Re: [Bioc-devel] Bioonductor package tracker has moved

[Kevin Rue-Albrecht]

Hi all, Tim,

Just for a second validation, I can log in again too while I couldn't
yesterday as described in this thread.

Anyway, thanks for fixing it so rapidly!
Cheers,
Kevin

On 16 October 2014 06:17, Tim Triche, Jr.  wrote:

> Looks like that fixed it, for me at least.  Thanks!
>
> Statistics is the grammar of science.
> Karl Pearson 
>
> On Wed, Oct 15, 2014 at 10:15 PM, Dan Tenenbaum 
> wrote:
>
> >
> >
> > - Original Message -
> > > From: "Tim Triche, Jr." 
> > > To: "Dan Tenenbaum" 
> > > Cc: "zhao shilin" , "bioc-devel" <
> > bioc-devel@r-project.org>
> > > Sent: Wednesday, October 15, 2014 9:32:14 PM
> > > Subject: Re: [Bioc-devel] Bioonductor package tracker has moved
> > >
> > >
> > > FWIW, I have the same problem. I created a "new" account with the
> > > login ttriche and when I went to confirm, it said "node exists". A
> > > password reset also did not work. No matter what, the system insists
> > > that I am not authorized to log in. This is odd, since I have in the
> > > past. But, I'm guessing there's something going on here.
> > >
> > >
> > >
> >
> > I fixed an issue where some users were not able to log in. I think this
> > should be resolved now.
> > Dan
> >
> >
> > >
> > >
> > > Statistics is the grammar of science.
> > > Karl Pearson
> > >
> > > On Wed, Oct 15, 2014 at 9:21 PM, Dan Tenenbaum < dtene...@fhcrc.org >
> > > wrote:
> > >
> > >
> > >
> > >
> > > - Original Message -
> > > > From: "zhao shilin" < zhaoshi...@gmail.com >
> > > > To: "Dan Tenenbaum" < dtene...@fhcrc.org >
> > > > Cc: "bioc-devel" < bioc-devel@r-project.org >
> > > > Sent: Wednesday, October 15, 2014 8:51:26 PM
> > > > Subject: Re: [Bioc-devel] Bioonductor package tracker has moved
> > > >
> > > >
> > > > Hello Dan,
> > > >
> > > >
> > > > It seems that I can't log in the new system. I tried to reset
> > > > password but still can't log in with new password.
> > > > My user name is "slzhao". Would you please help me to log in? Thank
> > > > you!
> > > >
> > > >
> > >
> > > Can you try the "Lost your login?" link?
> > >
> > > https://tracker.bioconductor.org/user?@template=forgotten
> > >
> > > Dan
> > >
> > >
> > >
> > >
> > >
> > > > Best,
> > > > Shilin
> > > >
> > > >
> > > > 2014-10-15 15:48 GMT-05:00 Dan Tenenbaum < dtene...@fhcrc.org > :
> > > >
> > > >
> > > > Hello Bioconductors,
> > > >
> > > > If you have ever submitted a package to Bioconductor, you know that
> > > > it is reviewed using our package tracker.
> > > >
> > > > This email is to let you know that the tracker has moved and the
> > > > new
> > > > url is:
> > > >
> > > > https://tracker.bioconductor.org/
> > > >
> > > > At the old URL there is a message telling you to go to the new URL,
> > > > but that message will not be there forever (in fact that old
> > > > machine
> > > > will be decomissioned soon) so please update your bookmarks.
> > > >
> > > > All the same data and user accounds, logins, etc., should be
> > > > present
> > > > at the new URL and it should work identically to the old one. You
> > > > may notice some cosmetic differences as we are using a newer
> > > > version
> > > > of the Roundup issue tracker software.
> > > >
> > > > If you have any issues, please let us know here on bioc-devel.
> > > >
> > > > Thanks,
> > > > Dan
> > > >
> > > > ___
> > > > Bioc-devel@r-project.org mailing list
> > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > >
> > > >
> > >
> > > ___
> > > Bioc-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >
> > >
> >
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
Kévin RUE-ALBRECHT
Wellcome Trust Computational Infection Biology PhD Programme
University College Dublin
Ireland
http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en

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[Bioc-devel] "'BiocInstaller' package not in repository" error during nightly build

[Kevin Rue-Albrecht]

Hi Bioconductors,

I got the *BUILD* ERROR report below on all platforms last night.

Given the fact that I didn't update my package since the last (successful)
build, and the error ''BiocInstaller' package not in repository'',  I have
a feeling this is due to a problem on the build platforms ?
In which case, I wonder how many other packages may be affected the same
way. Most of the packages seem fine though.

