23.4.1 Length = coercion to logical(1)

In R 4.3, a warning for a vector used in an if statement has increased to anERROR. So this:

 x = c(TRUE,TRUE, FALSE) > if (x) 1 [1] 1 Warning message: In if (x) 1 :   the condition has length > 1 and only the first element will be used

Will now be:

 > x = c(TRUE, TRUE, FALSE) > if (x) 1 Error in if (x) 1 : the condition has length > 1

Solution:In most cases this is a misjudgment in the length of the argument rather thanintentional use of checking if the value was assigned. The code should be reviewedto see if argument is being assigned correctly. In most cases the simplesolution might be to use anany( ) orall( ) surrounding the vector.

23.5.1 S3 method registration

Many packages are currently failing because of undeclared S3 methods in theNAMESPACE. There is some background information found on the R developers blogpost:S3 MethodLookup

This ERROR takes many different forms on the build report. Some of the morecommon forms include

• Cannot coerce class <structure> to a data.frame
• Cannot coerce type ‘S4’ to vector of type ‘double’
• No applicable method for <foo> applied to an object ofclass <bar>
• ‘X’ is a list, but does not have components ‘x’ and ‘y’
• Error in colMeans(x, na.rm = TRUE) : ‘x’ must be numeric
• Error in RG\[1:2, \] : incorrect number of dimensions
• formal argument <foo> matched by multiple actual arguments
• object <foo> of mode ‘function’ was not found
• ‘x’ and ‘y’ lengths differ

Solution: Register the S3 method in the NAMESPACE

S3method(<function>, <dispatch>)

A simple example which effects many packages is a S3 plotting method.The following line would be added to the package NAMESPACE.

S3method(plot, TCC)  # example from TCC package

23.5.2 Removed Setting in R CMD config

The source of the ERROR is utilizing settings in package configure script thathave been removed or replaced.There is a section of R NEWS “R CMD config no longer knows about the unusedsettings F77 and FCPIFCPLAGS, nor CXX98 and similar.”Executing the configuration script when installing the package fails, and theoutput contains lot of messages along the lines of the following:

• configure: WARNING: The flags FFLAGS=“” do not work
• checking whether the ERROR: no information for variable ‘F77’
• configure: WARNING: This value for FFLAGS does not work.

Solution: Replace instances of “${R} CMD config F77” with “${R} CMD config FC”

23.5.3 Conditional Length > 1

In R 4.0 a conditional with a length greater than 1 will produce a WARNING. Onthe Bioconductor Daily Builder and Single Package Builder this is increased toan ERROR.

Traditionallyif / while statements could accept vectors using the firstelement as the conditional value and ignoring the remaining values. This nowproduces a WARNING as seem in this dummy example and documented atConditions of Length Greater Than One

> if (c(TRUE, FALSE)) {}NULLWarning message:In if (c(TRUE, FALSE)) { :    the condition has length > 1 and only the first element will be used

Solution:Bioconductor increased the severity as in most cases this is a misjudgment inthe length of the argument rather than intentional. The code should be reviewedto see if argument is being assigned correctly. In most cases it might beappropriate to use anany( ) orall( ) surrounding the vector.

See alsomailing listpost

23.5.4 Scalar / Vector Logic

This is not a change in R yet but we have been notified that it is forth comingand have escalated to an ERROR on our daily builders in preparation. This typeof ERROR occurs with the misuse of&& and||. The double&& and||imply a scalar comparison rather than a vector comparison that the singular&and| expect. See the dummy example below:

> c(TRUE, TRUE) && TRUEError in c(TRUE, TRUE) && TRUE :   'length(x) = 2 > 1' in coercion to 'logical(1)'

Solution:Most cases are misjudgment and misunderstanding of the use of a scalarcomparison from a vector comparison. Changing the double&& /|| to a singular& /| will generally be sufficient if a vector comparison is intended or having the vector argument use anappropriateany( ) orall( ) surrounding the vector will result in theappropriate scalar comparison.Note: If this comparison is in a conditionalplease see the section above;any( ) orall( ) will most likely be a better alternative.

See alsomailing list post

23.5.5 Class == vs is/inherits

While this isn’t a change in R / Bioconductor as of yet, there is strong discussionabout the affects and consequences of this code structure. A better discussionand explanation can be foundWhen you thinkclass(.) == *, think again!

The sum up isclass( x ) == "foo" should be avoided. It can be misleading if classes extend other classes. Thebetter option is to useis( x , "foo") orinherits(x, "foo").

This is also advised inBioconductor best practices

Starting in R 4.0, a matrix is considered an extension of array.

