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the compilation failed with some issue reported by biber (see below) which is part of the dissertation file:

Snippet of log file

... 
Package biblatex Warning: Biber reported the following issues
(biblatex)                with 'malfertheiner_acute_2011':
(biblatex)                - Range field 'pages' in entry 'malfertheiner_acute_2
011' is malformed, skipping.


Package biblatex Warning: Biber reported the following issues
(biblatex)                with 'akdis_interleukins_2011':
(biblatex)                - Range field 'pages' in entry 'akdis_interleukins_20
11' is malformed, skipping.


Package biblatex Warning: Biber reported the following issues
(biblatex)                with 'cosmi_identification_2010':
(biblatex)                - Range field 'pages' in entry 'cosmi_identification_
2010' is malformed, skipping.

)

Runaway argument?
{Fisher-Rao linear discriminant analysis ({LDA)} is a valuable tool f\ETC.
! File ended while scanning use of \field.
<inserted text> 
                \par 
l.197 \begin{document}  

Snippet of the mentioned refs in the .bib file

@article{malfertheiner_acute_2011,
    title = {Acute infection with a {CagA} positive \textit{H. pylori} strain in healthy subjects -- effect on symptoms and gastric physiology},
    volume = {140},
    issn = {0016-5085},
    url = {http://www.gastrojournal.org/article/S0016-5085(11)60352-1/abstract},
    doi = {10.1016/S0016-5085(11)60352-1},
    abstract = {No abstract is available. To read the body of this article, please view the {PDF} online.},
    pages = {S-86-S-86},
    number = {5},
    journaltitle = {Gastroenterology},
    shortjournal = {Gastroenterology},
    author = {Malfertheiner, Peter and Selgrad, Michael and Wex, Thomas and Del Giudice, Giuseppe and Palla, Emanuela and Graham, David and Heaton, Penny M.},
    urldate = {2014-04-21},
    date = {2011-05},
    keywords = {allrefs, caga, cited, clinical, H. pylori, Human, Novartis, vaccine},
    file = {Malfertheiner et al. - 2011 - Acute infection with a CagA positive iH. pylori.pdf:D\:\\Documents\\Zotero_Backup\\storage\\3K8B7223\\Malfertheiner et al. - 2011 - Acute infection with a CagA positive iH. pylori.pdf:application/pdf}
}

