2

I'm trying to use biber/biblatex for the first time and have run into some problems. When I invoke biber on my document from inside TeXShop, the process appears to hang with the following appearing in the console:

INFO - This is Biber 1.8
INFO - Logfile is 'Main.blg'
INFO - Reading 'Main.bcf'
INFO - Found 1 citekeys in bib section 0
INFO - Processing section 0
INFO - Looking for bibtex format file 'Padraic.bib' for section 0

The bib file it's looking for is in my local texmf tree. It's my master bibliography file which I've been using for years (managed with BibDesk).

If I switch the biblatex backend to bibtex and invoke that engine in TeXShop then everything works fine.

Further, I tried running biber from the commandline with the debug option and got the following output:

INFO - This is Biber 1.8
INFO - Logfile is 'Main.blg'
INFO - DEBUG mode: all messages are logged to 'Main.blg'
INFO - Reading 'Main.bcf'
INFO - Found 1 citekeys in bib section 0
INFO - Processing section 0
INFO - Looking for bibtex format file 'Padraic.bib' for section 0
INFO - Found BibTeX data source '/Users/RPS/Library/texmf/bibtex/bib/Padraic.bib'
Abort trap: 6

So in this case it seems to have found the source, but I have no idea what that abort error means.

Any ideas as to what I should be doing differently?

Mac OS 10.8.5 TeXShop 3.36

EDIT:

Moving the bib file into the main document folder results in the same error from the command line, but TeXShop displays nothing in the console.

MWE:

% !BIB program = biber
\documentclass{report}

\usepackage[notes,backend=biber,noibid]{biblatex-chicago}
\addbibresource{Test.bib}

\author{Br.\ Samuel Springuel}
\title{Argument Analysis of \emph{Meno} 78b--79e}

\begin{document}
\maketitle

~\autocite{Dancy:2006}


\printbibliography

\end{document}

And the bib file that trips it:

%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/


%% Created for R. Padraic Springuel at 2014-04-06 15:08:02 -0400 


%% Saved with string encoding Western (ASCII) 



@article{Dancy:2006,
    Abstract = {This study investigates the effect of computer animation on assessment and the conditions under which animation may improve or hinder assessment of conceptual understanding in physics. An instrument was developed by replacing static pictures and descriptions of motion with computer animations on the Force Concept Inventory, a commonly used pencil and paper test. Both quantitative and qualitative data were collected. The animated and static versions of the test were given to students and the results were statistically analyzed. Think-aloud interviews were also conducted to provide additional insight into the statistical findings. We found that good verbal skills tended to increase performance on the static version but not on the animated version of the test. In general, students had a better understanding of the intent of the question when viewing an animation and gave an answer that was more indicative of their actual understanding, as reflected in separate interviews. In some situations this led students to the correct answer and in others it did not. Overall, we found that animation can improve assessment under some conditions by increasing the validity of the instrument.},
    Annote = {From the conclusions, animations are good under the following conditions:
"1) The animation is an integral part of the question and not just a good-looking addition. Students should have a need to use the animation to answer the question. From this it follows that questions about motion are the best candidates for animation. This result supports the findings of earlier research. 
2) It is likely that the static form of the question could be misread or misinterpreted in a way that could be clarified by an animation. If a question is vague, or unclear to a student, then the response that student gives may not be reflective of his or her understanding. Perhaps the greatest benefit offered by animation is that it can significantly decrease such problems. This is especially true for students with poor verbal skills. 
3) Students are likely to answer a question based on what they remember rather than what they know and understand. In this case the animation is helpful if it is not as recognizable to the student as the static question."},
    Author = {Dancy, Melissa H. and Beichner, Robert J.},
    Date-Added = {2014-04-06 19:07:59 +0000},
    Date-Modified = {2014-04-06 19:07:59 +0000},
    Doi = {10.1103/PhysRevSTPER.2.010104},
    Journal = {Physical Review Special Topics - Physics Education Research},
    Number = {010104},
    Pages = {1-7},
    Read = {Yes},
    Title = {Impact of animation on assessment of conceptual understanding in physics},
    Url = {http://link.aps.org/doi/10.1103/PhysRevSTPER.2.010104},
    Volume = {2},
    Year = {2006},
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@article{Finkelstein:2005a,
    Abstract = {We report a detailed study of the implementation of Tutorials in Introductory Physics at a large-scale research institution. Based on two successive semesters of evaluation, we observe students' improved conceptual mastery force and motion concept evaluation median normalized gain 0.77, N = 336, albeit with some student discontent. We replicate the results of original studies of tutorial effectiveness and document how and why these results occur. Additionally, using the Colorado Learning Attitudes about Science Survey we measure the support of students' expertlike beliefs about learning physics in our environment. We examine this implementation from a viewpoint that emphasizes varying contextual levels of this implementation, from students' engagement in individual tasks, to the situations in which these tasks are embedded, to the broader classroom, departmental, and educational structures. We document both obvious and subtle features that help ensure the successful implementation of these reforms.},
    Annote = {Implementation of UW tutorials at Colorado.  Success comperable to that seen at UW.

