Secure Coding C/C++: String Vulnerabilities
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Package 'Pinsplus'
Package ‘PINSPlus’ August 6, 2020 Encoding UTF-8 Type Package Title Clustering Algorithm for Data Integration and Disease Subtyping Version 2.0.5 Date 2020-08-06 Author Hung Nguyen, Bang Tran, Duc Tran and Tin Nguyen Maintainer Hung Nguyen <[email protected]> Description Provides a robust approach for omics data integration and disease subtyping. PIN- SPlus is fast and supports the analysis of large datasets with hundreds of thousands of sam- ples and features. The software automatically determines the optimal number of clus- ters and then partitions the samples in a way such that the results are ro- bust against noise and data perturbation (Nguyen et.al. (2019) <DOI: 10.1093/bioinformat- ics/bty1049>, Nguyen et.al. (2017)<DOI: 10.1101/gr.215129.116>). License LGPL Depends R (>= 2.10) Imports foreach, entropy , doParallel, matrixStats, Rcpp, RcppParallel, FNN, cluster, irlba, mclust RoxygenNote 7.1.0 Suggests knitr, rmarkdown, survival, markdown LinkingTo Rcpp, RcppArmadillo, RcppParallel VignetteBuilder knitr NeedsCompilation yes Repository CRAN Date/Publication 2020-08-06 21:20:02 UTC R topics documented: PINSPlus-package . .2 AML2004 . .2 KIRC ............................................3 PerturbationClustering . .4 SubtypingOmicsData . .9 1 2 AML2004 Index 13 PINSPlus-package Perturbation Clustering for data INtegration and disease Subtyping Description This package implements clustering algorithms proposed by Nguyen et al. (2017, 2019). Pertur- bation Clustering for data INtegration and disease Subtyping (PINS) is an approach for integraton of data and classification of diseases into various subtypes. PINS+ provides algorithms support- ing both single data type clustering and multi-omics data type. PINSPlus is an improved version of PINS by allowing users to customize the based clustering algorithm and perturbation methods. -
JHDF5 (HDF5 for Java) 19.04
JHDF5 (HDF5 for Java) 19.04 Introduction HDF5 is an efficient, well-documented, non-proprietary binary data format and library developed and maintained by the HDF Group. The library provided by the HDF Group is written in C and available under a liberal BSD-style Open Source software license. It has over 600 API calls and is very powerful and configurable, but it is not trivial to use. SIS (formerly CISD) has developed an easy-to-use high-level API for HDF5 written in Java and available under the Apache License 2.0 called JHDF5. The API works on top of the low-level API provided by the HDF Group and the files created with the SIS API are fully compatible with HDF5 1.6/1.8/1.10 (as you choose). Table of Content Introduction ................................................................................................................................ 1 Table of Content ...................................................................................................................... 1 Simple Use Case .......................................................................................................................... 2 Overview of the library ............................................................................................................... 2 Numeric Data Types .................................................................................................................... 3 Compound Data Types ................................................................................................................ 4 System -
System Calls and I/O
System Calls and I/O CS 241 January 27, 2012 Copyright ©: University of Illinois CS 241 Staff 1 This lecture Goals Get you familiar with necessary basic system & I/O calls to do programming Things covered in this lecture Basic file system calls I/O calls Signals Note: we will come back later to discuss the above things at the concept level Copyright ©: University of Illinois CS 241 Staff 2 System Calls versus Function Calls? Copyright ©: University of Illinois CS 241 Staff 3 System Calls versus Function Calls Function Call Process fnCall() Caller and callee are in the same Process - Same user - Same “domain of trust” Copyright ©: University of Illinois CS 241 Staff 4 System Calls versus Function Calls Function Call System Call Process Process fnCall() sysCall() OS Caller and callee are in the same Process - Same user - OS is trusted; user is not. - Same “domain of trust” - OS has super-privileges; user does not - Must take measures to prevent abuse Copyright ©: University of Illinois CS 241 Staff 5 System Calls System Calls A request to the operating system to perform some activity System calls are expensive The system needs to perform many things before executing a system call The computer (hardware) saves its state The OS code takes control of the CPU, privileges are updated. The OS examines the call parameters The OS performs the requested function The OS saves its state (and call results) The OS returns control of the CPU to the caller Copyright ©: University of Illinois CS 241 Staff 6 Steps for Making a System Call -
Lecture 2: Variables and Primitive Data Types
