R Error In Scan File
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Error In Read.table Duplicate 'row.names' Are Not Allowed
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In Scan(file = File, What = What, Sep = Sep, Quote = Quote, Dec = Dec, : Eof Within Quoted String
a minute: Sign up Confusing error in R: Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 42 elements) [duplicate] up vote 19 down vote favorite 10 This question already has an answer here: Error in reading in data set in R 5 answers I am new to R. I am trying to r fill = true read in a "CSV" file that is space-space delimited. The file does not have headers. It looks like this Element1 Element2 Element5 Element6 Element7 I am trying to read it in like this: > mydata <- read.table("/PathTo/file.csv") Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 14 elements Why does it expect 14 elements in the first row? How do I import this file? r share|improve this question asked Oct 18 '13 at 16:55 bernie2436 3,9551866145 marked as duplicate by Frank, rcs, liyakat, Jilber, Dour High Arch Oct 19 '13 at 16:28 This question has been asked before and already has an answer. If those answers do not fully address your question, please ask a new question. @SimonO101 if you put that as an answer I will accept –bernie2436 Oct 18 '13 at 17:19 Your data is not in the table format, why use read.table? –Fernando Oct 18 '13 at 17:20 add a comment| 2 Answers 2 active oldest votes up vote 39 down vote accepted read.table wants to re
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R Read Table Fill
workings and policies of this site About Us Learn more about Stack Overflow the company read table fill true Business Learn more about hiring developers or posting ads with us Stack Overflow Questions Jobs Documentation Tags Users Badges Ask Question x Dismiss Join the http://stackoverflow.com/questions/19455070/confusing-error-in-r-error-in-scanfile-what-nmax-sep-dec-quote-skip-nli Stack Overflow Community Stack Overflow is a community of 6.2 million programmers, just like you, helping each other. Join them; it only takes a minute: Sign up Reading in .csv file to R. Error in Scan up vote 0 down vote favorite Reading in a .csv file, but got the http://stackoverflow.com/questions/20226437/reading-in-csv-file-to-r-error-in-scan following error: Books <- read.table(file.choose(),header=TRUE,sep=";") Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 21688 did not have 3 elements .csv file name BX-Book-Ratings.csv Original - 1 column and 1048576 rows Shown - 1 column and 10 rows User-ID;"ISBN";"Book-Rating" 276725;"034545104X";"0" 276726;"0155061224";"5" 276727;"0446520802";"0" 276729;"052165615X";"3" 276729;"0521795028";"6" 276733;"2080674722";"0" 276736;"3257224281";"8" 276737;"0600570967";"6" 276744;"038550120X";"7" Area with the error - rows 21687:21694 4376;"0345378490";"0" 4376;"38208715X";"5" 4377;"\"0210000010";"8" 4385;"0061042331";"0" 4385;"0061083402";"10" 4385;"0061083577";"0" 4385;"0061093343";"9" 4385;"0061096156";"10" Please let me know if I can provide additional information. Thank you. r csv share|improve this question edited Nov 27 '13 at 20:56 asked Nov 26 '13 at 19:41 Scott Davis 316624 7 What happens on row 21688? –Justin Nov 26 '13 at 19:46 3 So what's preventing you from opening the file in a text editor and going to line 21688 (or near there)? –joran Nov 26 '13 at 19:46 2 Better to see what ha
using R and the shell: a casestudy Once in a while, you embark on what looks like a simple computational procedure only to encounter frustration very early on. "I can't even read my file into R!" you cry. Step back, take a deep breath and take note of what the software is https://nsaunders.wordpress.com/2011/04/08/fixing-aberrant-files-using-r-and-the-shell/ trying to tell you. Most times, you've just missed something very straightforward. Here's an example. Update: this post is not about how best to perform the task; it's about how to cope with frustration. Please stop sending me your solutions :-) Recently, I was trying to retrieve some data describing characteristics of microbial genomes from the NCBI FTP site. The file, lproks_0.txt (direct link), looked like a regular tab-delimited file with a couple of header lines: error in head lproks_0.txt ## Microbial Organism Information Page ## Columns: "RefSeq project ID" "Project ID" "Taxonomy ID" "Organism Name" "Super Kingdom" "Group" "Sequence Status" "Genome Size" "GC Content" "Gram Stain" "Shape" "Arrangment" "Endospores" "Motility" "Salinity" "Oxygen Req" "Habitat" "Temp. range" "Optimal temp." "Pathogenic in" "Disease" "Genbank accessions" "Refseq accessions" 49725 30807 551115 'Nostoc azollae' 0708 Bacteria Cyanobacteria complete 5.532 38.3 Filaments Filaments Yes Aerobic Multiple Mesophilic - CP002059,CP002060,CP002061 - 55729 33011 592010 Abiotrophia defectiva ATCC 49176 Bacteria Firmicutes : eof within assembly 3.4774 37.1 + Cocci NoNo Facultative - ACIN00000000 - Sharp eyes will notice a problem right there, on the first line of data. Less sharp-eyed users like me will open an R console to read the file, expecting no issues: genomes <- read.table("lproks_0.txt", header = F, skip = 2, stringsAsFactors = F, sep = "\t") Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 376 did not have 23 elements
"I can't even read my file into R!" My first mistake: reach for the tool that I know best, not the tool which is appropriate. In this case, my instinct was to count the fields in a line using awk. Since we skipped the first 2 lines in R, we want to examine line 378 in the original file: awk '{FS="\t"; print NF}' lproks_0.txt | head -n 378 | nl | tail -n1 378 23 Sure looks like line 378 has 23 elements to me. Replacing "NF" with "$0", we can examine the line content: awk '{FS="\t"; print $0}' lproks_0.txt | head -n 378 tail -n1 49969 40633 376219 Arthrospira sp. PCC 8005 Bacteria Cyanobacteria unfinished 6.14555 44.7 Spiral Yes Facultative Aquatic Mesophilic - - - Looks fine. What is the problem? As it happens, R comes with several useful functions to examine the structure of files. One of these is c