I am having trouble getting my publication list to render in my CV using vitae. I have read a previous post https://github.com/mitchelloharawild/vitae/issues/70 but cannot resolve the issue with the information provided. I have tried deleting the *.tex file in the output folder. I have tried updating my version of vitae to the latest version. New to R so appreciate pointers on where I am going wrong, thanks.
scholar::get_publications("EmD_lTEAAAAJ&EmD_lTEAAAAJ&") %>%
filter(cites > 30) %>%
distinct(title, .keep_all = TRUE) %>%
transmute(bibtype = "Article", author = as.character(author),
title = as.character(title),
journaltitle = as.character(journal), year, key = row_number()) %>%
RefManageR::as.BibEntry() %>%
RefManageR::WriteBib("curie.bib")
bibliography_entries("curie.bib")
Error message:
Can't decode ill-formed UTF-8 octet sequence <E9> at C:\Users\nicho\AppData\Local\Temp\par-6e6963686f\cache-3fdda9ab9b6106ff01fe44df85bbc368a2e8d9e0\inc\lib/File/Slurper.pm line 59.
Error: Failed to build the bibliography via biber
In addition: Warning messages:
1: package 'tibble' was built under R version 3.6.3
2: In RefManageR::as.BibEntry(.) :
rownames of data.frame not meaningful for creating keys
Execution halted
Warning message:
LaTeX Warning: Empty bibliography on input line 194.
LaTeX Warning: Citation '1' undefined on input line 209.
LaTeX Warning: Citation '2' undefined on input line 209.
LaTeX Warning: Citation '3' undefined on input line 209.
LaTeX Warning: Citation '4' undefined on input line 209.
LaTeX Warning: Citation '5' undefined on input line 209.
LaTeX Warning: Citation '6' undefined on input line 209.
LaTeX Warning: Citation '7' undefined on input line 209.
LaTeX Warning: Citation '8' undefined on input line 209.
LaTeX Warning: Citation '9' undefined on input line 209.
LaTeX Warning: Citation '10' undefined on input line 209.
LaTeX Warning: Citation '11' undefined on input line 209.
LaTeX Warning: Citation '12' undefined on input line 209.
LaTeX Warning: Citation '13' undefined on input line 209.
LaTeX Warning: Citation '14' undefined on input line 209.
Package rerunfilecheck Warning: File `Untitled.out' has changed.
(rerunfilecheck) Rerun to get outlines right
(rerunfilecheck) [... truncated]
Related
Starting a few days ago, after months without issue, I began having a giant error box keep popping up when editing my code in Atom. I believe it is from the Hydrogen plugin, the weird thing is even with this error the code still runs and does what I want it too.
I created a new conda environment, installing only what I needed (pandas, geopandas, descartes, jupyter) and even when using the new environment in Atom I am getting this issue. I've tried upgrading ipykernel but it is already the most recent version.
Error Message
[IPKernelApp] ERROR | Exception in message handler: Traceback (most recent call last): File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/ipykernel/kernelbase.py", line 268, in dispatch_shell yield gen.maybe_future(handler(stream, idents, msg)) File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/tornado/gen.py", line 762, in run value = future.result() File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/tornado/gen.py", line 234, in wrapper yielded = ctx_run(next, result) File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/ipykernel/kernelbase.py", line 583, in complete_request matches = yield gen.maybe_future(self.do_complete(code, cursor_pos)) File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/ipykernel/ipkernel.py", line 360, in do_complete return self._experimental_do_complete(code, cursor_pos) File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/ipykernel/ipkernel.py", line 385, in _experimental_do_complete completions = list(_rectify_completions(code, raw_completions)) File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/IPython/core/completer.py", line 484, in rectify_completions completions = list(completions) File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/IPython/core/completer.py", line 1818, in completions for c in self._completions(text, offset, _timeout=self.jedi_compute_type_timeout/1000): File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/IPython/core/completer.py", line 1861, in _completions matched_text, matches, matches_origin, jedi_matches = self._complete( File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/IPython/core/completer.py", line 2029, in _complete completions = self._jedi_matches( File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/IPython/core/completer.py", line 1373, in _jedi_matches interpreter = jedi.Interpreter( File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/jedi/api/init.py", line 725, in init super().init(code, environment=environment, TypeError: init() got an unexpected keyword argument 'column'
The latest jedi (0.18) release is incompatible with IPython 7.19 see this discussion. IPython: 7.20 (released Feb 1st 2020) and 8.0 (not yet released) have a compatibility fix.