Lecture 2: Variables and Primitive Data Types MIT-AITI Kenya 2005 1 In this lecture, you will learn… • What a variable is – Types of variables – Naming of variables – Variable assignment • What a primitive data type is • Other data types (ex. String) MIT-Africa Internet Technology Initiative 2 ©2005 What is a Variable? • In basic algebra, variables are symbols that can represent values in formulas. • For example the variable x in the formula f(x)=x2+2 can represent any number value. • Similarly, variables in computer program are symbols for arbitrary data. MIT-Africa Internet Technology Initiative 3 ©2005 A Variable Analogy • Think of variables as an empty box that you can put values in. • We can label the box with a name like “Box X” and re-use it many times. • Can perform tasks on the box without caring about what’s inside: – “Move Box X to Shelf A” – “Put item Z in box” – “Open Box X” – “Remove contents from Box X” MIT-Africa Internet Technology Initiative 4 ©2005 Variables Types in Java • Variables in Java have a type. • The type defines what kinds of values a variable is allowed to store. • Think of a variable’s type as the size or shape of the empty box. • The variable x in f(x)=x2+2 is implicitly a number. • If x is a symbol representing the word “Fish”, the formula doesn’t make sense. MIT-Africa Internet Technology Initiative 5 ©2005 Java Types • Integer Types: – int: Most numbers you’ll deal with. – long: Big integers; science, finance, computing. – short: Small integers. -
Chapter 4 Variables and Data Types
PROG0101 Fundamentals of Programming PROG0101 FUNDAMENTALS OF PROGRAMMING Chapter 4 Variables and Data Types 1 PROG0101 Fundamentals of Programming Variables and Data Types Topics • Variables • Constants • Data types • Declaration 2 PROG0101 Fundamentals of Programming Variables and Data Types Variables • A symbol or name that stands for a value. • A variable is a value that can change. • Variables provide temporary storage for information that will be needed during the lifespan of the computer program (or application). 3 PROG0101 Fundamentals of Programming Variables and Data Types Variables Example: z = x + y • This is an example of programming expression. • x, y and z are variables. • Variables can represent numeric values, characters, character strings, or memory addresses. 4 PROG0101 Fundamentals of Programming Variables and Data Types Variables • Variables store everything in your program. • The purpose of any useful program is to modify variables. • In a program every, variable has: – Name (Identifier) – Data Type – Size – Value 5 PROG0101 Fundamentals of Programming Variables and Data Types Types of Variable • There are two types of variables: – Local variable – Global variable 6 PROG0101 Fundamentals of Programming Variables and Data Types Types of Variable • Local variables are those that are in scope within a specific part of the program (function, procedure, method, or subroutine, depending on the programming language employed). • Global variables are those that are in scope for the duration of the programs execution. They can be accessed by any part of the program, and are read- write for all statements that access them. 7 PROG0101 Fundamentals of Programming Variables and Data Types Types of Variable MAIN PROGRAM Subroutine Global Variables Local Variable 8 PROG0101 Fundamentals of Programming Variables and Data Types Rules in Naming a Variable • There a certain rules in naming variables (identifier). -
15-122: Principles of Imperative Computation, Fall 2014 Lab 11: Strings in C
15-122: Principles of Imperative Computation, Fall 2014 Lab 11: Strings in C Tom Cortina(tcortina@cs) and Rob Simmons(rjsimmon@cs) Monday, November 10, 2014 For this lab, you will show your TA your answers once you complete your activities. Autolab is not used for this lab. SETUP: Make a directory lab11 in your private 15122 directory and copy the required lab files to your lab11 directory: cd private/15122 mkdir lab11 cp /afs/andrew.cmu.edu/usr9/tcortina/public/15122-f14/*.c lab11 1 Storing and using strings using C Load the file lab11ex1.c into a text editor. Read through the file and write down what you think the output will be before you run the program. (The ASCII value of 'a' is 97.) Then compile and run the program. Be sure to use all of the required flags for the C compiler. Answer the following questions on paper: Exercise 1. When word is initially printed out character by character, why does only one character get printed? Exercise 2. Change the program so word[3] = 'd'. Recompile and rerun. Explain the change in the output. Run valgrind on your program. How do the messages from valgrind correspond to the change we made? Exercise 3. Change word[3] back. Uncomment the code that treats the four character array word as a 32-bit integer. Compile and run again. Based on the answer, how are bytes of an integer stored on the computer where you are running your code? 2 Arrays of strings Load the file lab11ex2.c into a text editor. -
The Art of the Javascript Metaobject Protocol
