Re: LaTeX warning explanation needed [RESOLVED]

[Dr Eberhard Lisse]

Rich,

Good that it's working now.


In large documents, I find it helpful to pull out every section into its
own child document and have other than the ToC only Include statements
generated by

Insert --> File --> Child Document...

in the main file.

I then put my preamble into an include.tex which I pull into the
preamble of each file.

This is very helpful in my little "handbook" (888 pages currently),
where I can compile a section individually when making changes (and am
too impatient to wait the 2 1/2 minutes for the Makefile (570 lines
:-)-O) to do its thing)

greetings, el

On 2021-10-14 23:49 , Rich Shepard wrote:

On Wed, 13 Oct 2021, Rich Shepard wrote:

[...]

I copied the main doc's .lyx to bit-by-bit.lyx and deleted everything
but the title page and the paragraphs with the citations from this
copied file.

Then I copied the old file to the new one section-by-section, saving
and compiling each addition.  The bibliography was in the resulting
PDF with each addition.

No differences in the two files in the copied sections, but the new
one is 2K smaller in size.  So there must be something invisible in
the original file, but I'm not going to spend time looking for it
since I now have a complete copy.

[...]

--
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed [RESOLVED]

[Rich Shepard]

On Thu, 14 Oct 2021, Rich Shepard wrote:


No differences in the two files in the copied sections, but the new one is
2K smaller in size.


Nope. that file was mis-saved with a .lys suffix. Whatever that is.

Both the original and copied files have the same size.

Rich

--
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed [RESOLVED]

[Rich Shepard]

On Wed, 13 Oct 2021, Rich Shepard wrote:


The document now compiles without error using TeXLive2021 (and the 2020
version of texlive-extra), but the bibliography still does not print in the
PDF.


I copied the main doc's .lyx to bit-by-bit.lyx and deleted everything but
the title page and the paragraphs with the citations from this copied file.

Then I copied the old file to the new one section-by-section, saving and
compiling each addition. The bibliography was in the resulting PDF with each
addition.

No differences in the two files in the copied sections, but the new one is
2K smaller in size. So there must be something invisible in the original
file, but I'm not going to spend time looking for it since I now have a
complete copy.

Wow! Not before in the 20+ years I've used LyX have I had this issue.

Thanks to all of you who offered help.

Stay well everyone,

Rich

--
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Rich Shepard]

On Thu, 14 Oct 2021, Paul A. Rubin wrote:


Just to be clear, is the attached log from the same MWE that we have (just
references, nothing else) and does the MWE (with input encoding set to
UTF-8) compile for you? The log seems to indicate that it does.


Paul,

The file, latex.log, is for the main document. The file, mwe-latex.log, is
for the MWE.

Yes, the MWE displays the bibliography while the main file still does not.

Rich
--
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Paul A. Rubin]

On 10/14/21 4:21 PM, Rich Shepard wrote:

On Thu, 14 Oct 2021, Rich Shepard wrote:


I'll scroll through it, too.


Latest latex.log:
Package biblatex Info: Trying to load language 'english'...
Package biblatex Info: ... file 'english.lbx' found.
(/usr/share/texmf-dist/tex/latex/biblatex/lbx/english.lbx
File: english.lbx 2019/12/01 v3.14 biblatex localization (PK/MW)
)
Package biblatex Info: Input encoding 'utf8' detected.
Package biblatex Info: Automatic encoding selection.
(biblatex) Assuming data encoding 'utf8'.
\openout3 = `biological-evaluation.bcf'.

But,
Package biblatex Info: Trying to load bibliographic data...
Package biblatex Info: ... file 'biological-evaluation.bbl' not found.
No file biological-evaluation.bbl.

The MWE latex.log:
Package biblatex Info: Trying to load biblatex default data model...
Package biblatex Info: ... file 'blx-dm.def' found.
(/usr/share/texmf-dist/tex/latex/biblatex/blx-dm.def
File: blx-dm.def 2019/12/01 v3.14 biblatex localization (PK/MW)
)
Package biblatex Info: Trying to load biblatex style data model...
Package biblatex Info: ... file 'authoryear.dbx' not found.
Package biblatex Info: Trying to load biblatex custom data model...
Package biblatex Info: ... file 'biblatex-dm.cfg' not found.

Other than the page style in the MWE, what else might account for the
differences?

Rich

Just to be clear, is the attached log from the same MWE that we have 
(just references, nothing else) and does the MWE (with input encoding 
set to UTF-8) compile for you? The log seems to indicate that it does.


-- 
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Rich Shepard]

On Thu, 14 Oct 2021, Rich Shepard wrote:


I'll scroll through it, too.


Latest latex.log:
Package biblatex Info: Trying to load language 'english'...
Package biblatex Info: ... file 'english.lbx' found.
(/usr/share/texmf-dist/tex/latex/biblatex/lbx/english.lbx
File: english.lbx 2019/12/01 v3.14 biblatex localization (PK/MW)
)
Package biblatex Info: Input encoding 'utf8' detected.
Package biblatex Info: Automatic encoding selection.
(biblatex) Assuming data encoding 'utf8'.
\openout3 = `biological-evaluation.bcf'.

But,
Package biblatex Info: Trying to load bibliographic data...
Package biblatex Info: ... file 'biological-evaluation.bbl' not found.
No file biological-evaluation.bbl.

The MWE latex.log:
Package biblatex Info: Trying to load biblatex default data model...
Package biblatex Info: ... file 'blx-dm.def' found.
(/usr/share/texmf-dist/tex/latex/biblatex/blx-dm.def
File: blx-dm.def 2019/12/01 v3.14 biblatex localization (PK/MW)
)
Package biblatex Info: Trying to load biblatex style data model...
Package biblatex Info: ... file 'authoryear.dbx' not found.
Package biblatex Info: Trying to load biblatex custom data model...
Package biblatex Info: ... file 'biblatex-dm.cfg' not found.

Other than the page style in the MWE, what else might account for the
differences?

