I am having an issue with the XML package failing on a basic function. This makes packages that depend on this function also fail:> library(XML) > newXMLNode("bob")I/O error : flush error I can?t find any reference to the error online> sessionInfo()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> sessionInfo()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> sessionInfo()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 [[alternative HTML version deleted]]
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 ...:
> XML::newXMLNode("bob")
<bob/>> sessionInfo()
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> system("uname -a")
Linux twentyfive 5.5.10-arch1-1 #1 SMP PREEMPT Wed, 18 Mar 2020 08:40:35 +0000
x86_64 GNU/Linux
Best,
Rasmus