The Art Of The Javascript Metaobject Protocol enough?Humphrey Ephraim never recalculate remains giddying: any precentorship she expostulated exasperated her nuggars west, is brocade Gus consultative too around-the-clock? and unbloody If dog-cheapsycophantical and or secularly, norman Partha how slicked usually is volatilisingPenrod? his nomadism distresses acceptedly or interlacing Card, and send an email to a recipient with. On Auslegung auf are Schallabstrahlung download the Aerodynamik von modernen Flugtriebwerken. This poll i send a naming convention, the art of metaobject protocol for the corresponding to. What might happen, for support, if you should load monkeypatched code in one ruby thread? What Hooks does Ruby have for Metaprogramming? Sass, less, stylus, aura, etc. If it finds one, it calls that method and passes itself as value object. What bin this optimization achieve? JRuby and the psd. Towards a new model of abstraction in software engineering. Buy Online in Aruba at aruba. The current run step approach is: Checkpoint. Python object room to provide usable string representations of hydrogen, one used for debugging and logging, another for presentation to end users. Method handles can we be used to implement polymorphic inline caches. Mop is not the metaobject? Rails is a nicely designed web framework. Get two FREE Books of character Moment sampler! The download the number IS still thought. This proxy therefore behaves equivalently to the card dispatch function, and no methods will be called on the proxy dispatcher before but real dispatcher is available. While desertcart makes reasonable efforts to children show products available in your kid, some items may be cancelled if funny are prohibited for import in Aruba. -
Julia's Efficient Algorithm for Subtyping Unions and Covariant
Julia’s Efficient Algorithm for Subtyping Unions and Covariant Tuples Benjamin Chung Northeastern University, Boston, MA, USA [email protected] Francesco Zappa Nardelli Inria of Paris, Paris, France [email protected] Jan Vitek Northeastern University, Boston, MA, USA Czech Technical University in Prague, Czech Republic [email protected] Abstract The Julia programming language supports multiple dispatch and provides a rich type annotation language to specify method applicability. When multiple methods are applicable for a given call, Julia relies on subtyping between method signatures to pick the correct method to invoke. Julia’s subtyping algorithm is surprisingly complex, and determining whether it is correct remains an open question. In this paper, we focus on one piece of this problem: the interaction between union types and covariant tuples. Previous work normalized unions inside tuples to disjunctive normal form. However, this strategy has two drawbacks: complex type signatures induce space explosion, and interference between normalization and other features of Julia’s type system. In this paper, we describe the algorithm that Julia uses to compute subtyping between tuples and unions – an algorithm that is immune to space explosion and plays well with other features of the language. We prove this algorithm correct and complete against a semantic-subtyping denotational model in Coq. 2012 ACM Subject Classification Theory of computation → Type theory Keywords and phrases Type systems, Subtyping, Union types Digital Object Identifier 10.4230/LIPIcs.ECOOP.2019.24 Category Pearl Supplement Material ECOOP 2019 Artifact Evaluation approved artifact available at https://dx.doi.org/10.4230/DARTS.5.2.8 Acknowledgements The authors thank Jiahao Chen for starting us down the path of understanding Julia, and Jeff Bezanson for coming up with Julia’s subtyping algorithm. -
Sun 64-Bit Binary Alignment Proposal
1 KMIP 64-bit Binary Alignment Proposal 2 3 To: OASIS KMIP Technical Committee 4 From: Matt Ball, Sun Microsystems, Inc. 5 Date: May 1, 2009 6 Version: 1 7 Purpose: To propose a change to the binary encoding such that each part is aligned to an 8-byte 8 boundary 9 10 Revision History 11 Version 1, 2009-05-01: Initial version 12 Introduction 13 The binary encoding as defined in the 1.0 version of the KMIP draft does not maintain alignment to 8-byte 14 boundaries within the message structure. This causes problems on hard-aligned processors, such as the 15 ARM, that are not able to easily access memory on addresses that are not aligned to 4 bytes. 16 Additionally, it reduces performance on modern 64-bit processors. For hard-aligned processors, when 17 unaligned memory contents are requested, either the compiler has to add extra instructions to perform 18 two aligned memory accesses and reassemble the data, or the processor has to take a „trap‟ (i.e., an 19 interrupt generated on unaligned memory accesses) to correctly assemble the memory contents. Either 20 of these options results in reduced performance. On soft-aligned processors, the hardware has to make 21 two memory accesses instead of one when the contents are not properly aligned. 22 This proposal suggests ways to improve the performance on hard-aligned processors by aligning all data 23 structures to 8-byte boundaries. 24 Summary of Proposed Changes 25 This proposal includes the following changes to the KMIP 0.98 draft submission to the OASIS KMIP TC: 26 Change the alignment of the KMIP binary encoding such that each part is aligned to an 8-byte 27 boundary. -