I can see that the BiocInstaller package got *CHECK* ERROR on all platforms
in the most recent report. Could that be the origin of the problem?
In my vignette, I give the typical installation code "biocLite(GOexpress)"
which likely caused the build error when trying to load the BiocInstaller
library.

Thanks in advance for advising me

Kind regards,
Kevin


##
##
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD build --keep-empty-dirs
--no-resave-data GOexpress
###
##
##


* checking for file ‘GOexpress/DESCRIPTION’ ... OK
* preparing ‘GOexpress’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Bioconductor version 3.1 (BiocInstaller 1.17.0), ?biocLite for help

Error: processing vignette 'GOexpress-UsersGuide.Rnw' failed with diagnostics:
 chunk 2
Error : ''BiocInstaller' package not in repository' while trying
  http://bioconductor.org/packages/3.1/bioc
Execution halted


-- 
Kévin RUE-ALBRECHT
Wellcome Trust Computational Infection Biology PhD Programme
University College Dublin
Ireland
http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en

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Re: [Bioc-devel] "'BiocInstaller' package not in repository" error during nightly build

[Robert Castelo]

hi Kevin,

if you're talking about the devel version of BiocInstaller, the SVN logs 
show a commit yesterday with some correction on the BiocInstaller 
package, just svn the last version if you don't want to wait until the 
newer version gets built:


vn export --username readonly --password readonly 
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocInstaller BiocInstaller


and R CMD build and INSTALL this newer version (1.17.1).


cheers,

robert.

On 10/16/2014 11:45 AM, Kevin Rue-Albrecht wrote:

Hi Bioconductors,

I got the *BUILD* ERROR report below on all platforms last night.

Given the fact that I didn't update my package since the last (successful)
build, and the error ''BiocInstaller' package not in repository'',  I have
a feeling this is due to a problem on the build platforms ?
In which case, I wonder how many other packages may be affected the same
way. Most of the packages seem fine though.

I can see that the BiocInstaller package got *CHECK* ERROR on all platforms
in the most recent report. Could that be the origin of the problem?
In my vignette, I give the typical installation code "biocLite(GOexpress)"
which likely caused the build error when trying to load the BiocInstaller
library.

Thanks in advance for advising me

Kind regards,
Kevin


##
##
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD build --keep-empty-dirs
--no-resave-data GOexpress
###
##
##


* checking for file ‘GOexpress/DESCRIPTION’ ... OK
* preparing ‘GOexpress’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Bioconductor version 3.1 (BiocInstaller 1.17.0), ?biocLite for help

Error: processing vignette 'GOexpress-UsersGuide.Rnw' failed with diagnostics:
  chunk 2
Error : ''BiocInstaller' package not in repository' while trying
   http://bioconductor.org/packages/3.1/bioc
Execution halted




--
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550

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Re: [Bioc-devel] "'BiocInstaller' package not in repository" error during nightly build

[Dan Tenenbaum]

- Original Message -
> From: "Robert Castelo" 
> To: "Kevin Rue-Albrecht" 
> Cc: bioc-devel@r-project.org
> Sent: Thursday, October 16, 2014 3:24:32 AM
> Subject: Re: [Bioc-devel] "'BiocInstaller' package not in repository" error 
> during nightly build
> 
> hi Kevin,
> 
> if you're talking about the devel version of BiocInstaller, the SVN
> logs
> show a commit yesterday with some correction on the BiocInstaller
> package, just svn the last version if you don't want to wait until
> the
> newer version gets built:
> 
> vn export --username readonly --password readonly
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocInstaller
> BiocInstaller
> 
> and R CMD build and INSTALL this newer version (1.17.1).
> 

Yes, this was an issue with the build system, resolved now. 

I wouldn't worry too much about the brand new devel builds; they usually start 
off a bit unstable.

BTW, I don't advise that you have an evaluated vignette chunk that calls 
biocLite(). 

