r-devel January 2015

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Bug in foreign::read.arff()?
by Guillaume MULLER 22 Jan '15

22 Jan '15

Hi, I am currently trying to open an ARFF file created with Weka 3-7-12 (latest) with foreign::read.arff(). Unfortunately, it fails. The problem lies in the management of the (separator and mostly) quote char(s), inside quoted strings. Indeed, apparently foreign.arff() acts like read.csv, which documentation (that points to scan()'s documentation) says: If ‘sep’ is the default (‘""’), the character ‘\’ in a quoted string escapes the following character, so quotes may be included in the string by escaping them. If ‘sep’ is non-default, the fields may be quoted in the style of ‘.csv’ files where separators inside quotes (‘''’ or ‘""’) are ignored and quotes may be put inside strings by doubling them. However, if ‘sep = "\n"’ it is assumed by default that one wants to read entire lines verbatim. Unfortunately, Weka does not follow these rules when generating a CSV/ARFF file! According to the discussion I had with its developers: http://weka.8497.n7.nabble.com/Trying-to-reconciliate-R-and-Weka-a-k-a-on-t… and their specification of ARFF files (*): http://weka.wikispaces.com/ARFF+%28developer+version%29 Weka always use "," as the sep char and "'" as the quoting char. But when it comes to using a quote char inside a quoted string, they simply precede it with a "\". I've joined a set of files to demonstrate the problem: - plop3.arff uses \' to use quote char inside a quoted string. It opens with Weka/RWeka::read.arff() but fails with foreign::read.arff(). - plop4.arff uses '' to use quote char inside a quoted string. It opens with foreign::read.arff() but not Weka/RWeka::read.arff(). Would it be possible to change the default behaviour of foreign::read.arff() to follow the "specifications" from the Weka team, or to provide configuration options, so that valid arff files can be loaded with foreign? Also, since there does not exist any complete CSV file specification, the same problem occurs with opening CSV files created with Weka in R. I've asked them to parametrize their CSV generator, but it seems difficult to do, so they don't seem willing to do it. As you have the most complete/parametrizeable CSV reader I've seen so far, can I ask you also if it would be possible to parametrize read.csv/read.csv2/read.table to allow for both uses of the quoting char in quoted strings (doubling vs. backquoting)? Cheers GM (*) (The code suggests that double-quotes are acceptable and that a backslash will escape individual characters.) -- Guillaume MULLER, PhD Office 0375 Presans / X-Technologies / École Polytechnique 91128 Palaiseau CEDEX France http://www.presans.com http://feeds.feedburner.com/OYI/fr plop3.arff @relation InstancesFromHashTable @attribute Filename string @attribute AllKeywordsMatches numeric @attribute AllKeywordsMatchesNrmlzd numeric @attribute Class {0,1,2} @attribute CreatorApp numeric @attribute DateMatches numeric @attribute DateMatchesNrmlzd numeric @attribute FileSize100k numeric @attribute MostUsedFont numeric @attribute MostUsedFontNrmlzd numeric @attribute NbPages numeric @attribute NbPagesNrmlzd numeric @attribute PageOrientation numeric @attribute PageSize numeric @attribute RawPageWidth numeric @attribute ReferenceMatches numeric @attribute ReferenceMatchesNrmlzd numeric @attribute abstract numeric @attribute abstractNrmlzd numeric @attribute acknowledg numeric 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numeric @attribute comparisonNrmlzd numeric @attribute contribut numeric @attribute contributNrmlzd numeric @attribute doi numeric @attribute doiNrmlzd numeric @attribute 'e mail' numeric @attribute 'e mailNrmlzd' numeric @attribute email numeric @attribute emailNrmlzd numeric @attribute equat numeric @attribute equatNrmlzd numeric @attribute evalu numeric @attribute evaluNrmlzd numeric @attribute experi numeric @attribute experiNrmlzd numeric @attribute figur numeric @attribute