> m = matrix()> class(m)[1] "matrix" "array"> class(m) == "matrix"[1]  TRUE FALSE> if ( class(m) == "matrix"){}Error in if (class(m) == "matrix") { : the condition has length > 1

This change along with the previous section regarding conditional length resultsin many errors where users were doing something along the lines ofif (class(m) == "matrix"); This is an excellent example where the following isthe appropriate changeif(is(m, "matrix")) orif(inherits(m, "matrix")) orif(is.matrix(m)).

Another common ERROR now occurring because of this change is something similarto the following:

Error in vapply(experiments(object), class, character(1)) :  values must be length 1, but FUN(X[[4]]) result is length 2

23.5.6 data.frame stringsAsFactors

In R 4.0, the default for data.frame argumentstringsAsFactors changed fromTRUE to FALSE. This changes is causing the most breakage in tests where thereare checks for particular factor levels or constructing factor levels.The ERROR’s take many different forms. The simple solution is to change or addthestringAsFactors=TRUE to the data.frame call, however maintainers may wantto re-evaluate code for potential restructuring or ease of use.

23.5.7 stats::smoothEnds

A recent change tostats::smoothEnds(), now returns an integer vector with theinput is an integer vector. Previously it could return a number vector.

Example R 3.6.3

> class(smoothEnds(c(401:403)))[1] "integer"> class(smoothEnds(c(401:403, 555L)))[1] "numeric"

Example from 4.0.0

> class(smoothEnds(c(401:403)))[1] "integer"> class(smoothEnds(c(401:403, 555L)))[1] "integer"

This has the potential to cause ERROR’s if a class type was checked.

23.5.8 Grid package changes

We do not have a lot of specifics on what has changed but were notified byemail. Important sections of the email as follows:

    I am about to commit some internal changes to 'grid' units        (for, in some cases, 100x speed-up of unit operations).        A number of packages have already been fixed to work with these        changes, but, according to my testing, the following CRAN        packages will still fail R CMD check.    Some of those are cascades ('armada', 'countToFPKM', and 'wilson'        from 'ComplexHeatmap' - see below - and 'fingertipscharts' from 'lemon'        and 'xpose' is actually a 'ggforce' problem), but all of the other        package authors have been notified and several are already working on        fixes.        The most serious of those is 'ComplexHeatmap' because it causes multiple        follow-on failures, the CRAN ones above and others on BioConductor:    Again, the main package authors have been notified and the    'ComplexHeatmap' author is working on an update.

23.5.9 plot generic moved

The plot generic has moved from graphics to base. The ERROR’s seen from thischange are non specific and can take many forms. Some of the ERROR’s we seeare

Error in getGeneric(f, TRUE, envir, package) : no generic function found for 'plot'

or

Error in as.double(y) :      cannot coerce type 'S4' to vector of type 'double'

The explanation given:

  “The namespace controls the search strategy for variables used by  functions in the package. If not found locally, R searches the package  namespace first, then the imports, then the base namespace and then  the  normal search path." as per  https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Package-namespaces):  CRAN and Bioconductor  had a few packages that "worked" because the right  plot() was found in the normal search path, but now fail because it's  calling the one in base instead.

23.5.10 Partial Argument Matching

There is now more strict checking of argument matching with regards to partialargument matching. Best described with the following example

setGeneric(“mycoolfunction”,   function(object,  breaks)    standardGeneric(“mycoolfunction”)setMethod(“mycoolfunction”,    signature=c(object=”GRanges”, break=”GRanges”),    <code>)

Notice the generic usesbreaks while the setMethod usesbreak; This is anexample of a partial argument match that will no longer be valid.

Partial argument matching when envoking functions should also be avoided aspart of best practices. For example

mycoolfunction <- function( x, myargum, secondarg ) { code }mycoolfunction(x=2, myar=1:2, second=3)          # BAD Coding!mycoolfunction(x=2, myargum=1:2, secondarg=3)    # Good Practice!

23.5.11 Package inputenc Error: Invalid UTF-8

This ERROR started to appear on tokay2 (windows) in Spring 2020. We are not surethe exact source of the ERROR (change in MiKTek, Change in R, other?) but thesolution is simple:

Please place\usepackage[utf8]{inputenc} in the beginning of your Sweavevignette right after the\documentclass line.

23.5.12 Dependency Issues

Dependency Issues can fall into a few sub-categories:

23.5.13 Deprecated Functions

Functions can be deprecated, defunct, and eventually removed. Bioconductor triesto enforce this progression to allow maintainers to adjust code. Most deprecatedor defunct functions will (should) suggest the alternative. The following arenoted in Bioconductor 3.11

Error : RangedData objects are defunct. Please migrate your code to use GRanges  or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData

Error:'normalize' is defunct.Use ''normalize,SingleCellExperiment-method' is defunct.Use 'logNormCounts' instead' instead.

Error:'calculateQCMetrics' is defunct.Use 'perCellQCMetrics' instead.