[Bioc-devel] Build OK in devel, Mac OS error in release (CausalR)
Hi All, We currently have the same version of our package CausalR up in devel and release, but while devel is showing build OK for all 3 platforms, release is showing an build error for Mac OS. The error is related to the vignette building: * creating vignettes ... ERROR Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'CausalR.tex' failed. Any ideas why we're only getting it in release, or more importantly how we make it go away? Many thanks, Glyn This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. GSK monitors email communications sent to and from GSK in order to protect GSK, our employees, customers, suppliers and business partners, from cyber threats and loss of GSK Information. GSK monitoring is conducted with appropriate confidentiality controls and in accordance with local laws and after appropriate consultation. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Issues uploading our updated package (CausalR)
Hi, We’ve got CausalR back up both in the 3.2 release and devel, but although we committed the same package (with different version number) to both release and devel, the landing pages are showing build:OK in release but build:warnings in devel. Does anyone know why this might be, and more importantly, would the build:warnings in devel affect the release of the package in v3.3? Thanks, Glyn From: Glyn Bradley Sent: 16 March 2016 13:22 To: 'Kasper Daniel Hansen' Cc: bioc-devel@r-project.org Subject: RE: [Bioc-devel] Issues uploading our updated package (CausalR) Thanks, we’ve already read that. I was more hoping for a response from the Bioconductor team Glyn From: Kasper Daniel Hansen [mailto:kasperdanielhan...@gmail.com] Sent: 16 March 2016 13:20 To: Glyn Bradley Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> Subject: Re: [Bioc-devel] Issues uploading our updated package (CausalR) I don't know much about deprecated packages and how to deal with them, but for your svn questions, start by reading the howto: https://www.bioconductor.org/developers/source-control/ Kasper On Wed, Mar 16, 2016 at 6:19 AM, Glyn Bradley mailto:glyn.x.brad...@gsk.com>> wrote: Hi All, Our package, CausalR, broke when igraph was updated last year. We have now fixed this, but are having problems uploading the new version. The package had become depreciated in devel, but there's still a landing page in release. We checked out the existing Bioconductor version (via SVN) to a local directory from https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR The new, fixed, version was uploaded via SVN commit [Revision: 114806*] back to https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR But if you open https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR in a web browser it's still showing old data from Revision: 114827 (we don't understand why our new upload had a revision number lower than this) Also, because CausalR had become depreciated in devel, we were previously told we would have to update the package in both the devel and release trunks, but we only have the one url (https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR) So separately to the issues above about our update not seeming to stay on the system, could someone please advise how we update both trunks? Many thanks. Feel free to email me directly if this isn't a suitable discussion for the mailing list. Glyn This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Issues uploading our updated package (CausalR)
Thanks, we’ve already read that. I was more hoping for a response from the Bioconductor team Glyn From: Kasper Daniel Hansen [mailto:kasperdanielhan...@gmail.com] Sent: 16 March 2016 13:20 To: Glyn Bradley Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Issues uploading our updated package (CausalR) I don't know much about deprecated packages and how to deal with them, but for your svn questions, start by reading the howto: https://www.bioconductor.org/developers/source-control/ Kasper On Wed, Mar 16, 2016 at 6:19 AM, Glyn Bradley mailto:glyn.x.brad...@gsk.com>> wrote: Hi All, Our package, CausalR, broke when igraph was updated last year. We have now fixed this, but are having problems uploading the new version. The package had become depreciated in devel, but there's still a landing page in release. We checked out the existing Bioconductor version (via SVN) to a local directory from https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR The new, fixed, version was uploaded via SVN commit [Revision: 114806*] back to https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR But if you open https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR in a web browser it's still showing old data from Revision: 114827 (we don't understand why our new upload had a revision number lower than this) Also, because CausalR had become depreciated in devel, we were previously told we would have to update the package in both the devel and release trunks, but we only have the one url (https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR) So separately to the issues above about our update not seeming to stay on the system, could someone please advise how we update both trunks? Many thanks. Feel free to email me directly if this isn't a suitable discussion for the mailing list. Glyn This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Issues uploading our updated package (CausalR)
