Basic XML function not working

Tue, Apr 7, 2020 7:23 AM #

I am having an issue with the XML package failing on a basic function.  This makes packages that depend on this function also fail:

I/O error : flush error

I can?t find any reference to the error online

R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin18.6.0 (64-bit)
Running under: macOS  10.15.3

Matrix products: default
BLAS:   /Users/gabrielhoffman/Downloads/R-3.6.0/lib/libRblas.dylib
LAPACK: /Users/gabrielhoffman/Downloads/R-3.6.0/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] XML_3.99-0.3

loaded via a namespace (and not attached):
[1] compiler_3.6.0 tools_3.6.0    tcltk_3.6.0

# The expected result is: <bob/>
# This works fine in R 3.5.1 on the same machine

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.15.3

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] XML_3.99-0.3

loaded via a namespace (and not attached):
[1] compiler_3.5.1 tools_3.5.1

# It also fails on R development version

R Under development (unstable) (2020-03-16 r77979)
Platform: x86_64-apple-darwin19.3.0 (64-bit)
Running under: macOS Catalina 10.15.3

Matrix products: default
BLAS:   /Users/gabrielhoffman/Downloads/R-devel/lib/libRblas.dylib
LAPACK: /Users/gabrielhoffman/Downloads/R-devel/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] XML_3.99-0.3

loaded via a namespace (and not attached):
[1] compiler_4.0.0


Best
- Gabriel

Rasmus Liland

Tue, Apr 7, 2020 7:56 AM #

On 2020-04-07 14:23 +0000, Hoffman, Gabriel wrote:

| I am having an issue with the XML package 
| failing on a basic function.  This makes 
| packages that depend on this function also 
| fail:

Hi!  So XML::newXMLNode("bob") only works on 
the R 3.5.1, or r77979 as well?

So the question might be what is the 
difference between the R versions in 
Accelerate.framework compared to those in 
~/Downloads ?  Maybe the different versions 
of apple-darwin has something to do with it, 
but this remains speculation on my part ... 
quoted from your email:

| R version 3.6.0 (2019-04-26)
| Platform: x86_64-apple-darwin18.6.0 (64-bit)
| 
| R version 3.5.1 (2018-07-02)
| Platform: x86_64-apple-darwin15.6.0 (64-bit)
| 
| R Under development (unstable) (2020-03-16 r77979)
| Platform: x86_64-apple-darwin19.3.0 (64-bit)


This might not matter much, but I get the 
expected result here on 3.6.3 ...:

<bob/>

R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux

Matrix products: default
BLAS:   /usr/lib/libopenblasp-r0.3.9.so
LAPACK: /usr/lib/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8
 [2] LC_NUMERIC=C
 [3] LC_TIME=en_DK.UTF-8
 [4] LC_COLLATE=en_GB.UTF-8
 [5] LC_MONETARY=nb_NO.UTF-8
 [6] LC_MESSAGES=en_GB.UTF-8
 [7] LC_PAPER=nb_NO.UTF-8
 [8] LC_NAME=C
 [9] LC_ADDRESS=C
[10] LC_TELEPHONE=C
[11] LC_MEASUREMENT=nb_NO.UTF-8
[12] LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils
[5] datasets  methods   base

other attached packages:
[1] XML_3.99-0.3

loaded via a namespace (and not attached):
[1] compiler_3.6.3 tools_3.6.3

Linux twentyfive 5.5.10-arch1-1 #1 SMP PREEMPT Wed, 18 Mar 2020 08:40:35 +0000 x86_64 GNU/Linux

Best,
Rasmus