RichThis is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021 on Slint) 
(preloaded format=pdflatex 2021.10.13)  14 OCT 2021 12:58
entering extended mode
 restricted \write18 enabled.
 %&-line parsing enabled.
**mwe.tex
(./mwe.tex
LaTeX2e <2020-10-01> patch level 4
L3 programming layer <2021-02-18>
(/usr/share/texmf-dist/tex/latex/koma-script/scrreprt.cls
Document Class: scrreprt 2021/03/17 v3.33 KOMA-Script document class (report)
(/usr/share/texmf-dist/tex/latex/koma-script/scrkbase.sty
Package: scrkbase 2021/03/17 v3.33 KOMA-Script package (KOMA-Script-dependent b
asics and keyval usage)
(/usr/share/texmf-dist/tex/latex/koma-script/scrbase.sty
Package: scrbase 2021/03/17 v3.33 KOMA-Script package (KOMA-Script-independent 
basics and keyval usage)
(/usr/share/texmf-dist/tex/latex/koma-script/scrlfile.sty
Package: scrlfile 2021/03/17 v3.33 KOMA-Script package (file load hooks)
(/usr/share/texmf-dist/tex/latex/koma-script/scrlfile-hook.sty
Package: scrlfile-hook 2021/03/17 v3.33 KOMA-Script package (using LaTeX hooks)


LaTeX3 Info: Defining command \BeforeFile with sig. 'm' on line 61.


LaTeX3 Info: Defining command \AfterFile with sig. 'm' on line 65.


LaTeX3 Info: Defining command \BeforeClass with sig. 'm' on line 69.


LaTeX3 Info: Defining command \BeforePackage with sig. 'm' on line 73.


LaTeX3 Info: Defining command \AfterAtEndOfClass with sig. 'smo+m' on line 83.


LaTeX3 Info: Defining command \AfterAtEndOfPackage with sig. 'smo+m' on line
(LaTeX3) 93.


LaTeX3 Info: Defining command \scrlfile@AfterClass with sig. 'smo+m' on line
(LaTeX3) 173.


LaTeX3 Info: Defining command \AfterClass with sig. '' on line 174.


LaTeX3 Info: Defining command \scrlfile@AfterPackage with sig. 'smo+m' on line
(LaTeX3) 191.


LaTeX3 Info: Defining command \AfterPackage with sig. '' on line 192.


LaTeX3 Info: Defining command \ReplaceInput with sig. '' on line 193.


LaTeX3 Info: Defining command \ReplaceClass with sig. 'mm' on line 196.


LaTeX3 Info: Defining command \ReplacePackage with sig. 'mm' on line 199.


LaTeX3 Info: Defining command \UnReplaceInput with sig. '' on line 200.


LaTeX3 Info: Defining command \UnReplaceClass with sig. 'm' on line 203.


LaTeX3 Info: Defining command \UnReplacePackage with sig. 'mm' on line 206.


LaTeX3 Info: Defining command \PreventPackageFromLoading with sig. 's+om' on
(LaTeX3) line 234.


LaTeX3 Info: Defining command \StorePreventPackageFromLoading with sig. 'm' on
(LaTeX3) line 242.


LaTeX3 Info: Defining command \ResetPreventPackageFromLoading with sig. '' on
(LaTeX3) line 247.


LaTeX3 Info: Defining command \UnPreventPackageFromLoading with sig. 'sm' on
(LaTeX3) line 261.


LaTeX3 Info: Defining command \BeforeClosingMainAux with sig. 'om' on line
(LaTeX3) 274.


LaTeX3 Info: Defining command \AfterReadingMainAux with sig. 'om' on line 287.


LaTeX3 Info: Defining command \protected@immediate@write with sig. 'm+m+m' on
(LaTeX3) line 298.

(/usr/share/texmf-dist/tex/latex/koma-script/scrlogo.sty
Package: scrlogo 2021/03/17 v3.33 KOMA-Script package (logo)
))) (/usr/share/texmf-dist/tex/latex/graphics/keyval.sty
Package: keyval 2014/10/28 v1.15 key=value parser (DPC)
\KV@toks@=\toks15
)
Skipping: [2021/05/01] Usage of raw option list on input line 252.
Applying: [/00/00] compatibility for LaTeX before 2021/05/01 on input line 
337.
)) (/usr/share/texmf-dist/tex/latex/koma-script/tocbasic.sty
Package: tocbasic 2021/03/17 v3.33 KOMA-Script package (handling toc-files)
\scr@dte@tocline@numberwidth=\skip47
\scr@dte@tocline@numbox=\box47
)
Package tocbasic Info: babel extension for `toc' omitted
(tocbasic) because of missing 

Re: LaTeX warning explanation needed

[Rich Shepard]

On Thu, 14 Oct 2021, Paul A. Rubin wrote:


Just checked the modified MWE and confirmed that setting UTF-8 as the
input encoding still fixes things.


Paul,

While the MWE might be working, the main document still does not have the
bibliography with the Unicode (utf8) language setting.

If it's not the citations themselves it must be elsewhere. Most current
latex.log attached. I'll scroll through it, too.

RichThis is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021 on Slint) 
(preloaded format=pdflatex 2021.10.13)  14 OCT 2021 12:57
entering extended mode
 restricted \write18 enabled.
 %&-line parsing enabled.
**biological-evaluation.tex
(./biological-evaluation.tex
LaTeX2e <2020-10-01> patch level 4
L3 programming layer <2021-02-18>
(/usr/share/texmf-dist/tex/latex/koma-script/scrreprt.cls
Document Class: scrreprt 2021/03/17 v3.33 KOMA-Script document class (report)
(/usr/share/texmf-dist/tex/latex/koma-script/scrkbase.sty
Package: scrkbase 2021/03/17 v3.33 KOMA-Script package (KOMA-Script-dependent b
asics and keyval usage)
(/usr/share/texmf-dist/tex/latex/koma-script/scrbase.sty
Package: scrbase 2021/03/17 v3.33 KOMA-Script package (KOMA-Script-independent 
basics and keyval usage)
(/usr/share/texmf-dist/tex/latex/koma-script/scrlfile.sty
Package: scrlfile 2021/03/17 v3.33 KOMA-Script package (file load hooks)
(/usr/share/texmf-dist/tex/latex/koma-script/scrlfile-hook.sty
Package: scrlfile-hook 2021/03/17 v3.33 KOMA-Script package (using LaTeX hooks)


LaTeX3 Info: Defining command \BeforeFile with sig. 'm' on line 61.


