assignment of an object of class null is not valid

I'm wrestling with tximport/DESeq2. I've create a small experiment dataset of 2 paired end fastq, generated counts with salmon, and successfully read them in with tximport (or so I think). "files" is my list of 2 quant.sf files. tx2gene is the obvious.

> dds <- DESeqDataSetFromTximport(txi, sampleTable, ~tissue) Error in checkSlotAssignment(object, name, value) :    assignment of an object of class "NULL" is not valid for slot 'NAMES' in an object of class "DESeqDataSet"; is(value, "characterORNULL") is not TRUE

I've just recently installed R 3.4.0 and have update all packages. I see that there was some changes in S4 of renaming characterORNULL to character_OR_NULL; is this the issue?

Hi Michael,

Thanks for the response.

biocLite() looks clean:

For a brief time, I thought my problem was that I was no pulling in tximportData. But adding that did not help.

Should I be concerned that the Class is -none- in the DESeqDataSet?

The error message almost makes sense if it's happening from trying to act on a null class.

Incidentally, I see that makeExampleDESeqDataSet() also returns the same error for me

That's useful for debugging, isolating the problem to DESeq2 or its depends. Can you call traceback() after the error and post here?

RangedSummarizedExperiment has character_OR_NULL and DESeq2 has characterORNULL. I thought the latter was obsolete. This is also the one that shows up in the error message.

I'm starting to get more suspicious of the change in the S4Vectors package. Renaming characterORNULL to character_OR_NULL happened in 0.14.0 9 days ago.

What is your version of S4Vectors?

Does BiocInstaller::biocValid() point to any problems?

@JWCarlson found the workaround.. (he hit the 5-post limit)

The DESeq2 package will need to be tweaked to account for the latest change in S4Vectors. Creating the class definitions: setClassUnion("characterORNULL", c("character", "NULL”)) setClassUnion(“DataTableORNULL", c(“DataTable", "NULL”)) These were defined in the old S4Vectors but not in the latest version.

That is not the right solution. The slot NAMES comes from SummarizedExperiment; does SummarizedExperiment::SummarizedExperiment() work? Does getClass("SummarizedExperiment") show character_or_NULL ? Are there two versions of SummarizedExperiment installed, maybe tested with

Thanks Martin for helping to dive into this.

I just updated all Bioc packages on my machine and DESeq2 builds and passes CHECK as it does on Bioc servers.

I recognize that my setClassUnion call is a hack. It's a workaround until this gets sorted out and something to convince me that this really is the issue.

In answer to your questions, the constructor works and it shows character_OR_NULL. (As does RangedSummarizedExperiment; DESeqDataSet show NAMES is characterORNULL). And it looks like I have only 1 version installed.

Here is what I get for the NAMES slot of DESeqDataSet today. I don't believe that the version bump in SummarizedExperiment is relevant. 

Can you run biocLite() once again to grab any changes since the release?

The DESeqDataSetFromTximport example is working fine on the Bioc machines and on mine:

https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#deseq2

Thanks for your work on this Michael.

This is what I upgraded:

I updated all. If I take out my setClassUnion hack, I still see:

It still works with my hack in place.

I'm kind of baffled. It seems like there is an older version of some packages sneaking in, but I don't know how or why.

Yes. It's a strange thing. When I look at showClass("DESeqDataSet"), NAMES is charcterORNULL. But your results show that it is character_OR_NULL.

I agree that from all appearances, my initialization of DESeqDataSet looks like it's pulling in an older version of S4Vectors. I've stepped through the initialization of DESeqDataSet and it looks to me that NAMES in S4Vectors inside the initialization of DESeqDataSet is characterORNULL. But I cannot find where that is done. I'll look some more and see if I can find it.

I had this issue. Turns out I had the new version installed on my machine as the root user but an older version of DESeq2 and BioCinstaller in my ~/R/x86_64-pc-linux-gnu-library/3.4. Manually removed the packages from my users local R library and reran bioClite() then it worked.

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SyntaxError: invalid assignment left-hand side

The JavaScript exception "invalid assignment left-hand side" occurs when there was an unexpected assignment somewhere. It may be triggered when a single = sign was used instead of == or === .

SyntaxError or ReferenceError , depending on the syntax.

What went wrong?

