Package check result: OK Changes to worse in reverse depends: Package: gpcp Check: examples New result: ERROR Running examples in ‘gpcp-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: runGPCP > ### Title: Genomic Prediction of Cross Performance This function performs > ### genomic prediction of cross performance using genotype and phenotype > ### data. > ### Aliases: runGPCP > > ### ** Examples > > # Load phenotype data from CSV > phenotypeFile <- read.csv(system.file("extdata", "phenotypeFile.csv", package = "gpcp")) > genotypeFile <- system.file("extdata", "genotypeFile_Chr9and11.vcf", package = "gpcp") > finalcrosses <- runGPCP( + phenotypeFile = phenotypeFile, + genotypeFile = genotypeFile, + genotypes = "Accession", + traits = "YIELD,DMC", + weights = c(3, 1), + userFixed = "LOC,REP", + Ploidy = 2, + NCrosses = 150 + ) READING VARIANT FILE GENETIC PREDICTIONS... DISTANCE MATRIX... Initial data: Number of Individuals: 799 Number of Markers: 331 Missing data check: Total SNPs: 331 0 SNPs dropped due to missing data threshold of 0.5 Total of: 331 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 331 SNPs Final: 331 SNPs ( 0 SNPs removed) Completed! Time = 0.99 seconds processing phenotypic data... Fitting mixed model in sommer User response: YIELD Generating formula... Fit mixed GBLUP model... ~sommer::vsr(Accession, Gu = A) + sommer::vsr(Accession2, Gu = D) This function has been deprecated. Please start using 'mme' and its auxiliary functions (e.g., 'vsm', 'usm', 'dsm', 'ism', etc.). This function will be no longer maintained. Error: 'vsr' is not an exported object from 'namespace:sommer' Execution halted Package: IPLGP Check: dependencies in R code New result: WARNING Missing or unexported object: ‘sommer::vsr’ Package: IPLGP Check: examples New result: ERROR Running examples in ‘IPLGP-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: GBLUP.fit > ### Title: Muti-trait GBLUP Model > ### Aliases: GBLUP.fit > > ### ** Examples > > # generate simulated data > set.seed(2000) > t1 <- rnorm(50,30,10) > t2 <- rnorm(50,10,5) > t3 <- rnorm(50,20,20) > t4 <- NULL > t5 <- NULL > > # run with the marker score matrix > geno.test <- matrix(sample(c(1, -1), 5000, replace = TRUE), 50, 100) > result1 <- GBLUP.fit(t1, t2, t3, t4, t5, geno = geno.test) This function has been deprecated. Please start using 'mme' and its auxiliary functions (e.g., 'vsm', 'usm', 'dsm', 'ism', etc.). This function will be no longer maintained. Error: 'vsr' is not an exported object from 'namespace:sommer' Execution halted Package: lmDiallel Check: examples New result: ERROR Running examples in ‘lmDiallel-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: mmer.diallel > ### Title: Fitting random diallel linear models > ### Aliases: mmer.diallel > ### Keywords: diallel genetic effects > > ### ** Examples > > data("hayman54") > rMod <- mmer.diallel(Ftime ~ Par1 + Par2, Block = Block, + data = hayman54, + fct = "HAYMAN1") This function has been deprecated. Please start using 'mme' and its auxiliary functions (e.g., 'vsm', 'usm', 'dsm', 'ism', etc.). This function will be no longer maintained. Error in summary(modh)$varcomp : $ operator is invalid for atomic vectors Calls: mmer.diallel Execution halted Package: lucid Check: tests New result: ERROR Running ‘testthat.R’ [2s/2s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(lucid) > > test_check("lucid") id P1 P2 P3 1 A a -1 3.3175e-140 2 B b 0 1.0637e-165 3 C c 1 1.1279e-157 id P1 P2 1 A a -1 2 B b 0 3 C c 1 P3 1 0.0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000332 2 0 3 0 effect variance stddev (Intercept) 615.3 24.81 Residual 16.17 4.021 grp var1 var2 vcov sdcor Rail (Intercept) 615.3 24.81 Residual 16.17 4.021 grp var1 var2 vcov sdcor Rail (Intercept) 1.638 1.28 Residual 11.11 3.333 iteration LogLik wall cpu(sec) restrained 1 -5.78344 22:13:7 0 0 2 1.8756 22:13:7 0 0 3 8.51187 22:13:7 0 0 4 9.74181 22:13:7 0 0 5 9.75215 22:13:7 0 0 6 9.75225 22:13:7 0 0 [ FAIL 1 | WARN 1 | SKIP 2 | PASS 21 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • empty test (2): 'test_lucid.R:150:1', 'test_vc.R:74:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_vc.R:98:3'): mmer ────────────────────────────────────────────── Error in `summary(object)$varcomp`: $ operator is invalid for atomic vectors Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test_vc.R:98:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─lucid::vc(m1s) 5. └─lucid:::vc.mmer(m1s) [ FAIL 1 | WARN 1 | SKIP 2 | PASS 21 ] Error: Test failures Execution halted Package: MoBPS Check: dependencies in R code New result: WARNING Missing or unexported object: ‘sommer::vs’ Package: pcgen Check: whether package can be installed New result: ERROR Installation failed. Package: statgenGWAS Check: dependencies in R code New result: WARNING Missing or unexported object: ‘sommer::vsr’ Package: statgenGWAS Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘GWAS.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_recheck/statgenGWAS.Rcheck/vign_test/statgenGWAS/vignettes/GWAS_files/figure-html/plotGData-1.png 672x384 pixels, 8 bits/pixel, 255 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 11238 bytes Input file size = 12105 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9676 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9676 Output IDAT size = 9676 bytes (1562 bytes decrease) Output file size = 9754 bytes (2351 bytes = 19.42% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/statgenGWAS.Rcheck/vign_test/statgenGWAS/vignettes/GWAS_files/figure-html/plotGDataHL-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 23568 bytes Input file size = 23670 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18895 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18895 Output IDAT size = 18895 bytes (4673 bytes decrease) Output file size = 18973 bytes (4697 bytes = 19.84% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/statgenGWAS.Rcheck/vign_test/statgenGWAS/vignettes/GWAS_files/figure-html/qqStg-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 22827 bytes Input file size = 22929 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19212 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19212 Output IDAT size = 19212 bytes (3615 bytes decrease) Output file size = 19290 bytes (3639 bytes = 15.87% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/statgenGWAS.Rcheck/vign_test/statgenGWAS/vignettes/GWAS_files/figure-html/manhattanStg-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 58604 bytes Input file size = 58766 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 40268 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 40268 Output IDAT size = 40268 bytes (18336 bytes decrease) Output file size = 40346 bytes (18420 bytes = 31.34% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/statgenGWAS.Rcheck/vign_test/statgenGWAS/vignettes/GWAS_files/figure-html/manhattanStgThr-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 53092 bytes Input file size = 53242 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36138 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36138 Output IDAT size = 36138 bytes (16954 bytes decrease) Output file size = 36216 bytes (17026 bytes = 31.98% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/statgenGWAS.Rcheck/vign_test/statgenGWAS/vignettes/GWAS_files/figure-html/manhattanStgPos-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 44048 bytes Input file size = 44186 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30207 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30207 Output IDAT size = 30207 bytes (13841 bytes decrease) Output file size = 30285 bytes (13901 bytes = 31.46% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/statgenGWAS.Rcheck/vign_test/statgenGWAS/vignettes/GWAS_files/figure-html/manhattanLod-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 79192 bytes Input file size = 79378 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 50241 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 50241 Output IDAT size = 50241 bytes (28951 bytes decrease) Output file size = 50319 bytes (29059 bytes = 36.61% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/statgenGWAS.Rcheck/vign_test/statgenGWAS/vignettes/GWAS_files/figure-html/manhattanEffects-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 58643 bytes Input file size = 58805 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 40301 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 40301 Output IDAT size = 40301 bytes (18342 bytes decrease) Output file size = 40379 bytes (18426 bytes = 31.33% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/statgenGWAS.Rcheck/vign_test/statgenGWAS/vignettes/GWAS_files/figure-html/qtlStg-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 15634 bytes Input file size = 15724 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13493 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13493 Output IDAT size = 13493 bytes (2141 bytes decrease) Output file size = 13571 bytes (2153 bytes = 13.69% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/statgenGWAS.Rcheck/vign_test/statgenGWAS/vignettes/GWAS_files/figure-html/qtlStgThr-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 20842 bytes Input file size = 20944 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17356 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17356 Output IDAT size = 17356 bytes (3486 bytes decrease) Output file size = 17434 bytes (3510 bytes = 16.76% decrease) ** Processing: /home/hornik/tmp/CRAN_recheck/statgenGWAS.Rcheck/vign_test/statgenGWAS/vignettes/GWAS_files/figure-html/qtlStgNorm-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 20994 bytes Input file size = 21096 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17480 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17480 Output IDAT size = 17480 bytes (3514 bytes decrease) Output file size = 17558 bytes (3538 bytes = 16.77% decrease) Quitting from GWAS.Rmd:406-413 [stgSNPNR] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! 