MidnightBSD Magus

textproc/R-cran-XML

Tools for parsing and generating XML

License Permissions: dist-mirror dist-sell pkg-mirror pkg-sell auto-accept

Events

Log

===>  Testing for R-cran-XML-3.99.0.18
* using log directory ‘/magus/work/usr/mports/textproc/R-cran-XML/work/XML.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: amd64-portbld-midnightbsd4.0.2
* R was compiled by
    MidnightBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2)
    GNU Fortran (MidnightBSD Ports Collection) 14.2.0
* running under: MidnightBSD defiant.midnightbsd.org 4.0.2 MidnightBSD 4.0.2 stable/4.0-n13746-7f13a92583 GENERIC amd64
* using session charset: UTF-8
* using options ‘--no-manual --no-build-vignettes’
* checking for file ‘XML/DESCRIPTION’ ... OK
* this is package ‘XML’ version ‘3.99-0.18’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking: 'bitops', 'RCurl'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘XML’ can be installed ... WARNING
Found the following significant warnings:
  DocParse.c:67:25: warning: '__xmlDoValidityCheckingDefaultValue' is deprecated [-Wdeprecated-declarations]
  DocParse.c:70:6: warning: '__xmlDoValidityCheckingDefaultValue' is deprecated [-Wdeprecated-declarations]
  HTMLParse.c:143:14: warning: 'use' is deprecated [-Wdeprecated-declarations]
  HTMLParse.c:152:67: warning: 'content' is deprecated [-Wdeprecated-declarations]
  RSDTD.c:121:9: warning: 'validate' is deprecated [-Wdeprecated-declarations]
  RSDTD.c:134:7: warning: 'xmlSkipBlankChars' is deprecated [-Wdeprecated-declarations]
  RSDTD.c:135:7: warning: 'xmlParseMarkupDecl' is deprecated [-Wdeprecated-declarations]
  RUtils.c:142:13: warning: 'xmlSubstituteEntitiesDefault' is deprecated [-Wdeprecated-declarations]
  XMLTree.c:1439:14: warning: 'use' is deprecated [-Wdeprecated-declarations]
  XMLTree.c:1442:105: warning: 'content' is deprecated [-Wdeprecated-declarations]
  XMLTree.c:1444:57: warning: 'content' is deprecated [-Wdeprecated-declarations]
See ‘/magus/work/usr/mports/textproc/R-cran-XML/work/XML.Rcheck/00install.out’ for details.
* used C compiler: ‘MidnightBSD clang version 19.1.7 (https://github.com/llvm/llvm-project.git llvmorg-19.1.7-0-gcd708029e0b2)’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... OK
* checking examples ... ERROR
Running examples in ‘XML-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xmlTreeParse
> ### Title: XML Parser
> ### Aliases: xmlTreeParse htmlTreeParse htmlParse xmlInternalTreeParse
> ###   xmlNativeTreeParse xmlParse xmlSchemaParse
> ### Keywords: file IO
> 
> ### ** Examples
> 
>  fileName <- system.file("exampleData", "test.xml", package="XML")
>    # parse the document and return it in its standard format.
> 
>  xmlTreeParse(fileName)
$doc
$file
[1] "/magus/work/usr/mports/textproc/R-cran-XML/work/XML.Rcheck/XML/exampleData/test.xml"

$version
[1] "1.0"

$children
$children$comment


$children$foo

 
  test entity bar 
 
  
  %extEnt;
 
 
 Note that this caused a segmentation fault if replaceEntities was 
not TRUE.
That is,
 xmlTreeParse("test.xml", replaceEntities = TRUE)
 works, but
 xmlTreeParse("test.xml")
 does not if this is called before the one above.
This is now fixed and was caused by
treating an xmlNodePtr in the C code 
that had type XML_ELEMENT_DECL
and so was in fact an xmlElementPtr.
Aaah, C and casting!



attr(,"class")
[1] "XMLDocumentContent"

