* using log directory ‘/srv/hornik/tmp/CRAN_pretest/tidyGenR.Rcheck’ * using R Under development (unstable) (2026-02-08 r89382) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 21.1.8 (1+b1) Debian flang version 21.1.8 (1+b1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * current time: 2026-02-09 19:54:36 UTC * checking for file ‘tidyGenR/DESCRIPTION’ ... OK * this is package ‘tidyGenR’ version ‘0.1.6’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/5s] NOTE Maintainer: ‘Miguel Camacho ’ New submission Possibly misspelled words in DESCRIPTION: Amplicon (2:24) Illumina (10:64) MiSeq (10:73) amplicon (10:21) demultiplex (11:64) Found the following (possibly) invalid URLs: URL: https://codecov.io/gh/csmiguel/tidyGenR (moved to https://app.codecov.io/gh/csmiguel/tidyGenR) From: README.md Status: 301 Message: Moved Permanently For content that is 'Moved Permanently', please change http to https, add trailing slashes, or replace the old by the new URL. The Description field should start with a capital letter. * 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 ‘tidyGenR’ can be installed ... [23s/23s] OK * checking package directory ... OK * checking for future file timestamps ... 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [7s/7s] OK * checking whether the package can be loaded with stated dependencies ... [7s/7s] OK * checking whether the package can be unloaded cleanly ... [7s/7s] OK * checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK * checking whether the namespace can be unloaded cleanly ... [7s/7s] OK * checking loading without being on the library search path ... [7s/7s] OK * checking use of S3 registration ... 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 ... [31s/31s] OK * checking Rd files ... [0s/0s] 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 ... [2s/2s] OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [32s/32s] ERROR Running examples in ‘tidyGenR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: out_popart > ### Title: Format MSA and traits for PopArt > ### Aliases: out_popart > > ### ** Examples > > data("genotypes") > x <- + dplyr::filter(genotypes, locus == "abcg8") > nr <- seq_len(nrow(x)) > y <- + dplyr::mutate(x, sname = paste0("seq_", nr)) > msa <- + tidy2sequences(y, fasta_header = "{sname}") |> + DECIPHER::AlignSeqs() Sequences have not been written to fasta file. Determining distance matrix based on shared 8-mers: ================================================================================ Time difference of 0.01 secs Clustering into groups by similarity: ================================================================================ Time difference of 0.01 secs Aligning Sequences: ================================================================================ Time difference of 0.2 secs Iteration 1 of 2: Determining distance matrix based on alignment: ================================================================================ Time difference of 0 secs Reclustering into groups by similarity: ================================================================================ Time difference of 0.01 secs Realigning Sequences: ================================================================================ Time difference of 0.01 secs Alignment converged - skipping remaining iteration. > out_popart(msa, y, + outnex = "abcg8.nex", + sname = "sname", + xgroups = "sample", + blocks = c("DATA", "TRAITS") + ) Error in `vroom::vroom_write()`: ! `quote` must be a character vector, not `NULL`. Backtrace: ▆ 1. └─tidyGenR::out_popart(...) 2. └─tidyGenR (local) ftraits() 3. ├─utils::capture.output(...) 4. │ └─base::withVisible(...elt(i)) 5. └─readr::write_delim(...) 6. └─vroom::vroom_write(quote = quote) 7. └─rlang::arg_match(quote) 8. └─rlang:::check_character(arg, arg = error_arg, call = error_call) 9. └─rlang:::stop_input_type(...) 