Question

KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"

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AR3513 • 0

@ar3513-11025

Last seen 4.3 years ago

Hello,

I have been recently getting a warning message with KEGGgraph. See the following example:

library(KEGGgraph)

library(RCurl)

path = "rno00010"

file = paste("http://rest.kegg.jp/get/", path, "/kgml", sep = "")
pathway = try(getURL(file), silent = TRUE)
reactions = try(getReactions(parseKGML(pathway)), silent = TRUE)

Then I get loads of warnings like:

warnings()

48: In structure(x$children, class = "XMLNodeList") :
Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
49: In structure(x$children, class = "XMLNodeList") :
Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
50: In structure(x$children, class = "XMLNodeList") :
Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.

Any help?

Thanks very much,

Andrea

kegggraph • 3.5k views

ADD COMMENT • link 7.6 years ago • updated 7.5 years ago AR3513 • 0

score 0 · Answer 1 · 2017-06-08

Dear Andrea, I will have a look. This should not affect the functionality of the package, though. Best wishes, David On Thu, Jun 8, 2017 at 11:00 AM, AR3513 [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User AR3513 <https: support.bioconductor.org="" u="" 11025=""/> wrote Question: > KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :" > <https: support.bioconductor.org="" p="" 96798=""/>: > > Hello, > > I have been recently getting a warning message with KEGGgraph. See the > following example: > > library(KEGGgraph) > > library(RCurl) > > path = "rno00010" > > file = paste("http://rest.kegg.jp/get/", path, "/kgml", sep = "") > pathway = try(getURL(file), silent = TRUE) > reactions = try(getReactions(parseKGML(pathway)), silent = TRUE) > > Then I get loads of warnings like: > > warnings() > > 48: In structure(x$children, class = "XMLNodeList") : > Calling 'structure(NULL, *)' is deprecated, as NULL cannot have > attributes. > Consider 'structure(list(), *)' instead. > 49: In structure(x$children, class = "XMLNodeList") : > Calling 'structure(NULL, *)' is deprecated, as NULL cannot have > attributes. > Consider 'structure(list(), *)' instead. > 50: In structure(x$children, class = "XMLNodeList") : > Calling 'structure(NULL, *)' is deprecated, as NULL cannot have > attributes. > Consider 'structure(list(), *)' instead. > > Any help? > > Thanks very much, > > Andrea > > ------------------------------ > > Post tags: kegggraph > > You may reply via email or visit KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :" > -- *Dr. Jitao David Zhang | 张继涛 | Computational Biology and Bioinformatics* *Roche Pharmaceutical Research and Early Development (pRED) | Pharmaceutical Sciences, Translational Technologies and Bioinformatics (PS-TTB) | Roche Innovation Center Basel | F. Hoffmann-La-Roche AG | CH-4070 Basel | Switzerland* *Building 93/3.34* *Tel +41 61 688 62 51* Confidentiality Note: This message is intended only for the use of the named recipient(s) and may contain confidential and/or privileged information. If you are not the intended recipient, please contact the sender and delete this message. Any unauthorized use of the information contained in this message is prohibited. *Please inform me immediately in case attached documents are missing!*

score 0 · Answer 2 · 2017-06-09

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AR3513 • 0

@ar3513-11025

Last seen 4.3 years ago

Thanks very much for your reply. Yes, I know the code is working without problems, but it would be great if you could fix it (if possible) to avoid getting all these warnings.

Best wishes,

Andrea

ADD COMMENT • link 7.6 years ago AR3513 • 0

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Dear Andrea, Would you mind providing me the information of sessionInfo()? Because I cannot replicate the findings on my machine, i.e. I did not receive the warnings. My sessionInfo() is as follows: R version 3.3.2 (2016-10-31) > Platform: i686-pc-linux-gnu (32-bit) > Running under: Linux Mint 18 > locale: > [1] LC_CTYPE=de_CH.UTF-8 LC_NUMERIC=C > [3] LC_TIME=de_CH.UTF-8 LC_COLLATE=de_CH.UTF-8 > [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_CH.UTF-8 > [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] RCurl_1.95-4.8 bitops_1.0-6 KEGGgraph_1.35.0 > loaded via a namespace (and not attached): > [1] compiler_3.3.2 tools_3.3.2 parallel_3.3.2 > [4] BiocGenerics_0.20.0 stats4_3.3.2 XML_3.98-1.6 > [7] graph_1.52.0 Best wishes, David On Fri, Jun 9, 2017 at 11:42 AM, AR3513 [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User AR3513 <https: support.bioconductor.org="" u="" 11025=""/> wrote Answer: > KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :" > <https: support.bioconductor.org="" p="" 96798="" #96860="">: > > Thanks very much for your reply. Yes, I know the code is working without > problems, but it would be great if you could fix it (if possible) to avoid > getting all these warnings. > > Best wishes, > > Andrea > > > > ------------------------------ > > Post tags: kegggraph > > You may reply via email or visit https://support.bioconductor. > org/p/96798/#96860 > -- *Dr. Jitao David Zhang | 张继涛 | Computational Biology and Bioinformatics* *Roche Pharmaceutical Research and Early Development (pRED) | Pharmaceutical Sciences, Translational Technologies and Bioinformatics (PS-TTB) | Roche Innovation Center Basel | F. Hoffmann-La-Roche AG | CH-4070 Basel | Switzerland* *Building 93/3.34* *Tel +41 61 688 62 51* Confidentiality Note: This message is intended only for the use of the named recipient(s) and may contain confidential and/or privileged information. If you are not the intended recipient, please contact the sender and delete this message. Any unauthorized use of the information contained in this message is prohibited. *Please inform me immediately in case attached documents are missing!*