$dtd
$external
NULL

$internal
$elements
$elements$x
$name
[1] "x"

$type
mixed 
   15 

$contents
$type
PCData 
     1 

$ocur
Once 
   1 

$elements
NULL

attr(,"class")
[1] "XMLElementContent"

$attributes
NULL

attr(,"class")
[1] "XMLElementDef"

$elements$y
$name
[1] "y"

$type
element 
     15 

$contents
$type
Element 
      2 

$ocur
Mult 
   3 

$elements
[1] "x"

attr(,"class")
[1] "XMLElementContent"

$attributes
NULL

attr(,"class")
[1] "XMLElementDef"


$entities
$entities$testEnt
$name
[1] "testEnt"

$value
[1] "test entity bar"

$original
[1] "test entity bar"

attr(,"class")
[1] "XMLEntity"

$entities$logo
$name
[1] "logo"

$value
[1] "gif"

$original
NULL

attr(,"class")
[1] "XMLEntity"


attr(,"class")
[1] "InternalDTD"

attr(,"class")
[1] "DTDList"

attr(,"class")
[1] "XMLDocument"         "XMLAbstractDocument"
> 
>    # parse the document, discarding comments.
>   
>  xmlTreeParse(fileName, handlers=list("comment"=function(x,...){NULL}), asTree = TRUE)
$doc
$file
[1] "/magus/work/usr/mports/textproc/R-cran-XML/work/XML.Rcheck/XML/exampleData/test.xml"

$version
[1] "1.0"

$children
$children$foo

 
  test entity bar 
 
  %extEnt;
 
 
 Note that this caused a segmentation fault if replaceEntities was 
not TRUE.
That is,
 xmlTreeParse("test.xml", replaceEntities = TRUE)
 works, but
 xmlTreeParse("test.xml")
 does not if this is called before the one above.
This is now fixed and was caused by
treating an xmlNodePtr in the C code 
that had type XML_ELEMENT_DECL
and so was in fact an xmlElementPtr.
Aaah, C and casting!



attr(,"class")
[1] "XMLDocumentContent"

$dtd
$external
NULL

$internal
$elements
$elements$y
$name
[1] "y"

$type
element 
     15 

$contents
$type
Element 
      2 

$ocur
Mult 
   3 

$elements
[1] "x"

attr(,"class")
[1] "XMLElementContent"

$attributes
NULL

attr(,"class")
[1] "XMLElementDef"

$elements$x
$name
[1] "x"

$type
mixed 
   15 

$contents
$type
PCData 
     1 

$ocur
Once 
   1 

$elements
NULL

attr(,"class")
[1] "XMLElementContent"

$attributes
NULL

attr(,"class")
[1] "XMLElementDef"


$entities
$entities$logo
$name
[1] "logo"

$value
[1] "gif"

$original
NULL

attr(,"class")
[1] "XMLEntity"

$entities$testEnt
$name
[1] "testEnt"

$value
[1] "test entity bar"

$original
[1] "test entity bar"

attr(,"class")
[1] "XMLEntity"


attr(,"class")
[1] "InternalDTD"

attr(,"class")
[1] "DTDList"

attr(,"class")
[1] "XMLDocument"         "XMLAbstractDocument"
> 
>    # print the entities
>  invisible(xmlTreeParse(fileName,
+             handlers=list(entity=function(x) {
+                                     cat("In entity",x$name, x$value,"\n")
+                                     x}
+                                   ), asTree = TRUE
+                           )
+           )
In entity testEnt test entity bar 
> 
>  # Parse some XML text.
>  # Read the text from the file
>  xmlText <- paste(readLines(fileName), "\n", collapse="")
> 
>  print(xmlText)
[1] " \n \n   \n \n   \n   \n      \n \n   \n   \n]> \n \n \n  \n &testEnt; \n  \n  \n   \n    \n    %extEnt; \n   \n  \n \n \nNote that this caused a segmentation fault if replaceEntities was  \nnot TRUE. \nThat is, \n \nxmlTreeParse(\"test.xml\", replaceEntities = TRUE) \n \nworks, but  \n \nxmlTreeParse(\"test.xml\") \n \ndoes not if this is called before the one above. \nThis is now fixed and was caused by \ntreating an xmlNodePtr in the C code  \nthat had type XML_ELEMENT_DECL \nand so was in fact an xmlElementPtr. \nAaah, C and casting! \n \n"
>  xmlTreeParse(xmlText, asText=TRUE)
$doc
$file
[1] ""