'vsr' is not an exported object from 'namespace:sommer' --- Backtrace: ▆ 1. └─statgenGWAS::runSingleTraitGwas(...) 2. └─statgenGWAS:::estVarComp(...) 3. └─statgenGWAS:::estVarCompNR(...) 4. └─sommer::mmer(...) 5. └─base::eval(parse(text = rtermss[u]), data, parent.frame()) 6. └─base::eval(parse(text = rtermss[u]), data, parent.frame()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'GWAS.Rmd' failed with diagnostics: 'vsr' is not an exported object from 'namespace:sommer' --- failed re-building ‘GWAS.Rmd’ SUMMARY: processing the following file failed: ‘GWAS.Rmd’ Error: Vignette re-building failed. Execution halted Package: statgenGWAS Check: tests New result: ERROR Running ‘tinytest.R’ [3s/2s] Running the tests in ‘tests/tinytest.R’ failed. Complete output: > > if ( requireNamespace("tinytest", quietly=TRUE) ){ + tinytest::test_package("statgenGWAS") + } test_GWAS.R................... 0 tests test_GWAS.R................... 0 tests test_GWAS.R................... 0 tests test_GWAS.R................... 0 tests test_GWAS.R................... 1 tests OK test_GWAS.R................... 2 tests OK test_GWAS.R................... 2 tests OK test_GWAS.R................... 3 tests OK test_GWAS.R................... 4 tests OK test_GWAS.R................... 5 tests OK test_GWAS.R................... 6 tests OK test_GWAS.R................... 7 tests OK test_GWAS.R................... 8 tests OK test_GWAS.R................... 9 tests OK test_GWAS.R................... 10 tests OK test_GWAS.R................... 11 tests OK test_GWAS.R................... 11 tests OK test_GWAS.R................... 12 tests OK test_GWAS.R................... 13 tests OK test_GWAS.R................... 14 tests OK test_GWAS.R................... 15 tests OK test_GWAS.R................... 15 tests OK test_GWAS.R................... 16 tests OK test_GWAS.R................... 17 tests OK 0.2s test_STG.R.................... 0 tests test_STG.R.................... 0 tests test_STG.R.................... 0 tests test_STG.R.................... 0 tests test_STG.R.................... 0 tests test_STG.R.................... 0 tests test_STG.R.................... 0 tests test_STG.R.................... 0 tests test_STG.R.................... 1 tests OK test_STG.R.................... 2 tests OK test_STG.R.................... 3 tests OK test_STG.R.................... 4 tests OK test_STG.R.................... 5 tests OK test_STG.R.................... 6 tests OK test_STG.R.................... 7 tests OK test_STG.R.................... 8 tests OK test_STG.R.................... 9 tests OK test_STG.R.................... 10 tests OK test_STG.R.................... 11 tests OK test_STG.R.................... 12 tests OK test_STG.R.................... 13 tests OK test_STG.R.................... 14 tests OK test_STG.R.................... 15 tests OK test_STG.R.................... 16 tests OK test_STG.R.................... 17 tests OK test_STG.R.................... 17 tests OK test_STG.R.................... 17 tests OK test_STG.R.................... 17 tests OK test_STG.R.................... 17 tests OK test_STG.R.................... 17 tests OK test_STG.R.................... 18 tests OK test_STG.R.................... 19 tests OK test_STG.R.................... 20 tests OK test_STG.R.................... 21 tests OK test_STG.R.................... 22 tests OK test_STG.R.................... 23 tests OK test_STG.R.................... 24 tests OK test_STG.R.................... 25 tests OK test_STG.R.................... 26 tests OK test_STG.R.................... 27 tests OK test_STG.R.................... 28 tests OK test_STG.R.................... 29 tests OK test_STG.R.................... 30 tests OK test_STG.R.................... 31 tests OK test_STG.R.................... 32 tests OK test_STG.R.................... 33 tests OK test_STG.R.................... 34 tests OK test_STG.R.................... 35 tests OK test_STG.R.................... 36 tests OK test_STG.R.................... 37 tests OK 0.5s test_STGHelper.R.............. 0 tests test_STGHelper.R.............. 0 tests test_STGHelper.R.............. 0 tests test_STGHelper.R.............. 1 tests OK test_STGHelper.R.............. 2 tests OK test_STGHelper.R.............. 3 tests OK test_STGHelper.R.............. 3 tests OK test_STGHelper.R.............. 