LaTeX3 Info: Defining command \AfterFile with sig. 'm' on line 65.


LaTeX3 Info: Defining command \BeforeClass with sig. 'm' on line 69.


LaTeX3 Info: Defining command \BeforePackage with sig. 'm' on line 73.


LaTeX3 Info: Defining command \AfterAtEndOfClass with sig. 'smo+m' on line 83.


LaTeX3 Info: Defining command \AfterAtEndOfPackage with sig. 'smo+m' on line
(LaTeX3) 93.


LaTeX3 Info: Defining command \scrlfile@AfterClass with sig. 'smo+m' on line
(LaTeX3) 173.


LaTeX3 Info: Defining command \AfterClass with sig. '' on line 174.


LaTeX3 Info: Defining command \scrlfile@AfterPackage with sig. 'smo+m' on line
(LaTeX3) 191.


LaTeX3 Info: Defining command \AfterPackage with sig. '' on line 192.


LaTeX3 Info: Defining command \ReplaceInput with sig. '' on line 193.


LaTeX3 Info: Defining command \ReplaceClass with sig. 'mm' on line 196.


LaTeX3 Info: Defining command \ReplacePackage with sig. 'mm' on line 199.


LaTeX3 Info: Defining command \UnReplaceInput with sig. '' on line 200.


LaTeX3 Info: Defining command \UnReplaceClass with sig. 'm' on line 203.


LaTeX3 Info: Defining command \UnReplacePackage with sig. 'mm' on line 206.


LaTeX3 Info: Defining command \PreventPackageFromLoading with sig. 's+om' on
(LaTeX3) line 234.


LaTeX3 Info: Defining command \StorePreventPackageFromLoading with sig. 'm' on
(LaTeX3) line 242.


LaTeX3 Info: Defining command \ResetPreventPackageFromLoading with sig. '' on
(LaTeX3) line 247.


LaTeX3 Info: Defining command \UnPreventPackageFromLoading with sig. 'sm' on
(LaTeX3) line 261.


LaTeX3 Info: Defining command \BeforeClosingMainAux with sig. 'om' on line
(LaTeX3) 274.


LaTeX3 Info: Defining command \AfterReadingMainAux with sig. 'om' on line 287.


LaTeX3 Info: Defining command \protected@immediate@write with sig. 'm+m+m' on
(LaTeX3) line 298.

(/usr/share/texmf-dist/tex/latex/koma-script/scrlogo.sty
Package: scrlogo 2021/03/17 v3.33 KOMA-Script package (logo)
))) (/usr/share/texmf-dist/tex/latex/graphics/keyval.sty
Package: keyval 2014/10/28 v1.15 key=value parser (DPC)
\KV@toks@=\toks15
)
Skipping: [2021/05/01] Usage of raw option list on input line 252.
Applying: [/00/00] compatibility for LaTeX before 2021/05/01 on input line 
337.
)) (/usr/share/texmf-dist/tex/latex/koma-script/tocbasic.sty
Package: tocbasic 2021/03/17 v3.33 KOMA-Script package (handling toc-files)
\scr@dte@tocline@numberwidth=\skip47
\scr@dte@tocline@numbox=\box47
)
Package tocbasic Info: babel extension for `toc' omitted
(tocbasic) because of missing \bbl@set@language on input line 137.
Class scrreprt Info: File `scrsize11pt.clo' used instead of
(scrreprt)   file `scrsize11.clo' to setup font sizes on input line 245
1.
(/usr/share/texmf-dist/tex/latex/koma-script/scrsize11pt.clo
File: scrsize11pt.clo 2021/03/17 v3.33 KOMA-Script font size class option (11pt
)
) (/usr/share/texmf-dist/tex/latex/koma-script/typearea.sty
Package: typearea 2021/03/17 v3.33 KOMA-Script package (type area)
\ta@bcor=\skip48
\ta@div=\count179
\ta@hblk=\skip49
\ta@vblk=\skip50
\ta@temp=\skip51
\footheight=\skip52
Package typearea Info: These are the values describing the layout:
(typearea) DIV  = 10
(typearea) BCOR = 0.0pt
(typearea) \paperwidth  = 597.50793pt
(typearea)  \textwidth  = 418.2pt
(typearea)  DIV departure   = -6%
(typearea)  

Re: LaTeX warning explanation needed

[Rich Shepard]

On Thu, 14 Oct 2021, Paul A. Rubin wrote:


OK, after fixing the paragraph setting for the Van Doornik reference, I
got the MWE to compile by doing the following: in Document > Settings... >
Language > Encoding, I switched from Language default to "Other" and
selected "Unicode (utf8)".


Paul,

I wonder how that encoding was changed. The LyX document I last worked on
has the Language default selected; the Other shows a grey-out Unicode
(utf8).

So, the MWE displays the bibliography but the main document still does not
after changing the Language to Unicode (utf8).


I suspect there are some characters in the .bib file that are UTF-8 (which
is my default locale setting) but not "latin9".


$ locale
LANG=en_US.UTF-8
LC_CTYPE="en_US.UTF-8"
LC_NUMERIC="en_US.UTF-8"
LC_TIME="en_US.UTF-8"
LC_COLLATE=C
LC_MONETARY="en_US.UTF-8"
LC_MESSAGES="en_US.UTF-8"
LC_PAPER="en_US.UTF-8"
LC_NAME="en_US.UTF-8"
LC_ADDRESS="en_US.UTF-8"
LC_TELEPHONE="en_US.UTF-8"
LC_MEASUREMENT="en_US.UTF-8"
LC_IDENTIFICATION="en_US.UTF-8"
LC_ALL=

There's no latin9 here, either.


So the log file contained some nonspecific bitching and moaning about
latin9, which led me to discover that the default encoding (at least on my
system) was latin9, and that wasn't cutting it.