$version
[1] "1.0"

$children
$children$comment


$children$foo

 
  test entity bar 
 
  
  %extEnt;
 
 
 Note that this caused a segmentation fault if replaceEntities was  
not TRUE. 
That is,
 xmlTreeParse("test.xml", replaceEntities = TRUE)
 works, but
 xmlTreeParse("test.xml")
 does not if this is called before the one above. 
This is now fixed and was caused by 
treating an xmlNodePtr in the C code  
that had type XML_ELEMENT_DECL 
and so was in fact an xmlElementPtr. 
Aaah, C and casting!



attr(,"class")
[1] "XMLDocumentContent"

$dtd
$external
NULL

$internal
$elements
$elements$x
$name
[1] "x"

$type
mixed 
   15 

$contents
$type
PCData 
     1 

$ocur
Once 
   1 

$elements
NULL

attr(,"class")
[1] "XMLElementContent"

$attributes
NULL

attr(,"class")
[1] "XMLElementDef"

$elements$y
$name
[1] "y"

$type
element 
     15 

$contents
$type
Element 
      2 

$ocur
Mult 
   3 

$elements
[1] "x"

attr(,"class")
[1] "XMLElementContent"

$attributes
NULL

attr(,"class")
[1] "XMLElementDef"


$entities
$entities$logo
$name
[1] "logo"

$value
[1] "gif"

$original
NULL

attr(,"class")
[1] "XMLEntity"

$entities$testEnt
$name
[1] "testEnt"

$value
[1] "test entity bar"

$original
[1] "test entity bar"

attr(,"class")
[1] "XMLEntity"


attr(,"class")
[1] "InternalDTD"

attr(,"class")
[1] "DTDList"

attr(,"class")
[1] "XMLDocument"         "XMLAbstractDocument"
> 
> 
>     # with version 1.4.2 we can pass the contents of an XML
>     # stream without pasting them.
>  xmlTreeParse(readLines(fileName), asText=TRUE)
$doc
$file
[1] ""

$version
[1] "1.0"

$children
$children$comment


$children$foo

 
  test entity bar 
 
  
  %extEnt;
 
 
 Note that this caused a segmentation fault if replaceEntities was 
not TRUE.
That is,
 xmlTreeParse("test.xml", replaceEntities = TRUE)
 works, but
 xmlTreeParse("test.xml")
 does not if this is called before the one above.
This is now fixed and was caused by
treating an xmlNodePtr in the C code 
that had type XML_ELEMENT_DECL
and so was in fact an xmlElementPtr.
Aaah, C and casting!



attr(,"class")
[1] "XMLDocumentContent"

$dtd
$external
NULL

$internal
$elements
$elements$y
$name
[1] "y"

$type
element 
     15 

$contents
$type
Element 
      2 

$ocur
Mult 
   3 

$elements
[1] "x"

attr(,"class")
[1] "XMLElementContent"

$attributes
NULL

attr(,"class")
[1] "XMLElementDef"

$elements$x
$name
[1] "x"

$type
mixed 
   15 

$contents
$type
PCData 
     1 

$ocur
Once 
   1 

$elements
NULL

attr(,"class")
[1] "XMLElementContent"

$attributes
NULL

attr(,"class")
[1] "XMLElementDef"


$entities
$entities$logo
$name
[1] "logo"

$value
[1] "gif"

$original
NULL

attr(,"class")
[1] "XMLEntity"