10. └─rlang::abort(message, ..., call = call, arg = arg) Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed genotype 9.071 0 9.084 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [56s/56s] ERROR Running ‘testthat.R’ [56s/56s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # This file tells testthat what to do. > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(tidyGenR) > library(dplyr) Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union > > test_check("tidyGenR") Loci detected: 'abcg8', 'alkbh7', 'apeh17'. Files detected: /srv/hornik/tmp/CRAN_pretest/tidyGenR.Rcheck/tidyGenR/extdata/amplisas/abcg8.txt /srv/hornik/tmp/CRAN_pretest/tidyGenR.Rcheck/tidyGenR/extdata/amplisas/alkbh7.txt /srv/hornik/tmp/CRAN_pretest/tidyGenR.Rcheck/tidyGenR/extdata/amplisas/apeh17.txt All F and (R files) passed check on number of reads above 10. Sample names are unique. All F files have their corresponding R file. All F and (R files) passed check on number of reads above 10. Sample names are unique. Only F reads in check 3: orphan reads cannot be evaluated. Sample names are unique. Only F reads in check 3: orphan reads cannot be evaluated. Sample names are unique. Only F reads in check 3: orphan reads cannot be evaluated. All F and (R files) passed check on number of reads above 10. All F and (R files) passed check on number of reads above 10. Sample names are unique. 'td' is a named list with 2 or more dataframes that contain sample locus sequence. No output EXCEL file has been written. Change this behaviour by setting a path to 'dest_file'. 'td' is a named list with 2 or more dataframes that contain sample locus sequence. No output EXCEL file has been written. Change this behaviour by setting a path to 'dest_file'. 'td' is a named list with 2 or more dataframes that contain sample locus sequence. No output EXCEL file has been written. Change this behaviour by setting a path to 'dest_file'. 'td' is a named list with 2 or more dataframes that contain sample locus sequence. 'td' is a named list with 2 or more dataframes that contain sample locus sequence. De-replicated sequences written to /tmp/RtmpYVRaDQ/working_dir/RtmpXhKO85/test.xlsx. If the number of sheets in too large EXCEL might crash at opening. Initializing error rates to maximum possible estimate. selfConsist step 1 .. selfConsist step 2 Convergence after 2 rounds. Initializing error rates to maximum possible estimate. selfConsist step 1 ... selfConsist step 2 Convergence after 2 rounds. All loci are assumed to have a ploidy of 2 popdata is formatted correctly. STRUCTURE file written to /tmp/RtmpYVRaDQ/working_dir/RtmpXhKO85/test1.str Ploidy attribute in genotypes is set to 2. popdata is formatted correctly. GENALEX genotypes have been written to /tmp/RtmpYVRaDQ/working_dir/RtmpXhKO85/out.txt Ploidy attribute in genotypes is set to 2. popdata is formatted correctly. GENALEX genotypes have been written to /tmp/RtmpYVRaDQ/working_dir/RtmpXhKO85/out.xlsx ADt is ignored when ploidy != 2. ADt is ignored when ploidy != 2. Sequences have not been written to fasta file. Determining distance matrix based on shared 8-mers: ================================================================================ Time difference of 0.01 secs Clustering into groups by similarity: ================================================================================ Time difference of 0.01 secs Aligning Sequences: ================================================================================ Time difference of 0.21 secs Iteration 1 of 2: Determining distance matrix based on alignment: ================================================================================ Time difference of 0 secs Reclustering into groups by similarity: ================================================================================ Time difference of 0.01 secs Realigning Sequences: ================================================================================ Time difference of 0.01 secs Alignment converged - skipping remaining iteration. 'all.variants' and 'var_id' are ignored when setting 'path' to a folder. 'all.variants' and 'var_id' are ignored when setting 'path' to a folder. 'var_id' is ignored when 'all.variants' is FALSE. Loci alkbh7 apeh17 dhrs3 fancg irf5 ms4a2 mycbpap pipox ptgs2 rogdi ssfa2 are monomorphic. A total of 16 polymorphic loci have been returned. Loci alkbh7 apeh17 dhrs3 fancg irf5 ms4a2 mycbpap pipox ptgs2 rogdi ssfa2 are monomorphic. A total of 11 monomorphic loci have been returned. 