Here, the JabRef settings also specify UTF8 (see attached) so I've no idea
where LyX is seeing latin9.

Thanks,

Rich-- 
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Paul A. Rubin]

On 10/14/21 2:27 PM, Rich Shepard wrote:

On Thu, 14 Oct 2021, Paul A. Rubin wrote:


Assuming your .bib file does not contain state secrets, how about the
following? Create a new LyX doc (MWE) in which you just cite everything
that gets cited in the actual document. We don't need headings, images,
text etc., just the citations. Try compiling that. Assuming the same
problems occur, post the LyX MWE and the .bib file and let our resident
biblatex experts (of whom I am decidedly not one) try for themselves.


Paul,

Good idea, I might have thought of this instead of chasing my tail in
circles. See both mwe.lyx and mwe.pdf attached.

Looks like the issue is with Keefer, et al. 2008.

I'll look at that while folks examine the .lyx file.

Thanks,

Rich

OK, after fixing the paragraph setting for the Van Doornik reference, I 
got the MWE to compile by doing the following: in Document > Settings... 
> Language > Encoding, I switched from Language default to "Other" and 
selected "Unicode (utf8)". I suspect there are some characters in the 
.bib file that are UTF-8 (which is my default locale setting) but not 
"latin9". So the log file contained some nonspecific bitching and 
moaning about latin9, which led me to discover that the default encoding 
(at least on my system) was latin9, and that wasn't cutting it.


Paul

-- 
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Paul A. Rubin]

On 10/14/21 2:27 PM, Rich Shepard wrote:

On Thu, 14 Oct 2021, Paul A. Rubin wrote:


Assuming your .bib file does not contain state secrets, how about the
following? Create a new LyX doc (MWE) in which you just cite everything
that gets cited in the actual document. We don't need headings, images,
text etc., just the citations. Try compiling that. Assuming the same
problems occur, post the LyX MWE and the .bib file and let our resident
biblatex experts (of whom I am decidedly not one) try for themselves.


Paul,

Good idea, I might have thought of this instead of chasing my tail in
circles. See both mwe.lyx and mwe.pdf attached.

Looks like the issue is with Keefer, et al. 2008.

I'll look at that while folks examine the .lyx file.

Thanks,

Rich

Fair warning to others: There's a bug in the MWE that is probably 
separate from what is actually ailing Rich's document. In the MWE, the 
Van Doornik reference is in a "Titlehead" environment (the others are 
"Standard"), and that causes it's own set of problems.


Paul

-- 
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Rich Shepard]

On Thu, 14 Oct 2021, Paul A. Rubin wrote:


The runaway string messages suggest that biblatex is choking on something
in your reference file, but as I mentioned just now on the list, without
the .bib file we can't diagnose anything specific. Note that copying from
the .bib file and pasting into an email message may not help, because the
copy/paste sequence has been known to change the encodings of some
strings. I periodically need to copy stuff from an IDE (such as RStudio)
and paste it into an email address, and quotation marks and a few other
characters get mangled in the process. So I copy from RStudio, paste into
a text editor, copy from the text editor, paste into the email message,
and everything magically works.


Paul,

I view/edit the database .bib file in emacs. It's all plain ASCII text.

Regardless, there're no secrets in my scientific references database. I just
uploaded a copy to fileconvoy from where it can be downloaded over the next
5 days:


I'd sure like to get this all fixed once-and-for-all.

Thanks,

Rich
--
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Paul A. Rubin]

On 10/14/21 2:27 PM, Rich Shepard wrote:

On Thu, 14 Oct 2021, Paul A. Rubin wrote:


Assuming your .bib file does not contain state secrets, how about the
following? Create a new LyX doc (MWE) in which you just cite everything
that gets cited in the actual document. We don't need headings, images,
text etc., just the citations. Try compiling that. Assuming the same
problems occur, post the LyX MWE and the .bib file and let our resident
biblatex experts (of whom I am decidedly not one) try for themselves.


Paul,

Good idea, I might have thought of this instead of chasing my tail in
circles. See both mwe.lyx and mwe.pdf attached.

Looks like the issue is with Keefer, et al. 2008.

I'll look at that while folks examine the .lyx file.

Thanks,

Rich

I created a .bib file with just your Keefer entry (from your next 
message in the thread), stripped all cites other than Keefer out of you 
LyX file, and it compiled OK.


To diagnose this, we need your "jabrefdb" file.

Paul

-- 
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Rich Shepard]

On Thu, 14 Oct 2021, Rich Shepard wrote:


Looks like the issue is with Keefer, et al. 2008.


Here's the biblatex entry for that paper:
@Article{Keefer2008,
  author   = {Keefer, M.L. and Boggs, C.T. and Peery, C.A. and Caudill, C.C.},
  journal  = {North American Journal of Fisheries Management},
  title= {Overwintering Distribution, Behavior, and Survival of Adult 
Summer Steelhead: Variability among Columbia River Populations},
  year = {2008},
  pages= {81--96},
  volume   = {28},
  abstract = {Unlike most anadromous salmonids, summer steelhead Oncorhynchus
  mykiss overwinter in rivers rather than the ocean for 6--10
  months prior to spring spawning. Overwintering in rivers may
  make summer steelhead more vulnerable to harvest and other
  mortality sources than are other anadromous populations, but
  there has been little systematic study of this life history
  strategy. Here, we used a large-scale radiotelemetry study
  to examine the overwintering behaviors and distributions of
  26 summer steelhead stocks within the regulated lower
  Columbia-Snake River hydrosystem. Over 6 years, we monitored
  5,939 fish, of which 3,399 successfully reached spawning
  tributaries or the upper Columbia River basin and were
  assigned to specific populations. An estimated 12.\% of fish
  that reached spawning areas overwintered at least partially
  within the hydrosystem (annual estimates = 6.8--19.6\%),
  while the remainder overwintered in tributaries. Across all
  populations, later-arriving fish were more likely to
  overwinter in the hydrosystem; overwintering percentages
  ranged from less than 1\% for fish tagged in June to over
  40\% for those tagged in October. Proportionately more
  interior-basin steelhead (Clearwater, Salmon, and Snake
  River metapopulations) overwintered in the hydrosystem than
  did fish from lower-river populations. Steelhead were
  distributed in mixed-stock assemblages throughout the
  hydrosystem during winter, usually in reservoirs closest to
  their home rivers but also in nonnatal tributaries.
  Overwintering fish moved upstream and downstream between
  reaches in all months; a nadir occurred in early January and
  peak egress into spawning tributaries was in March. The
  estimated survival to tributaries was higher for fish that
  overwintered in the hydrosystem (82\%) than for fish that
  did not (62\%); this difference was largely attributable to
  low winter harvest rates. Our results suggest that large
  main-stem habitats, including reservoirs, may be widely used
  by overwintering summer steelhead. The complex migration
  behaviors of steelhead indicate both the potential for
  adaptation and possible susceptibility to future river
  environment changes.},
  keywords = {fish, salmon, steelhead, trout, rivers, Columbia River, 
distribution, behavior, survival, adults},
}

