Closed itsvetkova closed 3 years ago
Hi,
The error message says argument compress = “auto” is not valid for fwrite. This makes no sense, as this is indeed a valid argument, at least for the versions I have. Try to write just
?fwrite
In the console, and see if the Help-file for fwrite from data.table pops up. Please copy the text under Usage and send me.
You may try to update all packages. If you use RStudio, there is an update-button on the Packages window. This is always a good idea anyway,,,
LS
From: itsvetkova notifications@github.com Sent: tirsdag 4. august 2020 21:34 To: larssnip/micropan micropan@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [larssnip/micropan] unused argument (compress = "auto") (#7)
Hi! I encounter a problem at the stage of writing files with translated sequences. I'm not a very experienced R user. Please, help to find a solution to this problem. Here's the code:
R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit)
setwd("/home/biouser/Documents/Tsvetkova/rworkdir/invasive_pangenome") library(microseq) library(micropan) library(R.utils) library(ggdendro) library(tibble) library(dplyr) library(readr) library(Rcpp) library(data.table) library(igraph) library(rlang) library(tidyverse) ── Attaching packages ─────────────────────────────────────── tidyverse 1.2.1 ── ✔ ggplot2 3.3.2 ✔ readr 1.3.1 ✔ tidyr 1.1.1 ✔ purrr 0.3.2 ✔ ggplot2 3.3.2 ✔ forcats 0.4.0 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ rlang:::=() masks data.table:::=() ✖ purrr::%@%() masks rlang::%@%() ✖ igraph::as_data_frame() masks dplyr::as_data_frame(), tibble::as_data_frame() ✖ purrr::as_function() masks rlang::as_function() ✖ data.table::between() masks dplyr::between() ✖ purrr::compose() masks igraph::compose() ✖ tidyr::crossing() masks igraph::crossing() ✖ dplyr::filter() masks stats::filter() ✖ data.table::first() masks dplyr::first() ✖ purrr::flatten() masks rlang::flatten() ✖ purrr::flatten_chr() masks rlang::flatten_chr() ✖ purrr::flatten_dbl() masks rlang::flatten_dbl() ✖ purrr::flatten_int() masks rlang::flatten_int() ✖ purrr::flatten_lgl() masks rlang::flatten_lgl() ✖ purrr::flatten_raw() masks rlang::flatten_raw() ✖ igraph::groups() masks dplyr::groups() ✖ purrr::invoke() masks rlang::invoke() ✖ igraph::is_named() masks rlang::is_named() ✖ dplyr::lag() masks stats::lag() ✖ data.table::last() masks dplyr::last() ✖ purrr::list_along() masks rlang::list_along() ✖ purrr::modify() masks rlang::modify() ✖ purrr::prepend() masks rlang::prepend() ✖ purrr::simplify() masks igraph::simplify() ✖ purrr::splice() masks rlang::splice() ✖ purrr::transpose() masks data.table::transpose()
options(stringsAsFactors=FALSE) gnm.tbl <- read.table("/home/biouser/Documents/Tsvetkova/rworkdir/invasive_pangenome/Samples_for_pangenome_table.txt", sep=",", header=TRUE) dir.create("tmp_new") set.seed(2020) for(i in 1:nrow(gnm.tbl)){
· filter(Score > 40) %>%
·
*
· gff2fasta(genome) %>%
·
*
· mutate(Sequence = translate(Sequence)) %>%
·
*
· writeFasta(file.path("tmp_new", str_c(gnm.tbl$Name[i], ".faa")))
·
*
Error in fwrite(tibble(unlist(lst)), file = out.file, compress = "auto", : unused argument (compress = "auto")
Samples_for_pangenome_table.txthttps://github.com/larssnip/micropan/files/5024101/Samples_for_pangenome_table.txt
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/larssnip/micropan/issues/7, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADJZZFWHLZASPCNCK3EC2J3R7BPCDANCNFSM4PUXJYRQ.