The correct workaround at this time is to upgrade IPython:
pip install -U ipython==7.20
In future you can search for the final two lines of the trackback after removing all path fragments specific to your installation, this is searching for:
line 2029, in _complete completions = self._jedi_matches IPython/core/completer.py, line 1373, in _jedi_matches interpreter = jedi.Interpreter( jedi/api/init.py, line 725, in init super().init(code, environment=environment, TypeError: init() got an unexpected keyword argument 'column'
This will give you the relevant issues on GitHub in the first two Google result as for today.
I am trying to read a column of integers in a spreadsheet into Octave using the code
A = odsread('Data.ods', 'Sheet1', 'A1:A946');
But it fails and I get a message with warnings and errors as :
> unzip: cannot find or open Data.ods, Data.ods.zip or Data.ods.ZIP.
file Data.ods couldn't be unpacked. Is it the proper file format?
warning: UnZip failed with error 9
Output:
error: warning: STATE structure must have fields 'identifier' and 'state'
error: called from
__OCT_spsh_open__ at line 72 column 7
odsopen at line 267 column 30
odsread at line 179 column 7
So the error says that "STATE structure must have fields 'identifier' and 'state'" , what does this mean?
Apparently the full path to the file should be included to make it work. It cannot load the file itself even when the file is in the same directory.
I'm knitting some beamer slides in an RMarkdown script in Rstudio on a Windows 7 PC. The slides are in the directory
C:/me/slides/myslides.Rmd
I have a master bibliography that lives in
C:/me/bib/masterbib.bib
I cannot figure out how to link to the bibliography file from the RMarkdown document. Here's the YAML from my attempt:
---
title: "Slides"
author: "me"
date: "2016-12-20"
bibliography: C:/me/bib/masterbib.bib
biblio-style: "apalike"
output:
beamer_presentation:
citation_package: natbib
---
Here's the error:
! Undefined control sequence.
<write> \string \bibdata {C:\me\bib\masterbib}
l.174 \end{frame}
Error: Failed to compile Slides.tex. See Slides.log for more info.
In addition: Warning message:
running command '"pdflatex" -halt-on-error -interaction=batchmode "Slides.tex"' had status 1
Execution halted
I've tried a couple other ways to specify the directory for masterbib.bib, but none have worked. I would prefer to keep the masterbib.bib file where it is, and not make an extra copy in the C:/me/slides/ directory. Thanks for your help!
Edit
When attempting to pass the following into YAML (quoteed with forward slashes):
bibliography: "C:/LaTeXstuff/BibTexLibrary/BrianBib.bib"
I get a fatal error with log output:
! Undefined control sequence.
<write> \string \bibdata {C:\me
\bib\masterbib}
l.174 \end{frame}
Here is how much of TeX's memory you used:
18047 strings out of 494045
334241 string characters out of 3145937
424206 words of memory out of 3000000
20891 multiletter control sequences out of 15000+200000
31808 words of font info for 44 fonts, out of 3000000 for 9000
715 hyphenation exceptions out of 8191
56i,11n,55p,434b,376s stack positions out of 5000i,500n,10000p,200000b,50000s
! ==> Fatal error occurred, no output PDF file produced!
When passing the following into YAML (quoted with backslashes)
bibliography: "C:\me\bib\masterbib.bib"
I get the following error in the Rstudio console
Error in yaml::yaml.load(enc2utf8(string), ...) :
Scanner error: while parsing a quoted scalar at line 4, column 15found unknown escape character at line 4, column 29
Calls: <Anonymous> ... yaml_load_utf8 -> mark_utf8 -> <Anonymous> -> .Call
Execution halted
When passing the following into YAML (unquoted with backslashes)
bibliography: C:\me\bib\masterbib.bib
I get the following error in the Rstudio console
! Undefined control sequence.