figurNrmlzd numeric @attribute follow numeric @attribute followNrmlzd numeric @attribute formal numeric @attribute formalNrmlzd numeric @attribute goal numeric @attribute goalNrmlzd numeric @attribute grant numeric @attribute grantNrmlzd numeric @attribute hypothes numeric @attribute hypothesNrmlzd numeric @attribute hypothesi numeric @attribute hypothesiNrmlzd numeric @attribute institut numeric @attribute institutNrmlzd numeric @attribute introduct numeric @attribute introductNrmlzd numeric @attribute 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LearningBasev3_1000/In/Papers/1306.4384.pdf,67,0.023717,1,0,1,0.000354,4,11,0.003894,21,0.007434,1,6,612,0,0,0,0,0,0,0,0,8,0.002832,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0.000354,1,0.000354,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0.000708,0,0,0,0,0,0,23,0.008142,0,0,0,0,0,0,0,0,0,0,115,0.040708,2456,0.869381,20,0.00708,0,0,5,0.00177,0,0,0,0,5,0.00177,0,0,0,0,0,0,5,0.00177,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0.003186,13,0.004602,155,0.054867,42,0.014867,2,0.000708,0,0,115,0.040708,42,0.014867,155,0.054867,13,0.004602,9,0.003186,0,0,0,0,0,0,0,0,2456,0.869381,0,0,20,0.00708,0,0,5,0.00177,0,0,0,0,5,0.00177,0,0,0,0,5,0.00177,0,0,0,0,0,0,0,0,0,0,6,0.002124,0,0,0,0,0,0,0,0,20,0.00708,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,4,0.001416 'LearningBasev3_1000/In/OtherPDFs/Modern Britain\'s, Lecture 8, The Victorians (Part 2).pdf',1,0.003257,0,5,1,0.003257,35,18,0.058632,34,0.110749,1,7,538,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0.003257,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0.003257,0,0,0,0,0,0,0,0,143,0.465798,1,0.003257,0,0,61,0.198697,0,0,0,0,0,0,0,0,0,0,0,0,0,0,61,0.198697,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0.003257,0,0,0,0,0,0,0,0,143,0.465798,61,0.198697,1,0.003257,61,0.198697,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 plop4.arff @relation InstancesFromHashTable @attribute Filename string @attribute AllKeywordsMatches numeric @attribute AllKeywordsMatchesNrmlzd numeric @attribute Class {0,1,2} @attribute CreatorApp numeric @attribute DateMatches numeric @attribute DateMatchesNrmlzd numeric @attribute FileSize100k numeric 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numeric @attribute universNrmlzd numeric @attribute volum numeric @attribute volumNrmlzd numeric @attribute work numeric @attribute workNrmlzd numeric @data LearningBasev3_1000/In/Papers/1306.4384.pdf,67,0.023717,1,0,1,0.000354,4,11,0.003894,21,0.007434,1,6,612,0,0,0,0,0,0,0,0,8,0.002832,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0.000354,1,0.000354,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0.000708,0,0,0,0,0,0,23,0.008142,0,0,0,0,0,0,0,0,0,0,115,0.040708,2456,0.869381,20,0.00708,0,0,5,0.00177,0,0,0,0,5,0.00177,0,0,0,0,0,0,5,0.00177,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0.003186,13,0.004602,155,0.054867,42,0.014867,2,0.000708,0,0,115,0.040708,42,0.014867,155,0.054867,13,0.004602,9,0.003186,0,0,0,0,0,0,0,0,2456,0.869381,0,0,20,0.00708,0,0,5,0.00177,0,0,0,0,5,0.00177,0,0,0,0,5,0.00177,0,0,0,0,0,0,0,0,0,0,6,0.002124,0,0,0,0,0,0,0,0,20,0.00708,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,4,0.001416 'LearningBasev3_1000/In/OtherPDFs/Modern Britain''s, Lecture 8, The Victorians (Part 2).pdf',1,0.003257,0,5,1,0.003257,35,18,0.058632,34,0.110749,1,7,538,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0.003257,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0.003257,0,0,0,0,0,0,0,0,143,0.465798,1,0.003257,0,0,61,0.198697,0,0,0,0,0,0,0,0,0,0,0,0,0,0,61,0.198697,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0.003257,0,0,0,0,0,0,0,0,143,0.465798,61,0.198697,1,0.003257,61,0.198697,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -- Guillaume MULLER, PhD Office 0375 Presans / X-Technologies / École Polytechnique 91128 Palaiseau CEDEX France http://www.presans.com http://feeds.feedburner.com/OYI/fr

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r-devel January 2015