[Bioc-devel] builds of last 2 days

[Karim Mezhoud]

Dear all,
I re-cloned my package (canceR
),
following this tutorial
.
And I commit some changes (05 May), and I bump version from 1.18.2 to
1.18.3.
Actually I am seeing the version 1.18.2.

>git checkout RELEASE_3_9
#Switched to branch 'RELEASE_3_9'
#Your branch is up-to-date with 'upstream/RELEASE_3_9'.

Thanks,
Karim

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[Bioc-devel] Fwd: canceR problems reported in the Multiple platform build/check report for BioC 3.6

[Karim Mezhoud]

Dear Admin,
Following this link
https://master.bioconductor.org/checkResults/3.6/bioc-LATEST/canceR/malbec1-
buildsrc.html,
I did not find any built issue in malbec1 for 3.6 version.
Thanks,
Karim


-- Forwarded message --
From: 
Date: Mon, Dec 11, 2017 at 8:57 PM
Subject: canceR problems reported in the Multiple platform build/check
report for BioC 3.6
To: kmezh...@gmail.com


[This is an automatically generated email. Please don't reply.]

Hi canceR maintainer,

According to the Multiple platform build/check report for BioC 3.6,
the canceR package has the following problem(s):

  o TIMEOUT for 'R CMD build' on malbec1. See the details here:
  https://master.bioconductor.org/checkResults/3.6/bioc-
LATEST/canceR/malbec1-buildsrc.html

Please take the time to address this by committing and pushing
changes to your package at git.bioconductor.org

Notes:

  * This was the status of your package at the time this email was sent to
you.
Given that the online report is updated daily (in normal conditions) you
could see something different when you visit the URL(s) above,
especially if
you do so several days after you received this email.

  * It is possible that the problems reported in this report are false
positives,
either because another package (from CRAN or Bioconductor) breaks your
package (if yours depends on it) or because of a Build System problem.
If this is the case, then you can ignore this email.

  * Please check the report again 24h after you've committed your changes
to the
package and make sure that all the problems have gone.

  * If you have questions about this report or need help with the
maintenance of your package, please use the Bioc-devel mailing list:

  https://bioconductor.org/help/mailing-list/

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Re: [Bioc-devel] Creating an org.Hs.uniprot.db package

[Karim Mezhoud]

Hi,
Simply, for LCMSMS protein identification, it is better to use curated, and
verified protein sequence database (from experiments, assays and
publications).
Uniprot KnowledgeBase is known to be the most curated one (even manually)
It will be possible to convert ans improve  uniprotKB (Hs) to
org.Hs.uniprot.db if not yet done.
Karim



On Wed, Sep 13, 2017 at 12:00 PM, Aditya Bhagwat <
adb2...@qatar-med.cornell.edu> wrote:

> Hey guys,
>
>
>
> Thanks for your responses!
>
> Exactly the kind of feedback I wanted, to ensure that what is being
> intended makes sense.
>
>
>
> Resource to be used is UniprotKB.  Preview the first 10 entries:
>
> http://www.uniprot.org/uniprot/?sort=&desc=&compress=
> no&query=&fil=organism:%22Homo%20sapiens%20(Human)%20[
> 9606]%22&limit=10&force=no&preview=true&format=txt
> <http://www.uniprot.org/uniprot/?sort=&desc=&compress=no&query=&fil=organism:%22Homo%20sapiens%20(Human)%20%5b9606%5d%22&limit=10&force=no&preview=true&format=txt>
>
>
>
> How it will look like? Similar to org.Hs.eg.db, using the
> AnnotationDbi::select interface etc.
>
>
>
> Why not org.Hs.eg.db?
>
> · Many uniprot accessions are simply not present in org.Hs.eg.db.
> Take non-canonical isoforms. They are badly represented in org.Hs.eg.db,
> but are essential in LCMS proteomics.
>
> · org.Hs.eg.db does not offer an easy way to map uniprot
> accessions to uniprot summary. I would include that in the
> org.Hs.uniprot.db package
>
> · In LCMS proteomics, protein identification is performed by
> comparing the observed MS spectra to those you would expect from an
> organism-specific protein sequence database. Using the same protein
> sequence database for annotation as is being used for identification would
> provide a one-to-one mapping between analysis and annotation..
>
>
>
> Why not biomaRt
>
> · A reasonably deep LCMS proteomics experiment quantifies 7000
> proteins. Retrieving annotation for these through biomaRt would be slow (an
> overnight activity). I want something that works instantaneously.
>
> · From what I remember you can actually not access the uniprot
> summary (which gives a paragraph on current known knowledge for a protein)
> field from within biomaRt.
>
>
>
> What do you guys think?
>
> Thanks for your feedback!
>
>
>
> Cheers,
>
>
>
> Aditya
>
>
>
>
>
> *From:* Karim Mezhoud [mailto:kmezh...@gmail.com]
> *Sent:* Wednesday, September 13, 2017 1:35 PM
> *To:* Vincent Carey
> *Cc:* Aditya Bhagwat; bioc-devel@r-project.org
> *Subject:* Re: [Bioc-devel] Creating an org.Hs.uniprot.db package
>
>
>
> Hi,
>
> I general LCMSMS generate mass/charge data of Amino Acid or peptides.
>
> The goal in to identify which  protein belong the peptides.
>
> The Software used with LCMSMS can match the peptides to Uniprot database ,
> and ranks putative proteins by scores.
>
> Could the tell us what is the interest of org.Hs.uniprot.db versus default
> UniprotKB?
>
> Thanks,
>
> Karim
>
>
>
>
>
> On Wed, Sep 13, 2017 at 11:19 AM, Vincent Carey <
> st...@channing.harvard.edu> wrote:
>
> can you say a little more about what resource will be tapped and what it
> will look like?  you can
> already use uniprot identifiers as keys into org.Hs.eg.db
>
> On Tue, Sep 12, 2017 at 9:05 AM, Aditya Bhagwat <
> adb2...@qatar-med.cornell.edu> wrote:
>
> > Hey guys,
> >
> > I love the org.Hs.eg.db package (and similar others for other organisms).
> >
> > I work a lot with LCMSMS proteomics data, and I have always missed a
> > similar org.Hs.uniprot.db package, so I am thinking of creating that (and
> > then sharing it on BioC, to benefit fellow proteomics R users).
> >
> > Would you agree that this is of general interest? (Or does this in some
> > form already exist and have I overlooked it?)
> >
> > Thanks for your feedback!
> >
> > Cheers,
> >
> > Aditya
> >
> >
> >
> > Disclaimer: This email and its attachments may be confidential and are
> > intended solely for the use of the individual to whom it is addressed. If
> > you are not the intended recipient, any reading, printing, storage,
> > disclosure, copying or any other action taken in respect of this e-mail
> is
> > prohibited and may be unlawful. If you are not the intended recipient,
> > please notify the sender immediately by using the reply function and then
> > permanently delete what you have received..
> >
> > [[alternative HTML version 

Re: [Bioc-devel] Creating an org.Hs.uniprot.db package

[Karim Mezhoud]

Hi,
I general LCMSMS generate mass/charge data of Amino Acid or peptides.
The goal in to identify which  protein belong the peptides.
The Software used with LCMSMS can match the peptides to Uniprot database ,
and ranks putative proteins by scores.
Could the tell us what is the interest of org.Hs.uniprot.db versus default
UniprotKB?
Thanks,
Karim


On Wed, Sep 13, 2017 at 11:19 AM, Vincent Carey 
wrote:

> can you say a little more about what resource will be tapped and what it
> will look like?  you can
> already use uniprot identifiers as keys into org.Hs.eg.db
>
> On Tue, Sep 12, 2017 at 9:05 AM, Aditya Bhagwat <
> adb2...@qatar-med.cornell.edu> wrote:
>
> > Hey guys,
> >
> > I love the org.Hs.eg.db package (and similar others for other organisms).
> >
> > I work a lot with LCMSMS proteomics data, and I have always missed a
> > similar org.Hs.uniprot.db package, so I am thinking of creating that (and
> > then sharing it on BioC, to benefit fellow proteomics R users).
> >
> > Would you agree that this is of general interest? (Or does this in some
> > form already exist and have I overlooked it?)
> >
> > Thanks for your feedback!
> >
> > Cheers,
> >
> > Aditya
> >
> >
> >
> > Disclaimer: This email and its attachments may be confidential and are
> > intended solely for the use of the individual to whom it is addressed. If
> > you are not the intended recipient, any reading, printing, storage,
> > disclosure, copying or any other action taken in respect of this e-mail
> is
> > prohibited and may be unlawful. If you are not the intended recipient,
> > please notify the sender immediately by using the reply function and then
> > permanently delete what you have received..
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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>
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>

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Re: [Bioc-devel] denied access to git

[Karim Mezhoud]

Thank You Dr. Morgan,

When I cloned a repository with git clone , it automatically creates a
remote connection called *origin* pointing back to the cloned repository.

I tried to update bioCancer using old scenario 1:

   -  git clone https://github.com/Bioconductor-mirror/bioCancer
   - cd bioCancer/
   - ../update_remotes.sh
   - get changes to code
   - commit -m "just vignette" -a
   - git svn rebase
   - git svn dcommit --add-author-f

I removed the 'origin' remote but still can not push updates.

git remote remove origin
 git remote -v
upstreamg...@git.bioconductor.org:packages/bioCancer.git (fetch)
upstreamg...@git.bioconductor.org:packages/bioCancer.git (push)

 git push upstream master
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights and the repository
exists.

Thanks,
Karim

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[Bioc-devel] denied access to git

[Karim Mezhoud]

Dear admin,
I re-submit my ssh key to the google form.
Maybe I need to wait to get approved.

Actually I do not have access to push updates for bioCancer package.

bioCancer Mezhoud$  git remote -v
originhttps://github.com/Bioconductor-mirror/bioCancer (fetch)
originhttps://github.com/Bioconductor-mirror/bioCancer (push)
upstreamg...@git.bioconductor.org:packages/bioCancer.git (fetch)
upstreamg...@git.bioconductor.org:packages/bioCancer.git (push)

git checkout master
Already on 'master'
Your branch is ahead of 'origin/master' by 1 commit.
  (use "git push" to publish your local commits)

git push origin master
remote: Permission to Bioconductor-mirror/bioCancer.git denied to kmezhoud.
fatal: unable to access 'https://github.com/Bioconductor-mirror/bioCancer/':
The requested URL returned error: 403


Thanks,
Karim

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Re: [Bioc-devel] commit changes with scenario 1

[Karim Mezhoud]

Thanks Dr Dan,
I have multiple files to commit. How can I specify multiple files names?

git commit -m " resolve prblm" -a "file1.R, file2.R"

Thanks
karim


On Mon, Aug 8, 2016 at 6:33 PM, Dan Tenenbaum 
wrote:

>
>
> - Original Message -
> > From: "Karim Mezhoud" 
> > To: "bioc-devel" 
> > Sent: Tuesday, August 2, 2016 2:53:53 PM
> > Subject: [Bioc-devel] commit changes with scenario 1
>
> > I am trying to commit some changes to bioCancer
> > <https://github.com/Bioconductor-mirror/bioCancer>. the issue is no
> changes
> > added to commit.
> >
> > Please, here is commands. Thanks
> >
> >   -  git clone https://github.com/Bioconductor-mirror/bioCancer
> >   - cd bioCancer/
> >   - ../update_remotes.sh
> >
> >
> > Already on 'master'
> > Your branch is up-to-date with 'origin/master'.
> > Rebuilding
> > .git/svn/refs/remotes/git-svn/.rev_map.bc3139a8-67e5-0310-
> 9ffc-ced21a209358
> > ...
> > r117706 = 3d3efd35ec0406c4aaa4be764cf4ccb36a77d132
> > Done rebuilding
> > .git/svn/refs/remotes/git-svn/.rev_map.bc3139a8-67e5-0310-
> 9ffc-ced21a209358
> > Current branch master is up to date.
> > Commit to git as normal, when you want to push your commits to svn
> >  1. `git svn rebase` to get the latest SVN changes.
> >  2. `git svn dcommit --add-author-from` to commit your changes to SVN.
> >
> >
> >
> >   - Change manually  vignette.Rmd file
> >   - git commit -m "just vignette"
>
> In your git commit command you are not specifying a file to commit.
> You should either add the -a flag to commit all changed files (which have
> already been added) or specify the file(s) you want to commit on the
> command line.
>
> Dan
>
>
>
>
> >
> > On branch master
> > Your branch is up-to-date with 'origin/master'.
> > Changes not staged for commit:
> >modified:   vignettes/bioCancer.Rmd
> >
> > no changes added to commit
> >
> >   - git svn rebase
> >
> > vignettes/bioCancer.Rmd: needs update
> > update-index --refresh: command returned error: 1
> >
> >
> >
> >   - git svn dcommit --add-author-from
> >
> > vignettes/bioCancer.Rmd: needs update
> > update-index --refresh: command returned error: 1
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Bioc-devel] commit changes with scenario 1

[Karim Mezhoud]

I am trying to commit some changes to bioCancer
. the issue is no changes
added to commit.

Please, here is commands. Thanks

   -  git clone https://github.com/Bioconductor-mirror/bioCancer
   - cd bioCancer/
   - ../update_remotes.sh


Already on 'master'
Your branch is up-to-date with 'origin/master'.
Rebuilding
.git/svn/refs/remotes/git-svn/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358
...
r117706 = 3d3efd35ec0406c4aaa4be764cf4ccb36a77d132
Done rebuilding
.git/svn/refs/remotes/git-svn/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358
Current branch master is up to date.
Commit to git as normal, when you want to push your commits to svn
  1. `git svn rebase` to get the latest SVN changes.
  2. `git svn dcommit --add-author-from` to commit your changes to SVN.