@article{akdis_interleukins_2011,
    title = {Interleukins, from 1 to 37, and interferon-γ: receptors, functions, and roles in diseases},
    volume = {127},
    issn = {1097-6825},
    doi = {10.1016/j.jaci.2010.11.050},
    shorttitle = {Interleukins, from 1 to 37, and interferon-γ},
    abstract = {Advancing our understanding of mechanisms of immune regulation in allergy, asthma, autoimmune diseases, tumor development, organ transplantation, and chronic infections could lead to effective and targeted therapies. Subsets of immune and inflammatory cells interact via {ILs} and {IFNs;} reciprocal regulation and counter balance among T(h) and regulatory T cells, as well as subsets of B cells, offer opportunities for immune interventions. Here, we review current knowledge about {ILs} 1 to 37 and {IFN-γ.} Our understanding of the effects of {ILs} has greatly increased since the discoveries of monocyte {IL} (called {IL-1)} and lymphocyte {IL} (called {IL-2);} more than 40 cytokines are now designated as {ILs.} Studies of transgenic or knockout mice with altered expression of these cytokines or their receptors and analyses of mutations and polymorphisms in human genes that encode these products have provided important information about {IL} and {IFN} functions. We discuss their signaling pathways, cellular sources, targets, roles in immune regulation and cellular networks, roles in allergy and asthma, and roles in defense against infections.},
    pages = {701-721.e1-70},
    number = {3},
    journaltitle = {The Journal of allergy and clinical immunology},
    shortjournal = {J Allergy Clin Immunol},
    author = {Akdis, Mübeccel and Burgler, Simone and Crameri, Reto and Eiwegger, Thomas and Fujita, Hiroyuki and Gomez, Enrique and Klunker, Sven and Meyer, Norbert and {O'Mahony}, Liam and Palomares, Oscar and Rhyner, Claudio and Ouaked, Nadia and Quaked, Nadia and Schaffartzik, Anna and Van De Veen, Willem and Zeller, Sabine and Zimmermann, Maya and Akdis, Cezmi A},
    date = {2011-03},
    pmid = {21377040},
    keywords = {allrefs, Animals, cited, cytokine, expression source, figure, Humans, {IL-12}, {IL-12} family, {IL-17}, {IL-23}, {IL-27}, {IL-35}, {IL-8}, Immune System Diseases, Immunity, Interferon-gamma, Interleukins, Mice, Receptors, Interferon, Receptors, Interleukin, review, Th differentiation},
    file = {Akdis et al. - 2011 - Interleukins, from 1 to 37, and interferon-γ rece.pdf:D\:\\Documents\\Zotero_Backup\\storage\\PCM6FBJX\\Akdis et al. - 2011 - Interleukins, from 1 to 37, and interferon-γ rece.pdf:application/pdf}
}  
@article{cosmi_identification_2010,
    title = {Identification of a novel subset of human circulating memory {CD4(+)} T cells that produce both {IL-17A} and {IL-4}},
    volume = {125},
    issn = {1097-6825},
    doi = {10.1016/j.jaci.2009.10.012},
    abstract = {{BACKGROUND:} {IL-17A} has been suggested to play a pathogenic role in bronchial asthma and other allergic disorders.
{OBJECTIVE:} Study of the relationship between human {IL-17A-producing} {CD4(+)} T(H) cells (T(H)17) and {IL-4-producing} {CD4(+)} T(H) (T(H)2) cells.
{METHODS:} T-cell clones generated from the {CCR6(+)CD161(+)} fraction of human circulating {CD4(+)} T cells, which contains virtually all T(H)17 cells, as well as circulating {CD4(+)} T cells from both healthy subjects and patients with asthma, were assessed by flow cytometry for their cytokine production profile.
{RESULTS:} A small proportion of {CCR6(+)CD161(+)CD4(+)} T-cell clones showed the ability to produce both {IL-17A} and {IL-4} (T({H)17/T(H)2).} T({H)17/T(H)2} clones also produced {IL-5}, {IL-8}, {IL-9}, {IL-13}, {IL-21}, and {IL-22} and displayed the ability to induce the in vitro secretion of {IgE.} A very few T({H)17/T(H)2} cells were found among circulating {CD4(+)} T cells from normal subjects, but their proportions were significantly increased in the circulation of patients with chronic asthma. T({H)17/T(H)2} cells could not be derived from naive umbilical cord blood {CD4(+)} T cells under any experimental condition. However, when circulating memory {CCR6(+)CD161(+)CD4(+)} T cells were cloned under appropriate polarizing conditions, T({H)17/T(H)2} clones originated in the presence of {IL-4}, suggesting that an {IL-4-rich} microenvironment may induce the shifting of memory T(H)17 cells into T({H)17/T(H)2} cells.
{CONCLUSION:} Because of its peculiar functional properties and the increased numbers in the circulation of patients with bronchial asthma, this previously unknown population of T({H)17/T(H)2} cells may play some role in the pathogenesis of this disease.},
    pages = {222-230.e1-4},
    number = {1},
    journaltitle = {The Journal of allergy and clinical immunology},
    shortjournal = {J Allergy Clin Immunol},
    author = {Cosmi, Lorenzo and Maggi, Laura and Santarlasci, Veronica and Capone, Manuela and Cardilicchia, Elisa and Frosali, Francesca and Querci, Valentina and Angeli, Roberta and Matucci, Andrea and Fambrini, Massimiliano and Liotta, Francesco and Parronchi, Paola and Maggi, Enrico and Romagnani, Sergio and Annunziato, Francesco},
    date = {2010},
    pmid = {20109749},
    keywords = {17definition, 17plasticity, allrefs, Asthma, {CD4-Positive} T-Lymphocytes, cited, Clone Cells, Cytokines, Flow Cytometry, {groupTh17wTh2}, Humans, Immunologic Memory, Interleukin-17, Interleukin-4, key reference, {NK} Cell Lectin-Like Receptor Subfamily B, plasticity, Receptors, {CCR6}, Th17, Th2, T-Lymphocyte Subsets},
    file = {Cosmi et al. - 2010 - Identification of a novel subset of human circulat.pdf:D\:\\Documents\\Zotero_Backup\\storage\\DW6HV2VI\\Cosmi et al. - 2010 - Identification of a novel subset of human circulat.pdf:application/pdf}
}

I use biber version 1.9 - TexLive 2014 - Perl 5.18.2 and compile with xetex.