Hi All, Our package, CausalR, broke when igraph was updated last year. We have now fixed this, but are having problems uploading the new version. The package had become depreciated in devel, but there's still a landing page in release. We checked out the existing Bioconductor version (via SVN) to a local directory from https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR The new, fixed, version was uploaded via SVN commit [Revision: 114806*] back to https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR But if you open https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR in a web browser it's still showing old data from Revision: 114827 (we don't understand why our new upload had a revision number lower than this) Also, because CausalR had become depreciated in devel, we were previously told we would have to update the package in both the devel and release trunks, but we only have the one url (https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CausalR) So separately to the issues above about our update not seeming to stay on the system, could someone please advise how we update both trunks? Many thanks. Feel free to email me directly if this isn't a suitable discussion for the mailing list. Glyn This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Updating CausalR package after igraph fix
Hi All, Our package CausalR depends on igraph and so broke when igraph was updated last year. We have now fixed CausalR to work with the latest igraph, but we're not sure how we need to go about updating it on Bioconductor, - can we just submit our fixed package as an update, or do we need to do a new submission? We may have one small new function in the new package, which simply processes the results of CausalR to produce .sif text files to load into Cytoscape. It's only a few lines of code. It probably goes without saying, but we're keen to try to make this updating process as pain free and quick as possible - the initial submission/ acceptance of the package last year became quite time consuming, and even if we did have the motivation for a similar process again, I'm not sure we could justify spending the resource. There is still a landing page in the 3.2 release for CausalR, even though that version doesn't work with the latest igraph. We weren't sure if that was still supposed to be there or not. Any guidance would be much appreciated. Many thanks, Glyn This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Package deprecation and reacceptance
Hi All, Our package CausalR is currently broke due to the igraph updates. We're working on fixing it, but other commitments mean I'm really not sure when we'll get it done, and we've been told it will be depreciated before the upcoming release. Should that happen, will it be possible for us to get it reaccepted once we do get the igraph issues fixed? Thanks Glyn This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] changes to igraph break many Bioconductor packages (in release and devel)
Hi All Is it acceptable to specify a particular version of igraph for our package to use, even as a temporary fix? Failing that, does anyone know of any way I can get R to tell me which functions in our package (CausalR) call which igraph functions? Thanks Glyn -Original Message- From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of bioc-devel-requ...@r-project.org Sent: 20 July 2015 11:00 To: bioc-devel@r-project.org Subject: Bioc-devel Digest, Vol 136, Issue 20 Send Bioc-devel mailing list submissions to bioc-devel@r-project.org To subscribe or unsubscribe via the World Wide Web, visit https://stat.ethz.ch/mailman/listinfo/bioc-devel or, via email, send a message with subject or body 'help' to bioc-devel-requ...@r-project.org You can reach the person managing the list at bioc-devel-ow...@r-project.org When replying, please edit your Subject line so it is more specific than "Re: Contents of Bioc-devel digest..." Today's Topics: 1. changes to igraph break many Bioconductor packages (in release and devel) (Dan Tenenbaum) -- Message: 1 Date: Sun, 19 Jul 2015 14:38:39 -0700 (PDT) From: Dan Tenenbaum To: bioc-devel Subject: [Bioc-devel] changes to igraph break many Bioconductor packages (in release and devel) Message-ID: <622339655.4339608.1437341919035.javamail.r...