I am using MikTeX 2.9 (up-to-date) with TeXStudio. A file that compiled correctly in March 2019 now fails with the following error message:
!pdfTeX error: pdflatex.exe (file tcst1000): Font tcst1000 at 1200 not found
==> Fatal error occurred, no output PDF file produced!
Here is the MWE (from SWeave you can tell that it was produced by R):
\documentclass{article}
\RequirePackage{amsmath}
\RequirePackage{booktabs}
\usepackage{Sweave}
%\usepackage{lmodern}
\begin{document}
In this paper, I estimate loss in mean-variance efficiency due to estimation error by running simulations along the lines described in {Jori#1986-JFQA}.
\begin{Schunk}
\begin{Sinput}
> #Load the needed libraries.
> #I use H. Seltman's \texttt{cor2cov} function to get the covariance
> library(MASS)
> library(rJava)
> library(xlsxjars)
> library(xlsx)
\end{Sinput}
\end{Schunk}
\end{document}
If I remove the apostrophe after Seltman, the file compiles without error.
The error persists even if I uncomment the \usepackage{lmodern} line.
Thank you.
Related
I am trying to use FIX (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX) to denoise my functional MRI data, but after running the command to train the classifier:
/usr/local/fix/fix -t classifier_name -l <path I manually classified>
I get these errors:
/usr/local/fix/fix -t WP2a_classifier_training -l
sub-01/ses-w01pol03day01Pre/func/swsub-01_ses-w01pol03day01Pre_task-joystickPre_bold.ica
FIX Training classifier with output training file: ./WP2a_classifier_training and Melodic outputs list: sub-01/ses-w01pol03day01Pre/func/swsub-01_ses-w01pol03day01Pre_task-joystickPre_bold.ica
copy true labels and features into training directory
FIX features not already generated, so creating them now.
FIX Feature extraction for Melodic output directory: sub-01/ses-w01pol03day01Pre/func/swsub-01_ses-w01pol03day01Pre_task-joystickPre_bold.ica
create edge masks
run FAST
registration of standard space masks
error: inv(): matrix appears to be singular
terminate called after throwing an instance of 'std::runtime_error'
what(): inv(): matrix appears to be singular
/usr/local/fix/fix_0c_reg_masks: line 32: 26064 Aborted (core dumped) convert_xfm -omat $folders/fix/std2highres.mat -inverse $folders/fix/highres2std.mat
Could not open matrix file sub-01/ses-w01pol03day01Pre/func/swsub-01_ses-w01pol03day01Pre_task-joystickPre_bold.ica/fix/std2highres.mat
Cannot read input-matrix
Could not open matrix file sub-01/ses-w01pol03day01Pre/func/swsub-01_ses-w01pol03day01Pre_task-joystickPre_bold.ica/fix/std2exfunc.mat
error: matrix multiplication: incompatible matrix dimensions: 4x4 and 0x0
Any tip would be helpful as I'm quite stuck with this.
EDIT:
I am referring to this program https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX
Thanks.
I had compiled my work without any error in Latex a few months ago on a PC. However, it does work correctly on my new PC. My book.tex file looks like this:
\documentclass[graybox,envcountchap,sectrefs]{svmono}
\usepackage[sort, numbers]{natbib}
\usepackage{chapterbib}
%some packages are added
\begin{document}
\author{XYZ}
\title{abc}
\maketitle
\include{chapter1}
\include{chapter2}
\end{document}
My chapter1.tex and chapter2.tex look like the followings:
\chapter{Chapter one}
\cite[ref1]
\bibliographystyle{spbasic}
\bibliography{refCH1}
and
\chapter{Chapter two}
\cite[ref2]
\bibliographystyle{spbasic}
\bibliography{refCH2}
The refCH1.bib and refCH2.bib look like as:
#article{ref1,
title={ABC1},
author={AAA}
}
and
#article{ref2,
title={ABC2},
author={BBB}
}
The result of production pdf file, book.pdf, does not contain the references at the end of each chapter. Moreover, [?]’s appear instead of correct citations (e.g., [1], [2], …). The following messages appear in the console:
Command Line: makeindex.exe "book.idx"
Startup Folder: C:\...\SpringerBook\Springer_book_latex\templates
This is makeindex, version 2.15 [MiKTeX 2.9 64-bit] (kpathsea + Thai support).
Scanning input file book.idx...done (0 entries accepted, 0 rejected).
Nothing written in book.ind.
Transcript written in book.ilg.
Command Line: pdflatex.exe --interaction=errorstopmode --synctex=-1 "book.tex"
Startup Folder: C:\...\SpringerBook\Springer_book_latex\templates
This is pdfTeX, Version 3.14159265-2.6-1.40.15 (MiKTeX 2.9 64-bit)
entering extended mode
(book.tex
LaTeX2e <2014/05/01>
Babel <3.9l> and hyphenation patterns for 68 languages loaded.
(svmono.cls
Document Class: svmono 2009/12/17 v5.5
Springer Verlag global LaTeX document class for monographs
("C:\Program Files\MiKTeX 2.9\tex\latex\base\article.cls"
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
LaTeX Warning: Citation `ref1' in file `chapter1' on page 1 undefined on input line 20.