Dan


> 
> cheers,
> 
> robert.
> 
> On 10/16/2014 11:45 AM, Kevin Rue-Albrecht wrote:
> > Hi Bioconductors,
> >
> > I got the *BUILD* ERROR report below on all platforms last night.
> >
> > Given the fact that I didn't update my package since the last
> > (successful)
> > build, and the error ''BiocInstaller' package not in repository'',
> >  I have
> > a feeling this is due to a problem on the build platforms ?
> > In which case, I wonder how many other packages may be affected the
> > same
> > way. Most of the packages seem fine though.
> >
> > I can see that the BiocInstaller package got *CHECK* ERROR on all
> > platforms
> > in the most recent report. Could that be the origin of the problem?
> > In my vignette, I give the typical installation code
> > "biocLite(GOexpress)"
> > which likely caused the build error when trying to load the
> > BiocInstaller
> > library.
> >
> > Thanks in advance for advising me
> >
> > Kind regards,
> > Kevin
> >
> >
> > ##
> > ##
> > ###
> > ### Running command:
> > ###
> > ###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD build
> > --keep-empty-dirs
> > --no-resave-data GOexpress
> > ###
> > ##
> > ##
> >
> >
> > * checking for file ‘GOexpress/DESCRIPTION’ ... OK
> > * preparing ‘GOexpress’:
> > * checking DESCRIPTION meta-information ... OK
> > * installing the package to build vignettes
> > * creating vignettes ... ERROR
> > Bioconductor version 3.1 (BiocInstaller 1.17.0), ?biocLite for help
> >
> > Error: processing vignette 'GOexpress-UsersGuide.Rnw' failed with
> > diagnostics:
> >   chunk 2
> > Error : ''BiocInstaller' package not in repository' while trying
> >http://bioconductor.org/packages/3.1/bioc
> > Execution halted
> >
> >
> 
> --
> Robert Castelo, PhD
> Associate Professor
> Dept. of Experimental and Health Sciences
> Universitat Pompeu Fabra (UPF)
> Barcelona Biomedical Research Park (PRBB)
> Dr Aiguader 88
> E-08003 Barcelona, Spain
> telf: +34.933.160.514
> fax: +34.933.160.550
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 

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Re: [Bioc-devel] "'BiocInstaller' package not in repository" error during nightly build

[Kevin Rue-Albrecht]

Hi Dan, Robert,

Thanks for the answer and fix, Dan. I thought it might be to do with the
recent release.  I just wanted to make sure whether I should be doing
something on my part. Setting the "biocLite" code in my vignette to
"eval=FALSE" crossed my mind, I was just afraid to raise a warning or
something during the build if I had unevaluated code. Since you say it's
fine, then I'll push that with the next substantial fix. It's added to my
GitHub issues to remind me.

Robert, I didn't want to update my local BiocInstaller package, but thanks
for your answer as well. Might be useful in the future for other types of
problems.

Cheers
Kevin



On 16 October 2014 15:34, Dan Tenenbaum  wrote:

>
>
> - Original Message -
> > From: "Robert Castelo" 
> > To: "Kevin Rue-Albrecht" 
> > Cc: bioc-devel@r-project.org
> > Sent: Thursday, October 16, 2014 3:24:32 AM
> > Subject: Re: [Bioc-devel] "'BiocInstaller' package not in repository"
> error during nightly build
> >
> > hi Kevin,
> >
> > if you're talking about the devel version of BiocInstaller, the SVN
> > logs
> > show a commit yesterday with some correction on the BiocInstaller
> > package, just svn the last version if you don't want to wait until
> > the
> > newer version gets built:
> >
> > vn export --username readonly --password readonly
> >
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocInstaller
> > BiocInstaller
> >
> > and R CMD build and INSTALL this newer version (1.17.1).
> >
>
> Yes, this was an issue with the build system, resolved now.
>
> I wouldn't worry too much about the brand new devel builds; they usually
> start off a bit unstable.
>
> BTW, I don't advise that you have an evaluated vignette chunk that calls
> biocLite().
>
> Dan
>
>
> >
> > cheers,
> >
> > robert.
> >
> > On 10/16/2014 11:45 AM, Kevin Rue-Albrecht wrote:
> > > Hi Bioconductors,
> > >
> > > I got the *BUILD* ERROR report below on all platforms last night.
> > >
> > > Given the fact that I didn't update my package since the last
> > > (successful)
> > > build, and the error ''BiocInstaller' package not in repository'',
> > >  I have
> > > a feeling this is due to a problem on the build platforms ?
> > > In which case, I wonder how many other packages may be affected the
> > > same
> > > way. Most of the packages seem fine though.
> > >
> > > I can see that the BiocInstaller package got *CHECK* ERROR on all
> > > platforms
> > > in the most recent report. Could that be the origin of the problem?
> > > In my vignette, I give the typical installation code
> > > "biocLite(GOexpress)"
> > > which likely caused the build error when trying to load the
> > > BiocInstaller
> > > library.
> > >
> > > Thanks in advance for advising me
> > >
> > > Kind regards,
> > > Kevin
> > >
> > >
> > >
> ##
> > >
> ##
> > > ###
> > > ### Running command:
> > > ###
> > > ###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD build
> > > --keep-empty-dirs
> > > --no-resave-data GOexpress
> > > ###
> > >
> ##
> > >
> ##
> > >
> > >
> > > * checking for file ‘GOexpress/DESCRIPTION’ ... OK
> > > * preparing ‘GOexpress’:
> > > * checking DESCRIPTION meta-information ... OK
> > > * installing the package to build vignettes
> > > * creating vignettes ... ERROR
> > > Bioconductor version 3.1 (BiocInstaller 1.17.0), ?biocLite for help
> > >
> > > Error: processing vignette 'GOexpress-UsersGuide.Rnw' failed with
> > > diagnostics:
> > >   chunk 2
> > > Error : ''BiocInstaller' package not in repository' while trying
> > >http://bioconductor.org/packages/3.1/bioc
> > > Execution halted
> > >
> > >
> >
> > --
> > Robert Castelo, PhD
> > Associate Professor
> > Dept. of Experimental and Health Sciences
> > Universitat Pompeu Fabra (UPF)
> > Barcelona Biomedical Research Park (PRBB)
> > Dr Aiguader 88
> > E-08003 Barcelona, Spain
> > telf: +34.933.160.514
> > fax: +34.933.160.550
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>