1 files have been KEPT. 1 files REMOVED: /tmp/RtmpYVRaDQ/working_dir/RtmpXhKO85/empty_file.fastq Sequences have not been written to fasta file. Sequences have been written to: /tmp/RtmpYVRaDQ/working_dir/RtmpXhKO85/test.fasta Samples detected: BOR1061, BOR1063, BOR1069 Loci detected: chrna9, nfkbia, rogdi Sequencing files matching patterns seem to conform the required naming format 'sample.locus.[1|2].fastq.gz' Truncating chrna9 Creating output directory: /tmp/RtmpYVRaDQ/working_dir/RtmpXhKO85/truncated Forwards reads of chrna9 truncated at 200 nt. Reverse reads of chrna9 truncated at 200 nt. Truncating nfkbia Forwards reads of nfkbia truncated at 200 nt. Reverse reads of nfkbia truncated at 200 nt. Samples detected: BOR1061, BOR1063, BOR1069 Loci detected: chrna9, nfkbia, rogdi Sequencing files matching patterns seem to conform the required naming format 'sample.locus.[1|2].fastq.gz' Truncating chrna9 Forwards reads of chrna9 truncated at 200 nt. Reverse reads of chrna9 truncated at 200 nt. Truncating nfkbia Forwards reads of nfkbia truncated at 200 nt. Reverse reads of nfkbia truncated at 200 nt. Truncating rogdi Forwards reads of rogdi truncated at 200 nt. Reverse reads of rogdi truncated at 200 nt. Samples detected: BOR1061, BOR1063, BOR1069 Loci detected: chrna9, nfkbia, rogdi Sequencing files matching patterns seem to conform the required naming format 'sample.locus.[1|2].fastq.gz' Truncating chrna9 Samples detected: BOR1061, BOR1063, BOR1069 Loci detected: chrna9, nfkbia, rogdi Sequencing files matching patterns seem to conform the required naming format 'sample.locus.[1|2].fastq.gz' Truncating chrna9 Forwards reads of chrna9 truncated at 200 nt. Reverse reads of chrna9 truncated at 200 nt. Samples detected: BOR1061, BOR1063, BOR1069 Loci detected: chrna9, nfkbia, rogdi Sequencing files matching patterns seem to conform the required naming format 'sample.locus.[1|2].fastq.gz' Truncating chrna9 Forwards reads of chrna9 truncated at 200 nt. Reverse reads of chrna9 truncated at 200 nt. Samples detected: BOR1061, BOR1063, BOR1069 Loci detected: chrna9, nfkbia, rogdi Sequencing files matching patterns seem to conform the required naming format 'sample.locus.[1|2].fastq.gz' Truncating chrna9 Forwards reads of chrna9 truncated at 200 nt. Reverse reads of chrna9 truncated at 200 nt. Samples detected: BOR1061, BOR1063, BOR1069 Loci detected: chrna9, nfkbia, rogdi Sequencing files matching patterns seem to conform the required naming format 'sample.locus.[1|2].fastq.gz' Truncating chrna9 Forwards reads of chrna9 truncated at 200 nt. Reverse reads of chrna9 truncated at 200 nt. Samples detected: BOR1061, BOR1063, BOR1069 Loci detected: chrna9, nfkbia, rogdi Sequencing files matching patterns seem to conform the required naming format 'sample.locus.[1|2].fastq.gz' Truncating chrna9 Forwards reads of chrna9 truncated at 200 nt. Samples detected: BOR1061, BOR1063, BOR1069 Loci detected: chrna9, nfkbia, rogdi Sequencing files matching patterns seem to conform the required naming format 'sample.locus.[1|2].fastq.gz' Truncating chrna9 Forwards reads of chrna9 truncated at 100 nt. Samples detected: BOR1061, BOR1063, BOR1069 Loci detected: chrna9, nfkbia, rogdi Sequencing files matching patterns seem to conform the required naming format 'sample.locus.[1|2].fastq.gz' Truncating chrna9 Samples detected: BOR1061, BOR1063, BOR1069 Loci detected: chrna9, nfkbia, rogdi Sequencing files matching patterns seem to conform the required naming format 'sample.locus.