   - Change manually  vignette.Rmd file
   - git commit -m "just vignette"



On branch master
Your branch is up-to-date with 'origin/master'.
Changes not staged for commit:
modified:   vignettes/bioCancer.Rmd

no changes added to commit

   - git svn rebase

vignettes/bioCancer.Rmd: needs update
update-index --refresh: command returned error: 1



   - git svn dcommit --add-author-from

vignettes/bioCancer.Rmd: needs update
update-index --refresh: command returned error: 1

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Re: [Bioc-devel] check shiny app: issue with global variables: input$Vars is not found

[Karim Mezhoud]

Hi Stefan,
Thanks,
Yes you are right.
I mean r_data$globalVar2 instead input$globalVar2.
which r_data is a new env used to store global variables.
The question is:
Some functions run with  variables returned from ui.R  (input$var1) and in
some case theses variables are saved as global variable to avoid
re-computing.

when I check R CMD, the input$var1 is not found.

How to avoid this issue?

Thanks,
Karim



On Tue, May 3, 2016 at 3:46 PM, Stefan Haunsberger <
stefan.haunsber...@gmail.com> wrote:

> Hi Karim,
>
> I assume this is because the input parameter only assess the ones that are
> passed on from the ui-environment.
> The global variables are available without the 'input' prefix anyways.
>
> For example, if you declared *globalVar2* as a global variable (let's say
> in a global.r) then you don't need the input$ prefix.
> Variables declared within the ui-function body need to be addressed by
> input$.
>
> I hope that helps.
>
> Cheers,
>
> Stefan
>
> On Tue, May 3, 2016 at 1:57 PM Karim Mezhoud  wrote:
>
>> Dear R,
>> usually, Shiny app uses global variables saved in a session.
>> These variables can be returned by client web page (checkbox or select).
>>
>> for example:
>>  FUN1 <- function(input$var1){
>>  a <-  input$car1 + input$globalVar2
>> return (a)
>> }
>> when I run check package I got error like
>> object input$globalVar2 not found.
>>
>> Also the error is possible in running examples. The global variable or
>> input$var are not found in shiny app.
>>
>> How we can avoid these issues.
>> Thanks,
>> Karim
>>
>> [[alternative HTML version deleted]]
>>
>> ___
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>

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[Bioc-devel] check shiny app: issue with global variables: input$Vars is not found

[Karim Mezhoud]

Dear R,
usually, Shiny app uses global variables saved in a session.
These variables can be returned by client web page (checkbox or select).

for example:
 FUN1 <- function(input$var1){
 a <-  input$car1 + input$globalVar2
return (a)
}
when I run check package I got error like
object input$globalVar2 not found.

Also the error is possible in running examples. The global variable or
input$var are not found in shiny app.

How we can avoid these issues.
Thanks,
Karim

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Re: [Bioc-devel] package submission - problem with vignette

[Karim Mezhoud]

Hi,
I don't know why I have to use
%\VignetteEncoding{UTF-8}
instead
%\usepackage[UTF8]{inputenc}

it works.

On Tue, Apr 12, 2016 at 8:38 AM, Karim Mezhoud  wrote:

> Dear Lara and Dan,
> In my case I am having this error.  Thanks
>
> * creating vignettes ... ERROR
> Error: Vignette 'bioCancer.Rmd' is non-ASCII but has no declared encoding
> Execution halted
> Error: Command failed (1)
> Execution halted
>
> Exited with status 1.
>
> I am setting vignette using knitr package.
>
> In DESCRIPTION file I added:
>
> Suggests:
> BiocStyle,
> AnnotationHub,
> knitr,
> rmarkdown,
> testthat (>= 0.10.0),
> rappdirs
> VignetteBuilder: knitr
>
> In Rmd file, I started by:
>
> ---
> title: "bioCancer: Interactive Multi-OMICS Cancers Data Visualization and
> Analysis"
> author: "\\
> Karim Mezhoud ()\\
> Nuclear Science Center of Tunisia, Nuclear Safety & Security
> Department"
> date: "`r Sys.Date()`"
> output:
>   BiocStyle::html_document:
> toc: true
>   BiocStyle::pdf_document:
> toc: true
> vignette: >
>   %\VignetteIndexEntry{bioCancer: Interactive Multi-OMICS Cancers Data
> Visualization and Analysis}
>   %\VignetteEngine{knitr::rmarkdown}
>   %\VignetteDepends{AnnotationHub}
>   %\usepackage[utf8]{inputenc}
> ---
>
>
> On Mon, Apr 11, 2016 at 9:52 PM, Lara Urban 
> wrote:
>
>> Dear Dan,
>>
>> Many thanks, apparently I just had to update one of the knitr-associated
>> components.
>>
>> I hope it will go through now.
>>
>> Many thanks again and enjoy your evening,
>> Lara
>>
>> 2016-04-11 17:39 GMT+01:00 Dan Tenenbaum :
>>
>> >
>> >
>> > - Original Message -
>> > > From: "Dan Tenenbaum" 
>> > > To: "Lara Urban" 
>> > > Cc: "bioc-devel" 
>> > > Sent: Monday, April 11, 2016 9:29:30 AM
>> > > Subject: Re: [Bioc-devel] package submission - problem with vignette
>> >
>> > > It means that when you run R CMD build YourPackageName, the vignette
>> is
>> > not
>> > > built.
>> > >
>> > > It simply looks in the output of R CMD build for a line that starts:
>> > >
>> > >* creating vignettes ...
>> > >
>> > > If this line is present, it means `R` has not detected that a vignette
>> > > needs to be built.
>> >
>> > Oops, that should say: "If this line is NOT present..."
>> >
>> > Dan
>> >
>> > >
>> > > It's `REQUIRED` that the vignette be built.
>> > >
>> > > If you have vignette sources yet still get this message, there could
>> > > be several causes:
>> > >
>> > > * Missing or invalid `VignetteBuilder` line in the `DESCRIPTION` file.
>> > > * Missing or invalid `VignetteEngine` line in the vignette source.
>> > >
>> > > See `knitr`'s [package vignette](
>> http://yihui.name/knitr/demo/vignette/)
>> > > page, or the
>> > > [Non-Sweave
>> > > vignettes](
>> >
>> https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Non_002dSweave-vignettes
>> > )
>> > > section of "Writing R Extensions" for more information.
>> > >
>> > > Dan
>> > >
>> > >
>> > > - Original Message -
>> > >> From: "Lara Urban" 
>> > >> To: "bioc-devel" 
>> > >> Sent: Monday, April 11, 2016 8:58:14 AM
>> > >> Subject: [Bioc-devel] package submission - problem with vignette
>> > >
>> > >> Dear BiocDevel,
>> > >>
>> > >> I have a question regarding the submission of my package; thank you
>> very
>> > >> much in advance.
>> > >>
>> > >> I have submitted my package to Bioconductor a few days ago and it
>> passed
>> > >> build, check and bioccheck. Now, that I had to change just one line
>> in
>> > my R
>> > >> code and submitted it again, I get an error on all three platforms,
>> > because
>> > >> it is required that my vignette is built by R CMD build; however, I
>> > still
>> > >> have my Rmd file in the order vignettes as before. Shouldn't it build
>> > >> automatically? Do you have any ideas what is going wrong here?
>> > >>
&

Re: [Bioc-devel] package submission - problem with vignette

[Karim Mezhoud]

Dear Lara and Dan,
In my case I am having this error.  Thanks

* creating vignettes ... ERROR
Error: Vignette 'bioCancer.Rmd' is non-ASCII but has no declared encoding
Execution halted
Error: Command failed (1)
Execution halted

Exited with status 1.

I am setting vignette using knitr package.

In DESCRIPTION file I added:

Suggests:
BiocStyle,
AnnotationHub,
knitr,
rmarkdown,
testthat (>= 0.10.0),
rappdirs
VignetteBuilder: knitr

In Rmd file, I started by:

---
title: "bioCancer: Interactive Multi-OMICS Cancers Data Visualization and
Analysis"
author: "\\
Karim Mezhoud ()\\
Nuclear Science Center of Tunisia, Nuclear Safety & Security
Department"
date: "`r Sys.Date()`"
output:
  BiocStyle::html_document:
toc: true
  BiocStyle::pdf_document:
toc: true
vignette: >
  %\VignetteIndexEntry{bioCancer: Interactive Multi-OMICS Cancers Data
Visualization and Analysis}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteDepends{AnnotationHub}
  %\usepackage[utf8]{inputenc}
---


On Mon, Apr 11, 2016 at 9:52 PM, Lara Urban  wrote:

> Dear Dan,
>
> Many thanks, apparently I just had to update one of the knitr-associated
> components.
>
> I hope it will go through now.
>
> Many thanks again and enjoy your evening,
> Lara
>
> 2016-04-11 17:39 GMT+01:00 Dan Tenenbaum :
>
> >
> >
> > - Original Message -
> > > From: "Dan Tenenbaum" 
> > > To: "Lara Urban" 
> > > Cc: "bioc-devel" 
> > > Sent: Monday, April 11, 2016 9:29:30 AM
> > > Subject: Re: [Bioc-devel] package submission - problem with vignette
> >
> > > It means that when you run R CMD build YourPackageName, the vignette is
> > not
> > > built.
> > >
> > > It simply looks in the output of R CMD build for a line that starts:
> > >
> > >* creating vignettes ...
> > >
> > > If this line is present, it means `R` has not detected that a vignette
> > > needs to be built.
> >
> > Oops, that should say: "If this line is NOT present..."
> >
> > Dan
> >
> > >
> > > It's `REQUIRED` that the vignette be built.
> > >
> > > If you have vignette sources yet still get this message, there could
> > > be several causes:
> > >
> > > * Missing or invalid `VignetteBuilder` line in the `DESCRIPTION` file.
> > > * Missing or invalid `VignetteEngine` line in the vignette source.
> > >
> > > See `knitr`'s [package vignette](
> http://yihui.name/knitr/demo/vignette/)
> > > page, or the
> > > [Non-Sweave
> > > vignettes](
> >
> https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Non_002dSweave-vignettes
> > )
> > > section of "Writing R Extensions" for more information.
> > >
> > > Dan
> > >
> > >
> > > - Original Message -
> > >> From: "Lara Urban" 
> > >> To: "bioc-devel" 
> > >> Sent: Monday, April 11, 2016 8:58:14 AM
> > >> Subject: [Bioc-devel] package submission - problem with vignette
> > >
> > >> Dear BiocDevel,
> > >>
> > >> I have a question regarding the submission of my package; thank you
> very
> > >> much in advance.
> > >>
> > >> I have submitted my package to Bioconductor a few days ago and it
> passed
> > >> build, check and bioccheck. Now, that I had to change just one line in
> > my R
> > >> code and submitted it again, I get an error on all three platforms,
> > because
> > >> it is required that my vignette is built by R CMD build; however, I
> > still
> > >> have my Rmd file in the order vignettes as before. Shouldn't it build
> > >> automatically? Do you have any ideas what is going wrong here?
> > >>
> > >> Many thanks and kind regards,
> > >> Lara
> > >>
> > >>
> > >> --
> > >> Lara Urban
> > >>
> > >> Predoctoral Fellow
> > >> EMBL-European Bioinformatics Institute
> > >> Wellcome Trust Genome Campus
> > >> Hinxton, Cambridge
> > >> CB10 1SD
> > >> United Kingdom
> > >>
> > >> PhD Student
> > >> Wolfson College
> > >> University of Cambridge
> > >>
> > >> phone:  + 49 (0) 176 76 37 99 03
> > <%2B%2044%20%280%29%201223%20494%20655>
> > >> email: lara.h.ur...@ebi.ac.uk 
> > >>
>

Re: [Bioc-devel] import except on Window Machine

[Karim Mezhoud]

# ##BUILT &   RELOAD
==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer

* installing to library
‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
ERROR: failed to lock directory
‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’ for
modifying
Try removing
‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/00LOCK-bioCancer’

Exited with status 3.