Are the '%' symbols not correctly escaped?

Rich
--
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Rich Shepard]

On Thu, 14 Oct 2021, Paul A. Rubin wrote:


Assuming your .bib file does not contain state secrets, how about the
following? Create a new LyX doc (MWE) in which you just cite everything
that gets cited in the actual document. We don't need headings, images,
text etc., just the citations. Try compiling that. Assuming the same
problems occur, post the LyX MWE and the .bib file and let our resident
biblatex experts (of whom I am decidedly not one) try for themselves.


Paul,

Good idea, I might have thought of this instead of chasing my tail in
circles. See both mwe.lyx and mwe.pdf attached.

Looks like the issue is with Keefer, et al. 2008.

I'll look at that while folks examine the .lyx file.

Thanks,

Rich#LyX 2.3 created this file. For more info see http://www.lyx.org/
\lyxformat 544
\begin_document
\begin_header
\save_transient_properties true
\origin unavailable
\textclass scrreprt
\begin_preamble
\date{}
\end_preamble
\use_default_options false
\maintain_unincluded_children false
\language english
\language_package default
\inputencoding auto
\fontencoding global
\font_roman "palatino" "default"
\font_sans "default" "default"
\font_typewriter "default" "default"
\font_math "auto" "auto"
\font_default_family default
\use_non_tex_fonts false
\font_sc false
\font_osf false
\font_sf_scale 100 100
\font_tt_scale 100 100
\use_microtype false
\use_dash_ligatures true
\graphics default
\default_output_format pdf2
\output_sync 0
\bibtex_command default
\index_command default
\paperfontsize default
\spacing single
\use_hyperref false
\papersize letterpaper
\use_geometry true
\use_package amsmath 1
\use_package amssymb 1
\use_package cancel 1
\use_package esint 0
\use_package mathdots 0
\use_package mathtools 1
\use_package mhchem 1
\use_package stackrel 1
\use_package stmaryrd 1
\use_package undertilde 1
\cite_engine biblatex-natbib
\cite_engine_type authoryear
\biblio_style plain
\biblatex_bibstyle authoryear
\biblatex_citestyle authoryear
\use_bibtopic false
\use_indices false
\paperorientation portrait
\suppress_date false
\justification true
\use_refstyle 0
\use_minted 0
\index Index
\shortcut idx
\color #008000
\end_index
\leftmargin 2cm
\topmargin 4cm
\bottommargin 2cm
\headsep 1.5cm
\secnumdepth 3
\tocdepth 3
\paragraph_separation skip
\defskip medskip
\is_math_indent 0
\math_numbering_side default
\quotes_style english
\dynamic_quotes 0
\papercolumns 1
\papersides 2
\paperpagestyle fancy
\tracking_changes false
\output_changes false
\html_math_output 0
\html_css_as_file 0
\html_be_strict false
\end_header

\begin_body

\begin_layout Standard
MWE
\end_layout

\begin_layout Standard
\begin_inset CommandInset citation
LatexCommand cite
key "Groot1991"
literal "true"

\end_inset


\end_layout

\begin_layout Standard
\begin_inset CommandInset citation
LatexCommand cite
key "Marcoe2018"
literal "true"

\end_inset


\end_layout

\begin_layout Titlehead
\begin_inset CommandInset citation
LatexCommand cite
key "VanDoornik2019"
literal "true"

\end_inset


\end_layout

\begin_layout Standard
\begin_inset CommandInset citation
LatexCommand cite
key "Keefer2008"
literal "true"

\end_inset


\end_layout

\begin_layout Standard
\begin_inset CommandInset citation
LatexCommand cite
key "Johnson2005"
literal "true"

\end_inset


\end_layout

\begin_layout Standard
\begin_inset CommandInset citation
LatexCommand cite
key "McCabe1994"
literal "true"

\end_inset


\end_layout

\begin_layout Standard
\begin_inset CommandInset citation
LatexCommand cite
key "Poole2001"
literal "true"

\end_inset


\end_layout

\begin_layout Standard

\end_layout

\begin_layout Standard
\begin_inset CommandInset bibtex
LatexCommand bibtex
btprint "btPrintCited"
bibfiles "/home/rshepard/documents/jabrefdb"
options "bibtotoc,plain"

\end_inset


\end_layout

\end_body
\end_document


mwe.pdf
Description: Adobe PDF document
-- 
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Paul A. Rubin]

On 10/14/21 1:28 PM, Rich Shepard wrote:

On Thu, 14 Oct 2021, Rich Shepard wrote:


But after that I'm getting an error re-running pdflatex. It refers to a
runaway argument in a text paragraph. Since this happened on the 
second run
which has a bibliographic citation at the end the issue might be with 
that

entry in the database.


Fixed the bibliography database entry ... I think.

I need to confirm what I'm doing; there's an issue with the bibliography
insert at the end of the document.

1. pdflatex file.tex
2. biber file.bcf
3. pdflatex file.tex

Output:
! Package inputenc Error: Keyboard character used is undefined
(inputenc)    in inputencoding `latin9'.

See the inputenc package documentation for explanation.
Type  H   for immediate help.
 ...

l.602 \printbibliography[heading=bibintoc]

?