[1|2].fastq.gz' Truncating chrna9 Forwards reads of chrna9 truncated at 196 nt. Reverse reads of chrna9 truncated at 182 nt. Truncating nfkbia Forwards reads of nfkbia truncated at 198 nt. Reverse reads of nfkbia truncated at 197 nt. A total of 3 locus/loci have/has been detected in file(s) with the pattern '_F_filt.fastq.gz' in the path '/srv/hornik/tmp/CRAN_pretest/tidyGenR.Rcheck/tidyGenR/extdata/truncated': chrna9 nfkbia rogdi Trying to call variants in single end mode. Calling variants for chrna9 39690 total bases in 147 reads from 3 samples will be used for learning the error rates. Sample 1 - 49 reads in 15 unique sequences. Sample 2 - 43 reads in 10 unique sequences. Sample 3 - 55 reads in 19 unique sequences. Identified 0 bimeras out of 2 input sequences. Calling variants for nfkbia 52110 total bases in 193 reads from 3 samples will be used for learning the error rates. Sample 1 - 58 reads in 17 unique sequences. Sample 2 - 67 reads in 21 unique sequences. Sample 3 - 68 reads in 18 unique sequences. Identified 0 bimeras out of 1 input sequences. Calling variants for rogdi 46710 total bases in 173 reads from 3 samples will be used for learning the error rates. Sample 1 - 55 reads in 13 unique sequences. Sample 2 - 60 reads in 22 unique sequences. Sample 3 - 58 reads in 24 unique sequences. Identified 0 bimeras out of 1 input sequences. A total of 3 locus/loci have/has been detected in file(s) with the pattern '_F_filt.fastq.gz' in the path '/srv/hornik/tmp/CRAN_pretest/tidyGenR.Rcheck/tidyGenR/extdata/truncated': chrna9 nfkbia rogdi Trying to call variants in single end mode. Calling variants for chrna9 39690 total bases in 147 reads from 3 samples will be used for learning the error rates. Sample 1 - 49 reads in 15 unique sequences. Sample 2 - 43 reads in 10 unique sequences. Sample 3 - 55 reads in 19 unique sequences. Identified 0 bimeras out of 2 input sequences. Calling variants for nfkbia 52110 total bases in 193 reads from 3 samples will be used for learning the error rates. Sample 1 - 58 reads in 17 unique sequences. Sample 2 - 67 reads in 21 unique sequences. Sample 3 - 68 reads in 18 unique sequences. Identified 0 bimeras out of 1 input sequences. Calling variants for rogdi 46710 total bases in 173 reads from 3 samples will be used for learning the error rates. Sample 1 - 55 reads in 13 unique sequences. Sample 2 - 60 reads in 22 unique sequences. Sample 3 - 58 reads in 24 unique sequences. Identified 0 bimeras out of 1 input sequences. A total of 1 locus/loci have/has been detected in file(s) with the pattern '_F_filt.fastq.gz' in the path '/srv/hornik/tmp/CRAN_pretest/tidyGenR.Rcheck/tidyGenR/extdata/truncated': chrna9 Trying to call variants in single end mode. Calling variants for chrna9 39690 total bases in 147 reads from 3 samples will be used for learning the error rates. Sample 1 - 49 reads in 15 unique sequences. Sample 2 - 43 reads in 10 unique sequences. Sample 3 - 55 reads in 19 unique sequences. Identified 0 bimeras out of 2 input sequences. A total of 1 locus/loci have/has been detected in file(s) with the pattern '_F_filt.fastq.gz' in the path '/srv/hornik/tmp/CRAN_pretest/tidyGenR.Rcheck/tidyGenR/extdata/truncated': rogdi Trying to call variants in single end mode. Calling variants for rogdi 46710 total bases in 173 reads from 3 samples will be used for learning the error rates. Sample 1 - 55 reads in 13 unique sequences. Sample 2 - 60 reads in 22 unique sequences. Sample 3 - 58 reads in 24 unique sequences. Identified 0 bimeras out of 1 input sequences. A total of 1 locus/loci have/has been detected in file(s) with the pattern '_F_filt.fastq.gz' in the path '/srv/hornik/tmp/CRAN_pretest/tidyGenR.Rcheck/tidyGenR/extdata/truncated': rogdi Trying to call variants in paired-end mode. Calling variants for rogdi 46710 total bases in 173 reads from 3 samples will be used for learning the error rates. Sample 1 - 55 reads in 13 unique sequences. Sample 2 - 60 reads in 22 unique sequences. Sample 3 - 58 reads in 24 unique sequences. All F/R file names match. Files with F/R reads: BOR1061_rogdi, BOR1063_rogdi, BOR1069_rogdi 31140 total bases in 173 reads from 3 samples will be used for learning the error rates. Sample 1 - 55 reads in 19 unique sequences. Sample 2 - 60 reads in 18 unique sequences. Sample 3 - 58 reads in 14 unique sequences. F and R reads found. Merging reads: 55 paired-reads (in 1 unique pairings) successfully merged out of 55 (in 1 pairings) input. 60 paired-reads (in 1 unique pairings) successfully merged out of 60 (in 1 pairings) input. 