Last updated on 2026-04-30 09:52:55 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 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.1 | 90.83 | ERROR | |||
| r-devel-windows-x86_64 | 1.1.1 | 11.00 | 81.00 | 92.00 | OK | |
| r-patched-linux-x86_64 | 1.1.1 | 4.55 | 51.25 | 55.80 | OK | |
| r-release-linux-x86_64 | 1.1.1 | 3.14 | 51.50 | 54.64 | OK | |
| r-release-macos-arm64 | 1.1.1 | 1.00 | 22.00 | 23.00 | OK | |
| r-release-macos-x86_64 | 1.1.1 | 5.00 | 74.00 | 79.00 | OK | |
| r-release-windows-x86_64 | 1.1.1 | 8.00 | 78.00 | 86.00 | 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 | 90.00 | 100.00 | OK |
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
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