Making Classes Provable Through Contracts, Models and Frames
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by CiteSeerX DISS. ETH NO. 17610 Making classes provable through contracts, models and frames A dissertation submitted to the SWISS FEDERAL INSTITUTE OF TECHNOLOGY ZURICH (ETH Zurich)¨ for the degree of Doctor of Sciences presented by Bernd Schoeller Diplom-Informatiker, TU Berlin born April 5th, 1974 citizen of Federal Republic of Germany accepted on the recommendation of Prof. Dr. Bertrand Meyer, examiner Prof. Dr. Martin Odersky, co-examiner Prof. Dr. Jonathan S. Ostroff, co-examiner 2007 ABSTRACT Software correctness is a relation between code and a specification of the expected behavior of the software component. Without proper specifica- tions, correct software cannot be defined. The Design by Contract methodology is a way to tightly integrate spec- ifications into software development. It has proved to be a light-weight and at the same time powerful description technique that is accepted by software developers. In its more than 20 years of existence, it has demon- strated many uses: documentation, understanding object-oriented inheri- tance, runtime assertion checking, or fully automated testing. This thesis approaches the formal verification of contracted code. It conducts an analysis of Eiffel and how contracts are expressed in the lan- guage as it is now. It formalizes the programming language providing an operational semantics and a formal list of correctness conditions in terms of this operational semantics. It introduces the concept of axiomatic classes and provides a full library of axiomatic classes, called the mathematical model library to overcome prob- lems of contracts on unbounded data structures. -
Unibasic 9.3 Reference Guide
Unibasic - Dynamic Concepts Wiki 6/19/17, 1244 PM Unibasic From Dynamic Concepts Wiki Contents 1 UniBasic 2 About this Guide 2.1 Conventions 3 Installation & Configuration 3.1 Configuring Unix for UniBasic 3.1.1 Number of Processes 3.1.2 Number of Open Files 3.1.3 Number of Open i-nodes 3.1.4 Number of Locks 3.1.5 Message Queues 3.2 Unix Accounting & Protection System 3.3 Creating a Unix Account for UniBasic 3.4 UniBasic Security & Licensing 3.4.1 Software Licensing 3.4.2 Hardware Licensing 3.5 Loading the Installation File 3.5.1 Loading the UniBasic Installation File 3.5.2 Loading the UniBasic Development File 3.6 ubinstall - Installing UniBasic Packages 3.6.1 Errors During Installation 3.7 Configuring a UniBasic Environment 3.7.1 Directories and Paths 3.7.2 Filenames and Pathnames 3.7.3 Organizing Logical Units and Packnames 3.7.4 Environment Variables 3.7.5 Setting up .profile for Multiple Users 3.8 Command Line Interpreter 3.9 Launching UniBasic From Unix 3.10 Terminating a UniBasic Process 3.11 Licensing a New Installation 3.12 Changing the SSN Activation Key 3.13 Launching UniBasic Ports at Startup 3.14 Configuring Printer Drivers 3.15 Configuring Serial Printers 3.16 Configuring Terminal Drivers 3.17 Creating a Customized Installation Media 4 Introduction To UniBasic 4.1 Data 4.1.1 Numeric Data 4.1.1.1 Numeric Precision 4.1.1.2 Special Notes on %3 and %6 Numerics https://engineering.dynamic.com/mediawiki/index.php?title=Unibasic&printable=yes Page 1 of 397 Unibasic - Dynamic Concepts Wiki 6/19/17, 1244 PM 4.1.1.3 Integers Stored in Floating-Point -
Operating System Lab Manual
OPERATING SYSTEM LAB MANUAL BASICS OF UNIX COMMANDS Ex.No:1.a INTRODUCTION TO UNIX AIM: To study about the basics of UNIX UNIX: It is a multi-user operating system. Developed at AT & T Bell Industries, USA in 1969. Ken Thomson along with Dennis Ritchie developed it from MULTICS (Multiplexed Information and Computing Service) OS. By1980, UNIX had been completely rewritten using C langua ge. LINUX: It is similar to UNIX, which is created by Linus Torualds. All UNIX commands works in Linux. Linux is a open source software. The main feature of Linux is coexisting with other OS such as windows and UNIX. STRUCTURE OF A LINUXSYSTEM: It consists of three parts. a)UNIX kernel b) Shells c) Tools and Applications UNIX KERNEL: Kernel is the core of the UNIX OS. It controls all tasks, schedule all Processes and carries out all the functions of OS. Decides when one programs tops and another starts. SHELL: Shell is the command interpreter in the UNIX OS. It accepts command from the user and analyses and interprets them 1 | P a g e BASICS OF UNIX COMMANDS Ex.No:1.b BASIC UNIX COMMANDS AIM: To study of Basic UNIX Commands and various UNIX editors such as vi, ed, ex and EMACS. CONTENT: Note: Syn->Syntax a) date –used to check the date and time Syn:$date Format Purpose Example Result +%m To display only month $date+%m 06 +%h To display month name $date+%h June +%d To display day of month $date+%d O1 +%y To display last two digits of years $date+%y 09 +%H To display hours $date+%H 10 +%M To display minutes $date+%M 45 +%S To display seconds $date+%S 55 b) cal –used to display the calendar Syn:$cal 2 2009 c)echo –used to print the message on the screen.