Hi, The error message says argument compress = “auto” is not valid for fwrite. This makes no sense, as this is indeed a valid argument, at least for the versions I have. Try to write just ?fwrite In the console, and see if the Help-file for fwrite from data.table pops up. Please copy the text under Usage and send me. You may try to update all packages. If you use RStudio, there is an update-button on the Packages window. This is always a good idea anyway,,, LS From: itsvetkova notifications@github.com Sent: tirsdag 4. august 2020 21:34 To: larssnip/micropan micropan@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [larssnip/micropan] unused argument (compress = "auto") (#7) Hi! I encounter a problem at the stage of writing files with translated sequences. I'm not a very experienced R user. Please, help to find a solution to this problem. Here's the code: R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) setwd("/home/biouser/Documents/Tsvetkova/rworkdir/invasive_pangenome") library(microseq) library(micropan) library(R.utils) library(ggdendro) library(tibble) library(dplyr) library(readr) library(Rcpp) library(data.table) library(igraph) library(rlang) library(tidyverse) ── Attaching packages ─────────────────────────────────────── tidyverse 1.2.1 ── heavy_check_mark ggplot2 3.3.2 heavy_check_mark readr 1.3.1 heavy_check_mark tidyr 1.1.1 heavy_check_mark purrr 0.3.2 heavy_check_mark ggplot2 3.3.2 heavy_check_mark forcats 0.4.0 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── heavy_multiplication_x rlang:::=() masks data.table:::=() heavy_multiplication_x purrr::%@%() masks rlang::%@%() heavy_multiplication_x igraph::as_data_frame() masks dplyr::as_data_frame(), tibble::as_data_frame() heavy_multiplication_x purrr::as_function() masks rlang::as_function() heavy_multiplication_x data.table::between() masks dplyr::between() heavy_multiplication_x purrr::compose() masks igraph::compose() heavy_multiplication_x tidyr::crossing() masks igraph::crossing() heavy_multiplication_x dplyr::filter() masks stats::filter() heavy_multiplication_x data.table::first() masks dplyr::first() heavy_multiplication_x purrr::flatten() masks rlang::flatten() heavy_multiplication_x purrr::flatten_chr() masks rlang::flatten_chr() heavy_multiplication_x purrr::flatten_dbl() masks rlang::flatten_dbl() heavy_multiplication_x purrr::flatten_int() masks rlang::flatten_int() heavy_multiplication_x purrr::flatten_lgl() masks rlang::flatten_lgl() heavy_multiplication_x purrr::flatten_raw() masks rlang::flatten_raw() heavy_multiplication_x igraph::groups() masks dplyr::groups() heavy_multiplication_x purrr::invoke() masks rlang::invoke() heavy_multiplication_x igraph::is_named() masks rlang::is_named() heavy_multiplication_x dplyr::lag() masks stats::lag() heavy_multiplication_x data.table::last() masks dplyr::last() heavy_multiplication_x purrr::list_along() masks rlang::list_along() heavy_multiplication_x purrr::modify() masks rlang::modify() heavy_multiplication_x purrr::prepend() masks rlang::prepend() heavy_multiplication_x purrr::simplify() masks igraph::simplify() heavy_multiplication_x purrr::splice() masks rlang::splice() heavy_multiplication_x purrr::transpose() masks data.table::transpose() options(stringsAsFactors=FALSE) gnm.tbl <- read.table("/home/biouser/Documents/Tsvetkova/rworkdir/invasive_pangenome/Samples_for_pangenome_table.txt", sep=",", header=TRUE) dir.create("tmp_new") set.seed(2020) for(i in 1:nrow(gnm.tbl)){ genome <- readFasta(file.path("genomes", str_c(gnm.tbl$Name[i], ".fa"))) findGenes(file.path("genomes", str_c(gnm.tbl$Name[i], ".fa"))) %>% · filter(Score > 40) %>% · · gff2fasta(genome) %>% · · mutate(Sequence = translate(Sequence)) %>% · · writeFasta(file.path("tmp_new", str_c(gnm.tbl$Name[i], ".faa"))) · * } Error in fwrite(tibble(unlist(lst)), file = out.file, compress = "auto", : unused argument (compress = "auto") Samples_for_pangenome_table.txthttps://github.com/larssnip/micropan/files/5024101/Samples_for_pangenome_table.txt — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#7>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADJZZFWHLZASPCNCK3EC2J3R7BPCDANCNFSM4PUXJYRQ.