Why is inputencoding `latin9' when local is en_US.UTF-8?

Where do I find the inputenc package docs?

Exporting the .lyx file to pdflatex produces the same message about 
running

biber:
Package biblatex Warning: Please (re)run Biber on the file:
(biblatex)    biological-evaluation
(biblatex)    and rerun LaTeX afterwards.

Exporting to latex (pdflatex) and building from that provides more 
explicit

error information so I need to learn how to fix it.

Should I provide all Settings -> Bibliography key:value pairs?

Rich
Assuming your .bib file does not contain state secrets, how about the 
following? Create a new LyX doc (MWE) in which you just cite everything 
that gets cited in the actual document. We don't need headings, images, 
text etc., just the citations. Try compiling that. Assuming the same 
problems occur, post the LyX MWE and the .bib file and let our resident 
biblatex experts (of whom I am decidedly not one) try for themselves.


Paul
--
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Rich Shepard]

On Thu, 14 Oct 2021, Herbert Voss wrote:


\texttt{foo
here comes another text with paragraphs and so on



The argument of \texttt is a "runaway argunent" , the closing }
wasn't found.


Herbert,

Thank you.

The jabrefdb has all key:value pairs for the citation at the end of that
paragraph enclosed in curley braces.

The issue now is the Biblatex Generated Bibliography box at the end of the
document highlighted with the input encoding error I provided in my recent
post.

Regards,

Rich
--
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Rich Shepard]

On Thu, 14 Oct 2021, Rich Shepard wrote:


But after that I'm getting an error re-running pdflatex. It refers to a
runaway argument in a text paragraph. Since this happened on the second run
which has a bibliographic citation at the end the issue might be with that
entry in the database.


Fixed the bibliography database entry ... I think.

I need to confirm what I'm doing; there's an issue with the bibliography
insert at the end of the document.

1. pdflatex file.tex
2. biber file.bcf
3. pdflatex file.tex

Output:
! Package inputenc Error: Keyboard character used is undefined
(inputenc)in inputencoding `latin9'.

See the inputenc package documentation for explanation.
Type  H   for immediate help.
 ...

l.602 \printbibliography[heading=bibintoc]

?

Why is inputencoding `latin9' when local is en_US.UTF-8?

Where do I find the inputenc package docs?

Exporting the .lyx file to pdflatex produces the same message about running
biber:
Package biblatex Warning: Please (re)run Biber on the file:
(biblatex)biological-evaluation
(biblatex)and rerun LaTeX afterwards.

Exporting to latex (pdflatex) and building from that provides more explicit
error information so I need to learn how to fix it.

Should I provide all Settings -> Bibliography key:value pairs?

Rich
--
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Herbert Voss]

Am 14.10.21 um 18:55 schrieb Rich Shepard:

On Thu, 14 Oct 2021, Axel Dessecker wrote:

I'm aware what a warning is. This one explicitly tells you what to 
do: you

have to "run Biber on the file biological-evaluation and rerun LaTeX
afterwards‟. Biber's messages tend to be very helpful in cases where you
don't get the bibliography you want.


Axel,

I exported to LaTeX (pdflatex) and ran pdflatex on the *.tex file. Didn't
know the file to feed to biber.

Now I do, and biber ran to completion without errors.

But after that I'm getting an error re-running pdflatex. It refers to a
runaway argument in a text paragraph. Since this happened on the 
second run
which has a bibliographic citation at the end the issue might be with 
that

entry in the database.

I'm looking at that entry after I understand 'runaway argument.'



\texttt{foo
here comes another text with paragraphs and so on


The argument of \texttt is a "runaway argunent" , the closing }
wasn't found.

Herbert
--
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Rich Shepard]

On Thu, 14 Oct 2021, Axel Dessecker wrote:


I'm aware what a warning is. This one explicitly tells you what to do: you
have to "run Biber on the file biological-evaluation and rerun LaTeX
afterwards‟. Biber's messages tend to be very helpful in cases where you
don't get the bibliography you want.


Axel,

I exported to LaTeX (pdflatex) and ran pdflatex on the *.tex file. Didn't
know the file to feed to biber.

Now I do, and biber ran to completion without errors.

But after that I'm getting an error re-running pdflatex. It refers to a
runaway argument in a text paragraph. Since this happened on the second run
which has a bibliographic citation at the end the issue might be with that
entry in the database.

I'm looking at that entry after I understand 'runaway argument.'

Thanks,

Rich

--
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Herbert Voss]

Am 14.10.21 um 17:47 schrieb Rich Shepard:

On Thu, 14 Oct 2021, Axel Dessecker wrote:


LaTeX Warning: There were undefined references.
Package biblatex Warning: Please (re)run Biber on the file:
(biblatex)    biological-evaluation
(biblatex)    and rerun LaTeX afterwards.


In the PWD are these files:
$ ls
#biological-evaluation.lyx#  biological-evaluation.lyx 
biological-evaluation.tex.dep-pdf
biological-evaluation.aux    biological-evaluation.lyx.bbl 
biological-evaluation.tex.log
biological-evaluation.bcf    biological-evaluation.lyx.blg 
biological-evaluation.toc

biological-evaluation.lof    biological-evaluation.pdf
biological-evaluation.log    biological-evaluation.run.xml

I copied the LaTeX/pdflatex output in the /tmp/lyx_* directory.

Then I ran biber on the *.lyx file:
$ biber biological-evaluation.lyx INFO - This is Biber 2.14
INFO - Logfile is 'biological-evaluation.lyx.blg'
ERROR - Cannot find 'biological-evaluation.lyx.bcf'!
INFO - ERRORS: 1

but the file is present in the same directory. And it's 102032 bytes in
size.

Please suggest how I trace the error source.