-- 
Kévin RUE-ALBRECHT
Wellcome Trust Computational Infection Biology PhD Programme
University College Dublin
Ireland
http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en

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Re: [Bioc-devel] "'BiocInstaller' package not in repository" error during nightly build

[Dan Tenenbaum]

- Original Message -
> From: "Kevin Rue-Albrecht" 
> To: "Dan Tenenbaum" 
> Cc: "Robert Castelo" , bioc-devel@r-project.org
> Sent: Thursday, October 16, 2014 8:07:02 AM
> Subject: Re: [Bioc-devel] "'BiocInstaller' package not in repository" error 
> during nightly build
> 
> 
> Hi Dan, Robert,
> 
> 
> Thanks for the answer and fix, Dan. I thought it might be to do with
> the recent release. I just wanted to make sure whether I should be
> doing something on my part. Setting the "biocLite" code in my
> vignette to "eval=FALSE" crossed my mind, I was just afraid to raise
> a warning or something during the build if I had unevaluated code.
> Since you say it's fine, then I'll push that with the next
> substantial fix. It's added to my GitHub issues to remind me.
> 
> 
> Robert, I didn't want to update my local BiocInstaller package, but
> thanks for your answer as well. Might be useful in the future for
> other types of problems.
> 


Just to clarify, BiocInstaller is now available in R-devel by the usual means 
of running:

source('http://bioconductor.org/biocLite.R')

You don't need to install via svn.

