assignment of an object of class null is not valid

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Weirdness with and without []: assignment of an object of class "numeric" is not valid for slot "values" in an object of class.

The following indicates that assignment of numeric values to an @values part of an mxMatrix only works when the [] are there. When they are not there (which used to work fine) we get an error:

> DirectionofCausationBcausesA$ACE.B@values [,1] [,2] [1,] 0 0 [2,] 0 0 > DirectionofCausationBcausesA$ACE.B@values[] [,1] [,2] [1,] 0 0 [2,] 0 0 > > DirectionofCausationBcausesA$ACE.B@values<-0 Error in checkSlotAssignment(object, name, value) : assignment of an object of class "numeric" is not valid for slot "values" in an object of class "FullMatrix"; is(value, "matrix") is not TRUE > > > DirectionofCausationBcausesA$ACE.B@values [,1] [,2] [1,] 0 0 [2,] 0 0 > > DirectionofCausationBcausesA$ACE.B@values[]<-0

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This is not a bug. The slots of a S4 object are typed objects. They are possibly the only objects in R that are typed objects. '0' is a numeric vector, while ACE.B@values expects a matrix type. Therefore the assignment ACE.B@values[] <- 0 is necessary.

An analogy would be:

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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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Private properties

Private properties are counterparts of the regular class properties which are public, including class fields , class methods, etc. Private properties get created by using a hash # prefix and cannot be legally referenced outside of the class. The privacy encapsulation of these class properties is enforced by JavaScript itself.

Private properties were not native to the language before this syntax existed. In prototypical inheritance, its behavior may be emulated with WeakMap objects or closures , but they can't compare to the # syntax in terms of ergonomics.

There are some additional syntax restrictions:

• All private identifiers declared within a class must be unique. The namespace is shared between static and instance properties. The only exception is when the two declarations define a getter-setter pair.
• The private identifier cannot be #constructor .

Description

Most class properties have their private counterparts:

Private fields

Private methods, private static fields, private static methods.

• Private getters
• Private setters
• Private static getters
• Private static setters

These features are collectively called private properties . However, constructors cannot be private in JavaScript. To prevent classes from being constructed outside of the class, you have to use a private flag .

Private properties are declared with # names (pronounced "hash names"), which are identifiers prefixed with # . The hash prefix is an inherent part of the property name — you can draw relationship with the old underscore prefix convention _privateField — but it's not an ordinary string property, so you can't dynamically access it with the bracket notation .

It is a syntax error to refer to # names from outside of the class. It is also a syntax error to refer to private properties that were not declared in the class body, or to attempt to remove declared properties with delete .

JavaScript, being a dynamic language, is able to perform this compile-time check because of the special hash identifier syntax, making it different from normal properties on the syntax level.

Note: Code run in the Chrome console can access private properties outside the class. This is a DevTools-only relaxation of the JavaScript syntax restriction.

If you access a private property from an object that doesn't have the property, a TypeError is thrown, instead of returning undefined as normal properties do.

This example also illustrates that you can access private properties within static functions too, and on externally defined instances of the class.

You can use the in operator to check whether an externally defined object possesses a private property. This will return true if the private field or method exists, and false otherwise.

Note a corollary of private names being always pre-declared and non-deletable: if you found that an object possesses one private property of the current class (either from a try...catch or an in check), it must possess all other private properties. An object possessing the private properties of a class generally means it was constructed by that class (although not always ).

Private properties are not part of the prototypical inheritance model since they can only be accessed within the current class's body and aren't inherited by subclasses. Private properties with the same name within different classes are entirely different and do not interoperate with each other. See them as external metadata attached to each instance, managed by the class. For this reason, Object.freeze() and Object.seal() have no effect on private properties.

For more information on how and when private fields are initialized, see public class fields .

Private fields include private instance fields and private static fields. Private fields are only accessible from inside the class declaration.

Private instance fields

Like their public counterparts, private instance fields:

• are added before the constructor runs in a base class, or immediately after super() is invoked in a subclass, and
• are only available on instances of the class.

Note: #privateField from the ClassWithPrivateField base class is private to ClassWithPrivateField and is not accessible from the derived Subclass .

Returning overriding object

A class's constructor can return a different object, which will be used as the new this for the derived class constructor. The derived class may then define private fields on that returned object — meaning it is possible to "stamp" private fields onto unrelated objects.

Warning: This is a potentially very confusing thing to do. You are generally advised to avoid returning anything from the constructor — especially something unrelated to this .

Like their public counterparts, private static fields:

• are added to the class constructor at class evaluation time, and
• are only available on the class itself.

There is a restriction on private static fields: only the class which defines the private static field can access the field. This can lead to unexpected behavior when using this . In the following example, this refers to the Subclass class (not the ClassWithPrivateStaticField class) when we try to call Subclass.publicStaticMethod() , and so causes a TypeError .

This is the same if you call the method with super , because super methods are not called with the super class as this .

You are advised to always access private static fields through the class name, not through this , so inheritance doesn't break the method.

Private methods include private instance methods and private static methods. Private methods are only accessible from inside the class declaration.

Private instance methods

Unlike their public counterparts, private instance methods:

• are installed immediately before the instance fields are installed, and
• are only available on instances of the class, not on its .prototype property.

Private instance methods may be generator, async, or async generator functions. Private getters and setters are also possible, and follow the same syntax requirements as their public getter and setter counterparts.

Unlike public methods, private methods are not accessible on the .prototype property of their class.

Like their public counterparts, private static methods:

Private static methods may be generator, async, and async generator functions.

The same restriction previously mentioned for private static fields holds for private static methods, and similarly can lead to unexpected behavior when using this . In the following example, when we try to call Subclass.publicStaticMethod() , this refers to the Subclass class (not the ClassWithPrivateStaticMethod class) and so causes a TypeError .

Simulating private constructors

Many other languages include the capability to mark a constructor as private, which prevents the class from being instantiated outside of the class itself — you can only use static factory methods that create instances, or not be able to create instances at all. JavaScript does not have a native way to do this, but it can be accomplished by using a private static flag.

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• Using classes guide
• Public class fields
• Private Syntax FAQ in the TC39 class-fields proposal
• The semantics of all JS class elements by Shu-yu Guo (2018)
• Public and private class fields on v8.dev (2018)

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Handle null for class's object

I have the following in my class which gets the data from my database:

The problem is that sometimes it's null and therefore the app will fail to run.

How can I handle the null here?

but it's not valid

Can you show us the logic that queries the DB/populates that field? What's the data type of the database column that this field maps to?

This is the error:

System.Text.Json.JsonException: The JSON value could not be converted to System.Collections.Generic.List`1[Root]. Path: $ | LineNumber: 0 | BytePositionInLine: 1.

The code is:

The class is for Stripe result and it's attached as PDF because it's large to paste here..

165505-stripe-class.pdf

Mind posting the JSON / Root class?

Sorry, updated in my reply above.

It's worth copying the JSON to a local file, then stripping out properties to isolate the offending part. It's hard to help diagnose without seeing the JSON

If this happens often and it's Deserialize which is throwing the exception, consider wrapping this in a try-catch, write the json to a log file then work backwards to the data in the database to see why there is an issue with the json.

Here is the JSON

165589-stripe-json.txt

Try deserialising as Root rather than List<Root> :

Yes it's working. Thank you

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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

No branches or pull requests

Error in (function (cl, name, valueClass) :assignment of an object of class “numeric” is not vali...

Error in (function (cl, name, valueClass) : assignment of an object of class “numeric” is not valid for @‘data.signaling’ in an object of class “CellChat”; is(value, "AnyMatrix") is not TRUE

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