Hi, Lars, Thank you for answer. Here's the text under Usage of fwrite in the console's popup:
fwrite(x, file = "", append = FALSE, quote = "auto", sep = ",", sep2 = c("","|",""), eol = if (.Platform$OS.type=="windows") "\r\n" else "\n", na = "", dec = ".", row.names = FALSE, col.names = TRUE, qmethod = c("double","escape"), logical01 = getOption("datatable.logical01", FALSE), # due to change to TRUE; see NEWS logicalAsInt = logical01, # deprecated dateTimeAs = c("ISO","squash","epoch","write.csv"), buffMB = 8L, nThread = getDTthreads(verbose), showProgress = getOption("datatable.showProgress", interactive()), verbose = getOption("datatable.verbose", FALSE))
I will try to update all packages today. Regards, Irina Tsvetkova
OK, it looks like compress is not an argument to this version of fwrite. Install the data.table package again, and I guess it all works.
LS
From: itsvetkova notifications@github.com Sent: onsdag 5. august 2020 12:01 To: larssnip/micropan micropan@noreply.github.com Cc: Lars-Gustav Snipen lars.snipen@nmbu.no; Comment comment@noreply.github.com Subject: Re: [larssnip/micropan] unused argument (compress = "auto") (#7)
Hi, The error message says argument compress = “auto” is not valid for fwrite. This makes no sense, as this is indeed a valid argument, at least for the versions I have. Try to write just ?fwrite In the console, and see if the Help-file for fwrite from data.table pops up. Please copy the text under Usage and send me. You may try to update all packages. If you use RStudio, there is an update-button on the Packages window. This is always a good idea anyway,,, LS From: itsvetkova notifications@github.commailto:notifications@github.com Sent: tirsdag 4. august 2020 21:34 To: larssnip/micropan micropan@noreply.github.commailto:micropan@noreply.github.com Cc: Subscribed subscribed@noreply.github.commailto:subscribed@noreply.github.com Subject: [larssnip/micropan] unused argument (compress = "auto") (#7https://github.com/larssnip/micropan/issues/7) Hi! I encounter a problem at the stage of writing files with translated sequences. I'm not a very experienced R user. Please, help to find a solution to this problem. Here's the code: R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) setwd("/home/biouser/Documents/Tsvetkova/rworkdir/invasive_pangenome") library(microseq) library(micropan) library(R.utils) library(ggdendro) library(tibble) library(dplyr) library(readr) library(Rcpp) library(data.table) library(igraph) library(rlang) library(tidyverse) ── Attaching packages ─────────────────────────────────────── tidyverse 1.2.1 ── heavy_check_mark ggplot2 3.3.2 heavy_check_mark readr 1.3.1 heavy_check_mark tidyr 1.1.1 heavy_check_mark purrr 0.3.2 heavy_check_mark ggplot2 3.3.2 heavy_check_mark forcats 0.4.0 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── heavy_multiplication_x rlang:::=() masks data.table:::=() heavy_multiplication_x purrr::%@%() masks rlang::%@%() heavy_multiplication_x igraph::as_data_frame() masks dplyr::as_data_frame(), tibble::as_data_frame() heavy_multiplication_x purrr::as_function() masks rlang::as_function() heavy_multiplication_x data.table::between() masks dplyr::between() heavy_multiplication_x purrr::compose() masks