CLASS results which show that attitude and learning gains are correlated.

Succesful adoption of a methodology involves more than just an adoption of material.  It als involves adoption, adaptation, and reinvention of the larger cultural/enviromental factors that made the original implementation successful.

},
    Author = {Finkelstein, Noah D. and Pollock, S. J.},
    Date-Added = {2014-04-06 19:07:59 +0000},
    Date-Modified = {2014-04-06 19:07:59 +0000},
    Doi = {10.1103/PhysRevSTPER.1.010101},
    Journal = {Physical Review Special Topics - Physics Education Research},
    Number = {010101},
    Pages = {1-13},
    Read = {Yes},
    Title = {Replicating and understanding successful innovations: Implementing tutorials in introductory physics},
    Url = {http://link.aps.org/doi/10.1103/PhysRevSTPER.1.010101},
    Volume = {1},
    Year = {2005},
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@article{Hake:1998,
    Abstract = {A survey of pre/post-test data using the Halloun -- Hestenes Mechanics Diagnostic test or more recent Force Concept Inventory is reported for 62 introductory physics courses enrolling a total number of students N=6542. A consistent analysis over diverse student populations in high schools, colleges, and universities is obtained if a rough measure of the average effectiveness of a course in promoting conceptual understanding is taken to be the average normalized gain <g>. The latter is defined as the ratio of the actual average gain (%<post>-%<pre>) to the maximum possible average gain (100-%<pre>) . Fourteen ``traditional'' ( T ) courses (N=2084) which made little or no use of interactive-engagement IE methods achieved an average gain  <g>_{T - ave}= 0.23+/-0.04 (std dev). In sharp contrast, 48 courses (N=4458) which made substantial use of IE methods achieved an average gain  <g>_{IE-ave}=0.48+/-0.14 (std dev), almost two standard deviations of  g  IE-ave above that of the traditional courses. Results for 30 (N=3259) of the above 62 courses on the problem-solving Mechanics Baseline test of Hestenes -- Wells imply that IE strategies enhance problem-solving ability. The conceptual and problem-solving test results strongly suggest that the classroom use of IE methods can increase mechanics-course effectiveness well beyond that obtained in traditional practice.},
    Annote = {Big colation of FCI data showing that interactive engagement is better than traditional instruction.

Considerable effort spent on showing that systematic errors did not influence the results},
    Author = {Hake, Richard R.},
    Date-Added = {2014-04-06 19:07:59 +0000},
    Date-Modified = {2014-04-06 19:07:59 +0000},
    Doi = {10.1119/1.18809},
    Journal = {American Journal of Physics},
    Month = {January},
    Number = {1},
    Pages = {64-74},
    Read = {Yes},
    Title = {Interactive-engagement versus traditional methods: A six-thousand-student survey of mechanics test data for introductory physics courses},
    Url = {http://dx.doi.org/10.1119/1.18809},
    Volume = {66},
    Year = {1998},
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@article{Lee:2008,
    Abstract = {We investigate short-term learning from hints and feedback in a Web-based physics tutoring system. Both the skill of students and the difficulty and discrimination of items were determined by applying item response theory IRT to the first answers of students who are working on for-credit homework items in an introductory Newtonian physics course. We show that after tutoring a shifted logistic item response function with lower discrimination fits the students' second responses to an item previously answered incorrectly. Student skill decreased by 1.0 standard deviation when students used no tutoring between their incorrect first and second attempts, which we attribute to ``item-wrong bias.'' On average, using hints or feedback increased students' skill by 0.8 standard deviation. A skill increase of 1.9 standard deviation was observed when hints were requested after viewing, but prior to attempting to answer, a particular item. The skill changes measured in this way will enable the use of IRT to assess students based on their second attempt in a tutoring environment.},
    Annote = {Item response theory used to show learning and how learning was different along different trajectories through a tutorial system.