<write> \string \bibdata {C:\me
\bib\masterbib}
l.174 \end{frame}
Error: Failed to compile BibTest.tex. See BibTest.log for more info.
In addition: Warning message:
running command '"pdflatex" -halt-on-error -interaction=batchmode "BibTest.tex"' had status 1
Execution halted
Try unquoted with two backslashes:
...
bibliography: C:\\me\\bib\\masterbib.bib
...
So I am really not a Fortran programmer at all, but I have some code I am working with that uses the pgplot graphics libraries in fortran. I am able to get the code running in fortran from the console using the following commands.
gfortran -o simple discrete.f -lpgplot -IX11
discrete.f is the name of the file. So this works when I run it from the console. However, I want to run the code in the eclipse photran plugin so that I can use the debugger so that I can step through the code and observe some of the variables. I tried to put the -lpgplot and -IX11 flags in Eclipse, but I am getting errors about pgbbuf and pgnumb_ functions as undefined reference (which means that the -lpgplot function is not working when called from eclipse.
Can anyone please tell me how to set the flags correctly to run this code in Photran so that I can compile it and see the pgplot figure come up?
I am adding the console output:
02:57:05 **** Clean-only build of configuration Debug for project burglar_code_martin ****
make clean
rm -rf ./burglary_model.o burglar_code_martin
02:57:05 Build Finished (took 61ms)
02:57:05 **** Build of configuration Debug for project burglar_code_martin ****
make all
Building file: ../burglary_model.f
Invoking: GNU Fortran Compiler
gfortran -funderscoring -I/usr/lib -O0 -g -Wall -c -fmessage-length=0 -lpgplot -IX11 -o "burglary_model.o" "../burglary_model.f"
Warning: Nonconforming tab character in column 1 of line 225
Warning: Nonconforming tab character in column 1 of line 228
../burglary_model.f:155.27:
call probcheck(frac,1,outc)
1
Warning: Rank mismatch in argument 'problist' at (1) (rank-1 and scalar)
../burglary_model.f:54.33:
call probcheck(robprob,1,outcome)
1
Warning: Rank mismatch in argument 'problist' at (1) (rank-1 and scalar)
../burglary_model.f:95.30:
call probcheck(placeprob,1,outcome)
1
Warning: Rank mismatch in argument 'problist' at (1) (rank-1 and scalar)
../burglary_model.f:206.36:
subroutine output(A,burgsatloc,t,l,pic,screen,A0,Bbar)
1
Warning: Unused dummy argument 'burgsatloc' at (1)
../burglary_model.f:206.44:
subroutine output(A,burgsatloc,t,l,pic,screen,A0,Bbar)
1
Warning: Unused dummy argument 'pic' at (1)
../burglary_model.f:206.51:
subroutine output(A,burgsatloc,t,l,pic,screen,A0,Bbar)
1
Warning: Unused dummy argument 'screen' at (1)
../burglary_model.f:145.32:
integer l,pic,screen,i,j,k,PGOPEN,burgsatloc(512,*),nbar,outc
1
Warning: Unused variable 'k' declared at (1)
../burglary_model.f:146.15:
real rand,red,green,blue
1
Warning: Unused variable 'rand' declared at (1)
../burglary_model.f:143.53:
subroutine initialize(burgsatloc,B,l,pic,screen,rbar,Bbar)
1
Warning: Unused dummy argument 'screen' at (1)
../burglary_model.f:4.58:
integer i,j,n,l,pic,screen,guy,burgsatloc(512,512),k,
1
Warning: Unused variable 'k' declared at (1)
Finished building: ../burglary_model.f
Building target: burglar_code_martin
Invoking: GNU Fortran Linker
gfortran -lpgplot -IX11 -o "burglar_code_martin" ./burglary_model.o
./burglary_model.o: In function `output_':
/media/jaimini/workspace/eclipsejuno/burglar_code_martin/Debug/../burglary_model.f:241: undefined reference to `pgbbuf_'
