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I am having issues with svjour3 the document is below. When I try to compile, I keep getting (and probably plenty more will come):

/usr/local/texlive/2018/texmf-dist/tex/latex/base/fontenc.sty|105 warning| LaTeX Font Warning: Font shape `T1/cmr/m/n' in size <9.5> not available size <9> substituted
/usr/local/texlive/2018/texmf-dist/tex/latex/amsmath/amsmath.sty|| Package amsmath Warning: Unable to redefine math accent \vec.
|51 warning| LaTeX Font Warning: Font shape `OT1/cmss/m/n' in size <9.5> not available size <9> substituted
|51 warning| LaTeX Font Warning: Font shape `OT1/cmtt/m/n' in size <9.5> not available size <9> substituted
frontmatter.tex|| Package mathptmx Warning: There are no bold math fonts on input line 13.
|| LaTeX Font Warning: Size substitutions with differences up to 0.5pt have occurred.

What do I have wrong (how to handle the vector symbol and the fonts?)?

\documentclass[smallcondensed,final,natbib]{svjour3}
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{graphicx}
\usepackage{mathptmx}% for type 1 fonts in math environment
\usepackage{amssymb}
\usepackage[sumlimits,intlimits]{mathtools}
\usepackage[version=4]{mhchem}% Chemical elements and equations
\usepackage{siunitx}
\usepackage{natbib}
\usepackage{apalike}
\usepackage{booktabs,tabularx}% general table environments
\usepackage{color}
\usepackage[table]{xcolor}% extending the color package
\usepackage{longtable}
\usepackage{makecell}
\usepackage{pdflscape}% to make the large data table in landscape mode
\usepackage{afterpage}% for the large data table
\usepackage[inline]{enumitem}% Control layout of itemize, enumerate, description
\usepackage{hyperref}

\begin{document}
    \title{my title}
    \author{me}
    \institute{someplace somewhere}
    \maketitle
    \begin{abstract}
        bla bla bla
        \keywords{nothing interesting}
        \PACS{1234}
    \end{abstract}
\end{document}
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The definition of \vec made by svjour3 is painfully wrong: it essentially does \mathbf, but in a very slow way.

Also mathptmx is a legacy of the olden times when there were very few fonts available. Use newtx instead.

Just undefine \vec before loading mathtools and redefine it later in a more sensible way. If you want bold italic for your vectors, load also \usepackage{bm} (after mathtools) and do \renewcommand{\vec}[1]{\bm{#1}}.

In order to avoid the spurious warning about size substitutions, load fix-cm.

\RequirePackage{fix-cm}
\documentclass[smallcondensed,final,natbib]{svjour3}
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}

\let\vec\relax % nullify the horrible definition of \vec
\DeclareMathAccent{\vec}{\mathord}{letters}{"7E} % restore the standard

\usepackage[sumlimits,intlimits]{mathtools}
\usepackage{newtxtext,newtxmath}% for type 1 fonts in math environment

\usepackage{graphicx}
\usepackage[version=4]{mhchem}% Chemical elements and equations
\usepackage{siunitx}
\usepackage{natbib}
\usepackage{apalike}
\usepackage{booktabs,tabularx}% general table environments
\usepackage{color}
\usepackage[table]{xcolor}% extending the color package
\usepackage{longtable}
\usepackage{makecell}
\usepackage{pdflscape}% to make the large data table in landscape mode
\usepackage{afterpage}% for the large data table
\usepackage[inline]{enumitem}% Control layout of itemize, enumerate, description
\usepackage{hyperref}

\renewcommand{\vec}[1]{\mathbf{#1}} % like Springer likes

\begin{document}
    \title{my title}
    \author{me}
    \institute{someplace somewhere}
    \maketitle
    \begin{abstract}
        bla bla bla
        \keywords{nothing interesting}
        \PACS{1234}
    \end{abstract}

This is a vector $\vec{v}$.

\end{document}

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