Extension of IRT beyond basic skill assessment after a single test.},
    Author = {Lee, Young-Jin and Palazzo, David J. and Warnakulasooriya, Rasil and Pritchard, David E.},
    Date-Added = {2014-04-06 19:07:59 +0000},
    Date-Modified = {2014-04-06 19:07:59 +0000},
    Doi = {10.1103/PhysRevSTPER.4.010102},
    Journal = {Physical Review Special Topics - Physics Education Research},
    Number = {010102},
    Pages = {1-6},
    Read = {Yes},
    Title = {Measuring student learning with item response theory},
    Url = {http://link.aps.org/doi/10.1103/PhysRevSTPER.4.010102},
    Volume = {4},
    Year = {2008},
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@article{Mobley:2007,
    Abstract = {The ultrasonic attenuation coefficient, phase velocity, and group velocity spectra are reported for a suspension that supports negative group velocities. The suspension consists of plastic microspheres with an average radius of 80 m in an aqueous medium at a volume fraction of 3%. The spectra are measured using a broadband method covering a range from 2 to 20 MHz. The suspension exhibits negative group delays over a band near 4.5 MHz, with the group velocity magnitude exceeding 4.3 x 10^8 m/s at one point. The causal consistency of these results is confirmed using Kramers-Kronig relations.},
    Annote = {Breaking the speed of light.},
    Author = {Mobley, Joel and Heithau, Robert Evans},
    Date-Added = {2014-04-06 19:07:59 +0000},
    Date-Modified = {2014-04-06 19:07:59 +0000},
    Journal = {PHYSICAL REVIEW LETTERS},
    Number = {124301},
    Pages = {1-4},
    Title = {Ultrasonic Properties of a Suspension of Microspheres Supporting Negative Group Velocities},
    Volume = {99},
    Year = {2007},
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@article{Podolefsky:2007,
    Abstract = {This paper describes a model of analogy, analogical scaffolding, which explains present and prior results of student learning with analogies. We build on prior models of representation, blending, and layering of ideas.  Extending this model's explanatory power, we propose ways in which the model can be applied to design a curriculum directed at teaching abstract ideas in physics using multiple, layered analogies. We report on a recent empirical study that motivates this model. Students taught about electromagnetic waves in a curriculum that builds on the model of analogical scaffolding posted substantially greater gains pre- to postinstruction than students taught using a more traditional non-analogy-based tutorial 21% vs 7%. },
    Annote = {Provides a model of how analogical reasoning is done

Shows that students taught with analogy do better than students not taught with analogy

Analogy cirriculum was designed based on model

Did not show that model based analogical instruction outperforms other analgocial instruction.},
    Author = {Podolefsky, Noah S. and Finkelstein, Noah D.},
    Date-Added = {2014-04-06 19:07:59 +0000},
    Date-Modified = {2014-04-06 19:07:59 +0000},
    Doi = {10.1103/PhysRevSTPER.3.010109},
    Journal = {Physical Review Special Topics - Physics Education Research},
    Month = {June},
    Number = {010109},
    Pages = {1-12},
    Read = {Yes},
    Title = {Analogical scaffolding and the learning of abstract ideas in physics: An example from electromagnetic waves},
    Url = {http://link.aps.org/doi/10.1103/PhysRevSTPER.3.010109},
    Volume = {3},
    Year = {2007},
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@article{Thornton:2009,
    Abstract = {In this paper we compare and contrast student's pretest/post-test performance on the Halloun-Hestenes force concept inventory FCI to the Thornton-Sokoloff force and motion conceptual evaluation FMCE. Both tests are multiple-choice assessment instruments whose results are used to characterize how well a first term, introductory physics course promotes conceptual understanding. However, the two exams have slightly different content domains, as well as different representational formats; hence, one exam or the other might better fit the interests of a given instructor or researcher. To begin the comparison, we outline how to determine a single-number score for the FMCE and present ranges of normalized gains on this exam. We then compare scores on the FCI and the FMCE for approximately 2000 students enrolled in the Studio Physics course at Rensselaer Polytechnic Institute over a period of eight years 1998--2006 that encompassed significant evolution of the course and many different instructors. We found that the mean score on the FCI is significantly higher than the mean score on the FMCE, however there is a very strong relationship between scores on the two exams. The slope of a best fit line drawn through FCI versus FMCE data is approximately 0.54, and the correlation coefficient is approximately r = 0.78, for preinstructional and postinstructional testings combined. In spite of this strong relationship, the assessments measure different normalized gains under identical circumstances. Additionally, students who scored well on one exam did not necessarily score well on the other. We use this discrepancy to uncover some subtle, but important, differences between the exams. We also present ranges of normalized gains for the FMCE in a variety of instructional settings.},
    Annote = {Scoring the FMCE (out of 33 points):
5, 6, 15, 33, 35, 37, 39, 44, 45, 46, & 47 don't count
27-29, 11-13, and 8-10 are scored as a group with 2 points for getting all three correct and 0 otherwise
other questions are 1 point per

Paper accepts Ramlo as validating the FMCE

FCI covers more topics in similar number of questions and therefore is easier to score higher on