 BUILT SOURCE PACKAGE
==> devtools::document(roclets=c('rd', 'collate', 'namespace'))

Updating bioCancer documentation
Loading bioCancer
Documentation completed

==> devtools::build()

'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file
--no-environ  \
  --no-save --no-restore CMD build '/Volumes/DATA/radiant/bioCancer'  \
  --no-resave-data --no-manual

* checking for file ‘/Volumes/DATA/radiant/bioCancer/DESCRIPTION’ ... OK
* preparing ‘bioCancer’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘bioCancer_0.99.0.tar.gz’

[1] "/Volumes/DATA/radiant/bioCancer_0.99.0.tar.gz"

Source package written to /Volumes/DATA/radiant

On Mon, Apr 11, 2016 at 6:10 PM, Dan Tenenbaum 
wrote:

> roxygen2 does not support the new syntax. Do you still get the same error
> if you write your NAMESPACE manually?
>
> - Original Message -
> > From: "Karim Mezhoud" 
> > To: "Dan Tenenbaum" 
> > Cc: "Lihua Zhu" , "Michael Lawrence" <
> lawrence.mich...@gene.com>, "bioc-devel"
> > 
> > Sent: Monday, April 11, 2016 10:08:15 AM
> > Subject: Re: [Bioc-devel] import except on Window Machine
>
> >> sessionInfo()
> > R version 3.3.0 beta (2016-04-06 r70435)
> > Platform: x86_64-apple-darwin13.4.0 (64-bit)
> > Running under: OS X 10.11.3 (El Capitan)
> >
> > locale:
> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >
> >
> > On Mon, Apr 11, 2016 at 6:07 PM, Dan Tenenbaum 
> > wrote:
> >
> >> Karim, What is the sessionInfo() in your R-3.3? It might be too old to
> >> have the new feature. It needs to be at svn rev r70426 or newer.
> >>
> >> Dan
> >>
> >>
> >> - Original Message -
> >> > From: "Karim Mezhoud" 
> >> > To: "Lihua Zhu" 
> >> > Cc: "Dan Tenenbaum" , "Michael Lawrence" <
> >> lawrence.mich...@gene.com>, "bioc-devel"
> >> > 
> >> > Sent: Monday, April 11, 2016 10:03:52 AM
> >> > Subject: Re: [Bioc-devel] import except on Window Machine
> >>
> >> > Dear Julie,
> >> > Are you using roxigen2 to edit NAMESPACE file?
> >> > Are you using R 3.4?
> >> > Thanks
> >> >
> >> > In my case, When I used R 3.3 I get this error:
> >> >
> >> >
> >> > ==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer
> >> >
> >> > * installing to library
> >> > ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
> >> > * installing *source* package ‘bioCancer’ ...
> >> > ** R
> >> > ** inst
> >> > ** preparing package for lazy loading
> >> > Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck =
> >> vI[[i]])
> >> > :
> >> >  there is no package called ‘c("dataTableOutput", "renderDataTable")’
> >> > ERROR: lazy loading failed for package ‘bioCancer’
> >> > * removing
> >> >
> >>
> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCancer’
> >> > * restoring previous
> >> >
> >>
> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCancer’
> >> >
> >> > Exited with status 1
> >> >
> >> > When I used R 3.4, I get :
> >> >
> >> > unfortunately,
> >> >
> >> > Bioconductor version 3.3 (BiocInstaller 1.21.4), ?biocLite for help
> >> > Bioconductor does not yet support R version 3.4.0
> >> >
> >> >
> >> >
> >> > On Mon, Apr 11, 2016 at 5:30 PM, Zhu, Lihua (Julie) <
> >> julie@umassmed.edu>
> >> > wrote:
> >> >
> >> >> Thanks, Dan!
> >> >>
> >> >> Best,
> >> >>
> >> >> Julie
> >> >>
> >> >> On 4/11/16 12:22 PM, "Dan Tenenba

Re: [Bioc-devel] import except on Window Machine

[Karim Mezhoud]

> sessionInfo()
R version 3.3.0 beta (2016-04-06 r70435)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.3 (El Capitan)

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


On Mon, Apr 11, 2016 at 6:07 PM, Dan Tenenbaum 
wrote:

> Karim, What is the sessionInfo() in your R-3.3? It might be too old to
> have the new feature. It needs to be at svn rev r70426 or newer.
>
> Dan
>
>
> - Original Message -
> > From: "Karim Mezhoud" 
> > To: "Lihua Zhu" 
> > Cc: "Dan Tenenbaum" , "Michael Lawrence" <
> lawrence.mich...@gene.com>, "bioc-devel"
> > 
> > Sent: Monday, April 11, 2016 10:03:52 AM
> > Subject: Re: [Bioc-devel] import except on Window Machine
>
> > Dear Julie,
> > Are you using roxigen2 to edit NAMESPACE file?
> > Are you using R 3.4?
> > Thanks
> >
> > In my case, When I used R 3.3 I get this error:
> >
> >
> > ==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer
> >
> > * installing to library
> > ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
> > * installing *source* package ‘bioCancer’ ...
> > ** R
> > ** inst
> > ** preparing package for lazy loading
> > Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck =
> vI[[i]])
> > :
> >  there is no package called ‘c("dataTableOutput", "renderDataTable")’
> > ERROR: lazy loading failed for package ‘bioCancer’
> > * removing
> >
> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCancer’
> > * restoring previous
> >
> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCancer’
> >
> > Exited with status 1
> >
> > When I used R 3.4, I get :
> >
> > unfortunately,
> >
> > Bioconductor version 3.3 (BiocInstaller 1.21.4), ?biocLite for help
> > Bioconductor does not yet support R version 3.4.0
> >
> >
> >
> > On Mon, Apr 11, 2016 at 5:30 PM, Zhu, Lihua (Julie) <
> julie@umassmed.edu>
> > wrote:
> >
> >> Thanks, Dan!
> >>
> >> Best,
> >>
> >> Julie
> >>
> >> On 4/11/16 12:22 PM, "Dan Tenenbaum"  wrote:
> >>
> >> >The windows machine is still running an older version of R that does
> not
> >> >support this NAMESPACE syntax. I will update it this week.
> >> >Dan
> >> >
> >> >
> >> >- Original Message -
> >> >> From: "Lihua Zhu" 
> >> >> To: "bioc-devel" 
> >> >> Cc: "Michael Lawrence" 
> >> >> Sent: Monday, April 11, 2016 9:18:31 AM
> >> >> Subject: [Bioc-devel] import except on Window Machine
> >> >
> >> >> Michael,
> >> >>
> >> >> For some reason,  adding except clause in import in the NAMESPACE
> file
> >> >>gives
> >> >> error on window server, although it runs fine on Linux and Mac OS X.
> >> >>
> >> >>
> >>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_chec
> >>
> >>kResults_devel_bioc-2DLATEST_CRISPRseek_moscato2-2Dbuildsrc.html&d=BQICaQ
> >>
> >>&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPH
> >>
> >>hwHHF5gJMlij5cC5bLU&m=t9rR8WHE_O0PrI0B-0ySt37UGJMdDhnwk0JFoVzS5Cw&s=lEJWy
> >> >>zN3zY_O2V1X3QmOZcPD25KidcjhIQMAky52xsA&e=
> >> >>
> >> >> Here is the line that gives error.
> >> >> import(S4Vectors, except=c(fold, values))
> >> >>
> >> >> Did I miss something? Thank!
> >> >>
> >> >> Best regards,
> >> >>
> >> >> Julie
> >> >>
> >> >>
> >> >>
> >> >>  [[alternative HTML version deleted]]
> >> >>
> >> >> ___
> >> >> Bioc-devel@r-project.org mailing list
> >> >>
> >> >>
> >>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman
> >>
> >>_listinfo_bioc-2Ddevel&d=BQICaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPl
> >>
> >>OmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=t9rR8WHE_O0PrI0B-0yS
> >>
> >>t37UGJMdDhnwk0JFoVzS5Cw&s=3ZMFBJ4XMwlGXkfXcB5spcBnnzqBDeqk05sf_TSi88g&e=
> >>
> >> ___
> >> Bioc-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] import except on Window Machine

[Karim Mezhoud]

Dear Julie,
Are you using roxigen2 to edit NAMESPACE file?
Are you using R 3.4?
Thanks

In my case, When I used R 3.3 I get this error:


==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer

* installing to library
‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
* installing *source* package ‘bioCancer’ ...
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
:
  there is no package called ‘c("dataTableOutput", "renderDataTable")’
ERROR: lazy loading failed for package ‘bioCancer’
* removing
‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCancer’
* restoring previous
‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCancer’

Exited with status 1

When I used R 3.4, I get :

unfortunately,

Bioconductor version 3.3 (BiocInstaller 1.21.4), ?biocLite for help
Bioconductor does not yet support R version 3.4.0



On Mon, Apr 11, 2016 at 5:30 PM, Zhu, Lihua (Julie) 
wrote:

> Thanks, Dan!
>
> Best,
>
> Julie
>
> On 4/11/16 12:22 PM, "Dan Tenenbaum"  wrote:
>
> >The windows machine is still running an older version of R that does not
> >support this NAMESPACE syntax. I will update it this week.
> >Dan
> >
> >
> >- Original Message -
> >> From: "Lihua Zhu" 
> >> To: "bioc-devel" 
> >> Cc: "Michael Lawrence" 
> >> Sent: Monday, April 11, 2016 9:18:31 AM
> >> Subject: [Bioc-devel] import except on Window Machine
> >
> >> Michael,
> >>
> >> For some reason,  adding except clause in import in the NAMESPACE file
> >>gives
> >> error on window server, although it runs fine on Linux and Mac OS X.
> >>
> >>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_chec
> >>kResults_devel_bioc-2DLATEST_CRISPRseek_moscato2-2Dbuildsrc.html&d=BQICaQ
> >>&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPH
> >>hwHHF5gJMlij5cC5bLU&m=t9rR8WHE_O0PrI0B-0ySt37UGJMdDhnwk0JFoVzS5Cw&s=lEJWy
> >>zN3zY_O2V1X3QmOZcPD25KidcjhIQMAky52xsA&e=
> >>
> >> Here is the line that gives error.
> >> import(S4Vectors, except=c(fold, values))
> >>
> >> Did I miss something? Thank!
> >>
> >> Best regards,
> >>
> >> Julie
> >>
> >>
> >>
> >>  [[alternative HTML version deleted]]
> >>
> >> ___
> >> Bioc-devel@r-project.org mailing list
> >>
> >>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman
> >>_listinfo_bioc-2Ddevel&d=BQICaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPl
> >>OmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=t9rR8WHE_O0PrI0B-0yS
> >>t37UGJMdDhnwk0JFoVzS5Cw&s=3ZMFBJ4XMwlGXkfXcB5spcBnnzqBDeqk05sf_TSi88g&e=
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Bioc-devel] mascato2 check error

[Karim Mezhoud]

Dear BioC devel,
I did not understand the following error check message.
http://www.bioconductor.org/checkResults/3.3/bioc-LATEST/canceR/moscato2-checksrc.html
Any suggestion is welcome.
Thank you
Karim

### Running command:
###
###   rm -rf canceR.buildbin-libdir canceR.Rcheck && mkdir
canceR.buildbin-libdir canceR.Rcheck &&
E:\biocbld\bbs-3.3-bioc\R\bin\R.exe
CMD INSTALL --build --merge-multiarch --library=canceR.buildbin-libdir
canceR_1.3.7.tar.gz >canceR.Rcheck\00install.out 2>&1 &&
cp canceR.Rcheck\00install.out canceR-install.out  &&
E:\biocbld\bbs-3.3-bioc\R\bin\R.exe
CMD check --library=canceR.buildbin-libdir
--install="check:canceR-install.out" --force-multiarch --no-vignettes
--timings canceR_1.3.7.tar.gz
###

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Re: [Bioc-devel] namespace question

[Karim Mezhoud]

unfortunately,

Bioconductor version 3.3 (BiocInstaller 1.21.4), ?biocLite for help
Bioconductor does not yet support R version 3.4.0

On Tue, Apr 5, 2016 at 9:17 PM, Michael Lawrence 
wrote:

> You need R 3.4 for right now.
>
> On Tue, Apr 5, 2016 at 1:16 PM, Karim Mezhoud  wrote:
> > ==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer
> >
> > * installing to library
> > ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
> > * installing *source* package ‘bioCancer’ ...
> > ** R
> > ** inst
> > ** preparing package for lazy loading
> > Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck =
> vI[[i]]) :
> >   there is no package called ‘c("dataTableOutput", "renderDataTable")’
> > ERROR: lazy loading failed for package ‘bioCancer’
> > * removing
> >
> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCancer’
> > * restoring previous
> >
> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCancer’
> >
> > Exited with status 1
> >
> > On Tue, Apr 5, 2016 at 8:58 PM, Michael Lawrence <
> lawrence.mich...@gene.com>
> > wrote:
> >>
> >> Yea, with the closing )
> >>
> >> On Tue, Apr 5, 2016 at 12:37 PM, Karim Mezhoud 
> wrote:
> >> > If I include manually the exception, I hve to write this?
> >> >
> >> > import(shiny, except=c('dataTableOutput','renderDataTable')
> >> > Thanks
> >> > Karim
> >> >
> >> > On Tue, Apr 5, 2016 at 7:28 PM, Michael Lawrence
> >> > 
> >> > wrote:
> >> >>
> >> >> Roxygen does not yet support the feature. For now you'll have to live
> >> >> with the warning or just importFrom(shiny, ...). Maybe there is some
> >> >> way to manually patch the NAMESPACE with Roxygen?
> >> >>
> >> >> Honestly, I would recommend against using Roxygen to manage your
> >> >> NAMESPACE. Just write the thing...
> >> >>
> >> >>
> >> >>
> >> >> On Tue, Apr 5, 2016 at 11:07 AM, Karim Mezhoud 
> >> >> wrote:
> >> >> > Hi,
> >> >> > Actually I have conflict between DT and shiny
> >> >> >  Warning: replacing previous import ‘shiny::dataTableOutput’ by
> >> >> > ‘DT::dataTableOutput’ when loading ‘bioCancer’
> >> >> >   Warning: replacing previous import ‘shiny::renderDataTable’ by
> >> >> > ‘DT::renderDataTable’ when loading ‘bioCancer’
> >> >> >
> >> >> > I would like to import shiny except dataTableOutput and
> >> >> > renderDataTable.
> >> >> >
> >> >> > #'@import shiny except dataTableOutput renderDataTable
> >> >> > I am using roxygen2
> >> >> > R Under development (unstable) (2016-03-11 r70310)
> >> >> > Which package Can I update to get the new import argument.
> >> >> > Thanks
> >> >> > Karim
> >> >> >
> >> >> >
> >> >> > On Tue, Apr 5, 2016 at 6:50 PM, Michael Lawrence
> >> >> > 
> >> >> > wrote:
> >> >> >>
> >> >> >> I will try to sneak that in since it seems to work and it would be
> >> >> >> nice to use it before this Fall.
> >> >> >>
> >> >> >> On Tue, Apr 5, 2016 at 10:32 AM, Dan Tenenbaum
> >> >> >> 
> >> >> >> wrote:
> >> >> >> > Michael, do you know if this change will be (or has already
> been)
> >> >> >> > backported into R-3.3.0?
> >> >> >> >
> >> >> >> > Thanks.
> >> >> >> > Dan
> >> >> >> >
> >> >> >> >
> >> >> >> > - Original Message -
> >> >> >> >> From: "Lihua Zhu" 
> >> >> >> >> To: "Dan Tenenbaum" , "Michael
> Lawrence"
> >> >> >> >> 
> >> >> >> >> Cc: "bioc-devel" 
> >> >> >> >> Sent: Tuesday, April 5, 2016 9:49:26 AM
> >> >> >> >> Subject: Re: [Bioc-devel] namespace question
> >> >> >> >
> >> >> >> >> Dan,
> >> >> >> &g