Dan


> 
> Cheers
> Kevin
> 
> 
> 
> 
> 
> 
> On 16 October 2014 15:34, Dan Tenenbaum < dtene...@fhcrc.org > wrote:
> 
> 
> 
> 
> - Original Message -
> > From: "Robert Castelo" < robert.cast...@upf.edu >
> > To: "Kevin Rue-Albrecht" < kevin@ucdconnect.ie >
> > Cc: bioc-devel@r-project.org
> > Sent: Thursday, October 16, 2014 3:24:32 AM
> > Subject: Re: [Bioc-devel] "'BiocInstaller' package not in
> > repository" error during nightly build
> > 
> > hi Kevin,
> > 
> > if you're talking about the devel version of BiocInstaller, the SVN
> > logs
> > show a commit yesterday with some correction on the BiocInstaller
> > package, just svn the last version if you don't want to wait until
> > the
> > newer version gets built:
> > 
> > vn export --username readonly --password readonly
> > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocInstaller
> > BiocInstaller
> > 
> > and R CMD build and INSTALL this newer version (1.17.1).
> > 
> 
> Yes, this was an issue with the build system, resolved now.
> 
> I wouldn't worry too much about the brand new devel builds; they
> usually start off a bit unstable.
> 
> BTW, I don't advise that you have an evaluated vignette chunk that
> calls biocLite().
> 
> Dan
> 
> 
> 
> 
> > 
> > cheers,
> > 
> > robert.
> > 
> > On 10/16/2014 11:45 AM, Kevin Rue-Albrecht wrote:
> > > Hi Bioconductors,
> > > 
> > > I got the *BUILD* ERROR report below on all platforms last night.
> > > 
> > > Given the fact that I didn't update my package since the last
> > > (successful)
> > > build, and the error ''BiocInstaller' package not in
> > > repository'',
> > > I have
> > > a feeling this is due to a problem on the build platforms ?
> > > In which case, I wonder how many other packages may be affected
> > > the
> > > same
> > > way. Most of the packages seem fine though.
> > > 
> > > I can see that the BiocInstaller package got *CHECK* ERROR on all
> > > platforms
> > > in the most recent report. Could that be the origin of the
> > > problem?
> > > In my vignette, I give the typical installation code
> > > "biocLite(GOexpress)"
> > > which likely caused the build error when trying to load the
> > > BiocInstaller
> > > library.
> > > 
> > > Thanks in advance for advising me
> > > 
> > > Kind regards,
> > > Kevin
> > > 
> > > 
> > > ##
> > > ##
> > > ###
> > > ### Running command:
> > > ###
> > > ### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD build
> > > --keep-empty-dirs
> > > --no-resave-data GOexpress
> > > ###
> > > ##
> > > ##
> > > 
> > > 
> > > * checking for file ‘GOexpress/DESCRIPTION’ ... OK
> > > * preparing ‘GOexpress’:
> > > * checking DESCRIPTION meta-information ... OK
> > > * installing the package to build vignettes
> > > * creating vignettes ... ERROR
> > > Bioconductor version 3.1 (BiocInstaller 1.17.0), ?biocLite for
> > > help
> > > 
> > > Error: processing vignette 'GOexpress-UsersGuide.Rnw' failed with
> > > diagnostics:
> > > chunk 2
> > > Error : ''BiocInstaller' package not in repository' while trying
> > > http://bioconductor.org/packages/3.1/bioc
> > > Execution halted
> > > 
> > > 
> > 
> > --
> > Robert Castelo, PhD
> > Associate Professor
> > Dept. of Experimental and Health Sciences
> > Universitat Pompeu Fabra (UPF)
> > Barcelona Biomedical Research Park (PRBB)
> > Dr Aiguader 88
> > E-08003 Barcelona, Spain
> > telf: +34.933.160.514
> > fax: +34.933.160.550
> > 
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > 
> 
> 
> 
> 
> --
> 
> 

Re: [Bioc-devel] Bioonductor package tracker has moved

[zhao shilin]

Yes. It works for me now. Thank you!

Best,
Shilin

2014-10-16 4:18 GMT-05:00 Kevin Rue-Albrecht :