58 paired-reads (in 1 unique pairings) successfully merged out of 58 (in 1 pairings) input. All samples have overlapping F/R reads that have been merged successfully. Identified 0 bimeras out of 1 input sequences. A total of 1 locus/loci have/has been detected in file(s) with the pattern '_F_filt.fastq.gz' in the path '/srv/hornik/tmp/CRAN_pretest/tidyGenR.Rcheck/tidyGenR/extdata/truncated': chrna9 Trying to call variants in paired-end mode. Calling variants for chrna9 39690 total bases in 147 reads from 3 samples will be used for learning the error rates. Sample 1 - 49 reads in 15 unique sequences. Sample 2 - 43 reads in 10 unique sequences. Sample 3 - 55 reads in 19 unique sequences. All F/R file names match. Files with F/R reads: BOR1061_chrna9, BOR1063_chrna9, BOR1069_chrna9 26460 total bases in 147 reads from 3 samples will be used for learning the error rates. Sample 1 - 49 reads in 12 unique sequences. Sample 2 - 43 reads in 14 unique sequences. Sample 3 - 55 reads in 19 unique sequences. F and R reads found. Merging reads: 28 paired-reads (in 1 unique pairings) successfully merged out of 49 (in 2 pairings) input. 43 paired-reads (in 1 unique pairings) successfully merged out of 43 (in 1 pairings) input. 28 paired-reads (in 1 unique pairings) successfully merged out of 55 (in 2 pairings) input. All samples have overlapping F/R reads that have been merged successfully. Identified 0 bimeras out of 2 input sequences. A total of 1 locus/loci have/has been detected in file(s) with the pattern '_F_filt.fastq.gz' in the path '/srv/hornik/tmp/CRAN_pretest/tidyGenR.Rcheck/tidyGenR/extdata/truncated': chrna9 Trying to call variants in paired-end mode. Calling variants for chrna9 39690 total bases in 147 reads from 3 samples will be used for learning the error rates. Sample 1 - 49 reads in 15 unique sequences. Sample 2 - 43 reads in 10 unique sequences. Sample 3 - 55 reads in 19 unique sequences. All F/R file names match. Files with F/R reads: BOR1061_chrna9, BOR1063_chrna9, BOR1069_chrna9 26460 total bases in 147 reads from 3 samples will be used for learning the error rates. Sample 1 - 49 reads in 12 unique sequences. Sample 2 - 43 reads in 14 unique sequences. Sample 3 - 55 reads in 19 unique sequences. F and R reads found. Merging reads: 28 paired-reads (in 1 unique pairings) successfully merged out of 49 (in 2 pairings) input. 43 paired-reads (in 1 unique pairings) successfully merged out of 43 (in 1 pairings) input. 28 paired-reads (in 1 unique pairings) successfully merged out of 55 (in 2 pairings) input. All samples have overlapping F/R reads that have been merged successfully. Identified 0 bimeras out of 2 input sequences. A total of 1 locus/loci have/has been detected in file(s) with the pattern '_F_filt.fastq.gz' in the path '/srv/hornik/tmp/CRAN_pretest/tidyGenR.Rcheck/tidyGenR/extdata/truncated': chrna9 Trying to call variants in single end mode. Calling variants for chrna9 39690 total bases in 147 reads from 3 samples will be used for learning the error rates. Sample 1 - 49 reads in 15 unique sequences. Sample 2 - 43 reads in 10 unique sequences. Sample 3 - 55 reads in 19 unique sequences. Identified 0 bimeras out of 2 input sequences. A total of 1 locus/loci have/has been detected in file(s) with the pattern '_F_filt.fastq.gz' in the path '/srv/hornik/tmp/CRAN_pretest/tidyGenR.Rcheck/tidyGenR/extdata/truncated': chrna9 Trying to call variants in single end mode. Calling variants for chrna9 39690 total bases in 147 reads from 3 samples will be used for learning the error rates. Sample 1 - 49 reads in 15 unique sequences. Sample 2 - 43 reads in 10 unique sequences. Sample 3 - 55 reads in 19 unique sequences. Identified 0 bimeras out of 2 input sequences. A total of 1 locus/loci have/has been detected in file(s) with the pattern '_F_filt.fastq.gz' in the path '/srv/hornik/tmp/CRAN_pretest/tidyGenR.Rcheck/tidyGenR/extdata/truncated': chrna9 Trying to call variants in paired-end mode. Calling variants for chrna9 All F/R file names match. Files with F/R reads: BOR1061_chrna9, BOR1063_chrna9, BOR1069_chrna9 F and R reads found. Merging reads: 49 paired-reads (in 2 unique pairings) successfully merged out of 49 (in 2 pairings) input. 43 paired-reads (in 1 unique pairings) successfully merged out of 43 (in 1 pairings) input. 