Re: [Bioc-devel] new package: annotate function interaction from Reactome DB

[Karim Mezhoud]

Dear bioC devel,
I write an annotate package named reactomeFI to avoid the big size files in
/extdata folder.
Finally when compressed the txt file to RDS format I reduce enough the size
of files.

reactomeFI provides annotation that do not exist in any other package (to
my knowledge).
Nor reactome.db nor PSICQUIC provide the arrow direction and the type of
interaction.

library(reactomeFI)
dim(ld_reactomeFI(2014))
[1] 217249  5
> dim(ld_reactomeFI(2015))
[1] 229300  5
> head(ld_reactomeFI(version= 2015))
  Gene1  Gene2Annotation Direction Score
116-5-5  CDC42 predicted -  0.82
216-5-5   RHOJ predicted -  0.82
316-5-5   RHOQ predicted -  0.82
4 FAS/APO-1/CD95BID  activate->  1.00
5 FAS/APO-1/CD95 CASP10   complex -  1.00
6 FAS/APO-1/CD95   DAXX complex; reaction -  1.00

> tail(ld_reactomeFI(2015))
Gene1  Gene2 Annotation Direction Score
229295ZP3ZP4complex -  1.00
229296   ZPR1ZYX  predicted -  0.59
229297   ZW10 ZWILCH complex; input -  1.00
229298   ZW10  ZWINT complex; input -  1.00
229299 ZWILCH  ZWINT complex; input -  1.00
229300   ZXDA   ZXDC  predicted -  0.59

I can add other argument to specify the type of interaction or direction as

ld_reactomeFI(version=2014, type=c(activated, complex),
direction="arrowhead")

I am ready to submit this package if you consider as new annotate
information.
Thank you,
Karim

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[Bioc-devel] annotate package not need vignette?

[Karim Mezhoud]

Hi,
if yes, how to a avoid biocCheck failure?
Thanks
Karim

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Re: [Bioc-devel] big file ReactomeFI --> bioC annotate package

[Karim Mezhoud]

Thank you Valerie,
TxDb uses sqlite format. Maybe I need to know how to convert reactomeFI.txt
to reactomeFI.sqlite.

I found frombioC workshop 2006 a  Lab: How to use SQLite
<http://master.bioconductor.org/help/course-materials/2006/rforbioinformatics/labs/thurs/SQLite-R-howto.pdf>
.
Is it a good starting tutorial?
Any tutorial is welcome.
Thanks
Karim




On Tue, Apr 5, 2016 at 4:11 PM, Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:

> Hi Karim,
>
> I can help you put together an annotation package.
>
> Here are the general guidelines:
>
> http://www.bioconductor.org/developers/package-guidelines/
>
> We ask that annotations packages implement the select() interface from
> AnnotationDbi (eg, keys(), columns(), keytypes(), etc.). You can see how
> select() works with the TxDb and OrgDb packages. Once you've got that
> working you can open a new ticket on the package tracker.
>
> Feel free to write me at valerie.obench...@roswellpark.org if you have
> other questions.
>
> Valerie
>
>
>
>
> On 04/05/2016 02:18 AM, Karim Mezhoud wrote:
> > Dear bioC developer,
> > I included in my bioCancer/inst/extdata a Reactome FI database (/
> >
> http://reactomews.oicr.on.ca:8080/caBigR3WebApp2015/FIsInGene_031516_with_annotations.txt.zip
> > )
> >
> > Gene1Gene2AnnotationDirectionScore
> > 16-5-5CDC42predicted-0.82
> > 16-5-5RHOJpredicted-0.82
> > 16-5-5RHOQpredicted-0.82
> > FAS/APO-1/CD95BIDactivate->1.00
> > FAS/APO-1/CD95CASP10complex-1.00
> > FAS/APO-1/CD95DAXXcomplex; reaction-1.00
> > FAS/APO-1/CD95DKFZP686N0154activate->1.00
> > FAS/APO-1/CD95FADDcomplex-1.00
> > FAS/APO-1/CD95FASLGcomplex; input-1.00
> > FAS/APO-1/CD95HSPB1reaction-1.00
> > FAS/APO-1/CD95MAP2K3activate->1.00
> > FAS/APO-1/CD95MAP2K4activate->1.00
> >
> > bioCancer uses this file to extract the Direction/arrowhead of gene-gene
> > interaction (activates, inhibits, predicted, complexe.).
> > This kind of data is not available in Reactome.db package nor by Reactome
> > API service (to my knowledge).
> >
> > I have to remove this file from my new package and may get annotate
> package
> > for ReactomeFI database.
> > How to?
> > Karim
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>
>
> This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
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Re: [Bioc-devel] namespace question

[Karim Mezhoud]

==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer

* installing to library
‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
* installing *source* package ‘bioCancer’ ...
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
:
  there is no package called ‘c("dataTableOutput", "renderDataTable")’
ERROR: lazy loading failed for package ‘bioCancer’
* removing
‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCancer’
* restoring previous
‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCancer’

Exited with status 1

On Tue, Apr 5, 2016 at 8:58 PM, Michael Lawrence 
wrote:

> Yea, with the closing )
>
> On Tue, Apr 5, 2016 at 12:37 PM, Karim Mezhoud  wrote:
> > If I include manually the exception, I hve to write this?
> >
> > import(shiny, except=c('dataTableOutput','renderDataTable')
> > Thanks
> > Karim
> >
> > On Tue, Apr 5, 2016 at 7:28 PM, Michael Lawrence <
> lawrence.mich...@gene.com>
> > wrote:
> >>
> >> Roxygen does not yet support the feature. For now you'll have to live
> >> with the warning or just importFrom(shiny, ...). Maybe there is some
> >> way to manually patch the NAMESPACE with Roxygen?
> >>
> >> Honestly, I would recommend against using Roxygen to manage your
> >> NAMESPACE. Just write the thing...
> >>
> >>
> >>
> >> On Tue, Apr 5, 2016 at 11:07 AM, Karim Mezhoud 
> wrote:
> >> > Hi,
> >> > Actually I have conflict between DT and shiny
> >> >  Warning: replacing previous import ‘shiny::dataTableOutput’ by
> >> > ‘DT::dataTableOutput’ when loading ‘bioCancer’
> >> >   Warning: replacing previous import ‘shiny::renderDataTable’ by
> >> > ‘DT::renderDataTable’ when loading ‘bioCancer’
> >> >
> >> > I would like to import shiny except dataTableOutput and
> renderDataTable.
> >> >
> >> > #'@import shiny except dataTableOutput renderDataTable
> >> > I am using roxygen2
> >> > R Under development (unstable) (2016-03-11 r70310)
> >> > Which package Can I update to get the new import argument.
> >> > Thanks
> >> > Karim
> >> >
> >> >
> >> > On Tue, Apr 5, 2016 at 6:50 PM, Michael Lawrence
> >> > 
> >> > wrote:
> >> >>
> >> >> I will try to sneak that in since it seems to work and it would be
> >> >> nice to use it before this Fall.
> >> >>
> >> >> On Tue, Apr 5, 2016 at 10:32 AM, Dan Tenenbaum <
> dtene...@fredhutch.org>
> >> >> wrote:
> >> >> > Michael, do you know if this change will be (or has already been)
> >> >> > backported into R-3.3.0?
> >> >> >
> >> >> > Thanks.
> >> >> > Dan
> >> >> >
> >> >> >
> >> >> > - Original Message -
> >> >> >> From: "Lihua Zhu" 
> >> >> >> To: "Dan Tenenbaum" , "Michael Lawrence"
> >> >> >> 
> >> >> >> Cc: "bioc-devel" 
> >> >> >> Sent: Tuesday, April 5, 2016 9:49:26 AM
> >> >> >> Subject: Re: [Bioc-devel] namespace question
> >> >> >
> >> >> >> Dan,
> >> >> >>
> >> >> >> That is great! Thanks for letting us know!
> >> >> >>
> >> >> >> Michael, thank for making it happen so quickly! It works like a
> >> >> >> charm!
> >> >> >>
> >> >> >> Best,
> >> >> >>
> >> >> >> Julie
> >> >> >>
> >> >> >> On 4/2/16 1:58 PM, "Bioc-devel on behalf of Dan Tenenbaum"
> >> >> >>  >> >> >> dtene...@fredhutch.org>
> >> >> >> wrote:
> >> >> >>
> >> >> >>>BTW, looks like the change has been made to R-devel:
> >> >> >>>
> >> >> >>> CHANGES IN R-devel NEW FEATURES
> >> >> >>>
> >> >> >>>  * The Œimport()¹ namespace directive now accepts an argument
> >> >> >>> Œexcept¹
> >> >> >>>which names symbols to exclude from the imports. The Œexcept¹

Re: [Bioc-devel] namespace question

[Karim Mezhoud]

If I include manually the exception, I hve to write this?

import(shiny, except=c('dataTableOutput','renderDataTable')
Thanks
Karim

On Tue, Apr 5, 2016 at 7:28 PM, Michael Lawrence 
wrote:

> Roxygen does not yet support the feature. For now you'll have to live
> with the warning or just importFrom(shiny, ...). Maybe there is some
> way to manually patch the NAMESPACE with Roxygen?
>
> Honestly, I would recommend against using Roxygen to manage your
> NAMESPACE. Just write the thing...
>
>
>
> On Tue, Apr 5, 2016 at 11:07 AM, Karim Mezhoud  wrote:
> > Hi,
> > Actually I have conflict between DT and shiny
> >  Warning: replacing previous import ‘shiny::dataTableOutput’ by
> > ‘DT::dataTableOutput’ when loading ‘bioCancer’
> >   Warning: replacing previous import ‘shiny::renderDataTable’ by
> > ‘DT::renderDataTable’ when loading ‘bioCancer’
> >
> > I would like to import shiny except dataTableOutput and renderDataTable.
> >
> > #'@import shiny except dataTableOutput renderDataTable
> > I am using roxygen2
> > R Under development (unstable) (2016-03-11 r70310)
> > Which package Can I update to get the new import argument.
> > Thanks
> > Karim
> >
> >
> > On Tue, Apr 5, 2016 at 6:50 PM, Michael Lawrence <
> lawrence.mich...@gene.com>
> > wrote:
> >>
> >> I will try to sneak that in since it seems to work and it would be
> >> nice to use it before this Fall.
> >>
> >> On Tue, Apr 5, 2016 at 10:32 AM, Dan Tenenbaum 
> >> wrote:
> >> > Michael, do you know if this change will be (or has already been)
> >> > backported into R-3.3.0?
> >> >
> >> > Thanks.
> >> > Dan
> >> >
> >> >
> >> > - Original Message -
> >> >> From: "Lihua Zhu" 
> >> >> To: "Dan Tenenbaum" , "Michael Lawrence"
> >> >> 
> >> >> Cc: "bioc-devel" 
> >> >> Sent: Tuesday, April 5, 2016 9:49:26 AM
> >> >> Subject: Re: [Bioc-devel] namespace question
> >> >
> >> >> Dan,
> >> >>
> >> >> That is great! Thanks for letting us know!
> >> >>
> >> >> Michael, thank for making it happen so quickly! It works like a
> charm!
> >> >>
> >> >> Best,
> >> >>
> >> >> Julie
> >> >>
> >> >> On 4/2/16 1:58 PM, "Bioc-devel on behalf of Dan Tenenbaum"
> >> >>  dtene...@fredhutch.org>
> >> >> wrote:
> >> >>
> >> >>>BTW, looks like the change has been made to R-devel:
> >> >>>
> >> >>> CHANGES IN R-devel NEW FEATURES
> >> >>>
> >> >>>  * The Œimport()¹ namespace directive now accepts an argument
> Œexcept¹
> >> >>>which names symbols to exclude from the imports. The Œexcept¹
> >> >>> expression
> >> >>>should evaluate to a character vector (after substituting symbols for
> >> >>>strings). See Writing R Extensions.
> >> >>>
> >> >>>URL:
> >>
> >> >>> >>>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__developer.r-2Dproject.
> >>
> >> >>>
> >>>org_blosxom.cgi_R-2Ddevel_NEWS_2016_04_02-23n2016-2D04-2D02&d=BQIGaQ&c=WJB
> >>
> >> >>>
> >>>j9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5g
> >>
> >> >>>
> >>>JMlij5cC5bLU&m=HCJuUKMo50mOyjfD0AtQzV69c0SnACXTGdX_iHcWRfo&s=MbBj5lNGwkIfP
> >> >>>hrHI2clfQd1aq1yPyROa3utKrCP4ug&e=
> >> >>>
> >> >>>
> >> >>>
> >> >>>- Original Message -
> >> >>>> From: "Michael Lawrence" 
> >> >>>> To: "Hervé Pagès" 
> >> >>>> Cc: "Michael Lawrence" , "bioc-devel"
> >> >>>>
> >> >>>> Sent: Saturday, April 2, 2016 4:10:10 AM
> >> >>>> Subject: Re: [Bioc-devel] namespace question
> >> >>>
> >> >>>> Also, just btw, there are two other places where arbitrary R code
> can
> >> >>>> be evaluated in the NAMESPACE, but no one has abused them yet. as
> far
> >> >>>> as I know. The first argument to if() and the .f

