larssnip
commented
4 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)){
- 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
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itsvetkova
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