55 paired-reads (in 2 unique pairings) successfully merged out of 55 (in 2 pairings) input. All samples have overlapping F/R reads that have been merged successfully. Identified 0 bimeras out of 2 input sequences. A total of 1 locus/loci have/has been detected in file(s) with the pattern '_F_filt.fastq.gz' in the path '/srv/hornik/tmp/CRAN_pretest/tidyGenR.Rcheck/tidyGenR/extdata/truncated': chrna9 Trying to call variants in paired-end mode. Calling variants for chrna9 All F/R file names match. Files with F/R reads: BOR1061_chrna9, BOR1063_chrna9, BOR1069_chrna9 F and R reads found. Merging reads: 28 paired-reads (in 1 unique pairings) successfully merged out of 49 (in 2 pairings) input. 43 paired-reads (in 1 unique pairings) successfully merged out of 43 (in 1 pairings) input. 28 paired-reads (in 1 unique pairings) successfully merged out of 55 (in 2 pairings) input. All samples have overlapping F/R reads that have been merged successfully. Identified 0 bimeras out of 2 input sequences. 39690 total bases in 147 reads from 3 samples will be used for learning the error rates. Sample 1 - 49 reads in 15 unique sequences. Sample 2 - 43 reads in 10 unique sequences. Sample 3 - 55 reads in 19 unique sequences. 26460 total bases in 147 reads from 3 samples will be used for learning the error rates. Sample 1 - 49 reads in 12 unique sequences. Sample 2 - 43 reads in 14 unique sequences. Sample 3 - 55 reads in 19 unique sequences. 39690 total bases in 147 reads from 3 samples will be used for learning the error rates. Sample 1 - 49 reads in 15 unique sequences. Sample 2 - 43 reads in 10 unique sequences. Sample 3 - 55 reads in 19 unique sequences. 26460 total bases in 147 reads from 3 samples will be used for learning the error rates. Sample 1 - 49 reads in 12 unique sequences. Sample 2 - 43 reads in 14 unique sequences. Sample 3 - 55 reads in 19 unique sequences. 39690 total bases in 147 reads from 3 samples will be used for learning the error rates. Sample 1 - 49 reads in 15 unique sequences. Sample 2 - 43 reads in 10 unique sequences. Sample 3 - 55 reads in 19 unique sequences. 26460 total bases in 147 reads from 3 samples will be used for learning the error rates. Sample 1 - 49 reads in 12 unique sequences. Sample 2 - 43 reads in 14 unique sequences. Sample 3 - 55 reads in 19 unique sequences. A total of 1 locus/loci have/has been detected in file(s) with the pattern '_F_filt.fastq.gz' in the path '/srv/hornik/tmp/CRAN_pretest/tidyGenR.Rcheck/tidyGenR/extdata/truncated': chrna9 Trying to call variants in single end mode. Calling variants for chrna9 39690 total bases in 147 reads from 3 samples will be used for learning the error rates. Sample 1 - 49 reads in 15 unique sequences. Sample 2 - 43 reads in 10 unique sequences. Sample 3 - 55 reads in 19 unique sequences. Identified 0 bimeras out of 2 input sequences. A total of 1 locus/loci have/has been detected in file(s) with the pattern '_F_filt.fastq.gz' in the path '/srv/hornik/tmp/CRAN_pretest/tidyGenR.Rcheck/tidyGenR/extdata/truncated': chrna9 Trying to call variants in single end mode. Calling variants for chrna9 39690 total bases in 147 reads from 3 samples will be used for learning the error rates. Sample 1 - 49 reads in 15 unique sequences. Sample 2 - 43 reads in 10 unique sequences. Sample 3 - 55 reads in 19 unique sequences. Identified 0 bimeras out of 2 input sequences. A total of 1 locus/loci have/has been detected in file(s) with the pattern '_F_filt.fastq.gz' in the path '/srv/hornik/tmp/CRAN_pretest/tidyGenR.Rcheck/tidyGenR/extdata/truncated': chrna9 Trying to call variants in paired-end mode. Calling variants for chrna9 39690 total bases in 147 reads from 3 samples will be used for learning the error rates. Sample 1 - 49 reads in 15 unique sequences. Sample 2 - 43 reads in 10 unique sequences. Sample 3 - 55 reads in 19 unique sequences. All F/R file names match. Files with F/R reads: BOR1061_chrna9, BOR1063_chrna9, BOR1069_chrna9 26460 total bases in 147 reads from 3 samples will be used for learning the error rates. Sample 1 - 49 reads in 12 unique sequences. Sample 2 - 43 reads in 14 unique sequences. Sample 3 - 55 reads in 19 unique sequences. F and R reads found. Merging reads: 49 paired-reads (in 2 unique pairings) successfully merged out of 49 (in 2 pairings) input. 