Re: [Bioc-devel] namespace question

[Karim Mezhoud]

>>>> Now we have a new category of errors that can happen at package
> >>>>> installation time: errors triggered by the evaluation of the R
> >>>>> expressions embedded in the NAMESPACE file. Hopefully 'R CMD INSTALL'
> >>>>> will report something that can be understood by mere mortals when
> this
> >>>>> happens.
> >>>>>
> >>>>> Once you create the feeling that a NAMESPACE file is just a file
> >>>>> that contains arbitrary R code then people expect import(), export()
> >>>>> etc.. to be ordinary R functions with a man page (being able to do
> >>>>> ?import would not hurt actually) and they'll naturally try to do
> >>>>> things like
> >>>>>
> >>>>>   unwanted_foo_symbols <- ... long and complicated expression
> >>>>>   eventually calling user-defined helper
> >>>>>   functions located in the NAMESPACE file
> >>>>>...
> >>>>>   import(foo, except=unwanted_foo_symbols)
> >>>>>
> >>>>> Can't blame them for that. But is this the kind of things that we're
> >>>>> ready to see in NAMESPACE files?
> >>>>>
> >>>>> Also once you've open that door, people will naturally wonder why
> they
> >>>>> can use an R expression in the 'except' part of import( , except=)
> but
> >>>>> not elsewhere e.g. in
> >>>>>
> >>>>>   import(foo, only=paste0("bar", 1:10))
> >>>>>
> >>>>> as a more elegant way of doing importFrom(foo, bar1, bar2, ...,
> bar10).
> >>>>> This dissymmetry between the syntax of "import only this" and "import
> >>>>> all except this" feels very arbitrary. If you don't support the
> >>>>> import( , only=) syntax, people might legitimately ask things like
> >>>>>
> >>>>>   do.call(importFrom, c(list("foo"), as.list(paste0("bar", 1:10
> >>>>>
> >>>>> to work. Again, can't blame them for that. But do we want this kind
> of
> >>>>> things to work? I'm worried debugging NAMESPACE files would become a
> >>>>> full-time job...
> >>>>>
> >>>>>> I guess one could have implemented NAMESPACE parsing by evaluating
> the
> >>>>>> code in an environment (inheriting from the base namespace) where
> >>>>>> import(), export(), etc, were defined. Maybe there's a good reason
> why
> >>>>>> it was not implemented that way.
> >>>>>
> >>>>>
> >>>>> I'm sure there is ;-)
> >>>>>
> >>>>> H.
> >>>>>
> >>>>>
> >>>>>>
> >>>>>> On Fri, Apr 1, 2016 at 12:55 PM, Hervé Pagès 
> >>>>>>wrote:
> >>>>>>>
> >>>>>>> On 03/31/2016 04:07 PM, Michael Lawrence wrote:
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> I agree. The importExcept idea also works that way:
> >>>>>>>>importExcept(foo,
> >>>>>>>> bar,
> >>>>>>>> baz)
> >>>>>>>>
> >>>>>>>> But import(foo, except=c(bar, baz)) reads better.
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> mmh... so R expressions with calls to base functions like base::c()
> >>>>>>>are
> >>>>>>> making their way in the NAMESPACE file. That's opening a big door.
> >>>>>>>Does
> >>>>>>> that mean that we'll be able to do things like:
> >>>>>>>
> >>>>>>> import(foo, except=paste0("bar", 1:10))
> >>>>>>>
> >>>>>>> Or maybe c(bar, baz) in your above example is just an arbitrary
> >>>>>>>syntax
> >>>>>>> that just happens to look like an R expression but won't be
> evaluated
> >>>>>>> as such?
> >>>>>>>
> >>>>>>>
> >>>&

[Bioc-devel] big file ReactomeFI --> bioC annotate package

[Karim Mezhoud]

Dear bioC developer,
I included in my bioCancer/inst/extdata a Reactome FI database (/
http://reactomews.oicr.on.ca:8080/caBigR3WebApp2015/FIsInGene_031516_with_annotations.txt.zip
)

Gene1Gene2AnnotationDirectionScore
16-5-5CDC42predicted-0.82
16-5-5RHOJpredicted-0.82
16-5-5RHOQpredicted-0.82
FAS/APO-1/CD95BIDactivate->1.00
FAS/APO-1/CD95CASP10complex-1.00
FAS/APO-1/CD95DAXXcomplex; reaction-1.00
FAS/APO-1/CD95DKFZP686N0154activate->1.00
FAS/APO-1/CD95FADDcomplex-1.00
FAS/APO-1/CD95FASLGcomplex; input-1.00
FAS/APO-1/CD95HSPB1reaction-1.00
FAS/APO-1/CD95MAP2K3activate->1.00
FAS/APO-1/CD95MAP2K4activate->1.00

bioCancer uses this file to extract the Direction/arrowhead of gene-gene
interaction (activates, inhibits, predicted, complexe.).
This kind of data is not available in Reactome.db package nor by Reactome
API service (to my knowledge).

I have to remove this file from my new package and may get annotate package
for ReactomeFI database.
How to?
Karim

[[alternative HTML version deleted]]

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Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

[Karim Mezhoud]

git clone https://github.com/Bioconductor-mirror/canceR
 cd canceR/
 bash ../update_remotes.sh
Already on 'master'
Your branch is up-to-date with 'origin/master'.
Rebuilding
.git/svn/refs/remotes/git-svn/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358
...
r100351 = 942469704de53586b277926f1b3d358ffd808152
r100809 = 0aa2b86471d49cace7d4baa504684c2e86f47830
r100810 = 3940d764844e9051172fd1d05fe606ee56764e67
r100984 = 55fba8349ef754fc51a78367c19a8bc8f29b881e
r100985 = b313b60029281d2c8486d0dc9e6a34c2f68fd9be
r100987 = a8cd3e44badee5b04548fff7a9faeca2f8448489
r101023 = f625ce6a1d225016103768be2e051593ba785832
r102448 = a2c8236451c5e04cc1e43f4568472de8ea8361ba
r102571 = f6fc58dd50aa611f3b1930fd850df9c5471c7f94
r102584 = fdd1ce259835d1325645a17e80affa4f0656fc41
r102591 = 2e2874d3ad1d00f3599dcdc6ef7347199dc8b651
r102594 = 363ea15b52e2c00cc063c1bffeb167c70390769c
r102693 = 535c658791a5218ad341b329c2e049c4b04c9584
r102694 = 26c26df43c2ddf12008543e4f647f135bde63cf7
r102695 = af7cd2771d0695bb92c4d6a433b545cf63940463
r102854 = 954b8510e0fe68211fc315787a1c866ad237e8a5
r103140 = f042db172a7f04f00c04ca9e233df54bbc1746a1
r103142 = efb740a41e489809c91cd6f3a42516adddb6b050
r103607 = 1b9435efea2dd8d14593ad500f59623bcecbe155
r106326 = c9a8e4f83e33c277e26b58b03848c8bb304b9571
r106461 = 9726cf88862426c96fbbd238321599e99444fd12
r109589 = 88ef0e88bb6ab106d53100787d698672d6f44bac
r109592 = a8299618231a8ce2891e20310f4cbf2fddc24526
r115378 = 1da8432c11ae9cbc38950c22e16093fc4c97853f
r115379 = 2592b6a5ac7c41003611ce44b93ff9b6ac8c5a54
r115385 = 7fbc307287b25ff7efe7235001921791f2668898
r115387 = 1fe033d9fdd765f6c7e6a2a884053721bbd5691a
r115608 = 025a596f5f717b527b9a5c92612d48a09e93f0a8
Done rebuilding
.git/svn/refs/remotes/git-svn/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358
Current branch master is up to date.
Commit to git as normal, when you want to push your commits to svn
  1. `git svn rebase` to get the latest SVN changes.
  2. `git svn dcommit --add-author-from` to commit your changes to SVN.


add files/forder to /vignette
pump version DESCRIPTION

git commit -m "fix vignette"
 git svn rebase
Current branch master is up to date.

 git svn dcommit --add-author-from
Committing to
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/canceR ...
Avignettes/canceR.Rnw
Avignettes/canceR.latex
Avignettes/image/BrstPrstGSEAlm.png
Avignettes/image/whichMSigDB2.jpeg
Avignettes/image/workspace.png
Mvignettes/.gitignore

ERROR from SVN:
A repository hook failed: Commit blocked by pre-commit hook (exit code 1)
with output:
Traceback (most recent call last):
  File
"/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",
line 283, in 
myexit(0)
TypeError: myexit() takes exactly 2 arguments (1 given)

W: 35d29461f59277e54461a31161c6522053c666ad and refs/remotes/git-svn
differ, using rebase:
:04 04 e29c612e777ebd221293caaccbfb810b293addd0
7865b7a8f6a9e5e3b0bba7605de8f9e3abfb070a Mvignettes
Current branch master is up to date.
ERROR: Not all changes have been committed into SVN, however the committed
ones (if any) seem to be successfully integrated into the working tree.
Please see the above messages for details.

git diff


No thing



On Fri, Apr 1, 2016 at 9:48 PM, Dan Tenenbaum 
wrote:

> Sorry, about that, please try again.
>
> Dan
>
>
> - Original Message -
> > From: "Karim Mezhoud" 
> > To: "Dan Tenenbaum" 
> > Sent: Friday, April 1, 2016 1:36:30 PM
> > Subject: Re: [Bioc-devel] 49 software packages either have no vignettes
> or their vignettes are not built by R CMD build!
>
> > git reset --hard HEAD~
> > bash ../update_remotes.sh
> >
> > add files/folder  to / vignette
> > pump version in DESCRIPTION
> > check all change
> > git commit -m "fix vignette"
> > git svn rebase
> > git svn dcommit --add-author-from
> > Committing to
> > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/canceR ...
> >Avignettes/canceR.Rnw
> >Avignettes/canceR.latex
> >Avignettes/image/BrstPrstGSEAlm.png
> >Avignettes/image/BrstPrstGSEAlm1.jpeg
> >Avignettes/image/BrstPrstGSEAlm2.jpeg
> >Avignettes/image/BrstPrstGSEAlm3.jpeg
> >Avignettes/image/BrstPrstGSEAlm4.jpeg
> >Avignettes/image/Circos.png
> >Avignettes/image/Coxph.png
> >Avignettes/image/stadGSEAlm2.jpeg
> >Avignettes/image/stadGSEAlm3.jpeg
> >Avignettes/image/stadGSEAlm4.jpeg
> >Avignettes/image/stadGSEAlm5.jpeg
> >Avignettes/image/stadGSEAlm6.jpeg
> >Avignettes/image/stadGSEAlm7.jpeg
> >Avignettes/image/stadGSEAlm8.jpeg
> >Avignettes/image/stadGSEAlm9.jpeg
&

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

[Karim Mezhoud]

NO thing in the file

On Fri, Apr 1, 2016 at 6:24 PM, Dan Tenenbaum 
wrote:

