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Question: KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
0
gravatar for AR3513
4 months ago by
AR35130
AR35130 wrote:

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

ADD COMMENTlink modified 3 months ago • written 4 months ago by AR35130
0
gravatar for Zhang, Jitao David
4 months ago by
Switzerland
Zhang, Jitao David100 wrote:
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!*
ADD COMMENTlink written 4 months ago by Zhang, Jitao David100
0
gravatar for AR3513
4 months ago by
AR35130
AR35130 wrote:

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 COMMENTlink written 4 months ago by AR35130
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 REPLYlink written 4 months ago by Zhang, Jitao David100

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 REPLYlink written 3 months ago by AR35130
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 REPLYlink written 3 months ago by Zhang, Jitao David100
0
gravatar for AR3513
3 months ago by
AR35130
AR35130 wrote:

Thanks very much!

ADD COMMENTlink written 3 months ago by AR35130
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