FCI better at evaluating overall progress in Intro Physics; FMCE better at evaluating progress towards Newtonian concept of forces},
    Author = {Thornton, Ronald K. and Kuhl, Dennis and Cummings, Karen and Marx, Jeffrey},
    Date-Added = {2014-04-06 19:07:59 +0000},
    Date-Modified = {2014-04-06 19:07:59 +0000},
    Doi = {10.1103/PhysRevSTPER.5.010105},
    Journal = {Physical Review Special Topics - Physics Education Research},
    Month = {March},
    Number = {1},
    Numpages = {8},
    Pages = {010105},
    Publisher = {American Physical Society},
    Read = {Yes},
    Title = {Comparing the force and motion conceptual evaluation and the force concept inventory},
    Url = {http://dx.doi.org/10.1103/PhysRevSTPER.5.010105},
    Volume = {5},
    Year = {2009},
    Bdsk-File-1 = {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}}

So far as I can tell, there is nothing unique about these entries in my master bib file (other than the fact that they trip the error. There are also no features in these entries that don't appear in at least one other entry.

  • Welcome to TeX.SX! Does the same issue occur with a .bib file in the same directory as your .tex file? In either case: Please help us to help you and add a minimal working example (MWE) that illustrates your problem. It will be much easier for us to reproduce your situation and find out what the issue is when we see compilable code, starting with \documentclass{...}, ending with \end{document}, and including a sample .bib file that produces the error. – Paul Gessler Apr 6 '14 at 0:57
  • Possibly related: tex.stackexchange.com/q/129014/21344 – Paul Gessler Apr 6 '14 at 1:02
  • 1
    It might be faster to subdivide the bib file to isolate the error rather than adding one entry at a time. Start with the first half of the bib; if the error occurs, you have the right half; if the error doesn't occur, use the other half and make sure the error shows up. Rinse and repeat until you've isolated the problem entry. – Paul Gessler Apr 6 '14 at 17:26
  • 2
    Hake:1998 and Mobley:2007 and Podolefsky:2007 have unescaped %, which will make the compilaiton fail ... though with a runaway argument problem, probably(?) not make biber fail with your weird abort trap 6. – jon Apr 6 '14 at 20:03
  • 2
    abort trap 6 seems to be Mac OS X's way of telling you that the process aborted thanks to a SIGABRT signal, it is used by some programming libraries to stop the programme after a fatal error (some memory overflows/allocation errors might trigger a SIGABRT). Such errors are notoriously hard to debug. In your case I'm confident though that the faulty abstract fields are the culprit, as without them the compilation of a document citing all seven sources above goes rather smoothly and displays as expected. – moewe Apr 7 '14 at 9:57
2

Based on the interactions in the comments above, I was able to all 7 entries to work and move them back to my main database. Further, I was able to re-enter the abstract and annote fields that were causing the problems, so long as I didn't copy and paste them.

So that other people can find the answer to this problem I summarize the steps I took here:

1) First, identify the entries which are causing the problem. As Paul suggested above, the best way to do this is to split your bib file, and test the splits. Splits that compile properly have nothing but good entries in them. Those that cause the error contain at least one bad entry. Continue this process until you've identified all the bad entries.

2) Edit the bad entries to remove the problematic fields. The most likely culprits are the abstract and annote field. Largely, I think, because there is so much text in these fields. However, I suspect that any field filled via Copy/Paste may cause problems. To make sure you're removing the right fields I recommend testing as you go. You probably also want to copy the removed information into a text document or another bib database so that you don't lose it.

3) Once you've got all the entries working, you can start filling back in the information removed. Do not use Copy/Paste for this process! In my case retyping the abstracts enabled me to get all the information back into the bib database without corrupting the entries. Again, test as you go.

Thanks to @PaulGessler, @jon, and @meowe for the help.

1

I was having exactly the same problem myself. However, I had a database of nearly 400 entries; trying to find the offending entries would be a daunting task. @jon's comments regarding unescaped LaTeX special characters inspired me to search for such characters in my .bib file.

I did not find any unescaped LaTeX special characters, but in the process I did discover 120 "other non-printable characters" using Textwrangler's "show invisibles" feature; these show up as upside-down question marks. Specifically, they were all the hexadecimal character \x{00}. A quick find-and-replace of these characters solved my problem. Biber properly processes the .bcf file now, producing the .bbl file, and my document now compiles as expected.

While I did not have any unescaped LaTeX special characters, which may also cause the same problem, It may be more productive to do a search for these known characters in a text editor rather than trying to isolate particular offending bib entries.

Also, regarding the comments about copy/paste in @rpspringuel's answer--I think this was definitely the cause of my problem. I'm sure that I copied abstracts from selected text in PDF documents, which would copy hidden, non-printable characters, such as \x{00}.

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