read csv warning EOF within quoted string prevents complete reading of file

Question

I have a CSV file  24 1 MB  that I cannot fully read into my R session  When I open the file in a spreadsheet program I can see 112 544 rows  When I read it into R with read csv I only get 56 952 rows and this warning   cit  lt - read csv  citations CSV   row names   NULL                   comment char       header   TRUE                   stringsAsFactors   FALSE                    colClasses   character   encoding   utf-8    Warning message  In scan file  what  nmax  sep  dec  quote  skip  nlines  na strings       EOF within quoted string   I can read the whole file into R with readLines   rl  lt - readLines file  citations CSV   encoding    utf-8    length rl   1  112545   But I can t get this back into R as a table  via read csv    write table rl   rl txt   quote   FALSE  row names   FALSE  rl in  lt - read csv  rl txt   skip   1  row names   NULL   Warning message  In scan file  what  nmax  sep  dec  quote  skip  nlines  na strings       EOF within quoted string   How can I solve or workaround this EOF message  which seems to be more of an error than a warning  to get the entire file into my R session   I have similar problems with other methods of reading CSV files   require sqldf  cit sql  lt - read csv sql  citations CSV   sql    select   from file   require data table  cit dt  lt - fread  citations CSV   require ff  cit ff  lt - read csv ffdf file  citations CSV     Here s my sessionInfo    R version 3 0 1  2013-05-16  Platform  x86 64-w64-mingw32 x64  64-bit   locale   1  LC COLLATE English United States 1252  LC CTYPE English United States 1252     3  LC MONETARY English United States 1252 LC NUMERIC C                            5  LC TIME English United States 1252      attached base packages   1  tools     tcltk     stats     graphics  grDevices utils     datasets  methods   base       other attached packages    1  ff 2 2-11             bit 1 1-10            data table 1 8 8      sqldf 0 4-6 4           5  RSQLite extfuns 0 0 1 RSQLite 0 11 4        chron 2 3-43          gsubfn 0 6-5            9  proto 0 3-10          DBI 0 2-7

User · Answer

In the R help section  as pointed out above  just disabling quoting altogether  by simply adding       quote         to the read csv   worked for me    The error   EOF within quoted string   occurred with        gt  iproscan 53A neg       read csv  interproscan 53A neg n csv                                colClasses c pb id         character                                             genLoc        character                                             icode         character                                             length        character                                             proteinDB     character                                             protein id    character                                             prot desc     character                                             start         character                                             end           character                                             evalue        character                                             tchar         character                                             date          character                                             ipro id       character                                             prot name     character                                             go cat        character                                             reactome id   character                                              as is T header F      Warning message      In scan file  what  nmax  sep  dec  quote  skip  nlines  na strings           EOF within quoted string      gt  dim iproscan 53A neg       1  69383    16   And the file read in was missing 6 619 lines   But by disabling quoting       gt  iproscan 53A neg       read csv  interproscan 53A neg n csv                                colClasses c pb id         character                                             genLoc        character                                             icode         character                                             length        character                                             proteinDB     character                                             protein id    character                                             prot desc     character                                             start         character                                             end           character                                             evalue        character                                             tchar         character                                             date          character                                             ipro id       character                                             prot name     character                                             go cat        character                                             reactome id   character                                              as is T header F   quote                gt        gt  dim iproscan 53A neg       1  76002    16   Worked without error and all lines were successfully read in

User · Answer

I too had the similar problem  But in my case  the cause of the issue was due to the presence of apostrophes  i e  single quotation marks  within some of the text values  This is especially frequent when working with data including texts in French  e g    L autre jour     So  the solution was simply to adjust the default setting of the quote argument to exclude the       symbol  and thus  using quote         i e  double quotation mark only   everything worked fine   I hope that can help some of you  Cheers

User · Answer

Actually  using read csv   to read a file with text content is not a good idea  disable the quote as set quote    is only a temporary solution  it only worked with Separate quotation marks  There are other reasons would cause the warning  such as some special characters    The permanent solution using read csv     finding out what those special characters are and use a regular expression to eliminate them is an idea   Have you ever think of installing the package  data table  and use fread   to read the file  it is much faster and would not bother you with this EOF warning  Note that the file it loads it will be stored as a data table object but not a data frame object  The class data table has many good features  but anyway  you can transform it using as data frame   if needed

User · Answer

You need to disable quoting   cit  lt - read csv  citations CSV   quote                         row names   NULL                    stringsAsFactors   FALSE   str cit      data frame      112543 obs  of  13 variables        row names      chr   10 2307 675394   10 2307 30007362   10 2307 4254931   10 2307 20537934            id             chr   10 2307 675394 t   10 2307 30007362 t   10 2307 4254931 t   10 2307 20537934 t            doi            chr   Archaeological Inference and Inductive Confirmation t   Sound and Sense in Cath Almaine t   Oak Galls Preserved by the Eruption of Mount Vesuvius in A D  79  and Their Probable Use t   The Arts Four Thousand Years Ago t            title          chr   Bruce D  Smith t   Tom  s    Cathasaigh t   Hiram G  Larew t    t            author         chr   American Anthropologist t     riu t   Economic Botany t   The Illustrated Magazine of Art t            journaltitle   chr   79 t   54 t   41 t   1 t            volume         chr   3 t    t   1 t   3 t            issue          chr   1977-09-01T00 00 00Z t   2004-01-01T00 00 00Z t   1987-01-01T00 00 00Z t   1853-01-01T00 00 00Z t            pubdate        chr   pp  598-617 t   pp  41-47 t   pp  33-40 t   pp  171-172 t            pagerange      chr   American Anthropological Association tWiley t   Royal Irish Academy t   New York Botanical Garden Press tSpringer t    t            publisher      chr   fla t   fla t   fla t   fla t            type           logi  NA NA NA NA NA NA           reviewed work  logi  NA NA NA NA NA NA       I think is because of this kind of lines  check  Thorn  and  Minus     readLines  citations CSV   82   1   10 2307 3642839 10 2307 3642839 t   Thorn   and   Minus   in Hieroglyphic Luvian Orthography t H  Craig Melchert t Anatolian Studies t 38 t  t 1988-01-01T00 00 00Z t pp  29-42 t British Institute at Ankara t fla t  t

User · Answer

The readr package will fix this issue    install packages  readr   library readr  readr  read csv  yourfile csv

User · Answer

I also ran into this problem  and was able to work around a similar EOF error using   read table      csv   sep             Notice that the separator parameter is defined within the more general read table

User · Answer

I had the similar problem  EOF -warning and only part of data was loading with read csv    I tried the quotes     but it only removed the EOF -warning   But looking at the first row that was not loading  I found that there was a special character  an arrow    hexadecimal value 0x1A  in one of the cells  After deleting the arrow I got the data to load normally

User · Answer

I m a new-ish R user and thought I d post  this in case it helps anyone else  I was trying to read in data from a text file  separated with commas  that included a few Spanish characters and it took me forever to figure it out  I knew I needed to use UTF-8 encoding  set the header arg to TRUE  and that I need to set the sep arguemnt to  quot   quot   but then I still got hang ups  After reading this post I tried setting the fill arg to TRUE  but then got the same  quot EOF within quoted string quot  which I was able to fix in the same manner as above  My successful read table looks like this  target  lt - read table  quot target2 txt quot   fill TRUE  header TRUE  quote  quot  quot   sep  quot   quot   encoding  quot UTF-8 quot   The result has Spanish language characters and same dims I had originally  so I m calling it a success  Thanks all

[r] read.csv warning 'EOF within quoted string' prevents complete reading of file

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