> Can  you send me the output of
>
> git diff?
>
> So:
>
> git diff > diff.txt
>
> and send me diff.txt?
>
> Dan
>
>
> - Original Message -
> > From: "Karim Mezhoud" 
> > To: "Dan Tenenbaum" 
> > Cc: "bioc-devel" 
> > Sent: Friday, April 1, 2016 9:27:52 AM
> > Subject: Re: [Bioc-devel] 49 software packages either have no vignettes
> or their vignettes are not built by R CMD build!
>
> > Hi,
> > I tried the scenario 1:
> > git clone https://github.com/Bioconductor-mirror/canceR
> > cd canceR
> >
> > bash ../update_remotes.sh
> > add files/dir  in /vignette
> > pump version in DESCRIPTION
> >
> > commit -m "fix vignette"
> > git svn rebase
> > git svn dcommit --add-author-from
> >
> >
> > MBP-de-MacBook:canceR Mezhoud$ git svn dcommit --add-author-from
> > Committing to
> > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/canceR ...
> >Ainst/doc/canceR.pdf
> >Avignettes/canceR.Rnw
> >Avignettes/canceR.latex
> >Avignettes/image/BrstPrstGSEAlm.png
> >Avignettes/image/BrstPrstGSEAlm1.jpeg
> >Avignettes/image/BrstPrstGSEAlm2.jpeg
> >Avignettes/image/BrstPrstGSEAlm3.jpeg
> >Avignettes/image/BrstPrstGSEAlm4.jpeg
> >Avignettes/image/Circos.png
> >Avignettes/image/Coxph.png
> >Avignettes/image/GSEA-R.png
> >Avignettes/image/Mutation1.png
> >Avignettes/image/clinicalDataDialog.png
> >Avignettes/image/dialogCircos.png
> >Avignettes/image/gct_cls.png
> > ..
> >Avignettes/image/setWorkspace.jpeg
> >Avignettes/image/stadGSEAlm4.jpeg
> >Avignettes/image/stadGSEAlm5.jpeg
> >Avignettes/image/stadGSEAlm6.jpeg
> >Avignettes/image/stadGSEAlm7.jpeg
> >Avignettes/image/stadGSEAlm8.jpeg
> >Avignettes/image/stadGSEAlm9.jpeg
> >Avignettes/image/stadGSEAlmCNA.png
> >Avignettes/image/starting.png
> >Avignettes/image/starting.svg
> >Avignettes/image/startingWindow.jpeg
> >Avignettes/image/whichMSigDB.png
> >Avignettes/image/whichMSigDB1.jpeg
> >Avignettes/image/whichMSigDB2.jpeg
> >Avignettes/image/workspace.png
> >MDESCRIPTION
> >
> > ERROR from SVN:
> > A repository hook failed: Commit blocked by pre-commit hook (exit code 1)
> > with output:
> > Traceback (most recent call last):
> >  File
> >
> "/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",
> > line 277, in 
> >process_diff(diff)
> >  File
> >
> "/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",
> > line 112, in process_diff
> >filename = segs0[1]
> > IndexError: list index out of range
> >
> > W: e980c09a87a818a1736f38304e18325b7c0362f5 and refs/remotes/git-svn
> > differ, using rebase:
> > :100755 100755 d4a308bbf85b4f0ba06ee27af51f1e76804bad2a
> > 6b7df529709f10184b376d69d5ea9f3ae9e1d3fe MDESCRIPTION
> > :04 04 de5dbdd606d8758565afcadbaf04e5821e71b461
> > 870588b10784e8f5169b2f7bf6377985edd3a735 Minst
> > :04 04 056451883aa9ba2af9e19f8dd2a285d412b9ae60
> > 7865b7a8f6a9e5e3b0bba7605de8f9e3abfb070a Mvignettes
> > Current branch master is up to date.
> > ERROR: Not all changes have been committed into SVN, however the
> committed
> > ones (if any) seem to be successfully integrated into the working tree.
> > Please see the above messages for details.
> >
> >
> > On Fri, Apr 1, 2016 at 4:27 PM, Dan Tenenbaum 
> > wrote:
> >
> >> Just because git tells you to push, doesn't mean you should push! ;)
> >> In the devel branch, the upstream repository is an svn repository, so
> >> instead of pushing you want to do
> >>
> >> git svn dcommit --add-author-from
> >>
> >> I'll take a look at your earlier email later today.
> >>
> >> Dan
> >>
> >>
> >> - Original Message -
> >> > From: "Karim Mezhoud" 
> >> > To: "Dan Tenenbaum" 
> >> > Cc: "bioc-devel" 
> >> > Sent: Friday, April 1, 2016 5:17:32 AM
> >> > Subject: Re: [Bioc-devel] 49 software packages either have no
> vig

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

[Karim Mezhoud]

Hi,
I tried the scenario 1:
git clone https://github.com/Bioconductor-mirror/canceR
cd canceR

bash ../update_remotes.sh
add files/dir  in /vignette
pump version in DESCRIPTION

commit -m "fix vignette"
git svn rebase
git svn dcommit --add-author-from


MBP-de-MacBook:canceR Mezhoud$ git svn dcommit --add-author-from
Committing to
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/canceR ...
Ainst/doc/canceR.pdf
Avignettes/canceR.Rnw
Avignettes/canceR.latex
Avignettes/image/BrstPrstGSEAlm.png
Avignettes/image/BrstPrstGSEAlm1.jpeg
Avignettes/image/BrstPrstGSEAlm2.jpeg
Avignettes/image/BrstPrstGSEAlm3.jpeg
Avignettes/image/BrstPrstGSEAlm4.jpeg
Avignettes/image/Circos.png
Avignettes/image/Coxph.png
Avignettes/image/GSEA-R.png
Avignettes/image/Mutation1.png
Avignettes/image/clinicalDataDialog.png
Avignettes/image/dialogCircos.png
Avignettes/image/gct_cls.png
 ..
Avignettes/image/setWorkspace.jpeg
Avignettes/image/stadGSEAlm4.jpeg
Avignettes/image/stadGSEAlm5.jpeg
Avignettes/image/stadGSEAlm6.jpeg
Avignettes/image/stadGSEAlm7.jpeg
Avignettes/image/stadGSEAlm8.jpeg
Avignettes/image/stadGSEAlm9.jpeg
Avignettes/image/stadGSEAlmCNA.png
Avignettes/image/starting.png
Avignettes/image/starting.svg
Avignettes/image/startingWindow.jpeg
Avignettes/image/whichMSigDB.png
Avignettes/image/whichMSigDB1.jpeg
Avignettes/image/whichMSigDB2.jpeg
Avignettes/image/workspace.png
MDESCRIPTION

ERROR from SVN:
A repository hook failed: Commit blocked by pre-commit hook (exit code 1)
with output:
Traceback (most recent call last):
  File
"/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",
line 277, in 
process_diff(diff)
  File
"/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",
line 112, in process_diff
filename = segs0[1]
IndexError: list index out of range

W: e980c09a87a818a1736f38304e18325b7c0362f5 and refs/remotes/git-svn
differ, using rebase:
:100755 100755 d4a308bbf85b4f0ba06ee27af51f1e76804bad2a
6b7df529709f10184b376d69d5ea9f3ae9e1d3fe MDESCRIPTION
:04 04 de5dbdd606d8758565afcadbaf04e5821e71b461
870588b10784e8f5169b2f7bf6377985edd3a735 Minst
:04 04 056451883aa9ba2af9e19f8dd2a285d412b9ae60
7865b7a8f6a9e5e3b0bba7605de8f9e3abfb070a Mvignettes
Current branch master is up to date.
ERROR: Not all changes have been committed into SVN, however the committed
ones (if any) seem to be successfully integrated into the working tree.
Please see the above messages for details.


On Fri, Apr 1, 2016 at 4:27 PM, Dan Tenenbaum 
wrote:

> Just because git tells you to push, doesn't mean you should push! ;)
> In the devel branch, the upstream repository is an svn repository, so
> instead of pushing you want to do
>
> git svn dcommit --add-author-from
>
> I'll take a look at your earlier email later today.
>
> Dan
>
>
> - Original Message -
> > From: "Karim Mezhoud" 
> > To: "Dan Tenenbaum" 
> > Cc: "bioc-devel" 
> > Sent: Friday, April 1, 2016 5:17:32 AM
> > Subject: Re: [Bioc-devel] 49 software packages either have no vignettes
> or their vignettes are not built by R CMD build!
>
> > Hi,
> > What is the meaning of this? Thanks
> >
> > git checkout devel
> >
> > Previous HEAD position was 1fe033d... add /image
> > Switched to branch 'devel'
> > Your branch is ahead of 'bioc/master' by 49 commits.
> >  (use "git push" to publish your local commits)
> >
> > git push
> >
> > fatal: The upstream branch of your current branch does not match
> > the name of your current branch.  To push to the upstream branch
> > on the remote, use
> >
> >git push bioc HEAD:master
> >
> > To push to the branch of the same name on the remote, use
> >
> > git push HEAD:master
> >
> >
> > ssh: Could not resolve hostname head: nodename nor servname provided, or
> > not known
> > fatal: Could not read from remote repository.
> >
> > Please make sure you have the correct access rights
> >
> >
> >
> > On Fri, Apr 1, 2016 at 1:09 AM, Karim Mezhoud 
> wrote:
> >
> >> Hi,
> >> I repeated several times the clone And I success for one time the
> >> commit but with mistakes. I can't repeat the steps again.
> >>
> >> git merge master --log
> >>
> >> And I had a conflict between versions. I omit conflicts and I
> >>
> >> git svn

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

[Karim Mezhoud]

Hi,
What is the meaning of this? Thanks

 git checkout devel

Previous HEAD position was 1fe033d... add /image
Switched to branch 'devel'
Your branch is ahead of 'bioc/master' by 49 commits.
  (use "git push" to publish your local commits)

 git push

fatal: The upstream branch of your current branch does not match
the name of your current branch.  To push to the upstream branch
on the remote, use

git push bioc HEAD:master

To push to the branch of the same name on the remote, use

git push HEAD:master


ssh: Could not resolve hostname head: nodename nor servname provided, or
not known
fatal: Could not read from remote repository.

Please make sure you have the correct access rights



On Fri, Apr 1, 2016 at 1:09 AM, Karim Mezhoud  wrote:

> Hi,
> I repeated several times the clone And I success for one time the
> commit but with mistakes. I can't repeat the steps again.
>
> git merge master --log
>
> And I had a conflict between versions. I omit conflicts and I
>
> git svn dcommit --add-author-from
>
> ##
> A
> A.
> A.
> All files are added
>
>
> ERROR from SVN:
> A repository hook failed: Commit blocked by pre-commit hook (exit code 1)
> with output:
> Traceback (most recent call last):
>   File
> "/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",
> line 277, in 
> process_diff(diff)
>   File
> "/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",
> line 112, in process_diff
> filename = segs0[1]
> IndexError: list index out of range
>
> W: bc9bed01f7b03d6da5b345d2699822d197b202b4 and refs/remotes/git-svn-devel
> differ, using rebase:
> :100644 100644 d4a2ec80b4623bc866606de39e06ff33e60056a8
> cea7fa70e88adf9033fce5d7a846944c3431ee85 M.gitignore
> :100755 100755 6b7df529709f10184b376d69d5ea9f3ae9e1d3fe
> 15ac213b3484b967cceabc0c0e22bda2d654b27a MDESCRIPTION
> :04 04 e2c182ee6256b99e4c83e2dac8e7576fedeef302
> 7865b7a8f6a9e5e3b0bba7605de8f9e3abfb070a Mvignettes
>
> It seems that there is already a rebase-apply directory, and
> I wonder if you are in the middle of another rebase.  If that is the
> case, please try
> git rebase (--continue | --abort | --skip)
> If that is not the case, please
> rm -fr "/Volumes/DATA/canceRwrksp3/canceR/.git/rebase-apply"
> and run me again.  I am stopping in case you still have something
> valuable there.
> rebase refs/remotes/git-svn-devel: command returned error: 1
> @#
>
>
>
>
> I removed
>
>
> rm -fr /Volumes/DATA/canceRwrksp3/canceR/.git/rebase-apply
>
> and
>
> git svn rebase
>
> ###
> First, rewinding head to replay your work on top of it...
> Applying: canceR0.99.1
> Using index info to reconstruct a base tree...
> .git/rebase-apply/patch:102: trailing whitespace.
>
> .git/rebase-apply/patch:103: trailing whitespace.
>
> .git/rebase-apply/patch:106: trailing whitespace.
>
> .git/rebase-apply/patch:113: trailing whitespace.
>
> .git/rebase-apply/patch:120: trailing whitespace.
>
> warning: squelched 7388 whitespace errors
> warning: 7393 lines add whitespace errors.
> Falling back to patching base and 3-way merge...
> error: The following untracked working tree files would be overwritten by
> merge:
> vignettes/._canceR.pdf
> Please move or remove them before you can merge.
> Aborting
> error: Failed to merge in the changes.
> Patch failed at 0001 canceR0.99.1
> The copy of the patch that failed is found in: .git/rebase-apply/patch
>
> When you have resolved this problem, run "git rebase --continue".
> If you prefer to skip this patch, run "git rebase --skip" instead.
> To check out the original branch and stop rebasing, run "git rebase
> --abort".
>
> rebase refs/remotes/git-svn-devel: command returned error: 128
> ###
>
> I did not found any whitespace in path file line: 102, 103, 106, 113, 120
>
> patch file from 112 to 120:
>
> *@@ -0,0 +1,73 @@*
>
> *+Match_GeneList_MSigDB <- function(){*
>
> *+*
>
> *+*
>
> *+ttdialogMSigDB<-tktoplevel()*
>
> *+tktitle(ttdialogMSigDB) <- "Setting MSigDB Directory"*
>
> *+*
>
> *+fromDir <- function(){*
>
> *+##Select directory which has MSigDB*
>
> *+myGlobalEnv$dirMSigDBPath <- tk_choose.dir()*
>
> *+tkdestroy(ttdialogMSigDB)*
>
> *+#return(dirMSigDBPath)*
>
> *+}*
>
> *+*
>
> *+fromExample <- f

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

[Karim Mezhoud]

Hi,
I repeated several times the clone And I success for one time the
commit but with mistakes. I can't repeat the steps again.

git merge master --log

And I had a conflict between versions. I omit conflicts and I

git svn dcommit --add-author-from

##
A
A.
A.
All files are added


ERROR from SVN:
A repository hook failed: Commit blocked by pre-commit hook (exit code 1)
with output:
Traceback (most recent call last):
  File
"/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",
line 277, in 
process_diff(diff)
  File
"/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",
line 112, in process_diff
filename = segs0[1]
IndexError: list index out of range

W: bc9bed01f7b03d6da5b345d2699822d197b202b4 and refs/remotes/git-svn-devel
differ, using rebase:
:100644 100644 d4a2ec80b4623bc866606de39e06ff33e60056a8
cea7fa70e88adf9033fce5d7a846944c3431ee85 M.gitignore
:100755 100755 6b7df529709f10184b376d69d5ea9f3ae9e1d3fe
15ac213b3484b967cceabc0c0e22bda2d654b27a MDESCRIPTION
:04 04 e2c182ee6256b99e4c83e2dac8e7576fedeef302
7865b7a8f6a9e5e3b0bba7605de8f9e3abfb070a Mvignettes

It seems that there is already a rebase-apply directory, and
I wonder if you are in the middle of another rebase.  If that is the
case, please try
git rebase (--continue | --abort | --skip)
If that is not the case, please
rm -fr "/Volumes/DATA/canceRwrksp3/canceR/.git/rebase-apply"
and run me again.  I am stopping in case you still have something
valuable there.
rebase refs/remotes/git-svn-devel: command returned error: 1
@#




I removed


rm -fr /Volumes/DATA/canceRwrksp3/canceR/.git/rebase-apply

and

git svn rebase

###
First, rewinding head to replay your work on top of it...
Applying: canceR0.99.1
Using index info to reconstruct a base tree...
.git/rebase-apply/patch:102: trailing whitespace.