There was an unexpected assignment somewhere. This might be due to a mismatch of an assignment operator and an equality operator , for example. While a single = sign assigns a value to a variable, the == or === operators compare a value.

Typical invalid assignments

In the if statement, you want to use an equality operator ( === ), and for the string concatenation, the plus ( + ) operator is needed.

Assignments producing ReferenceErrors

Invalid assignments don't always produce syntax errors. Sometimes the syntax is almost correct, but at runtime, the left hand side expression evaluates to a value instead of a reference , so the assignment is still invalid. Such errors occur later in execution, when the statement is actually executed.

Function calls, new calls, super() , and this are all values instead of references. If you want to use them on the left hand side, the assignment target needs to be a property of their produced values instead.

Note: In Firefox and Safari, the first example produces a ReferenceError in non-strict mode, and a SyntaxError in strict mode . Chrome throws a runtime ReferenceError for both strict and non-strict modes.

Using optional chaining as assignment target

Optional chaining is not a valid target of assignment.

Instead, you have to first guard the nullish case.

• Assignment operators
• Equality operators

• Web Development

What Is the JavaScript Logical Nullish Assignment Operator?

• Daniyal Hamid
• 24 Dec, 2021

Introduced in ES12, you can use the logical nullish assignment operator ( ??= ) to assign a value to a variable if it hasn't been set already. Consider the following examples, which are all equivalent:

The null coalescing assignment operator only assigns the default value if x is a nullish value (i.e. undefined or null ). For example:

In the following example, x already has a value, therefore, the logical nullish assignment operator would not set a default (i.e. it won't return the value on the right side of the assignment operator):

In case, you use the nullish assignment operator on an undeclared variable, the following ReferenceError is thrown:

This post was published 24 Dec, 2021 by Daniyal Hamid . Daniyal currently works as the Head of Engineering in Germany and has 20+ years of experience in software engineering, design and marketing. Please show your love and support by sharing this post .

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Cracking the Shell of Mystery

Basic_string _m_construct null not valid: What it is and how to fix it

The C++ standard library provides a number of string classes, including the `std::string` class. `std::string` is a powerful and flexible class that can be used to store and manipulate text data. However, it is important to understand the limitations of `std::string`, especially when it comes to constructing strings from null characters.

In this article, we will discuss the `std::string::_M_construct()` function, which is used to construct a `std::string` object from a null character. We will explain why it is not valid to construct a `std::string` from a null character, and we will show how to avoid this problem.

We will also discuss some of the other ways to construct `std::string` objects, and we will provide some tips for working with null characters in C++.

By the end of this article, you will have a good understanding of the `std::string::_M_construct()` function and how to use it safely. You will also be familiar with the other ways to construct `std::string` objects, and you will be able to avoid problems with null characters in your C++ code.

The basic_string::_m_construct null not valid error is a common error that occurs when an attempt is made to construct a basic_string object with a null pointer as the initial value. This error is caused by a number of different factors, including incorrect assignment statements, null pointer literals, and invalid casts.

In this article, we will discuss the causes of the basic_string::_m_construct null not valid error and how to avoid it. We will also provide some code examples to illustrate how to correctly construct basic_string objects.

What is the basic_string::_m_construct null not valid error?

The basic_string::_m_construct null not valid error occurs when an attempt is made to construct a basic_string object with a null pointer as the initial value. This is invalid because a null pointer cannot be dereferenced, and therefore the basic_string object cannot be initialized.

The error message typically includes the following information:

• The file name where the error occurred
• The line number where the error occurred
• The text of the invalid expression

For example, the following code will cause the basic_string::_m_construct null not valid error:

std::string str = nullptr;

This is because the assignment operator for basic_string objects requires a non-null pointer as its argument.

What causes the basic_string::_m_construct null not valid error?

The most common cause of the basic_string::_m_construct null not valid error is an incorrect assignment statement. For example, the following code will cause the error:

Another common cause of the basic_string::_m_construct null not valid error is an attempt to create a basic_string object with a null pointer literal. For example, the following code will also cause the error:

std::string str = NULL;

This is because the null pointer literal is converted to a null pointer before it is used to initialize the basic_string object.

Finally, the basic_string::_m_construct null not valid error can also be caused by invalid casts. For example, the following code will cause the error:

std::string str = static_cast (nullptr);

This is because the cast from a null pointer to a basic_string pointer is invalid.