igraph::compose() heavy_multiplication_x tidyr::crossing() masks igraph::crossing() heavy_multiplication_x dplyr::filter() masks stats::filter() heavy_multiplication_x data.table::first() masks dplyr::first() heavy_multiplication_x purrr::flatten() masks rlang::flatten() heavy_multiplication_x purrr::flatten_chr() masks rlang::flatten_chr() heavy_multiplication_x purrr::flatten_dbl() masks rlang::flatten_dbl() heavy_multiplication_x purrr::flatten_int() masks rlang::flatten_int() heavy_multiplication_x purrr::flatten_lgl() masks rlang::flatten_lgl() heavy_multiplication_x purrr::flatten_raw() masks rlang::flatten_raw() heavy_multiplication_x igraph::groups() masks dplyr::groups() heavy_multiplication_x purrr::invoke() masks rlang::invoke() heavy_multiplication_x igraph::is_named() masks rlang::is_named() heavy_multiplication_x dplyr::lag() masks stats::lag() heavy_multiplication_x data.table::last() masks dplyr::last() heavy_multiplication_x purrr::list_along() masks rlang::list_along() heavy_multiplication_x purrr::modify() masks rlang::modify() heavy_multiplication_x purrr::prepend() masks rlang::prepend() heavy_multiplication_x purrr::simplify() masks igraph::simplify() heavy_multiplication_x purrr::splice() masks rlang::splice() heavy_multiplication_x purrr::transpose() masks data.table::transpose() options(stringsAsFactors=FALSE) gnm.tbl <- read.table("/home/biouser/Documents/Tsvetkova/rworkdir/invasive_pangenome/Samples_for_pangenome_table.txt", sep=",", header=TRUE) dir.create("tmp_new") set.seed(2020) for(i in 1:nrow(gnm.tbl)){ genome <- readFasta(file.path("genomes", str_c(gnm.tbl$Name[i], ".fa"))) findGenes(file.path("genomes", str_c(gnm.tbl$Name[i], ".fa"))) %>% · filter(Score > 40) %>% · · gff2fasta(genome) %>% · · mutate(Sequence = translate(Sequence)) %>% · · writeFasta(file.path("tmp_new", str_c(gnm.tbl$Name[i], ".faa"))) · * } Error in fwrite(tibble(unlist(lst)), file = out.file, compress = "auto", : unused argument (compress = "auto") Samples_for_pangenome_table.txthttps://github.com/larssnip/micropan/files/5024101/Samples_for_pangenome_table.txt — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#7https://github.com/larssnip/micropan/issues/7>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADJZZFWHLZASPCNCK3EC2J3R7BPCDANCNFSM4PUXJYRQ.
Hi, Lars, Thank you for answer. Here's the text under Usage of fwrite in the console's popup:
fwrite(x, file = "", append = FALSE, quote = "auto", sep = ",", sep2 = c("","|",""), eol = if (.Platform$OS.type=="windows") "\r\n" else "\n", na = "", dec = ".", row.names = FALSE, col.names = TRUE, qmethod = c("double","escape"), logical01 = getOption("datatable.logical01", FALSE), # due to change to TRUE; see NEWS logicalAsInt = logical01, # deprecated dateTimeAs = c("ISO","squash","epoch","write.csv"), buffMB = 8L, nThread = getDTthreads(verbose), showProgress = getOption("datatable.showProgress", interactive()), verbose = getOption("datatable.verbose", FALSE))
I will try to update all packages today. Regards, Irina Tsvetkova
— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/larssnip/micropan/issues/7#issuecomment-669102455, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADJZZFR76IH4ZY5UAW3SYRDR7EUT5ANCNFSM4PUXJYRQ.