> Hi all, Tim,
>
> Just for a second validation, I can log in again too while I couldn't
> yesterday as described in this thread.
>
> Anyway, thanks for fixing it so rapidly!
> Cheers,
> Kevin
>
> On 16 October 2014 06:17, Tim Triche, Jr.  wrote:
>
> > Looks like that fixed it, for me at least.  Thanks!
> >
> > Statistics is the grammar of science.
> > Karl Pearson 
> >
> > On Wed, Oct 15, 2014 at 10:15 PM, Dan Tenenbaum 
> > wrote:
> >
> > >
> > >
> > > - Original Message -
> > > > From: "Tim Triche, Jr." 
> > > > To: "Dan Tenenbaum" 
> > > > Cc: "zhao shilin" , "bioc-devel" <
> > > bioc-devel@r-project.org>
> > > > Sent: Wednesday, October 15, 2014 9:32:14 PM
> > > > Subject: Re: [Bioc-devel] Bioonductor package tracker has moved
> > > >
> > > >
> > > > FWIW, I have the same problem. I created a "new" account with the
> > > > login ttriche and when I went to confirm, it said "node exists". A
> > > > password reset also did not work. No matter what, the system insists
> > > > that I am not authorized to log in. This is odd, since I have in the
> > > > past. But, I'm guessing there's something going on here.
> > > >
> > > >
> > > >
> > >
> > > I fixed an issue where some users were not able to log in. I think this
> > > should be resolved now.
> > > Dan
> > >
> > >
> > > >
> > > >
> > > > Statistics is the grammar of science.
> > > > Karl Pearson
> > > >
> > > > On Wed, Oct 15, 2014 at 9:21 PM, Dan Tenenbaum < dtene...@fhcrc.org
> >
> > > > wrote:
> > > >
> > > >
> > > >
> > > >
> > > > - Original Message -
> > > > > From: "zhao shilin" < zhaoshi...@gmail.com >
> > > > > To: "Dan Tenenbaum" < dtene...@fhcrc.org >
> > > > > Cc: "bioc-devel" < bioc-devel@r-project.org >
> > > > > Sent: Wednesday, October 15, 2014 8:51:26 PM
> > > > > Subject: Re: [Bioc-devel] Bioonductor package tracker has moved
> > > > >
> > > > >
> > > > > Hello Dan,
> > > > >
> > > > >
> > > > > It seems that I can't log in the new system. I tried to reset
> > > > > password but still can't log in with new password.
> > > > > My user name is "slzhao". Would you please help me to log in? Thank
> > > > > you!
> > > > >
> > > > >
> > > >
> > > > Can you try the "Lost your login?" link?
> > > >
> > > > https://tracker.bioconductor.org/user?@template=forgotten
> > > >
> > > > Dan
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > > Best,
> > > > > Shilin
> > > > >
> > > > >
> > > > > 2014-10-15 15:48 GMT-05:00 Dan Tenenbaum < dtene...@fhcrc.org > :
> > > > >
> > > > >
> > > > > Hello Bioconductors,
> > > > >
> > > > > If you have ever submitted a package to Bioconductor, you know that
> > > > > it is reviewed using our package tracker.
> > > > >
> > > > > This email is to let you know that the tracker has moved and the
> > > > > new
> > > > > url is:
> > > > >
> > > > > https://tracker.bioconductor.org/
> > > > >
> > > > > At the old URL there is a message telling you to go to the new URL,
> > > > > but that message will not be there forever (in fact that old
> > > > > machine
> > > > > will be decomissioned soon) so please update your bookmarks.
> > > > >
> > > > > All the same data and user accounds, logins, etc., should be
> > > > > present
> > > > > at the new URL and it should work identically to the old one. You
> > > > > may notice some cosmetic differences as we are using a newer
> > > > > version
> > > > > of the Roundup issue tracker software.
> > > > >
> > > > > If you have any issues, please let us know here on bioc-devel.
> > > > >
> > > > > Thanks,
> > > > > Dan
> > > > >
> > > > > ___
> > > > > Bioc-devel@r-project.org mailing list
> > > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > > >
> > > > >
> > > >
> > > > ___
> > > > Bioc-devel@r-project.org mailing list
> > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > >
> > > >
> > >
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>
>
> --
> Kévin RUE-ALBRECHT
> Wellcome Trust Computational Infection Biology PhD Programme
> University College Dublin
> Ireland
> http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en
>
> [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] How to update annotation packages

[Valerie Obenchain]

Hi Robert,

Annotation packages are generally updated before each release. You 
should have received an email from Marc (cc'd) last month asking if you 
had any updates. Updated packages are uploaded to our ftp server and 
Marc adds them to the repository.


If you need to make a change I think Marc needs to give you access to 
the server or maybe you already have it. He'll be able to fill in the 
details.


Valerie


On 10/15/2014 09:08 AM, Robert Castelo wrote:

Hi,


i submitted one release ago the following annotation packages:

MafDb.ALL.wgs.phase1.release.v3.20101123
MafDb.ESP6500SI.V2.SSA137.dbSNP138
phastCons100way.UCSC.hg19

for which i'm also the "maintainer".

while the functionality to access their annotation resides in another
software package i maintain (VariantFiltering), they contain some
functionality to help updating their annotations themselves. i need to
update those R scripts which are part of the annotation packages,
however, i found nowhere whether this is possible via svn.

how should i proceed with this, should i made the changes local and
submit the new version, or is there some 'svn' way to do it just like
with software or experiment data packages?

thanks,

robert.

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Re: [Bioc-devel] How to update annotation packages

[Marc Carlson]

Hi Robert,

I am sending you another invite now.

 Marc


On 10/16/2014 08:59 AM, Valerie Obenchain wrote:

Hi Robert,

Annotation packages are generally updated before each release. You 
should have received an email from Marc (cc'd) last month asking if 
you had any updates. Updated packages are uploaded to our ftp server 
and Marc adds them to the repository.


If you need to make a change I think Marc needs to give you access to 
the server or maybe you already have it. He'll be able to fill in the 
details.


Valerie


On 10/15/2014 09:08 AM, Robert Castelo wrote:

Hi,


i submitted one release ago the following annotation packages:

MafDb.ALL.wgs.phase1.release.v3.20101123
MafDb.ESP6500SI.V2.SSA137.dbSNP138
phastCons100way.UCSC.hg19

for which i'm also the "maintainer".

while the functionality to access their annotation resides in another
software package i maintain (VariantFiltering), they contain some
functionality to help updating their annotations themselves. i need to
update those R scripts which are part of the annotation packages,
however, i found nowhere whether this is possible via svn.

how should i proceed with this, should i made the changes local and
submit the new version, or is there some 'svn' way to do it just like
with software or experiment data packages?

thanks,

robert.