LaTeX Warning: Citation `ref2' in file `chapter2' on page 1 undefined on input line 20.
No file chapter1.bbl.
Command Line: bibtex.exe "book"
Startup Folder: C:\...\SpringerBook\Springer_book_latex\templates
This is BibTeX, Version 0.99d (MiKTeX 2.9 64-bit)
The top-level auxiliary file: book.aux
A level-1 auxiliary file: chapter1.aux
A level-1 auxiliary file: chapter2.aux
Illegal, another \bibstyle command---line 74 of file chapter1.aux
: \bibstyle
: {spbasic}
I'm skipping whatever remains of this command
Illegal, another \bibdata command---line 75 of file chapter2.aux
: \bibdata
: {refCH1}
I'm skipping whatever remains of this command
Database file #1: refCH1.bib
(There were # error messages)
I installed healthcareai from the instructions at the readthedocsURL
pip install https://github.com/HealthCatalyst/healthcareai-
py/zipball/master
After successfully running example_classification_1.py, I attempted to run example_classification_2.py. However, on example_classification_2.py, the code errored out at line 62:
factors = trained_model.make_factors(prediction_dataframe,
number_top_features=3)
The error in the console was:
File "/home/jdoe/anaconda3/lib/python3.5/site-packages/healthcareai/common/top_factors.py", line 55, in top_k_features
results = list(step2.values[:, :k])
IndexError: too many indices for array
I went back and looked at the documentation for "Choosing a Prediction Output" and it indicated the code should be run without the "number_top_features" option in the list:
factors = trained_model.make_factors(prediction_dataframe)
I did that, but it still threw an error.
Please advise. Thanks.
I get an error while building an image using Yocto (dizzy):
ERROR: Creation of tar /mnt/workspace/build/tmp/deploy/tar/xev-dbg-1.2.1-r0.tar.gz failed.
and bitbake command fails with the following report:
No currently running tasks (6291 of 6292)
NOTE: Tasks Summary: Attempted 6292 tasks of which 18 didn't need to be rerun and all succeeded.
Summary: There were 13 WARNING messages shown.
Summary: There were 3 ERROR messages shown, returning a non-zero exit code.
If I check the file xev-dbg-1.2.1-r0.tar.gz, I get:
$ file /mnt/workspace/build/tmp/deploy/tar/xev-dbg-1.2.1-r0.tar.gz
/mnt/workspace/build/tmp/deploy/tar/xev-dbg-1.2.1-r0.tar.gz: gzip compressed data, from Unix, last modified: Mon Mar 27 20:19:55 201
and it is the same case for the remaining two errors.
I am confused:
if there was an error, why bitbake is reporting that all tasks succeeded?
If the file were successfully created, why bitbake exits with non zero value?
Bitbake did not return a 0 exit-code. This mean that there are errors in the bitbake process.
There are 3 errors when it is trying to create the tar files as shown.
The compressed file is there but it is not complete. E.g. Just like how you could download a file and interrupt it and the download file is still there. So we usually use md5sum or some kind of hash number to check on the completeness of the file.
A better understanding might be: Bitbake attempted to run 6292 task. 18 of them do not need to rerun. Bitbake attempted to rerun the rest 6274(6292-18) and succeeded in rerunning them. This does not mean that all of them are successfully compiled. In the process of rerunning them, there are 13 warnings and and 3 errors appeared. Because of the 3 errors, bitbake returns with a non-zero exit code.
No currently running tasks (6291 of 6292)
NOTE: Tasks Summary: Attempted 6292 tasks of which 18 didn't need to be rerun and all succeeded.
Summary: There were 13 WARNING messages shown.
Summary: There were 3 ERROR messages shown, returning a non-zero exit code.
When I open an h5 file file.h5 with h5py and check for a certain key:
then this does not work:
found = "data" in h5File.keys() # warning on this line
if found:
a = h5File["data"][...]
and spits out the following warning:
HDF5-DIAG: Error detected in HDF5 (1.8.15-patch1) thread 0:
#000: /cluster/home/nuetzig/installHDF5/hdf5-1.8.15-patch1/src/H5Gdeprec.c line 893 in H5Gget_objinfo(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: /cluster/home/nuetzig/installHDF5/hdf5-1.8.15-patch1/src/H5Gloc.c line 173 in H5G_loc(): invalid file ID
major: Invalid arguments to routine
minor: Bad value
However making a set from h5File.keys() which is of type KeysViewWithLock(<HDF5 file "file.h5" (mode r)>)
works:
found = "data" in set(h5File.keys())
if found:
a = h5File["data"][...]
Anybody some idea where the problem is?
I have to say, that the file resides on a parallel network storage (Lustre) on a cluster...
Note: also "data" in h5File does not work
Problem solved:
Reinstalled h5py manually
by
python3 setup.py configure --hdf5-version=1.8.15
python3 install
Somehow the version did not get set and it used 1.8.4, dont know why...