ADD REPLY • link 7.5 years ago Zhang, Jitao David ▴ 120

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Thanks very much for your reply. See below:

> library(KEGGgraph)

Attaching package: ‘KEGGgraph’

The following object is masked from ‘package:graphics’:

plot

> library(RCurl)
Loading required package: bitops
> path = "rno00010"
> path = "rno00010"
> file = paste("http://rest.kegg.jp/get/", path, "/kgml", sep = "")
> pathway = try(getURL(file), silent = TRUE)
> reactions = try(getReactions(parseKGML(pathway)), silent = TRUE)
There were 50 or more warnings (use warnings() to see the first 50)
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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] RCurl_1.95-4.8 bitops_1.0-6 KEGGgraph_1.35.0

loaded via a namespace (and not attached):
[1] compiler_3.4.0 parallel_3.4.0 tools_3.4.0 BiocGenerics_0.23.0 stats4_3.4.0
[6] XML_3.98-1.7 graph_1.55.0

Best wishes,

Andrea

ADD REPLY • link 7.5 years ago AR3513 • 0

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Dear Andrea, I looked into the issue and confirm that it's observed in R 3.4 but not in older versions. In case anyone is interested in the cause: the warning is caused by XML::xmlChildren.xmlNode, which tries to build a structure out of NULL in case there's no children of a given XML node. As a work-around I implemented a simple checker to make sure that the warning is avoided. It's implemented in the subversion tree of KEGGgraph <https: hedgehog.fhcrc.org="" bioconductor="" trunk="" madman="" rpacks="" kegggraph="">. @Andrea: if you need a compiled package of the latest code I can also share with you directly. Thanks for reporting the issue and have a good day, David On Mon, Jun 19, 2017 at 1:14 PM, AR3513 [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User AR3513 <https: support.bioconductor.org="" u="" 11025=""/> wrote Comment: > KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :" > <https: support.bioconductor.org="" p="" 96798="" #97193="">: > > Thanks very much for your reply. See below: > > > library(KEGGgraph) > > Attaching package: ‘KEGGgraph’ > > The following object is masked from ‘package:graphics’: > > plot > > > library(RCurl) > Loading required package: bitops > > path = "rno00010" > > path = "rno00010" > > file = paste("http://rest.kegg.jp/get/", path, "/kgml", sep = "") > > pathway = try(getURL(file), silent = TRUE) > > reactions = try(getReactions(parseKGML(pathway)), silent = TRUE) > There were 50 or more warnings (use warnings() to see the first 50) > > sessionInfo() > R version 3.4.0 (2017-04-21) > Platform: x86_64-apple-darwin15.6.0 (64-bit) > Running under: OS X El Capitan 10.11.6 > > Matrix products: default > BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/ > A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib > LAPACK: /Library/Frameworks/R.framework/Versions/3.4/ > 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] RCurl_1.95-4.8 bitops_1.0-6 KEGGgraph_1.35.0 > > loaded via a namespace (and not attached): > [1] compiler_3.4.0 parallel_3.4.0 tools_3.4.0 > BiocGenerics_0.23.0 stats4_3.4.0 > [6] XML_3.98-1.7 graph_1.55.0 > > Best wishes, > > Andrea > > ------------------------------ > > Post tags: kegggraph > > You may reply via email or visit https://support.bioconductor. > org/p/96798/#97193 > -- *Dr. Jitao David Zhang | 张继涛 | Computational Biology and Bioinformatics* *Roche Pharmaceutical Research and Early Development (pRED) | Pharmaceutical Sciences, Translational Technologies and Bioinformatics (PS-TTB) | Roche Innovation Center Basel | F. Hoffmann-La-Roche AG | CH-4070 Basel | Switzerland* *Building 93/3.34* *Tel +41 61 688 62 51* Confidentiality Note: This message is intended only for the use of the named recipient(s) and may contain confidential and/or privileged information. If you are not the intended recipient, please contact the sender and delete this message. Any unauthorized use of the information contained in this message is prohibited. *Please inform me immediately in case attached documents are missing!*

ADD REPLY • link 7.5 years ago Zhang, Jitao David ▴ 120

score 0 · Answer 3 · 2017-06-22

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AR3513 • 0

@ar3513-11025

Last seen 4.3 years ago

Thanks very much!

ADD COMMENT • link 7.5 years ago AR3513 • 0