:44] 0 0 0 0 0 0 0 0 0 0 ... ..$ rpb003: num [1:44] 0 0 0 0 0 0 0 0 0 0 ... ..$ rpb004: num [1:44] 0 0 0 0 0 1 1 1 1 1 ... ..$ rpb006: num [1:44] 0 1 1 1 1 0 1 1 1 1 ... ..$ rpb007: num [1:44] 0 0 0 0 0 0 0 0 0 0 ... ..$ rpb009: int [1:44] 0 0 0 1 1 0 0 0 1 1 ... ..$ rpb014: int [1:44] 0 0 1 0 1 0 0 1 0 1 ... $ rvn:'data.frame': 13 obs. of 5 variables: ..$ p : num [1:13] 0.95714 0.00476 0.00476 0.00476 0.00952 ... ..$ rvn005: int [1:13] 0 0 0 0 0 1 1 1 1 1 ... ..$ rvn007: int [1:13] 0 0 0 0 1 0 0 0 0 1 ... ..$ rvn009: int [1:13] 0 0 1 1 0 0 0 1 1 0 ... ..$ rvn013: int [1:13] 0 1 0 1 0 0 1 0 1 0 ... $ thv:'data.frame': 16 obs. of 5 variables: ..$ p : num [1:16] 0.95595 0.00357 0.00357 0.00357 0.00357 ... ..$ thv005: int [1:16] 0 0 0 0 0 0 0 0 1 1 ... ..$ thv006: int [1:16] 0 0 0 0 1 1 1 1 0 0 ... ..$ thv011: int [1:16] 0 0 1 1 0 0 1 1 0 0 ... ..$ thv012: int [1:16] 0 1 0 1 0 1 0 1 0 1 ... $ wkt:'data.frame': 45 obs. of 9 variables: ..$ p : num [1:45] 0.942857 0.004762 0.004762 0.000595 0.000595 ... ..$ wkt004: num [1:45] 0 1 1 1 1 1 1 1 1 1 ... ..$ wkt007: num [1:45] 0 0 0 0 0 0 0 0 0 0 ... ..$ wkt008: num [1:45] 0 0 0 1 1 1 1 1 1 1 ... ..$ wkt011: num [1:45] 0 0 1 0 0 0 0 0 0 0 ... ..$ wkt012: num [1:45] 0 0 0 0 0 0 0 0 0 0 ... ..$ wkt013: num [1:45] 0 0 0 0 0 0 0 1 1 1 ... ..$ wkt014: num [1:45] 0 0 0 0 0 1 1 0 0 1 ... ..$ wkt015: num [1:45] 0 0 0 0 1 0 1 0 1 0 ... $ yiu:'data.frame': 47 obs. of 8 variables: ..$ p : num [1:47] 0.93575 0.00117 0.00117 0.00117 0.00584 ... ..$ yiu001: num [1:47] 0 0 0 0 0 0 0 0 0 0 ... ..$ yiu003: num [1:47] 0 0 0 0 0 0 0 0 0 0 ... ..$ yiu005: num [1:47] 0 0 0 0 0 0 0 0 1 1 ... ..$ yiu008: num [1:47] 0 0 0 0 1 1 1 1 0 0 ... ..$ yiu011: num [1:47] 0 0 0 0 0 0 0 0 0 0 ... ..$ yiu014: int [1:47] 0 0 1 1 0 0 1 1 0 0 ... ..$ yiu018: int [1:47] 0 1 0 1 0 1 0 1 0 1 ... $ yvf:'data.frame': 63 obs. of 9 variables: ..$ p : num [1:63] 0.93224 0.00234 0.00234 0.00234 0.00234 ... ..$ yvf001: num [1:63] 0 0 0 0 0 0 0 0 0 0 ... ..$ yvf004: num [1:63] 0 0 0 0 0 0 0 0 0 0 ... ..$ yvf006: num [1:63] 0 0 0 0 0 0 0 0 1 1 ... ..$ yvf007: num [1:63] 0 0 0 0 0 0 0 0 0 0 ... ..$ yvf008: num [1:63] 0 0 0 0 0 0 0 0 0 0 ... ..$ yvf011: int [1:63] 0 0 0 0 1 1 1 1 0 0 ... ..$ yvf013: int [1:63] 0 0 1 1 0 0 1 1 0 0 ... ..$ yvf014: int [1:63] 0 1 0 1 0 1 0 1 0 1 ... > > ## No test: > # Compute Delta l > MLEs <- ML_estimates(typed_genos, M_values, ncores = 4) Loading data Computing log-likelihood for the standard mixture model Error in .check_ncores(length(names)) : 4 simultaneous processes spawned Calls: ML_estimates ... em_mix -> -> makePSOCKcluster -> .check_ncores Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [8s/148s] 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/heritEWAS.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 2:53.68, 26.89 + 5.43