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[Bioc-devel] error about Display environment/ biomart for the build of my package

[Martin, Tiphaine]

Hi,


I have a type of warning message by bioconductor package tracker on Linux and 
Mac that I don't have when I did that  on my computers. So I don't know to 
correct or to check it on my computers. I think that it is related to the 
package trackViewer, which need to have tcl/tk package.


Error on Mac OS (check and BiocCheck steps)

** testing if installed package can be loaded
Warning in fun(libname, pkgname) :
  no display name and no $DISPLAY environment variable

Error on Linus (BiocCheck step)

* Installing package...
Warning in fun(libname, pkgname) :
  no DISPLAY variable so Tk is not available


I have an error message on window to connect to Biomart. In my package, I 
create Gviz's annotation tracks that connect to UCSC and ENSEMBL via Biomart 
connection.

This connection worked on Linux and Mac. So I would like to know if other 
people observed the biomart connection more difficulty under windows than under 
Mac and Linux or if it is just unlucky event.


Regards,

Tiphaine


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Re: [Bioc-devel] runnable examples for internal function ?

[Hervé Pagès]

Hi Tiphaine,

On 10/15/2014 06:30 AM, Martin, Tiphaine wrote:


Hi Herve,

Thank you for your email. very useful.
But I updated my NAMESPACE in order to list only functions that I want to 
export.
Even if I did that and if in addition, I keep different man files for functions 
that I do not want to export, I have this error message.
But if I removed them, I don't have error messages.
I kept different man files for functions that I do not want to export to help 
my colleagues. It seems that currently, it is not recommended in Bioconductor.


By "colleagues" I guess you mean "co-developers", not "users" of
your package right?

Yes it seems reasonable to expect 'R CMD BiocCheck' to only check
\value and \example for man pages that document exported things.
We should fix that.

Note that it's questionable whether it's a good idea or not to keep
around man pages for non exported things. IMO it's better to document
internal helpers using in-source comments. And since you already
have those in-source comments in place anyway (because you're
using roxygen2), all you need to do is find a way to block
roxygen2 from generating the man pages for these internal helpers.
Co-developers of your package will still be able to see useful
information and that information will be placed where developers
expect it to be: in the source code itself.

My 2 cents.

Cheers,
H.



thank you for your help,

Tiphaine

From: Hervé Pagès 
Sent: 14 October 2014 03:02
To: Martin, Tiphaine; Michael Lawrence; Dan Tenenbaum
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] runnable examples for internal function ?

Hi Tiphaine,

On 10/13/2014 04:31 PM, Martin, Tiphaine wrote:

Hi,


I wrote a list of functions used in my package called coMET. I decided with my 
colleagues to try to publish it in Bioconductor. Currently, it has not been yet 
submitted to bioconductor because I would like to be sure that it satisfies all 
your guidelines.
A list of functions is useful only internally. I saw that there are two methods to remove 
the function from the package index and to disable some of their automated tests: the 
first method is to put a dot as first letter, the second method is to put the 
"internal" keyword 
(http://cran.r-project.org/web/packages/roxygen2/vignettes/rdkeywords.html).


That link is to the documentation of the roxygen2 package. Are you
using roxygen2 to develop your package? You didn't say so.
You say that "you saw that prefixing the function name with a dot
or putting the 'internal' keyword in the man page will 'remove the
function from the package index and disable some of its automated
tests'". I guess that's something you saw in the roxygen2 documentation
right? I don't use roxygene2 myself so I don't know what's the roxygen2
way to control what's exposed or not to the user. However I know many
BioC developers use it for their package so maybe they'll be able to
provide some good advice here.

Keep in mind that using a tool like roxygen2 adds an extra layer of
convenience when developing your package but, unfortunately, it doesn't
completely exempt you from learning and understanding some basic
concepts like NAMESPACE, man pages aliases, keywords, etc...
The ultimate reference for these things is still the "Writing R
Extensions" manual:

http://cran.r-project.org/doc/manuals/r-release/R-exts.html

So, and FWIW, below I'll describe quickly how you need to proceed when
you don't use a fancy tool like roxygen2 to automatically generate
the NAMESPACE and man pages in your package:

1) The real true way to not expose a function to the user is to not
 export it. What one exports from a package is controlled via
 the NAMESPACE file. So first you need to learn about how to use
 the NAMESPACE file to control exactly what you want to expose to
 the user. See "Writing R Extensions" manual for the details.

