* using log directory 'd:/Rcompile/CRANpkg/local/4.7/ensembleTax.Rcheck' * using R Under development (unstable) (2026-05-01 r89993 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * current time: 2026-05-03 12:05:56 UTC * checking for file 'ensembleTax/DESCRIPTION' ... OK * this is package 'ensembleTax' version '1.1.1' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'ensembleTax' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... 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[0s] ERROR Running examples in 'ensembleTax-Ex.R' failed The error most likely occurred in: > ### Name: assign.ensembleTax > ### Title: Computes ensemble taxonomic assignments for each ASV in an > ### amplicon data set > ### Aliases: assign.ensembleTax > > ### ** Examples > > fake1.pr2 <- data.frame(ASV = c("AAAA", "ATCG", "GCGC", "TATA", "TCGA"), + kingdom = c("Eukaryota", "Eukaryota", "Eukaryota", "Eukaryota", + "Eukaryota"), + supergroup = c(NA, "Stramenopiles", "Rhizaria", "Stramenopiles", + "Alveolata"), + division = c(NA, "Ochrophyta", "Radiolaria", "Opalozoa", + "Dinoflagellata"), + class = c(NA, "Bacillariophyta", "Polycystinea", "MAST-12", + "Syndiniales"), + order = c(NA, "Bacillariophyta_X", "Collodaria", "MAST-12A", NA), + family = c(NA, "Polar-centric-Mediophyceae", "Collophidiidae", NA, + NA), + genus = c(NA, NA, "Collophidium", NA, NA), + species = as.character(c(NA, NA, NA, NA, NA)), + stringsAsFactors = FALSE) > fake2.pr2 <- data.frame(ASV = c("AAAA", "ATCG", "GCGC", "TATA", "TCGA"), + kingdom = c("Eukaryota", "Eukaryota", "Eukaryota", "Eukaryota", + "Eukaryota"), + supergroup = c(NA, "Stramenopiles", "Rhizaria", "Stramenopiles", + "Alveolata"), + division = c(NA, "Opalozoa", "Radiolaria", "Opalozoa", + "Dinoflagellata"), + class = c(NA, NA, "Polycystinea", NA, "Dinophycese"), + order = c(NA, NA, "Collodaria", NA, NA), + family = c(NA, NA, "Collophidiidae", NA, NA), + genus = c(NA, NA, "Collophidium", NA, NA), + species = as.character(c(NA, NA, NA, NA, NA)), + stringsAsFactors = FALSE) > head(fake1.pr2) ASV kingdom supergroup division class order 1 AAAA Eukaryota 2 ATCG Eukaryota Stramenopiles Ochrophyta Bacillariophyta Bacillariophyta_X 3 GCGC Eukaryota Rhizaria Radiolaria Polycystinea Collodaria 4 TATA Eukaryota Stramenopiles Opalozoa MAST-12 MAST-12A 5 TCGA Eukaryota Alveolata Dinoflagellata Syndiniales family genus species 1 2 Polar-centric-Mediophyceae 3 Collophidiidae Collophidium 4 5 > head(fake2.pr2) ASV kingdom supergroup division class order 1 AAAA Eukaryota 2 ATCG Eukaryota Stramenopiles Opalozoa 3 GCGC Eukaryota Rhizaria Radiolaria Polycystinea Collodaria 4 TATA Eukaryota Stramenopiles Opalozoa 5 TCGA Eukaryota Alveolata Dinoflagellata Dinophycese family genus species 1 2 3 Collophidiidae Collophidium 4 5 > xx <- list(fake1.pr2, fake2.pr2) > names(xx) <- c("fake1", "fake2") > xx $fake1 ASV kingdom supergroup division class order 1 AAAA Eukaryota 2 ATCG Eukaryota Stramenopiles Ochrophyta Bacillariophyta Bacillariophyta_X 3 GCGC Eukaryota Rhizaria Radiolaria Polycystinea Collodaria 4 TATA Eukaryota Stramenopiles Opalozoa MAST-12 MAST-12A 5 TCGA Eukaryota Alveolata Dinoflagellata Syndiniales family genus species 1 2 Polar-centric-Mediophyceae 3 Collophidiidae Collophidium 4 5 $fake2 ASV kingdom supergroup division class order 1 AAAA Eukaryota 2 ATCG Eukaryota Stramenopiles Opalozoa 3 GCGC Eukaryota Rhizaria Radiolaria Polycystinea Collodaria 4 TATA Eukaryota Stramenopiles Opalozoa 5 TCGA Eukaryota Alveolata Dinoflagellata Dinophycese family genus species 1 2 3 Collophidiidae Collophidium 4 5 > eTax <- assign.ensembleTax(xx, + tablenames = names(xx), + ranknames = c("kingdom", "supergroup", "division","class","order", + "family","genus","species"), + tiebreakz = NULL, + count.na=TRUE, + assign.threshold = 0.5, + weights=rep(1,length(xx))) Error in as.data.frame.integer(x[[i]], optional = TRUE) : row names contain missing values Calls: assign.ensembleTax ... data.frame -> as.data.frame -> as.data.frame.integer Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [10s] ERROR Error(s) in re-building vignettes: --- re-building 'assign.ensembleTax_tutorial.Rmd' using rmarkdown Quitting from assign.ensembleTax_tutorial.Rmd:89-103 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `as.data.frame.integer()`: ! row names contain missing values --- Backtrace: ▆ 1. └─ensembleTax::assign.ensembleTax(...) 2. ├─base::as.data.frame(base::table(taxs, exclude = NULL), stringsAsFactors = FALSE) 3. └─base::as.data.frame.table(...) 4. ├─base::eval(ex) 5. │ └─base::eval(ex) 6. └─base::data.frame(...) 7. ├─base::as.data.frame(x[[i]], optional = TRUE) 8. └─base::as.data.frame.integer(x[[i]], optional = TRUE) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'assign.ensembleTax_tutorial.Rmd' failed with diagnostics: row names contain missing values --- failed re-building 'assign.ensembleTax_tutorial.Rmd' --- re-building 'ensembleTax.Rmd' using rmarkdown Quitting from ensembleTax.Rmd:252-267 [unnamed-chunk-8] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `as.data.frame.integer()`: ! row names contain missing values --- Backtrace: ▆ 1. └─ensembleTax::assign.ensembleTax(...) 2. ├─base::as.data.frame(base::table(taxs, exclude = NULL), stringsAsFactors = FALSE) 3. └─base::as.data.frame.table(...) 4. ├─base::eval(ex) 5. │ └─base::eval(ex) 6. └─base::data.frame(...) 7. ├─base::as.data.frame(x[[i]], optional = TRUE) 8. └─base::as.data.frame.integer(x[[i]], optional = TRUE) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'ensembleTax.Rmd' failed with diagnostics: row names contain missing values --- failed re-building 'ensembleTax.Rmd' --- re-building 'taxmapper_tutorial.Rmd' using rmarkdown --- finished re-building 'taxmapper_tutorial.Rmd' SUMMARY: processing the following files failed: 'assign.ensembleTax_tutorial.Rmd' 'ensembleTax.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [19s] OK * checking HTML version of manual ... [4s] OK * DONE Status: 2 ERRORs