Your errors are only warnings and bad boxes.
Let us test another way. Please copy the following MWE (I used package filecontents to have bib file and TeX code together in one MWE) to your computer. Call the file mwe.tex.
\RequirePackage{filecontents}
\begin{filecontents}{\jobname.bib}
@book{browning2008basic,
title={Basic Plasma Physics},
author={Browning, B.},
isbn={9781409219194},
url={https://books.google.ie/books?id=pItUOwAACAAJ},
year={2008},
publisher={Lulu.com},
}
@inproceedings{Siegman:98,
author = {A. E. Siegman},
booktitle = {DPSS (Diode Pumped Solid State) Lasers: Applications and Issues},
journal = {DPSS (Diode Pumped Solid State) Lasers: Applications and Issues},
keywords = {},
pages = {MQ1},
publisher = {Optical Society of America},
title = {How to (Maybe) Measure Laser Beam Quality},
year = {1998},
url = {http://www.osapublishing.org/abstract.cfm?URI=DLAI-1998-MQ1},
doi = {10.1364/DLAI.1998.MQ1},
abstract = {},
}
@MastersThesis{lopez,
title = {No wayout},
school = {Universidad de Pamplona},
author = {P. Lopez},
year = {2007},
}
@misc{nistasd,
title = "",
author = "",
note = "\url{https://physics.nist.gov/PhysRefData/ASD/levels_form.html}",
year = ""
}
@article{doi:10.1063/1.2142102,
author = {Shinsuke Fujioka and Hiroaki Nishimura and Katsunobu Nishihara and Masakatsu Murakami and Youngces-G Kang and Qincui Gu and Keiji Nagai and Takayoshi Norimatsu and Noriaki Miyanaga and Yasukazu Izawa and Kunioki Mima and Yoshinori Shimada and Atsushi Sunahara and Hiroyuki Furukawa},
title = {Properties of ion debris emitted from laser-produced mass-limited tin plasmas for extreme ultraviolet light source applications},
journal = {Applied Physics Letters},
volume = {87},
number = {24},
pages = {241503},
year = {2005},
doi = {10.1063/1.2142102},
URL = {http://dx.doi.org/10.1063/1.2142102},
eprint = {http://dx.doi.org/10.1063/1.2142102}
}
\end{filecontents}
\documentclass[a4paper,12pt]{report}
%%%%%figure beyond 100
%\usepackage[titles]{tocloft}
%\cftsetindents{figure}{0em}{3.5em}
%\cftsetindents{table}{0em}{3.5em}
%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{graphicx,rotating}
\usepackage{multirow}
\usepackage{siunitx,booktabs}%for table decimals number
\sisetup{separate-uncertainty}%
\usepackage[export]{adjustbox}
\usepackage[sectionbib]{chapterbib}
\usepackage{setspace}
\onehalfspacing
\usepackage{amssymb}%checkmark on table
\usepackage{parskip}%paragraph separation
\setlength\parskip{5pt}%separation after title
\usepackage{fancyhdr}
\fancyfoot{}
\fancyhead{}
\pagestyle{fancy}
\fancyhead[R]{\textbf{\cfoot{\thepage}}}{\slshape \rightmark}
\renewcommand{\headrulewidth}{0pt} %lets the head rule disappear.
\lhead{\textbf{\nouppercase{\rightmark}}}
%\addtolength{\oddsidemargin}{2.cm}
\usepackage[left=3.5cm,right=2.5cm,top=3.5cm,bottom=4cm,headheight=1cm]{geometry}
\usepackage{wrapfig}
\usepackage{nccmath}
\usepackage{tabularx,ragged2e,booktabs,caption,makecell}
\usepackage[section]{placeins}
\usepackage[textfont=normalfont]{subcaption}
\usepackage{url}
\urlstyle{same}
\newcommand\apj{1925ApJ....61...38R} % Journal abbreviations
\addtolength{\topmargin}{.25in} %topmargin control
\setlength{\parindent}{0pt}
\setcounter{secnumdepth}{3} %to include subsection in table of cont.
\setcounter{tocdepth}{3}
\pagenumbering{roman} %change page number style
\flushbottom
\begin{document}
This is given problem to compile \cite{browning2008basic}
and this \cite{Siegman:98}.
and this \cite{lopez}
and this \cite{nistasd}
and this \cite{doi:10.1063/1.2142102}
\bibliographystyle{ieeetr}%\newpage\cleardoublepage
\bibliography{\jobname}
\end{document}
Then use the compiling chain
pdflatex mwe.tex
bibtex mwe
pdflatex mwe.tex
pdflatex mwe.tex
Do not forget bibtex mwe!