4 tests OK test_STGHelper.R.............. 5 tests OK test_STGHelper.R.............. 6 tests OK test_STGHelper.R.............. 7 tests OK test_STGHelper.R.............. 8 tests OK test_STGHelper.R.............. 9 tests OK test_STGHelper.R.............. 10 tests OK test_STGHelper.R.............. 11 tests OK test_STGHelper.R.............. 12 tests OK test_STGHelper.R.............. 13 tests OK test_STGHelper.R.............. 14 tests OK test_STGHelper.R.............. 14 tests OK test_STGHelper.R.............. 15 tests OK test_STGHelper.R.............. 16 tests OK test_STGHelper.R.............. 17 tests OK test_STGHelper.R.............. 18 tests OK test_STGHelper.R.............. 18 tests OK test_STGHelper.R.............. 19 tests OK test_STGHelper.R.............. 20 tests OK test_STGHelper.R.............. 20 tests OK test_STGHelper.R.............. 20 tests OK test_STGHelper.R.............. 21 tests OK test_STGHelper.R.............. 22 tests OK test_STGHelper.R.............. 23 tests OK test_STGHelper.R.............. 24 tests OK test_STGHelper.R.............. 25 tests OK test_STGHelper.R.............. 26 tests OK test_STGHelper.R.............. 27 tests OK test_STGHelper.R.............. 28 tests OK test_STGHelper.R.............. 29 tests OK test_STGHelper.R.............. 30 tests OK test_STGHelper.R.............. 31 tests OK 16ms test_STGoptions.R............. 0 tests test_STGoptions.R............. 1 tests OK This function has been deprecated. Please start using 'mme' and its auxiliary functions (e.g., 'vsm', 'usm', 'dsm', 'ism', etc.). This function will be no longer maintained. Error: 'vsr' is not an exported object from 'namespace:sommer' Execution halted Package: statgenQTLxT Check: dependencies in R code New result: WARNING Missing or unexported object: ‘sommer::vsr’ Package: statgenQTLxT Check: Rd cross-references Old result: NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: runMultiTraitGwas.Rd: GWAS Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. New result: WARNING Missing link(s) in Rd file 'runMultiTraitGwas.Rd': ‘GWAS’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: runMultiTraitGwas.Rd: GWAS Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. Package: statgenQTLxT Check: tests New result: ERROR Running ‘tinytest.R’ [1s/1s] Running the tests in ‘tests/tinytest.R’ failed. Complete output: > > if ( requireNamespace("tinytest", quietly=TRUE) ){ + tinytest::test_package("statgenQTLxT") + } test_chkFuncs.R............... 0 tests test_chkFuncs.R............... 0 tests test_chkFuncs.R............... 1 tests OK test_chkFuncs.R............... 2 tests OK test_chkFuncs.R............... 3 tests OK test_chkFuncs.R............... 3 tests OK test_chkFuncs.R............... 3 tests OK test_chkFuncs.R............... 4 tests OK test_chkFuncs.R............... 5 tests OK test_chkFuncs.R............... 6 tests OK test_chkFuncs.R............... 7 tests OK test_chkFuncs.R............... 8 tests OK test_chkFuncs.R............... 9 tests OK test_chkFuncs.R............... 10 tests OK test_chkFuncs.R............... 11 tests OK test_chkFuncs.R............... 12 tests OK test_chkFuncs.R............... 13 tests OK test_chkFuncs.R............... 14 tests OK test_chkFuncs.R............... 15 tests OK test_chkFuncs.R............... 16 tests OK test_chkFuncs.R............... 17 tests OK test_chkFuncs.R............... 18 tests OK test_chkFuncs.R............... 19 tests OK test_chkFuncs.R............... 20 tests OK test_chkFuncs.R............... 21 tests OK test_chkFuncs.R............... 22 tests OK test_chkFuncs.R............... 23 tests OK test_chkFuncs.R............... 24 tests OK test_chkFuncs.R............... 25 tests OK test_chkFuncs.R............... 26 tests OK test_chkFuncs.R............... 26 tests OK test_chkFuncs.R............... 27 tests OK test_chkFuncs.R............... 27 tests OK test_chkFuncs.R............... 28 tests OK test_chkFuncs.R............... 29 tests OK test_chkFuncs.R............... 30 tests OK test_chkFuncs.R............... 31 tests OK test_chkFuncs.R............... 32 tests OK test_chkFuncs.R............... 33 tests OK test_chkFuncs.R............... 34 tests OK test_chkFuncs.R............... 35 tests OK test_chkFuncs.R............... 36 tests OK test_chkFuncs.R............... 37 tests OK test_chkFuncs.R............... 38 tests OK test_chkFuncs.R............... 39 tests OK 0.2s test_runMultiTraitGwas.R...... 0 tests test_runMultiTraitGwas.R...... 0 tests test_runMultiTraitGwas.R...... 1 tests OK test_runMultiTraitGwas.R...... 2 tests OK This function has been deprecated. Please start using 'mme' and its auxiliary functions (e.g., 'vsm', 'usm', 'dsm', 'ism', etc.). This function will be no longer maintained. Error: 'vsr' is not an exported object from 'namespace:sommer' Execution halted