$entities$testEnt
$name
[1] "testEnt"

$value
[1] "test entity bar"

$original
[1] "test entity bar"

attr(,"class")
[1] "XMLEntity"


attr(,"class")
[1] "InternalDTD"

attr(,"class")
[1] "DTDList"

attr(,"class")
[1] "XMLDocument"         "XMLAbstractDocument"
> 
> 
>  # Read a MathML document and convert each node
>  # so that the primary class is 
>  #   MathML
>  # so that we can use method  dispatching when processing
>  # it rather than conditional statements on the tag name.
>  # See plotMathML() in examples/.
>  fileName <- system.file("exampleData", "mathml.xml",package="XML")
> m <- xmlTreeParse(fileName, 
+                   handlers=list(
+                    startElement = function(node){
+                    cname <- paste(xmlName(node),"MathML", sep="",collapse="")
+                    class(node) <- c(cname, class(node)); 
+                    node
+                 }))
> 
> 
> 
>   # In this example, we extract _just_ the names of the
>   # variables in the mtcars.xml file. 
>   # The names are the contents of the 
>   # tags. We discard all other tags by returning NULL
>   # from the startElement handler.
>   #
>   # We cumulate the names of variables in a character
>   # vector named 'vars'.
>   # We define this within a closure and define the 
>   # variable function within that closure so that it
>   # will be invoked when the parser encounters a 
>   # tag.
>   # This is called with 2 arguments: the XMLNode object (containing
>   # its children) and the list of attributes.
>   # We get the variable name via call to xmlValue().
> 
>   # Note that we define the closure function in the call and then 
>   # create an instance of it by calling it directly as
>   #   (function() {...})()
> 
>   # Note that we can get the names by parsing
>   # in the usual manner and the entire document and then executing
>   # xmlSApply(xmlRoot(doc)[[1]], function(x) xmlValue(x[[1]]))
>   # which is simpler but is more costly in terms of memory.
>  fileName <- system.file("exampleData", "mtcars.xml", package="XML")
>  doc <- xmlTreeParse(fileName,  handlers = (function() { 
+                                  vars <- character(0) ;
+                                 list(variable=function(x, attrs) { 
+                                                 vars <<- c(vars, xmlValue(x[[1]])); 
+                                                 NULL}, 
+                                      startElement=function(x,attr){
+                                                    NULL
+                                                   }, 
+                                      names = function() {
+                                                  vars
+                                              }
+                                     )
+                                })()
+                      )
> 
>   # Here we just print the variable names to the console
>   # with a special handler.
>  doc <- xmlTreeParse(fileName, handlers = list(
+                                   variable=function(x, attrs) {
+                                              print(xmlValue(x[[1]])); TRUE
+                                            }), asTree=TRUE)
[1] "mpg"
[1] "cyl"
[1] "disp"
[1] "hp"
[1] "drat"
[1] "wt"
[1] "qsec"
[1] "vs"
[1] "am"
[1] "gear"
[1] "carb"
> 
> 
>   # This should raise an error.
>   try(xmlTreeParse(
+             system.file("exampleData", "TestInvalid.xml", package="XML"),
+             validate=TRUE))

 *** caught segfault ***
address 0xe5728838, cause 'memory not mapped'

Traceback:
 1: xmlTreeParse(system.file("exampleData", "TestInvalid.xml", package = "XML"),     validate = TRUE)
 2: doTryCatch(return(expr), name, parentenv, handler)
 3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 4: tryCatchList(expr, classes, parentenv, handlers)
 5: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
 6: try(xmlTreeParse(system.file("exampleData", "TestInvalid.xml",     package = "XML"), validate = TRUE))
An irrecoverable exception occurred. R is aborting now ...
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/magus/work/usr/mports/textproc/R-cran-XML/work/XML.Rcheck/00check.log’
for details.

*** Error code 1

Stop.
make: stopped in /usr/mports/textproc/R-cran-XML