@fredhutch.org> Content-Type: text/plain; charset=utf-8 Hello, The igraph package (in CRAN) recently had a major API change. The changes are detailed in its NEWS file: https://cran.r-project.org/web/packages/igraph/news.html The changes cause many Bioconductor packages to break in both release and devel. If you are the maintainer of one of the following packages, please see our build report (release: http://bioconductor.org/checkResults/release/bioc-LATEST/ ; devel: http://bioconductor.org/checkResults/devel/bioc-LATEST/ ) for a report of the error and fix it right away in release (if your package is in release) and devel. You should increment the package version number as well in order to cause your changes to propagate. BioNet CausalR facopy FEM * FGNet * geNetClassifier GenomicInteractions GenoView HTSanalyzeR netbiov * - these packages also need to be sure to import (in DESCRIPTION and NAMESPACE) the graph package. If you have any questions, please send them to the bioc-devel mailing list. Thanks, Dan -- Subject: Digest Footer ___ Bioc-devel mailing list Bioc-devel@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-devel -- End of Bioc-devel Digest, Vol 136, Issue 20 *** This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] New package : CausalR
Hi All, We're pleased to announce the release of our package 'CausalR', which provides functions for causal reasoning (causal network analysis). The idea is to explain sets of observed endpoints by reasoning through causal interaction networks, so for example this type of analysis can be used to uncover the top regulators of high-throughput transcriptomics data. So far the use of these techniques has largely been limited to the commercial domain. We hope CausalR and the increasing availability of causal biological interaction data in the public domain will generate interest in their further development in the academic community also. We would be very pleased to discuss potential collaborations to that end, and to receive any other feedback about the package. All being well a publication will appear in the coming months, describing use cases and giving test input gene signatures along with a working public causal network. Best regards, Glyn This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Rtools warning on tracker page
Hi After uploading our package to the tracker, it built successfully on all systems with no errors. But we have the following Rtools related WARNING: WARNING: Rtools is required to build R packages, but no version of Rtools compatible with R 3.2.0 was found. (Only the following incompatible version(s) of Rtools were found:2.13,2.14,2.15,2.16) Is it possible this is related to the build environment on the tracker page? We can't think how it could be related to our package. I have already mailed the BioC team about this, but I thought I'd post it here also to see if anyone else has the same issue. (our package is called 'CausalR'). Best Regards, Glyn This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocCheck examples error when using imported package functions
Hi
Please disregard this thread, I've realised it's an error with our code
Thanks
Glyn
From: Glyn Bradley
Sent: 16 January 2015 15:32
To: 'bioc-devel@r-project.org'
Subject: BiocCheck examples error when using imported package functions
Hi,
Our package uses igraph.
We have
imports: igraph in the DESCRIPTION file and
import(igraph)in the NAMESPACE
But when we try to write examples for our functions that use igraph functions
to create then use igraph objects from our input, BiocCheck fails on them.
How can we use igraph in our examples?
The error is
> ### ** Examples
>
> network <- graph.formula( "node0" -+ "node1")
> network <- set.edge.attribute(network,"Weight", 1, 1)
> network <- set.vertex.attribute(network,"ID", 1:2, 1:2)
> predictions <- MakePredictions("node0", +1, network, 2)
Error in if (network$isCCG) { : argument is of length zero
Calls: MakePredictions
Execution halted
** running examples for arch 'x64' ... ERROR
Thanks,
Glyn
This e-mail was sent by GlaxoSmithKline Services Unlimited
(registered in England and Wales No. 1047315), which is a
member of the GlaxoSmithKline group of companies. The
registered address of GlaxoSmithKline Services Unlimited
is 980 Great West Road, Brentford, Middlesex TW8 9GS.
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[Bioc-devel] BiocCheck examples error when using imported package functions
Hi,
Our package uses igraph.
We have
imports: igraph in the DESCRIPTION file and
import(igraph)in the NAMESPACE
But when we try to write examples for our functions that use igraph functions
to create then use igraph objects from our input, BiocCheck fails on them.
How can we use igraph in our examples?
The error is
> ### ** Examples
>
> network <- graph.formula( "node0" -+ "node1")
> network <- set.edge.attribute(network,"Weight", 1, 1)
> network <- set.vertex.attribute(network,"ID", 1:2, 1:2)
> predictions <- MakePredictions("node0", +1, network, 2)
Error in if (network$isCCG) { : argument is of length zero
Calls: MakePredictions
Execution halted
** running examples for arch 'x64' ... ERROR
Thanks,
Glyn
This e-mail was sent by GlaxoSmithKline Services Unlimited
(registered in England and Wales No. 1047315), which is a
member of the GlaxoSmithKline group of companies. The
registered address of GlaxoSmithKline Services Unlimited
is 980 Great West Road, Brentford, Middlesex TW8 9GS.
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