/media/jaimini/workspace/eclipsejuno/burglar_code_martin/Debug/../burglary_model.f:242: undefined reference to `pgnumb_'
/media/jaimini/workspace/eclipsejuno/burglar_code_martin/Debug/../burglary_model.f:244: undefined reference to `pgenv_'
/media/jaimini/workspace/eclipsejuno/burglar_code_martin/Debug/../burglary_model.f:246: undefined reference to `pglab_'
/media/jaimini/workspace/eclipsejuno/burglar_code_martin/Debug/../burglary_model.f:247: undefined reference to `pgimag_'
/media/jaimini/workspace/eclipsejuno/burglar_code_martin/Debug/../burglary_model.f:253: undefined reference to `pgebuf_'
./burglary_model.o: In function `initialize_':
/media/jaimini/workspace/eclipsejuno/burglar_code_martin/Debug/../burglary_model.f:165: undefined reference to `pgopen_'
/media/jaimini/workspace/eclipsejuno/burglar_code_martin/Debug/../burglary_model.f:168: undefined reference to `pgpap_'
/media/jaimini/workspace/eclipsejuno/burglar_code_martin/Debug/../burglary_model.f:169: undefined reference to `pgask_'
/media/jaimini/workspace/eclipsejuno/burglar_code_martin/Debug/../burglary_model.f:170: undefined reference to `pgscir_'
/media/jaimini/workspace/eclipsejuno/burglar_code_martin/Debug/../burglary_model.f:175: undefined reference to `pgscr_'
/media/jaimini/workspace/eclipsejuno/burglar_code_martin/Debug/../burglary_model.f:181: undefined reference to `pgscr_'
/media/jaimini/workspace/eclipsejuno/burglar_code_martin/Debug/../burglary_model.f:187: undefined reference to `pgscr_'
/media/jaimini/workspace/eclipsejuno/burglar_code_martin/Debug/../burglary_model.f:193: undefined reference to `pgscr_'
/media/jaimini/workspace/eclipsejuno/burglar_code_martin/Debug/../burglary_model.f:199: undefined reference to `pgscr_'
./burglary_model.o: In function `implicit':
/media/jaimini/workspace/eclipsejuno/burglar_code_martin/Debug/../burglary_model.f:109: undefined reference to `pgclos_'
collect2: ld returned 1 exit status
make: *** [burglar_code_martin] Error 1
02:57:05 Build Finished (took 209ms)
I'm trying to run the simple "MongoDB:Tutorial" tutorial:
http://search.cpan.org/dist/MongoDB/lib/MongoDB/Tutorial.pod
My goal is to connect to a MongoDB database from a Perl script. I've installed MongoDB using cpanm:
$ sudo cpanm MongoDB
MongoDB is up to date. (0.501.1)
I created a simple Perl script called loadRaw.pl:
use strict;
use warnings;
use MongoDB;
use MongoDB::Connection;
use MongoDB::OID;
print "hello\n";
When I try to run the script, I get a bunch of errors:
$ perl ./loadRaw.pl
String found where operator expected at /usr/local/lib/perl/5.10.1/MongoDB/Cursor.pm line 271, near "confess "cannot set fields after querying""
(Do you need to predeclare confess?)
String found where operator expected at /usr/local/lib/perl/5.10.1/MongoDB/Cursor.pm line 273, near "confess 'not a hash reference'"
(Do you need to predeclare confess?)
String found where operator expected at /usr/local/lib/perl/5.10.1/MongoDB/Cursor.pm line 294, near "confess "cannot set sort after querying""
(Do you need to predeclare confess?)
String found where operator expected at /usr/local/lib/perl/5.10.1/MongoDB/Cursor.pm line 296, near "confess 'not a hash reference'"
(Do you need to predeclare confess?)
String found where operator expected at /usr/local/lib/perl/5.10.1/MongoDB/Cursor.pm line 317, near "confess "cannot set limit after querying""
(Do you need to predeclare confess?)