How to avoid the basic_string::_m_construct null not valid error

There are a few things you can do to avoid the basic_string::_m_construct null not valid error.

First, make sure that you are using the correct assignment operator for basic_string objects. The assignment operator for basic_string objects requires a non-null pointer as its argument.

Second, avoid using null pointer literals to initialize basic_string objects. Instead, use a non-null pointer or a string literal.

Finally, be careful with casts. Make sure that you are only casting from a valid type to a basic_string pointer.

The basic_string::_m_construct null not valid error is a common error that can be avoided by following a few simple guidelines. By understanding the causes of this error, you can write code that is free from this type of error.

Here are some additional resources that you may find helpful:

• [The C++ Programming Language, 4th Edition](https://www.pearson.com/us/higher-education/product/The-C-Programming-Language-4th-Edition/9780134197783.html)
• [The C++ Standard Library, 3rd Edition](https://www.pearson.com/us/higher-education/product/The-C-Standard-Library-3rd-Edition/9780134043636.html)
• [C++ Reference](https://en.cppreference.com/w/)

The basic_string::_m_construct null not valid error is a compile-time error that occurs when you attempt to construct a basic_string object with a null pointer. This error is caused by the fact that the basic_string class’s constructor requires a non-null pointer to a character array as its first argument. If you attempt to pass a null pointer to the constructor, the compiler will generate an error.

How can I fix the basic_string::_m_construct null not valid error?

To fix this error, you must ensure that the initial value of the basic_string object is not a null pointer. This can be done by either passing a non-null pointer to the constructor, or by initializing the object with a non-null string literal.

Example code

The following code demonstrates how to fix the basic_string::_m_construct null not valid error:

c++ include include

int main() { // Create a basic_string object with a non-null pointer. std::string str = “Hello world”;

// Print the contents of the basic_string object. std::cout

The basic_string::_m_construct null not valid error is a common error that can be easily avoided by ensuring that the initial value of the basic_string object is not a null pointer. By following the steps in this article, you can easily fix this error and continue on with your C++ programming.

Q: What does the error message “basic_string::_M_construct null not valid” mean?

A: This error message means that you are trying to create a C++ string object with a null pointer as the initial value. This is not allowed, as a null pointer cannot be used to store any data.

Q: How can I fix this error?

A: There are a few ways to fix this error. One way is to simply provide a non-null value for the initial value of the string object. For example, you could use the following code:

c++ std::string str(“Hello world”);

Another way to fix this error is to use the C++ `nullptr` keyword. The `nullptr` keyword is a special value that can be used to represent a null pointer. You can use the `nullptr` keyword to initialize a string object as follows:

c++ std::string str(nullptr);

Q: What are the consequences of using a null pointer to initialize a string object?

A: If you use a null pointer to initialize a string object, the string object will be empty. This means that it will not be able to store any data. If you try to access the data in a string object that has been initialized with a null pointer, you will get a compiler error.

Q: Can I use the `std::string::assign()` method to initialize a string object with a null pointer?

A: No, you cannot use the `std::string::assign()` method to initialize a string object with a null pointer. The `std::string::assign()` method takes a C-style string as its argument, and a null pointer is not a valid C-style string.

Q: What other errors can I get when working with C++ strings?

A: There are a number of other errors that you can get when working with C++ strings. Some of the most common errors include:

• Out-of-bounds errors: These errors occur when you try to access a character in a string that is outside of the bounds of the string.
• Invalid character encoding errors: These errors occur when you try to use a character encoding that is not supported by the C++ standard library.
• Memory allocation errors: These errors occur when the C++ standard library cannot allocate enough memory to store a string.

For more information on these errors, please refer to the C++ documentation.

In this article, we discussed the issue of std::basic_string::_M_construct(const char *, size_t) throwing an exception when the input string is null. We presented a possible solution to this problem, which involves using the std::string::npos constant to indicate that the string is null. We also discussed the potential performance implications of this solution, and concluded that it is a viable option for most applications.

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Error in checkSlotAssignment(object, name, value) #44

xuesongjing commented May 22, 2017

JEFworks commented May 22, 2017

Sorry, something went wrong.

mittalan commented Apr 2, 2020 • edited

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