.git/rebase-apply/patch:103: trailing whitespace.

.git/rebase-apply/patch:106: trailing whitespace.

.git/rebase-apply/patch:113: trailing whitespace.

.git/rebase-apply/patch:120: trailing whitespace.

warning: squelched 7388 whitespace errors
warning: 7393 lines add whitespace errors.
Falling back to patching base and 3-way merge...
error: The following untracked working tree files would be overwritten by
merge:
vignettes/._canceR.pdf
Please move or remove them before you can merge.
Aborting
error: Failed to merge in the changes.
Patch failed at 0001 canceR0.99.1
The copy of the patch that failed is found in: .git/rebase-apply/patch

When you have resolved this problem, run "git rebase --continue".
If you prefer to skip this patch, run "git rebase --skip" instead.
To check out the original branch and stop rebasing, run "git rebase
--abort".

rebase refs/remotes/git-svn-devel: command returned error: 128
###

I did not found any whitespace in path file line: 102, 103, 106, 113, 120

patch file from 112 to 120:

*@@ -0,0 +1,73 @@*

*+Match_GeneList_MSigDB <- function(){*

*+*

*+*

*+ttdialogMSigDB<-tktoplevel()*

*+tktitle(ttdialogMSigDB) <- "Setting MSigDB Directory"*

*+*

*+fromDir <- function(){*

*+##Select directory which has MSigDB*

*+myGlobalEnv$dirMSigDBPath <- tk_choose.dir()*

*+tkdestroy(ttdialogMSigDB)*

*+#return(dirMSigDBPath)*

*+}*

*+*

*+fromExample <- function(){*

*+##Or select MSigDB from package*

*+myGlobalEnv$dirMSigDBPath <-
paste(path.package("canceR"),"/extdata/MSigDB/",sep="")*

*+tkdestroy(ttdialogMSigDB)*

*+#return(dirMSigDBPath)*



 after Igit svn rebase

It seems that there is already a rebase-apply directory, and
I wonder if you are in the middle of another rebase.  If that is the
case, please try
git rebase (--continue | --abort | --skip)
If that is not the case, please
rm -fr "/Volumes/DATA/canceRwrksp3/canceR/.git/rebase-apply"
and run me again.  I am stopping in case you still have something
valuable there.
rebase refs/remotes/git-svn-devel: command returned error: 1

On Tue, Mar 29, 2016 at 8:12 PM, Dan Tenenbaum 
wrote:

>
>
>
>
> - Original Message -
> > From: "Karim Mezhoud" 
> > To: "Dan Tenenbaum" 
> > Cc: "bioc-devel" 
> > Sent: Tuesday, March 29, 2016 12:05:03 PM
> > Subject: Re: [Bioc-devel] 49 software packages either have no vignettes
> or their vignettes are not built by R CMD build!
>
> > Thank you,
> > I am in devel branch (git checkout devel) .
> >
> > when I "git svn rebase" I get all changed files with message: needs
> update.
>
> This doesn't happen with me:
&g

Re: [Bioc-devel] namespace question

[Karim Mezhoud]

I think "From" is needed to specify which package we want to exlude
functions.

I think  excludeFrom (package, function)  seems to be intuitive.

thanks,
Karim



On Thu, Mar 31, 2016 at 9:54 PM, Hervé Pagès  wrote:

> On 03/31/2016 12:55 PM, Michael Lawrence wrote:
>
>> Probably should just stick to exact symbols for now. If there is a
>> case where a pattern is actually useful, rather than just an
>> obfuscation, we can extend the feature set.
>>
>
> Fair enough. Not really intuitive that excludeImport uses the same
> syntax as (but does the opposite of) importFrom though. Maybe having
> the name of the directive start with "import" would help e.g.
>
> importExcept(hash, values)  # opposite of importFrom(hash, values)
>
> Thanks,
> H.
>
>
>
>> On Thu, Mar 31, 2016 at 12:11 PM, Zhu, Lihua (Julie)
>>  wrote:
>>
>>> Herve,
>>>
>>> That is a very interesting idea and works for me! Thanks!
>>>
>>> importPatternFrom(IRanges, "^values$")
>>>
>>>
>>> Best,
>>>
>>> Julie
>>>
>>> On 3/31/16 2:51 PM, "Bioc-devel on behalf of Hervé Pagès"
>>> 
>>> wrote:
>>>
>>> On 03/30/2016 08:35 PM, Michael Lawrence wrote:

> That would work, but R is not going to be happy about redundant
> imports. Interactively, users would balk at symbol qualification.
>
> There are two classes of conflict:
> 1) Same semantics, where a common generic would arbitrate, or one
> package could depend on the other, and
> 2) Different semantics, in which case one of the functions should
> probably be renamed, although that might not be practical or easy to
> agree upon.
>
> When those approaches fail, qualification is the only recourse.
>
> I will think about adding an excludeImport() or importAs().
>

 What about having something like an importPatternFrom() directive
 similar to the exportPattern() directive and have these directives
 support some of the grep() toggles like 'ignore.case', 'fixed',
 'invert' etc... ?

 Then Julie could just do:

 importPatternFrom(hash, "^values$", invert=TRUE)

 H.


>
> On Wed, Mar 30, 2016 at 8:20 PM, Robert M. Flight  >
> wrote:
>
>> In the cases of having conflicting names, is it not appropriate then
>> to use
>> the "package::function" form for calling a particular function?
>>
>> On Wed, Mar 30, 2016 at 11:14 PM Michael Lawrence
>> 
>> wrote:
>>
>> I can't find the hash function in IRanges. Are you sure it has one?
>>>
>>> On Wed, Mar 30, 2016 at 8:07 PM, Zhu, Lihua (Julie)
>>>  wrote:
>>>
 Michael,

 I have the same user case as Kasper. Another example is that both
 IRanges
 and hash packages have hash. I need to use the hash from the hash
 package
 instead of the one from IRanges.

 Best,

 Julie

 On Mar 30, 2016, at 7:57 PM, Kasper Daniel Hansen
  wrote:

 My usecase is when I import() two packages who has a conflict in a
 name.
 For example, both Biobase and matrixStats has both anyMissing and
 rowMedians. I am happy to get all of these two packages, but I need
 to
 resolve the conflict.  Since I want to keep the ones from
 matrixStats I

>>> know
>>>
 need to figure out how to import Biobase selectively.  Which I can,
 using
 the tools from codetoolsBioC, but I would also be happy with an
 importFromExcept(), which would make my life much easier.

 Best,
 Kasper

 On Wed, Mar 30, 2016 at 4:47 PM, Michael Lawrence
  wrote:

>
> I'm curious about which symbols you wouldn't want to import, and
> why.
>
> On Wed, Mar 30, 2016 at 12:19 PM, Zhu, Lihua (Julie)
>  wrote:
>
>> Hi,
>>
>> Is there a function to import all the exported objects from a
>> package
>> except a few named ones in NAMESPACE file?
>>
>> For example, I would like to import all the functions in S4Vectors
>> except fold. Is there a way to  specify this without listing all
>> other
>> functions using importFrom?
>>
>> Many thanks for your help!
>>
>> Best regards,
>>
>> Julie
>>
>> 
>> Lihua Julie Zhu, Ph.D
>> Research Professor
>> Department of Molecular, Cell and Cancer Biology (MCCB)
>> Head of MCCB Bioinformatics Core
>> Program in Molecular Medicine
>> Program in Bioinformatics and Integrative Biology
>> University of Massachusetts Medical School
>> 364 Plantation Street, Room 613
>> Worcester, MA 01605
>> 508-856-5256 phone
>> (508) 856 5460 fax
>>

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

[Karim Mezhoud]

Thank you,
I am in devel branch (git checkout devel) .

when I "git svn rebase" I get all changed files with message: needs update.
How can I update.
km




On Tue, Mar 29, 2016 at 4:16 PM, Dan Tenenbaum 
wrote:

>
>
> - Original Message -----
> > From: "Karim Mezhoud" 
> > To: "bioc-devel" 
> > Cc: "Dan Tenenbaum" 
> > Sent: Tuesday, March 29, 2016 6:11:15 AM
> > Subject: Re: [Bioc-devel] 49 software packages either have no vignettes
> or their vignettes are not built by R CMD build!
>
> > Dear Dr Dan,
> > Thank you for this note.
> > In my case (canceR), I am using sweave and having:
> >
> > checking PDF version of manual ... [8s/19s]   OK
> >
> > during R CMD Check.
> >
> > I need to sync devel version using git-mirrors (
> > https://www.bioconductor.org/developers/how-to/git-mirrors/).
> > I am following scenario 2.
> > When I fork bioc-mirror/canceR I get two repo with the same name in my
> > github.
> >
>
> It sounds like you already had a github repository before the fork. In
> this case, do not fork, just run the update_remotes.sh script.
> Dan
>
>
> > at step 4 of tutorial, I can not push some changes:
> >
> > error: unable to read askpass response from 'rpostback-askpass'
> > fatal: could not read Username for 'https://github.com': Device not
> > configured
> >
> > 1- How can I configure access to bioc-mirror/canceR.
> >
> > 2- What is the utility of the fork if we can commit directly to
> > bioc-mirror/canceR?
> >
> > Thank you
> > Karim
> >
> >
> > On Wed, Mar 23, 2016 at 10:44 PM, Dan Tenenbaum 
> > wrote:
> >
> >> Attention package maintainers,
> >>
> >> When building an R package, if R thinks there is a vignette, it will
> emit
> >> this line during R CMD build:
> >>
> >> * creating vignettes ... OK
> >>
> >> If there is either no vignette, or in the case of non-sweave vignettes,
> >> something is not set up correctly (there are many things that can go
> >> wrong), you won't see that line of output.
> >>
> >> This means your vignette will not be available on our web site, nor to
> end
> >> users who install your package.
> >>
> >> So going to the build system and looking through all R CMD build output
> to
> >> see which output files do NOT have that line, returns 49 matches:
> >>
> >> $ grep -L "creating vignettes ..." *.buildsrc-out.txt
> >> a4Base.buildsrc-out.txt
> >> a4Classif.buildsrc-out.txt
> >> a4Core.buildsrc-out.txt
> >> a4Preproc.buildsrc-out.txt
> >> a4Reporting.buildsrc-out.txt
> >> affxparser.buildsrc-out.txt
> >> affyio.buildsrc-out.txt
> >> AffyTiling.buildsrc-out.txt
> >> aroma.light.buildsrc-out.txt
> >> arrayQuality.buildsrc-out.txt
> >> bigmemoryExtras.buildsrc-out.txt
> >> BiocCaseStudies.buildsrc-out.txt
> >> BiocGenerics.buildsrc-out.txt
> >> BiocInstaller.buildsrc-out.txt
> >> BufferedMatrixMethods.buildsrc-out.txt
> >> canceR.buildsrc-out.txt
> >> CGHbase.buildsrc-out.txt
> >> CoCiteStats.buildsrc-out.txt
> >> daMA.buildsrc-out.txt
> >> dcGSA.buildsrc-out.txt
> >> DynDoc.buildsrc-out.txt
> >> ExperimentHub.buildsrc-out.txt
> >> flipflop.buildsrc-out.txt
> >> GraphAT.buildsrc-out.txt
> >> HDF5Array.buildsrc-out.txt
> >> hypergraph.buildsrc-out.txt
> >> Icens.buildsrc-out.txt
> >> impute.buildsrc-out.txt
> >> mcaGUI.buildsrc-out.txt
> >> microRNA.buildsrc-out.txt
> >> minet.buildsrc-out.txt
> >> MSstats.buildsrc-out.txt
> >> multtest.buildsrc-out.txt
> >> netresponse.buildsrc-out.txt
> >> nondetects.buildsrc-out.txt
> >> normalize450K.buildsrc-out.txt
> >> oligoClasses.buildsrc-out.txt
> >> parglms.buildsrc-out.txt
> >> plier.buildsrc-out.txt
> >> preprocessCore.buildsrc-out.txt
> >> ProtGenerics.buildsrc-out.txt
> >> QUALIFIER.buildsrc-out.txt
> >> RPA.buildsrc-out.txt
> >> scde.buildsrc-out.txt
> >> seqplots.buildsrc-out.txt
> >> SJava.buildsrc-out.txt
> >> spotSegmentation.buildsrc-out.txt
> >> stepNorm.buildsrc-out.txt
> >> XVector.buildsrc-out.txt
> >>
> >> Some of these (a4Base, a4Classif and many more) just have no vignettes/
> >> directory so no vignettes at all.
> >>
> >>
> >> 

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

[Karim Mezhoud]

Dear Dr Dan,
Thank you for this note.
In my case (canceR), I am using sweave and having:

 checking PDF version of manual ... [8s/19s]   OK

during R CMD Check.

I need to sync devel version using git-mirrors (
https://www.bioconductor.org/developers/how-to/git-mirrors/).
I am following scenario 2.
When I fork bioc-mirror/canceR I get two repo with the same name in my
github.

at step 4 of tutorial, I can not push some changes:

error: unable to read askpass response from 'rpostback-askpass'
fatal: could not read Username for 'https://github.com': Device not
configured

1- How can I configure access to bioc-mirror/canceR.