You have to _export_ the LyX file tp (pdf) latex and then run
pdflatex  file.tex
biber file
pdflatex file

Herbert

--
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Axel Dessecker]

Am Donnerstag, 14. Oktober 2021, 17:39:38 CEST schrieb Rich Shepard:
> On Thu, 14 Oct 2021, Axel Dessecker wrote:
> > starting from line 847 of your log file you find the following
> > information:
> > LaTeX Warning: There were undefined references.
> > Package biblatex Warning: Please (re)run Biber on the file:
> > (biblatex)biological-evaluation
> > (biblatex)and rerun LaTeX afterwards.
> 
> Axel,
> 
> Warnings are just that; they don't prevent compiling the document.
> 
> The error must be with biblatex, Biber, or the database. I scanned the
> latter for non-ASCII characters (it's in utf-8 encoding) and found none.
> 
> I'll read the biblatex.pdf again to learn how to run biber on the database;
> I guess that's the place to start.
> 
> Rich

Rich,

I'm aware what a warning is. This one explicitly tells you what to do: you 
have to "run Biber on the file biological-evaluation and rerun LaTeX 
afterwards‟. Biber's messages tend to be very helpful in cases where you don't 
get the bibliography you want.

Axel



-- 
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Rich Shepard]

On Thu, 14 Oct 2021, Axel Dessecker wrote:


LaTeX Warning: There were undefined references.
Package biblatex Warning: Please (re)run Biber on the file:
(biblatex)biological-evaluation
(biblatex)and rerun LaTeX afterwards.


In the PWD are these files:
$ ls
#biological-evaluation.lyx#  biological-evaluation.lyx  
biological-evaluation.tex.dep-pdf
biological-evaluation.auxbiological-evaluation.lyx.bbl  
biological-evaluation.tex.log
biological-evaluation.bcfbiological-evaluation.lyx.blg  
biological-evaluation.toc
biological-evaluation.lofbiological-evaluation.pdf
biological-evaluation.logbiological-evaluation.run.xml

I copied the LaTeX/pdflatex output in the /tmp/lyx_* directory.

Then I ran biber on the *.lyx file:
$ biber biological-evaluation.lyx 
INFO - This is Biber 2.14

INFO - Logfile is 'biological-evaluation.lyx.blg'
ERROR - Cannot find 'biological-evaluation.lyx.bcf'!
INFO - ERRORS: 1

but the file is present in the same directory. And it's 102032 bytes in
size.

Please suggest how I trace the error source.

Rich
--
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Rich Shepard]

On Thu, 14 Oct 2021, Axel Dessecker wrote:


starting from line 847 of your log file you find the following information:
LaTeX Warning: There were undefined references.
Package biblatex Warning: Please (re)run Biber on the file:
(biblatex)biological-evaluation
(biblatex)and rerun LaTeX afterwards.


Axel,

Warnings are just that; they don't prevent compiling the document.

The error must be with biblatex, Biber, or the database. I scanned the
latter for non-ASCII characters (it's in utf-8 encoding) and found none.

I'll read the biblatex.pdf again to learn how to run biber on the database;
I guess that's the place to start.

Rich
--
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Dr Eberhard Lisse]

LOG files don't help.

MWE's do :-)-O

el

On 14/10/2021 00:47, Rich Shepard wrote:

The document now compiles without error using TeXLive2021 (and the
2020 version of texlive-extra), but the bibliography still does not
print in the PDF.

The latex.log has these warnings:
LaTeX Warning: Citation 'Groot1991' on page 4 undefined on input line 151.
LaTeX Warning: Citation 'Marcoe2018' on page 4 undefined on input line 167.

Lines 149-151 in the .lyx file are:
\begin_layout Standard
\begin_inset ERT
status open

and lines 163-167 are:
\begin_inset CommandInset toc
LatexCommand tableofcontents

\end_inset

There are other warnings at the top of the (attached) latex.log file
and I need help understanding what the warnings mean.

TIA,

Rich



--
To email me replace 'nospam' with 'el'

--
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Axel Dessecker]

Am Donnerstag, 14. Oktober 2021, 01:16:53 CEST schrieb Rich Shepard:
> On Wed, 13 Oct 2021, Paul A. Rubin wrote:
> > The line numbers refer to lines in the .tex file being compiled, not lines
> > in the .lyx file. The .tex file will be hiding in the temp directory LyX
> > is using.
> 
> Paul,
> 
> Well, that makes sense. The .tex file and it's other files seem to have
> vanished when I closed lyx. There's nothing in /tmp/.
> 
> More investigation tomorrow.
> 
> Thanks,
> 
> Rich

Good morning,

starting from line 847 of your log file you find the following information:

LaTeX Warning: There were undefined references.
Package biblatex Warning: Please (re)run Biber on the file:
(biblatex)biological-evaluation
(biblatex)and rerun LaTeX afterwards.

Axel



-- 
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Rich Shepard]

On Wed, 13 Oct 2021, Paul A. Rubin wrote:


The line numbers refer to lines in the .tex file being compiled, not lines
in the .lyx file. The .tex file will be hiding in the temp directory LyX
is using.


Paul,

Well, that makes sense. The .tex file and it's other files seem to have
vanished when I closed lyx. There's nothing in /tmp/.

More investigation tomorrow.

Thanks,

Rich
--
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

Re: LaTeX warning explanation needed

[Paul A. Rubin]

On 10/13/21 6:47 PM, Rich Shepard wrote:

The document now compiles without error using TeXLive2021 (and the 2020
version of texlive-extra), but the bibliography still does not print 
in the

PDF.

The latex.log has these warnings:
LaTeX Warning: Citation 'Groot1991' on page 4 undefined on input line 
151.
LaTeX Warning: Citation 'Marcoe2018' on page 4 undefined on input line 
167.


Lines 149-151 in the .lyx file are:
\begin_layout Standard
\begin_inset ERT
status open

and lines 163-167 are:
\begin_inset CommandInset toc
LatexCommand tableofcontents

\end_inset

There are other warnings at the top of the (attached) latex.log file 
and I

need help understanding what the warnings mean.

TIA,

Rich


Rich,

The line numbers refer to lines in the .tex file being compiled, not 
lines in the .lyx file. The .tex file will be hiding in the temp 
directory LyX is using.


Paul

-- 
lyx-users mailing list
lyx-users@lists.lyx.org
http://lists.lyx.org/mailman/listinfo/lyx-users

LaTeX warning explanation needed

[Rich Shepard]

The document now compiles without error using TeXLive2021 (and the 2020
version of texlive-extra), but the bibliography still does not print in the
PDF.