OK, it looks like compress is not an argument to this version of fwrite. Install the data.table package again, and I guess it all works. LS From: itsvetkova notifications@github.com Sent: onsdag 5. august 2020 12:01 To: larssnip/micropan micropan@noreply.github.com Cc: Lars-Gustav Snipen lars.snipen@nmbu.no; Comment comment@noreply.github.com Subject: Re: [larssnip/micropan] unused argument (compress = "auto") (#7) Hi, The error message says argument compress = “auto” is not valid for fwrite. This makes no sense, as this is indeed a valid argument, at least for the versions I have. Try to write just ?fwrite In the console, and see if the Help-file for fwrite from data.table pops up. Please copy the text under Usage and send me. You may try to update all packages. If you use RStudio, there is an update-button on the Packages window. This is always a good idea anyway,,, LS From: itsvetkova notifications@github.commailto:notifications@github.com Sent: tirsdag 4. august 2020 21:34 To: larssnip/micropan micropan@noreply.github.commailto:micropan@noreply.github.com Cc: Subscribed subscribed@noreply.github.commailto:subscribed@noreply.github.com Subject: [larssnip/micropan] unused argument (compress = "auto") (#7<#7>) Hi! I encounter a problem at the stage of writing files with translated sequences. I'm not a very experienced R user. Please, help to find a solution to this problem. Here's the code: R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) setwd("/home/biouser/Documents/Tsvetkova/rworkdir/invasive_pangenome") library(microseq) library(micropan) library(R.utils) library(ggdendro) library(tibble) library(dplyr) library(readr) library(Rcpp) library(data.table) library(igraph) library(rlang) library(tidyverse) ── Attaching packages ─────────────────────────────────────── tidyverse 1.2.1 ── heavy_check_mark ggplot2 3.3.2 heavy_check_mark readr 1.3.1 heavy_check_mark tidyr 1.1.1 heavy_check_mark purrr 0.3.2 heavy_check_mark ggplot2 3.3.2 heavy_check_mark forcats 0.4.0 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── heavy_multiplication_x rlang:::=() masks data.table:::=() heavy_multiplication_x purrr::%@%() masks rlang::%@%() heavy_multiplication_x igraph::as_data_frame() masks dplyr::as_data_frame(), tibble::as_data_frame() heavy_multiplication_x purrr::as_function() masks rlang::as_function() heavy_multiplication_x data.table::between() masks dplyr::between() heavy_multiplication_x purrr::compose() masks igraph::compose() heavy_multiplication_x tidyr::crossing() masks igraph::crossing() heavy_multiplication_x dplyr::filter() masks stats::filter() heavy_multiplication_x data.table::first() masks dplyr::first() heavy_multiplication_x purrr::flatten() masks rlang::flatten() heavy_multiplication_x purrr::flatten_chr() masks rlang::flatten_chr() heavy_multiplication_x purrr::flatten_dbl() masks rlang::flatten_dbl() heavy_multiplication_x purrr::flatten_int() masks rlang::flatten_int() heavy_multiplication_x purrr::flatten_lgl() masks rlang::flatten_lgl() heavy_multiplication_x purrr::flatten_raw() masks rlang::flatten_raw() heavy_multiplication_x igraph::groups() masks dplyr::groups() heavy_multiplication_x purrr::invoke() masks rlang::invoke() heavy_multiplication_x igraph::is_named() masks rlang::is_named() heavy_multiplication_x dplyr::lag() masks stats::lag() heavy_multiplication_x data.table::last() masks dplyr::last() heavy_multiplication_x purrr::list_along() masks rlang::list_along() heavy_multiplication_x purrr::modify() masks rlang::modify() heavy_multiplication_x purrr::prepend() masks rlang::prepend() heavy_multiplication_x purrr::simplify() masks igraph::simplify() heavy_multiplication_x purrr::splice() masks rlang::splice() heavy_multiplication_x purrr::transpose() masks data.table::transpose() options(stringsAsFactors=FALSE) gnm.tbl <- read.table("/home/biouser/Documents/Tsvetkova/rworkdir/invasive_pangenome/Samples_for_pangenome_table.txt", sep=",", header=TRUE) dir.create("tmp_new") set.seed(2020) for(i in 1:nrow(gnm.tbl)){ genome <- readFasta(file.path("genomes", str_c(gnm.tbl$Name[i], ".fa"))) findGenes(file.path("genomes", str_c(gnm.tbl$Name[i], ".fa"))) %>% · filter(Score > 40) %>% · · gff2fasta(genome) %>% · · mutate(Sequence = translate(Sequence)) %>% · · writeFasta(file.path("tmp_new", str_c(gnm.tbl$Name[i], ".faa"))) · * } Error in fwrite(tibble(unlist(lst)), file = out.file, compress = "auto", : unused argument (compress = "auto") Samples_for_pangenome_table.txthttps://github.com/larssnip/micropan/files/5024101/Samples_for_pangenome_table.txt — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#7<#7>>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADJZZFWHLZASPCNCK3EC2J3R7BPCDANCNFSM4PUXJYRQ. Hi, Lars, Thank you for answer. Here's the text under Usage of fwrite in the console's popup: fwrite(x, file = "", append = FALSE, quote = "auto", sep = ",", sep2 = c("","|",""), eol = if (.Platform$OS.type=="windows") "\r\n" else "\n", na = "", dec = ".", row.names = FALSE, col.names = TRUE, qmethod = c("double","escape"), logical01 = getOption("datatable.logical01", FALSE), # due to change to TRUE; see NEWS logicalAsInt = logical01, # deprecated dateTimeAs = c("ISO","squash","epoch","write.csv"), buffMB = 8L, nThread = getDTthreads(verbose), showProgress = getOption("datatable.showProgress", interactive()), verbose = getOption("datatable.verbose", FALSE)) I will try to update all packages today. Regards, Irina Tsvetkova — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#7 (comment)>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADJZZFR76IH4ZY5UAW3SYRDR7EUT5ANCNFSM4PUXJYRQ.
Hi Lars,
I've detected and upgraded (as a root user) the versions of all package's with the commands: pkgs <- as.data.frame(installed.packages(), stringsAsFactors = FALSE, row.names = FALSE) pkgs[, c("Package", "Version", "Built")] update.packages(ask = FALSE, checkBuilt = TRUE)
It did not completely help fix conflicts:
library(tidyverse) ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ── ✔ ggplot2 3.3.2 ✔ purrr 0.3.4 ✔ tibble 3.0.3 ✔ dplyr 1.0.1 ✔ tidyr 1.1.1 ✔ stringr 1.4.0 ✔ readr 1.3.1 ✔ forcats 0.5.0 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::between() masks data.table::between() ✖ dplyr::filter() masks stats::filter() ✖ dplyr::first() masks data.table::first() ✖ dplyr::lag() masks stats::lag() ✖ dplyr::last() masks data.table::last() ✖ purrr::transpose() masks data.table::transpose() But upgrading the data.table package to v 1.13.0 has helped:
fwrite(x, file = "", append = FALSE, quote = "auto", sep = ",", sep2 = c("","|",""), eol = if (.Platform$OS.type=="windows") "\r\n" else "\n", na = "", dec = ".", row.names = FALSE, col.names = TRUE, qmethod = c("double","escape"), logical01 = getOption("datatable.logical01", FALSE), # due to change to TRUE; see NEWS logicalAsInt = logical01, # deprecated scipen = getOption('scipen', 0L), dateTimeAs = c("ISO","squash","epoch","write.csv"), buffMB = 8L, nThread = getDTthreads(verbose), showProgress = getOption("datatable.showProgress", interactive()), compress = c("auto", "none", "gzip"), yaml = FALSE, bom = FALSE, verbose = getOption("datatable.verbose", FALSE))
The code for extracting genes and writing protein sequences works. Thank you!
Regards, Irina Tsvetkova
Hi! I encounter a problem at the stage of writing files with translated sequences. I'm not a very experienced R user. Please, help to find a solution to this problem. Here's the code:
R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit)
Error in fwrite(tibble(unlist(lst)), file = out.file, compress = "auto", : unused argument (compress = "auto")
Samples_for_pangenome_table.txt