2- What is the utility of the fork if we can commit directly to
bioc-mirror/canceR?

Thank you
Karim


On Wed, Mar 23, 2016 at 10:44 PM, Dan Tenenbaum 
wrote:

> Attention package maintainers,
>
> When building an R package, if R thinks there is a vignette, it will emit
> this line during R CMD build:
>
> * creating vignettes ... OK
>
> If there is either no vignette, or in the case of non-sweave vignettes,
> something is not set up correctly (there are many things that can go
> wrong), you won't see that line of output.
>
> This means your vignette will not be available on our web site, nor to end
> users who install your package.
>
> So going to the build system and looking through all R CMD build output to
> see which output files do NOT have that line, returns 49 matches:
>
> $ grep -L "creating vignettes ..." *.buildsrc-out.txt
> a4Base.buildsrc-out.txt
> a4Classif.buildsrc-out.txt
> a4Core.buildsrc-out.txt
> a4Preproc.buildsrc-out.txt
> a4Reporting.buildsrc-out.txt
> affxparser.buildsrc-out.txt
> affyio.buildsrc-out.txt
> AffyTiling.buildsrc-out.txt
> aroma.light.buildsrc-out.txt
> arrayQuality.buildsrc-out.txt
> bigmemoryExtras.buildsrc-out.txt
> BiocCaseStudies.buildsrc-out.txt
> BiocGenerics.buildsrc-out.txt
> BiocInstaller.buildsrc-out.txt
> BufferedMatrixMethods.buildsrc-out.txt
> canceR.buildsrc-out.txt
> CGHbase.buildsrc-out.txt
> CoCiteStats.buildsrc-out.txt
> daMA.buildsrc-out.txt
> dcGSA.buildsrc-out.txt
> DynDoc.buildsrc-out.txt
> ExperimentHub.buildsrc-out.txt
> flipflop.buildsrc-out.txt
> GraphAT.buildsrc-out.txt
> HDF5Array.buildsrc-out.txt
> hypergraph.buildsrc-out.txt
> Icens.buildsrc-out.txt
> impute.buildsrc-out.txt
> mcaGUI.buildsrc-out.txt
> microRNA.buildsrc-out.txt
> minet.buildsrc-out.txt
> MSstats.buildsrc-out.txt
> multtest.buildsrc-out.txt
> netresponse.buildsrc-out.txt
> nondetects.buildsrc-out.txt
> normalize450K.buildsrc-out.txt
> oligoClasses.buildsrc-out.txt
> parglms.buildsrc-out.txt
> plier.buildsrc-out.txt
> preprocessCore.buildsrc-out.txt
> ProtGenerics.buildsrc-out.txt
> QUALIFIER.buildsrc-out.txt
> RPA.buildsrc-out.txt
> scde.buildsrc-out.txt
> seqplots.buildsrc-out.txt
> SJava.buildsrc-out.txt
> spotSegmentation.buildsrc-out.txt
> stepNorm.buildsrc-out.txt
> XVector.buildsrc-out.txt
>
> Some of these (a4Base, a4Classif and many more) just have no vignettes/
> directory so no vignettes at all.
>
>
> Others (ExperimentHub for example) have an empty vignettes directory.
>
> But others (QUALIFIER for example) have a vignettes directory with
> vignette files.
>
> If any packages you maintain do not have a vignette, please add one.
>
> If your package has a vignette in the vignettes/ directory but is in the
> above list, then you need to fix it.
>
> This page is a good place to start tracking down the problem:
>
> http://yihui.name/knitr/demo/vignette/
>
> For non-sweave (usually knitr) vignettes, the important things to check
> are:
>
> - knitr should be in the Suggests field in DESCRIPTION
>   (if using BiocStyle with rmarkdown, be sure BiocStyle and rmarkdown are
>   also in Suggests).
> - VignetteBuilder: knitr should be in DESCRIPTION
> - The actual vignette file should have a %\VignetteEngine line; see link
> above
>   for more information.
>
> How can you tell if you've fixed the problem?
> run R CMD build on your package and look for the line
>
> * creating vignettes ... OK
>
> In the output. If you don't see that line, your vignette has not been
> built.
>
> If you've tried all these things and are still running into problems,
> contact bioc-devel.
>
> Dan
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Bioc-devel] new package: canceR

[Karim Mezhoud]

Dear All,
I am pleased to announce the release of new package named canceR
<http://www.bioconductor.org/packages/devel/bioc/html/canceR.html>. The
main goal of this package is to facilitate to NOT R user the access of
complex cancer genomics data hosted by the MSKCC and available through
cgdsr CRAN package. By simple clic, the user can combine Cases (Samples)
and Genetic profiles to get rapidly without programming skills all
available cancer genomics data (CNA, mRNA, Methylation, Mutation, miRNA,
RPPA) in exportable table.
Compared to cBioportal <http://www.cbioportal.org/>, canceR allows user to
focus on some Studies and get specific data as Amino Acid changes in
Mutation Data for selected gene list.

The second part of canceR focus on modeling. I selected some interesting
fonctions from others packages (see Vignette) and I adapted them to
1-Associate phenotypes (gene / variable ) to disease
2-Classify genes by phenotype or disease
3-Enrichment gene expression data using GSEA-R (Broad Institute)

Other function is in progress to facilitated the visualization of multi
Dimensional Genomics Data  for multiples cancers using Circos styles.

Please fill free for any suggestions.

Karim Mezhoud

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Re: [Bioc-devel] Package submission with library requirement

[Karim Mezhoud]

Yes,
 just an error by copy/paste

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Re: [Bioc-devel] Package submission with library requirement

[Karim Mezhoud]

Hi,

Before you submit your package, please make sure that it satisfies all our

guidelines here.

http://www.bioconductor.org/developers/package­guidelines/

Be sure that you tested it with the appropriate version of R. To work

out which version that is, please have a look at this site here:

http://www.bioconductor.org/developers/how­to/useDevel/

Then use our tracking system for package submission (which can be

found here):

https://tracker.bioconductor.org/

recommended video:
https://www.youtube.com/watch?v=QfqaK_BHebU

Karim

  Ô__
 c/ /'_;kmezhoud
(*) \(*)   ⴽⴰⵔⵉⵎ  ⵎⴻⵣⵀⵓⴷ
http://bioinformatics.tn/



On Wed, Jan 21, 2015 at 2:24 PM, avinash sahu 
wrote:

> Hi all,
>
> I am trying to submit a package (https://github.com/vinash85/GOAL) in
> bioconductor. It requires a ransampl (
> http://sourceforge.net/projects/ransampl/) and gsl libraries already
> installed in system.
> The package is failing to install at automated package installer of
> bioconductor (
>
> http://bioconductor.org/spb_reports/GOAL_0.99.0_buildreport_20150121045701.html
> ).
> How to take care of additional Libraries?
>
> Further, the package is meant for Linux and Mac ( it is NOT currently
> compiling in windows). Is it possible to submit the package in pre-compiled
> binaries form for Mac and Linux.
>
> This is the first package that I am submitting to BioConductor, so I am not
> aware of these issues.
>
> thanks in advance
> avi
>
> [[alternative HTML version deleted]]
>
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>

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Re: [Bioc-devel] BiocCheck result

[Karim Mezhoud]

Dear Dr Dan,
Thanks,
With GUI package the vignette does not have chunks only for installation
paragraph.
Thanks
Karim

  Ô__
 c/ /'_;kmezhoud
(*) \(*)   ⴽⴰⵔⵉⵎ  ⵎⴻⵣⵀⵓⴷ
http://bioinformatics.tn/



On Fri, Jan 2, 2015 at 6:55 PM, Dan Tenenbaum 
wrote:

>
>
> - Original Message -----
> > From: "Karim Mezhoud" 
> > To: bioc-devel@r-project.org
> > Sent: Friday, January 2, 2015 4:22:44 AM
> > Subject: [Bioc-devel] BiocCheck result
> >
> > Dear all,
> >
> > I have these comments and did not found solution for silencing them.
> >
> > 1 - What about Vignette?
>
> The message (below) is saying you  need to evaluate more vignette chunks,
> as mentioned in the BiocCheck vignette (
> http://www.bioconductor.org/packages/devel/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#Interpreting_BiocCheck_output)
> at least 50% of vignette chunks need to be evaluated, otherwise you get
> this RECOMMENDation.
>
> > 2 - The version is "package.0.99.0.tar.gz"
> >
>
> Looks like you are running BiocCheck under Bioconductor 3.0 (the release
> version). You should be developing your package under the devel version of
> Bioconductor (currently 3.1, requires R-devel (R-3.2)). If you do that you
> won't see this message.
>
>
> > 3 - In wich file can I clarify permanent objects. To avoid <<- I
> > create new
> > Environment with
> > myGlobalEnv <- new.env(parent = emptyenv())
> >
> > I have many permanent objects because my package is a GUI. All these
> > objects are useful for different functions and reduce the computing
> > time
> > and the multiple running of the same function.
> >
>
> This is something that is best looked at during the package review process.
>
> > 4- Indenting, Tabs and long lines were not found.
>
> As mentioned in the BiocCheck output and in the vignette, the formatting
> suggestions are just suggestions. Some of them are more important than
> others, for example, most reviewers will insist on lines shorter than 80
> columns, for readability's sake.
>
> >
> > Can I submit with theses comments?
>
> You can submit, and these issues will be looked at as part of the package
> review process.
> Dan
>
> > Thanks
> > Karim
> >
> >
> > $requirements
> > character(0)
> >
> > $recommendations
> > [1] "Evaluate more vignette chunks."   "y of x.y.z
> > version
> > should be even in release"
> >
> > $considerations
> > [1] "Clarifying how objects Li, A, ttCasesGenProfs, EventTime,
> > Category,
> > Continu, Category, ttMain, CasesStudies, curselectCases, fname.GCT,
> > fname.CLS, ttMain, GenesDetails, CaseChoice, mSigDB_SubName,
> > GenesDetails,
> > lenght, ttCasesGenProfs, myGlobalEnv (used in canceR , dialogMut ,
> > dialogOptionPhenoTest, dialogOptionPhenoTest , getClinicalDataMatrix,
> > geteSet, getGCTCLSExample, getGeneExpMatrix, getGenesClassifier,
> > getGenesTree_MultipleCases, getGSEAlm_Diseases, getGSEAlm_Variables,
> > getMegaProfData, getMetDataMultipleGenes, getMSigDBExample ,
> > getMSigDBExample, GSEA, GSEA.Analyze.Sets, plot_1Gene_2GenProfs,
> > testCheckedCaseGenProf) were initialized. Maybe they are part of a
> > data set
> > loaded with data(), or perhaps part of an object referenced in with()
> > or
> > within()."
> > [2] "Shortening lines; 1227 lines (11%) are > 80 characters
> > long."
> >
> > [3] "Replacing tabs with 4 spaces; 6 lines (0%) contain
> > tabs."
> >
> > [4] "Indenting lines with a multiple of 4 spaces; 1752 lines (15%)
> > are
> > not."
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>

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[Bioc-devel] BiocCheck result

[Karim Mezhoud]

Dear all,

I have these comments and did not found solution for silencing them.

1 - What about Vignette?
2 - The version is "package.0.99.0.tar.gz"

3 - In wich file can I clarify permanent objects. To avoid <<- I create new
Environment with
myGlobalEnv <- new.env(parent = emptyenv())

I have many permanent objects because my package is a GUI. All these
objects are useful for different functions and reduce the computing time
and the multiple running of the same function.

4- Indenting, Tabs and long lines were not found.

Can I submit with theses comments?
Thanks
Karim


$requirements
character(0)

$recommendations
[1] "Evaluate more vignette chunks."   "y of x.y.z version
should be even in release"

$considerations
[1] "Clarifying how objects Li, A, ttCasesGenProfs, EventTime, Category,
Continu, Category, ttMain, CasesStudies, curselectCases, fname.GCT,
fname.CLS, ttMain, GenesDetails, CaseChoice, mSigDB_SubName, GenesDetails,
lenght, ttCasesGenProfs, myGlobalEnv (used in canceR , dialogMut ,
dialogOptionPhenoTest, dialogOptionPhenoTest , getClinicalDataMatrix,
geteSet, getGCTCLSExample, getGeneExpMatrix, getGenesClassifier,
getGenesTree_MultipleCases, getGSEAlm_Diseases, getGSEAlm_Variables,
getMegaProfData, getMetDataMultipleGenes, getMSigDBExample ,
getMSigDBExample, GSEA, GSEA.Analyze.Sets, plot_1Gene_2GenProfs,
testCheckedCaseGenProf) were initialized. Maybe they are part of a data set
loaded with data(), or perhaps part of an object referenced in with() or
within()."
[2] "Shortening lines; 1227 lines (11%) are > 80 characters
long."

[3] "Replacing tabs with 4 spaces; 6 lines (0%) contain
tabs."

[4] "Indenting lines with a multiple of 4 spaces; 1752 lines (15%) are
not."

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[Bioc-devel] built BioC packages using RStudio

[Karim Mezhoud]

Dear All,
I am trying to built for the first time a package. I am following this
tutorial:
https://support.rstudio.com/hc/en-us/articles/200486488-Developing-Packages-with-RStudio

I create a new Project (package) and I added 44 .R sources files
(functions).
After, I got error message when I built and reload the project;
In attached file the log informations.

Any suggestion?

I need to fill the doc informations (title, manual, vignette, description).
Can I do these directly from Rd files located in Man folder?
Thanks!
Karim Mezhoud
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