The latex.log has these warnings:
LaTeX Warning: Citation 'Groot1991' on page 4 undefined on input line 151.
LaTeX Warning: Citation 'Marcoe2018' on page 4 undefined on input line 167.

Lines 149-151 in the .lyx file are:
\begin_layout Standard
\begin_inset ERT
status open

and lines 163-167 are:
\begin_inset CommandInset toc
LatexCommand tableofcontents

\end_inset

There are other warnings at the top of the (attached) latex.log file and I
need help understanding what the warnings mean.

TIA,

Rich
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2021 on Slint) 
(preloaded format=pdflatex 2021.10.13)  13 OCT 2021 15:36
entering extended mode
 restricted \write18 enabled.
 %&-line parsing enabled.
**biological-evaluation.tex
(./biological-evaluation.tex
LaTeX2e <2020-10-01> patch level 4
L3 programming layer <2021-02-18>
(/usr/share/texmf-dist/tex/latex/koma-script/scrreprt.cls
Document Class: scrreprt 2021/03/17 v3.33 KOMA-Script document class (report)
(/usr/share/texmf-dist/tex/latex/koma-script/scrkbase.sty
Package: scrkbase 2021/03/17 v3.33 KOMA-Script package (KOMA-Script-dependent b
asics and keyval usage)
(/usr/share/texmf-dist/tex/latex/koma-script/scrbase.sty
Package: scrbase 2021/03/17 v3.33 KOMA-Script package (KOMA-Script-independent 
basics and keyval usage)
(/usr/share/texmf-dist/tex/latex/koma-script/scrlfile.sty
Package: scrlfile 2021/03/17 v3.33 KOMA-Script package (file load hooks)
(/usr/share/texmf-dist/tex/latex/koma-script/scrlfile-hook.sty
Package: scrlfile-hook 2021/03/17 v3.33 KOMA-Script package (using LaTeX hooks)


LaTeX3 Info: Defining command \BeforeFile with sig. 'm' on line 61.


LaTeX3 Info: Defining command \AfterFile with sig. 'm' on line 65.


LaTeX3 Info: Defining command \BeforeClass with sig. 'm' on line 69.


LaTeX3 Info: Defining command \BeforePackage with sig. 'm' on line 73.


LaTeX3 Info: Defining command \AfterAtEndOfClass with sig. 'smo+m' on line 83.


LaTeX3 Info: Defining command \AfterAtEndOfPackage with sig. 'smo+m' on line
(LaTeX3) 93.


LaTeX3 Info: Defining command \scrlfile@AfterClass with sig. 'smo+m' on line
(LaTeX3) 173.


LaTeX3 Info: Defining command \AfterClass with sig. '' on line 174.


LaTeX3 Info: Defining command \scrlfile@AfterPackage with sig. 'smo+m' on line
(LaTeX3) 191.


LaTeX3 Info: Defining command \AfterPackage with sig. '' on line 192.


LaTeX3 Info: Defining command \ReplaceInput with sig. '' on line 193.


LaTeX3 Info: Defining command \ReplaceClass with sig. 'mm' on line 196.


LaTeX3 Info: Defining command \ReplacePackage with sig. 'mm' on line 199.


LaTeX3 Info: Defining command \UnReplaceInput with sig. '' on line 200.


LaTeX3 Info: Defining command \UnReplaceClass with sig. 'm' on line 203.


LaTeX3 Info: Defining command \UnReplacePackage with sig. 'mm' on line 206.


LaTeX3 Info: Defining command \PreventPackageFromLoading with sig. 's+om' on
(LaTeX3) line 234.


LaTeX3 Info: Defining command \StorePreventPackageFromLoading with sig. 'm' on
(LaTeX3) line 242.


LaTeX3 Info: Defining command \ResetPreventPackageFromLoading with sig. '' on
(LaTeX3) line 247.


LaTeX3 Info: Defining command \UnPreventPackageFromLoading with sig. 'sm' on
(LaTeX3) line 261.


LaTeX3 Info: Defining command \BeforeClosingMainAux with sig. 'om' on line
(LaTeX3) 274.


LaTeX3 Info: Defining command \AfterReadingMainAux with sig. 'om' on line 287.


LaTeX3 Info: Defining command \protected@immediate@write with sig. 'm+m+m' on
(LaTeX3) line 298.

(/usr/share/texmf-dist/tex/latex/koma-script/scrlogo.sty
Package: scrlogo 2021/03/17 v3.33 KOMA-Script package (logo)
))) (/usr/share/texmf-dist/tex/latex/graphics/keyval.sty
Package: keyval 2014/10/28 v1.15 key=value parser (DPC)
\KV@toks@=\toks15
)
Skipping: [2021/05/01] Usage of raw option list on input line 252.
Applying: [/00/00] compatibility for LaTeX before 2021/05/01 on input line 
337.
)) (/usr/share/texmf-dist/tex/latex/koma-script/tocbasic.sty
Package: tocbasic 2021/03/17 v3.33 KOMA-Script package (handling toc-files)
\scr@dte@tocline@numberwidth=\skip47
\scr@dte@tocline@numbox=\box47
)
Package tocbasic Info: babel extension for `toc' omitted
(tocbasic) because of missing \bbl@set@language on input line 137.
Class scrreprt Info: File `scrsize11pt.clo' used instead of
(scrreprt)   file `scrsize11.clo' to setup font sizes on input line 245
1.
(/usr/share/texmf-dist/tex/latex/koma-script/scrsize11pt.clo
File: scrsize11pt.clo 2021/03/17 v3.33 KOMA-Script font size class option (11pt
)
) (/usr/share/texmf-dist/tex/latex/koma-script/typearea.sty
Package: typearea 2021/03/17 v3.33 KOMA-Script package (type area)
\ta@bcor=\skip48
\ta@div=\count179
\ta@hblk=\skip49
\ta@vblk=\skip50
\ta@temp=\skip51
\footheight=\skip52
Package typearea Info: These are the values describing the