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CRAN Package Check Results for Package ensembleTax

Last updated on 2026-05-04 05:51:47 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1.1 3.68 60.31 63.99 NOTE
r-devel-linux-x86_64-debian-gcc 1.1.1 3.00 44.06 47.06 NOTE
r-devel-linux-x86_64-fedora-clang 1.1.1 8.00 78.32 86.32 ERROR
r-devel-linux-x86_64-fedora-gcc 1.1.1 90.83 ERROR
r-devel-windows-x86_64 1.1.1 8.00 67.00 75.00 ERROR
r-patched-linux-x86_64 1.1.1 4.55 51.25 55.80 OK
r-release-linux-x86_64 1.1.1 3.91 50.97 54.88 OK
r-release-macos-arm64 1.1.1 1.00 22.00 23.00 OK
r-release-macos-x86_64 1.1.1 4.00 87.00 91.00 OK
r-release-windows-x86_64 1.1.1 9.00 88.00 97.00 OK
r-oldrel-macos-arm64 1.1.1 OK
r-oldrel-macos-x86_64 1.1.1 4.00 66.00 70.00 OK
r-oldrel-windows-x86_64 1.1.1 10.00 92.00 102.00 OK

Check Details

Version: 1.1.1
Check: CRAN incoming feasibility
Result: NOTE Maintainer: ‘Dylan Catlett <dcat4444@gmail.com>’ No Authors@R field in DESCRIPTION. Please add one, modifying Authors@R: c(person(given = "Dylan", family = "Catlett", role = c("aut", "cre"), email = "dcat4444@gmail.com"), person(given = "Kevin", family = "Son", role = "ctb"), person(given = "Connie", family = "Liang", role = "ctb")) as necessary. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.1.1
Check: dependencies in R code
Result: NOTE Namespaces in Imports field not imported from: ‘Biostrings’ ‘DECIPHER’ ‘ggplot2’ ‘reshape2’ ‘usethis’ All declared Imports should be used. Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.1.1
Check: examples
Result: 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 <NA> <NA> <NA> <NA> 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 <NA> family genus species 1 <NA> <NA> <NA> 2 Polar-centric-Mediophyceae <NA> <NA> 3 Collophidiidae Collophidium <NA> 4 <NA> <NA> <NA> 5 <NA> <NA> <NA> > head(fake2.pr2) ASV kingdom supergroup division class order 1 AAAA Eukaryota <NA> <NA> <NA> <NA> 2 ATCG Eukaryota Stramenopiles Opalozoa <NA> <NA> 3 GCGC Eukaryota Rhizaria Radiolaria Polycystinea Collodaria 4 TATA Eukaryota Stramenopiles Opalozoa <NA> <NA> 5 TCGA Eukaryota Alveolata Dinoflagellata Dinophycese <NA> family genus species 1 <NA> <NA> <NA> 2 <NA> <NA> <NA> 3 Collophidiidae Collophidium <NA> 4 <NA> <NA> <NA> 5 <NA> <NA> <NA> > xx <- list(fake1.pr2, fake2.pr2) > names(xx) <- c("fake1", "fake2") > xx $fake1 ASV kingdom supergroup division class order 1 AAAA Eukaryota <NA> <NA> <NA> <NA> 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 <NA> family genus species 1 <NA> <NA> <NA> 2 Polar-centric-Mediophyceae <NA> <NA> 3 Collophidiidae Collophidium <NA> 4 <NA> <NA> <NA> 5 <NA> <NA> <NA> $fake2 ASV kingdom supergroup division class order 1 AAAA Eukaryota <NA> <NA> <NA> <NA> 2 ATCG Eukaryota Stramenopiles Opalozoa <NA> <NA> 3 GCGC Eukaryota Rhizaria Radiolaria Polycystinea Collodaria 4 TATA Eukaryota Stramenopiles Opalozoa <NA> <NA> 5 TCGA Eukaryota Alveolata Dinoflagellata Dinophycese <NA> family genus species 1 <NA> <NA> <NA> 2 <NA> <NA> <NA> 3 Collophidiidae Collophidium <NA> 4 <NA> <NA> <NA> 5 <NA> <NA> <NA> > 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 Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Version: 1.1.1
Check: re-building of vignette outputs
Result: 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/rlang_error> 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/rlang_error> 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 Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

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