String found where operator expected at /usr/local/lib/perl/5.10.1/MongoDB/Cursor.pm line 343, near "confess "Cannot set tailable state""
(Do you need to predeclare confess?)
String found where operator expected at /usr/local/lib/perl/5.10.1/MongoDB/Cursor.pm line 366, near "confess "cannot set skip after querying""
(Do you need to predeclare confess?)
String found where operator expected at /usr/local/lib/perl/5.10.1/MongoDB/Cursor.pm line 390, near "confess "cannot set snapshot after querying""
(Do you need to predeclare confess?)
String found where operator expected at /usr/local/lib/perl/5.10.1/MongoDB/Cursor.pm line 408, near "confess "cannot set hint after querying""
(Do you need to predeclare confess?)
String found where operator expected at /usr/local/lib/perl/5.10.1/MongoDB/Cursor.pm line 410, near "confess 'not a hash reference'"
(Do you need to predeclare confess?)
syntax error at /usr/local/lib/perl/5.10.1/MongoDB/Cursor.pm line 90, near "has started_iterating"
syntax error at /usr/local/lib/perl/5.10.1/MongoDB/Cursor.pm line 271, near "confess "cannot set fields after querying""
syntax error at /usr/local/lib/perl/5.10.1/MongoDB/Cursor.pm line 294, near "confess "cannot set sort after querying""
syntax error at /usr/local/lib/perl/5.10.1/MongoDB/Cursor.pm line 317, near "confess "cannot set limit after querying""
syntax error at /usr/local/lib/perl/5.10.1/MongoDB/Cursor.pm line 343, near "confess "Cannot set tailable state""
syntax error at /usr/local/lib/perl/5.10.1/MongoDB/Cursor.pm line 366, near "confess "cannot set skip after querying""
syntax error at /usr/local/lib/perl/5.10.1/MongoDB/Cursor.pm line 390, near "confess "cannot set snapshot after querying""
syntax error at /usr/local/lib/perl/5.10.1/MongoDB/Cursor.pm line 408, near "confess "cannot set hint after querying""
BEGIN not safe after errors--compilation aborted at /usr/local/lib/perl/5.10.1/MongoDB/Cursor.pm line 564.
Compilation failed in require at /usr/local/lib/perl/5.10.1/MongoDB/Connection.pm line 26.
BEGIN failed--compilation aborted at /usr/local/lib/perl/5.10.1/MongoDB/Connection.pm line 26.
Compilation failed in require at /usr/local/lib/perl/5.10.1/MongoDB.pm line 30.
BEGIN failed--compilation aborted at /usr/local/lib/perl/5.10.1/MongoDB.pm line 30.
Compilation failed in require at ./loadRaw.pl line 7.
BEGIN failed--compilation aborted at ./loadRaw.pl line 7.
It seems like the MongoDB Perl module (specifically, the Cursor.pm file) has some syntax errors. The first batch of problems (those related to the confess keyword) are solved if I add the line use Carp; to the top of Cursor.pm. However, I don't think I should have to do this, and instead I'm doing something else incorrectly. Also, the second batch of errors (those related to the has keyword) are not solved by including Carp.
Has anyone else experienced this? Any ideas?
I never found out exactly what was going wrong, but it was surely unique to my system and my Perl configuration. Since others were able to execute the provided code without problem, I tried executing the code using Perlbrew (as suggested by friedo):
$ perlbrew install perl-5.16.0
(Output not shown)
$ perlbrew switch perl-5.16.0
(Output not shown)
$ perlbrew install-cpanm
(Output not shown)
$ /home/sthomas/perl5/perlbrew/bin/cpanm MongoDB
(Output not shown)
$ perlbrew exec perl ./loadRaw.pl
perl-5.16.0
==========
hello
Since it works fine with a Perlbrew installation, the problem is not with MongoDB or my sample code; it must be some weird quirk of my Perl environment. I guess I'll try a fresh install of Perl and all my required modules and see if that works.