43 paired-reads (in 1 unique pairings) successfully merged out of 43 (in 1 pairings) input. 55 paired-reads (in 2 unique pairings) successfully merged out of 55 (in 2 pairings) input. All samples have overlapping F/R reads that have been merged successfully. Identified 0 bimeras out of 2 input sequences. A total of 1 locus/loci have/has been detected in file(s) with the pattern '_F_filt.fastq.gz' in the path '/srv/hornik/tmp/CRAN_pretest/tidyGenR.Rcheck/tidyGenR/extdata/truncated': chrna9 Trying to call variants in paired-end mode. Calling variants for chrna9 39690 total bases in 147 reads from 3 samples will be used for learning the error rates. Sample 1 - 49 reads in 15 unique sequences. Sample 2 - 43 reads in 10 unique sequences. Sample 3 - 55 reads in 19 unique sequences. All F/R file names match. Files with F/R reads: BOR1061_chrna9, BOR1063_chrna9, BOR1069_chrna9 26460 total bases in 147 reads from 3 samples will be used for learning the error rates. Sample 1 - 49 reads in 12 unique sequences. Sample 2 - 43 reads in 14 unique sequences. Sample 3 - 55 reads in 19 unique sequences. F and R reads found. Merging reads: 28 paired-reads (in 1 unique pairings) successfully merged out of 49 (in 2 pairings) input. 43 paired-reads (in 1 unique pairings) successfully merged out of 43 (in 1 pairings) input. 28 paired-reads (in 1 unique pairings) successfully merged out of 55 (in 2 pairings) input. All samples have overlapping F/R reads that have been merged successfully. Identified 0 bimeras out of 2 input sequences. Determining distance matrix based on shared 8-mers: ================================================================================ Time difference of 0 secs Clustering into groups by similarity: ================================================================================ Time difference of 0 secs Aligning Sequences: ================================================================================ Time difference of 0.04 secs Iteration 1 of 2: Determining distance matrix based on alignment: ================================================================================ Time difference of 0 secs Reclustering into groups by similarity: ================================================================================ Time difference of 0 secs Realigning Sequences: ================================================================================ Time difference of 0 secs Alignment converged - skipping remaining iteration. Refining the alignment: ================================================================================ Time difference of 0.06 secs [ FAIL 1 | WARN 729 | SKIP 2 | PASS 144 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • On CRAN (2): 'test-gen_format_conversion.R:45:1', 'test-gen_format_conversion.R:61:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-out_popart.R:10:5'): popart nex is well formed ───────────────── Error in `vroom::vroom_write(x, file, delim = delim, col_names = col_names, append = append, na = na, eol = eol, quote = quote, escape = escape, num_threads = num_threads, progress = progress)`: `quote` must be a character vector, not `NULL`. Backtrace: ▆ 1. └─tidyGenR::out_popart(...) at test-out_popart.R:10:5 2. └─tidyGenR (local) ftraits() 3. ├─utils::capture.output(...) 4. │ └─base::withVisible(...elt(i)) 5. └─readr::write_delim(...) 6. └─vroom::vroom_write(quote = quote) 7. └─rlang::arg_match(quote) 8. └─rlang:::check_character(arg, arg = error_arg, call = error_call) 9. └─rlang:::stop_input_type(...) 10. └─rlang::abort(message, ..., call = call, arg = arg) [ FAIL 1 | WARN 729 | SKIP 2 | PASS 144 ] Deleting unused snapshots: 'out_popart/popart_test_nex' Error: ! Test failures. Warning message: In for (i in seq_len(n)) { : closing unused connection 4 (/tmp/RtmpYVRaDQ/working_dir/RtmpXhKO85/test_popart.nex) Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [24s/25s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘abcg8.nex’ ‘dataset1.txt’ ‘demultiplex.sh’ ‘genotypes.str’ * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 2 NOTEs