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I use the subcaption package in a 2-column document (specifically \documentclass[journal,twoside]{IEEEtran}) to create an overall figure that occupies one column and that consists of two side-by-side subfigures. I cannot get the two subfigures aligned; subfig(a) is on the lower left corner and ...

In case it helps resolve the "caption" warning message, here is the "pdflatex -v" output:
% pdflatex -v
pdfTeX using libpoppler 3.141592-1.40.3-2.2 (Web2C 7.5.6)
kpathsea version 3.5.6
Copyright 2007 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
Kpathsea is copyright 2007 Karl Berry and Olaf ...

I do not know what TeX distribution the system administrator installed on my system. Is there a way to find out?
Is it related to the "caption" warning message?

Yes, I did use copy-and-paste to save a couple dtx files!
Now that there is no error, I'd set aside the package manager issue.
Now I notice that the following message appears when I latex my .tex file:
"Package caption Warning: Unsupported document class (or package) detected,
(caption) usage of the ...

I re-installed it, using "latex caption.ins" and now there is no error. I don't know how to use "the package manager of [my] TeX distribution".

I installed the package by "latex caption.ins". And I reviewed the caption.log after installation and it does not indicate any error.
I am going to re-install it. Thanks.

I read that subfig is deprecated and one should use the subcaption package. I installed it and have the following files in my working directory:
% ls *sty
bicaption.sty caption2.sty caption3.sty caption.sty
ltcaption.sty newfloat.sty subcaption.sty

I also have them in ~/texmf/tex
I also did a ...

I have a my_fig.tex as follows:
\begin{figure}[tp]
\centering
\mbox{\input{my_code.tex}}
\caption[...]{....}
\end{figure}
and a my_code.tex as follows:
\fbox{\footnotesize
\parbox{1.5in}{\tt
\begin{tabbing}
...
\end{tabbing}
}}
I suspect that the combination of mbox , [url=http://latex-community ...

I tried \setlength{\fboxsep}{1pt} for example but it affects only the horizontal spacing, i.e., the spacing between the text and the box border on the left and right sides, but not the vertical spacing, i.e. top and bottom.
My figure is written as follows:

\begin{figure*}[!ht]
\begin{center ...

It is a common occurrence that text formatted in math mode in a regular text paragraph runs into the right margin. That is, it does not start in a new line. How to fix it? Thanks.