Then you should get the following pdf without errors and warnings (one warning comes from package filecontents, that is okay):

Check the result on your computer with mine results. If your result is different, add command \listfiles before \documentclass ... and check the log file. At the end you will find a list of used packages and version numbers. Please compare it with the following list, resulting with an current MiKTeX 2.9:
*File List*
filecontents.sty 2011/10/08 v1.3 Create an external file from within a LaTeX document
report.cls 2014/09/29 v1.4h Standard LaTeX document class
size12.clo 2014/09/29 v1.4h Standard LaTeX file (size option)
graphicx.sty 2017/06/01 v1.1a Enhanced LaTeX Graphics (DPC,SPQR)
keyval.sty 2014/10/28 v1.15 key=value parser (DPC)
graphics.sty 2017/06/25 v1.2c Standard LaTeX Graphics (DPC,SPQR)
trig.sty 2016/01/03 v1.10 sin cos tan (DPC)
graphics.cfg 2016/06/04 v1.11 sample graphics configuration
pdftex.def 2017/06/24 v1.0g Graphics/color driver for pdftex
rotating.sty 2016/08/11 v2.16d rotated objects in LaTeX
ifthen.sty 2014/09/29 v1.1c Standard LaTeX ifthen package (DPC)
multirow.sty 2016/11/25 v2.2 Span multiple rows of a table
siunitx.sty 2017/08/02 v2.7j A comprehensive (SI) units package
expl3.sty 2017/07/19 L3 programming layer (loader)
expl3-code.tex 2017/07/19 L3 programming layer
l3pdfmode.def 2017/03/18 v L3 Experimental driver: PDF mode
xparse.sty 2017/07/19 L3 Experimental document command parser
amstext.sty 2000/06/29 v2.01 AMS text
amsgen.sty 1999/11/30 v2.0 generic functions
array.sty 2016/10/06 v2.4d Tabular extension package (FMi)
l3keys2e.sty 2017/07/19 LaTeX2e option processing using LaTeX3 keys
translator.sty 2010/06/12 ver 1.10
translator-language-mappings.tex
booktabs.sty 2005/04/14 v1.61803 publication quality tables
adjustbox.sty 2012/05/21 v1.0 Adjusting TeX boxes (trim, clip, ...)
xkeyval.sty 2014/12/03 v2.7a package option processing (HA)
xkeyval.tex 2014/12/03 v2.7a key=value parser (HA)
adjcalc.sty 2012/05/16 v1.1 Provides advanced setlength with multiple back-ends (calc, etex, pgfmath)
trimclip.sty 2012/05/16 v1.0 Trim and clip general TeX material
collectbox.sty 2012/05/17 v0.4b Collect macro arguments as boxes
tc-pdftex.def 2012/05/13 v1.0 Clipping driver for pdftex
ifoddpage.sty 2016/04/23 v1.1 Conditionals for odd/even page detection
varwidth.sty 2009/03/30 ver 0.92; Variable-width minipages
chapterbib.sty 2010/09/18 v 1.17
setspace.sty 2011/12/19 v6.7a set line spacing
amssymb.sty 2013/01/14 v3.01 AMS font symbols
amsfonts.sty 2013/01/14 v3.01 Basic AMSFonts support
parskip.sty 2001/04/09 non-zero parskip adjustments
fancyhdr.sty 2017/06/30 v3.9a Extensive control of page headers and footers
geometry.sty 2010/09/12 v5.6 Page Geometry
ifpdf.sty 2017/03/15 v3.2 Provides the ifpdf switch
ifvtex.sty 2016/05/16 v1.6 Detect VTeX and its facilities (HO)
ifxetex.sty 2010/09/12 v0.6 Provides ifxetex conditional
geometry.cfg
wrapfig.sty 2003/01/31 v 3.6
nccmath.sty 2005/02/21 v1.2 Additional Math Commands (NCC)
amsmath.sty 2016/11/05 v2.16a AMS math features
amsbsy.sty 1999/11/29 v1.2d Bold Symbols
amsopn.sty 2016/03/08 v2.02 operator names
tabularx.sty 2016/02/03 v2.11 `tabularx' package (DPC)
ragged2e.sty 2009/05/21 v2.1 ragged2e Package (MS)
everysel.sty 2011/10/28 v1.2 EverySelectfont Package (MS)
caption.sty 2016/02/21 v3.3-144 Customizing captions (AR)
caption3.sty 2016/05/22 v1.7-166 caption3 kernel (AR)
makecell.sty 2009/08/03 V0.1e Managing of Tab Column Heads and Cells
placeins.sty 2005/04/18 v 2.2
subcaption.sty 2016/05/22 v1.1-161 Sub-captions (AR)
url.sty 2013/09/16 ver 3.4 Verb mode for urls, etc.
supp-pdf.mkii
epstopdf-base.sty 2016/05/15 v2.6 Base part for package epstopdf
infwarerr.sty 2016/05/16 v1.4 Providing info/warning/error messages (HO)
grfext.sty 2016/05/16 v1.2 Manage graphics extensions (HO)
kvdefinekeys.sty 2016/05/16 v1.4 Define keys (HO)
ltxcmds.sty 2016/05/16 v1.23 LaTeX kernel commands for general use (HO)
kvoptions.sty 2016/05/16 v3.12 Key value format for package options (HO)
kvsetkeys.sty 2016/05/16 v1.17 Key value parser (HO)
etexcmds.sty 2016/05/16 v1.6 Avoid name clashes with e-TeX commands (HO)
ifluatex.sty 2016/05/16 v1.4 Provides the ifluatex switch (HO)
pdftexcmds.sty 2017/03/19 v0.25 Utility functions of pdfTeX for LuaTeX (HO)
translator-basic-dictionary-English.dict
siunitx-abbreviations.cfg 2017/08/02 v2.7j siunitx: Abbreviated units
umsa.fd 2013/01/14 v3.01 AMS symbols A
umsb.fd 2013/01/14 v3.01 AMS symbols B
nistasd' in filechapter2/sourcespectra' on page 15 undefined and the same for the other one – user138824 Aug 30 '17 at 10:14authorfield to{NIST}and thetitlefield toAtomic Spectra Database Levels Form? – Mico Aug 30 '17 at 10:21bibtexorbiblatex, the former rarely support the@onlinetype, whereas the latter does. – daleif Aug 30 '17 at 10:29onlinetomisc– Mensch Aug 30 '17 at 11:18\citeinstructions. Please advise. – Mico Aug 30 '17 at 11:39