Update 1
the statement in the log file Fisher-Roa Fisher-Rao linear discriminant analysis ({LDA)} is a valuable tool for is a text part of one of the refs in the .bib file as below:

@article{hastie_discriminant_1996,
    title = {Discriminant analysis by gaussian mixtures},
    volume = {58},
    url = {http://www.jstor.org/discover/10.2307/2346171?uid=3737864&uid=2&uid=4&sid=21104276903573},
    abstract = {Fisher-Rao linear discriminant analysis ({LDA)} is a valuable tool for multigroup classification. {LDA} is equivalent to maximum likelihood classification assuming Gaussian distributions for each class. In this paper, we fit Gaussian mixtures to each class to facilitate effective classification in non-normal settings, especially when the classes are clustered. Low dimensional views are an important by-product of {LDA---our} new techniques inherit this feature. We are able to control the within-class spread of the subclass centers relative to the between-class spread. Our technique for fitting these models permits a natural blend with nonparametric versions of {LDA.}  Keywords: Classification, Pattern Recognition, Clustering, Nonparametric, Penalized. 1 Introduction  In the generic classification or discrimination problem, the outcome of interest  G falls into J unordered classes, which for convenience we denote by the set J =  f1; 2; 3; {\textbackslash}Delta {\textbackslash}Delta {\textbackslash}Delta Jg. We wish to build a rule for pred...},
    pages = {155–176},
    journaltitle = {Journal of the Royal Statistical Society, Series B},
    shortjournal = {J R Stat Soc},
    author = {Hastie, Trevor and Tibshirani, Robert},
    date = {1996},
    keywords = {allrefs, cited, first reference, {MDA}, statistics},
    file = {Hastie and Tibshirani - 1996 - Discriminant Analysis by Gaussian Mixtures.pdf:D\:\\Documents\\Zotero_Backup\\storage\\K9XXKTSJ\\Hastie and Tibshirani - 1996 - Discriminant Analysis by Gaussian Mixtures.pdf:application/pdf}
}

Update 2
now the errors considering page ranges disappeared after caring for them, but the error for abstract did not, perplexed! see the snippet below:

)

(./phdmain.bbl

)

Runaway argument?
{Fisher-Rao linear discriminant analysis ({LDA}) is a valuable tool f\ETC.
! File ended while scanning use of \field.
<inserted text> 
                \par 
l.197 \begin{document}

?

Question
How can I fix this error?

share|improve this question
    
The line that causes the compilation to fail is the one with Fisher-Rao linear discriminant analysis. You haven't included that in your .bib file, so it's not possible to tell what's wrong with it. Please post a MWE. –  Sverre Sep 2 at 15:56
    
In addition to that, the bits with Biber reported are due to your pages fields being malformed - see my answer. –  greyshade Sep 2 at 16:01
    
@Sverre, pls see the update considering that part of the log. –  doctorate Sep 2 at 16:05
    
@doctorate that one is simple: ({LDA)} should be ({LDA}) - for the rest, see my answer –  greyshade Sep 2 at 16:07

1 Answer 1

up vote 6 down vote accepted

There's two problems here:

1st: the reason compilation fails is due to wrong sequence of brackets in ({LDA)} in the abstract field of hastie_discriminant_1996.

2nd: the warnings with Biber reported the following issues are due to biber not recognising your page fields as ranges as they should be, according to the biblatex documentation:

Range fields consist of one or more ranges where all dashes are normalized and replaced by the command \bibrangedash . A range is something optionally followed by one or more dashes optionally followed by some non-dash (e.g. 5–7 ). Any number of consecutive dashes will only yield a single range dash. A typical example of a range field is the pages field. See also the \bibrangessep command which can be used to Biberonly customise the separator between multiple ranges. With Biber, range fields will be skipped and will generate a warning if they do not consist of one or more ranges. You can normalise messy range fields before they are parsed using \DeclareSourcemap (see § 4.5.2 ).

biber itself complains about that (using only the first entry of the .bib:

WARN - Range field 'pages' in entry 'malfertheiner_acute_2011' is malformed, skipping

In order to make things work you'll have to wrap the parts of the range in {}, i.e. in malfertheiner_acute_2011 write pages = {{S-86}-{S-86}}.

share|improve this answer
    
interesting that this problem has never occurred until I updated the TexLive to 2014. Is there any global way to fix this error without correcting the individual refs (i.e. protecting each page range with brackets)? that would be time saving since I am at final stage of the dissertation. –  doctorate Sep 2 at 16:08
    
@doctorate none that I would be aware of - the biblatex doc points to §4.5.2 in what I cited, which talks about mappings and cleaning up fields. But I'm not sure there's a 'quick' nor necessarily a 'global' way for that.. –  greyshade Sep 2 at 16:11
    
@doctorate a partial solution for those cases where there's three dashes in total in the pages field might be found with a regexp as mentioned in the doc, but the case of something like 222-230.e1-4 would already require another regexp, i.e. these things would definitely not be global. –  greyshade Sep 2 at 16:16
    
I am glad now, this way mistakes in typesetting were spotted in the bibliography where only the word pages is there but without numbers! so it deserves to hunt them one by one with more scrutiny. –  doctorate Sep 2 at 16:21
    
pls can you have a look at the update 2, still cannot fix it even after deleting the temp files of latex. –  doctorate Sep 2 at 16:31

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