2) Every symbol that is exported needs to be documented, that is, there
 must be a man page with an alias for this symbol. And of course
 opening the man page at the R prompt with ? should display
 useful information about that symbol.
 'R CMD check' is the tool that will check that every exported
 symbol is documented. It will also perform many checks on the
 man pages to make sure that they are formatted properly.

3) As Dan said previously, any function that is exported also needs
 to have runnable examples and a \value section in its man page.
 Note that this is a Bioconductor requirement, 'R CMD check'
 doesn't check that. 'R CMD BiocCheck' is the tool that will
 perform this check and any other Bioconductor specific check.


I decided to use the second method to reduce to rewrite now all my package.


Note that, for "plain package development" (i.e. without using a
a fancy tool like roxygen2), using the "internal" keyword in a man
page has no effect on whether the function is exported or not.




When I run the new versio

Re: [Bioc-devel] runnable examples for internal function ?

[Martin, Tiphaine]

Yep you guess well about my colleagues :) sorry.

Thank you for your advices.
Tiphaine

From: Hervé Pagès 
Sent: 16 October 2014 19:43
To: Martin, Tiphaine; Michael Lawrence; Dan Tenenbaum
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] runnable examples for internal function ?

Hi Tiphaine,

On 10/15/2014 06:30 AM, Martin, Tiphaine wrote:
>
> Hi Herve,
>
> Thank you for your email. very useful.
> But I updated my NAMESPACE in order to list only functions that I want to 
> export.
> Even if I did that and if in addition, I keep different man files for 
> functions that I do not want to export, I have this error message.
> But if I removed them, I don't have error messages.
> I kept different man files for functions that I do not want to export to help 
> my colleagues. It seems that currently, it is not recommended in Bioconductor.

By "colleagues" I guess you mean "co-developers", not "users" of
your package right?

Yes it seems reasonable to expect 'R CMD BiocCheck' to only check
\value and \example for man pages that document exported things.
We should fix that.

Note that it's questionable whether it's a good idea or not to keep
around man pages for non exported things. IMO it's better to document
internal helpers using in-source comments. And since you already
have those in-source comments in place anyway (because you're
using roxygen2), all you need to do is find a way to block
roxygen2 from generating the man pages for these internal helpers.
Co-developers of your package will still be able to see useful
information and that information will be placed where developers
expect it to be: in the source code itself.

My 2 cents.

Cheers,
H.

>
> thank you for your help,
>
> Tiphaine
> 
> From: Hervé Pagès 
> Sent: 14 October 2014 03:02
> To: Martin, Tiphaine; Michael Lawrence; Dan Tenenbaum
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] runnable examples for internal function ?
>
> Hi Tiphaine,
>
> On 10/13/2014 04:31 PM, Martin, Tiphaine wrote:
>> Hi,
>>
>>
>> I wrote a list of functions used in my package called coMET. I decided with 
>> my colleagues to try to publish it in Bioconductor. Currently, it has not 
>> been yet submitted to bioconductor because I would like to be sure that it 
>> satisfies all your guidelines.
>> A list of functions is useful only internally. I saw that there are two 
>> methods to remove the function from the package index and to disable some of 
>> their automated tests: the first method is to put a dot as first letter, the 
>> second method is to put the "internal" keyword 
>> (http://cran.r-project.org/web/packages/roxygen2/vignettes/rdkeywords.html).
>
> That link is to the documentation of the roxygen2 package. Are you
> using roxygen2 to develop your package? You didn't say so.
> You say that "you saw that prefixing the function name with a dot
> or putting the 'internal' keyword in the man page will 'remove the
> function from the package index and disable some of its automated
> tests'". I guess that's something you saw in the roxygen2 documentation
> right? I don't use roxygene2 myself so I don't know what's the roxygen2
> way to control what's exposed or not to the user. However I know many
> BioC developers use it for their package so maybe they'll be able to
> provide some good advice here.
>
> Keep in mind that using a tool like roxygen2 adds an extra layer of
> convenience when developing your package but, unfortunately, it doesn't
> completely exempt you from learning and understanding some basic
> concepts like NAMESPACE, man pages aliases, keywords, etc...
> The ultimate reference for these things is still the "Writing R
> Extensions" manual:
>
> http://cran.r-project.org/doc/manuals/r-release/R-exts.html
>
> So, and FWIW, below I'll describe quickly how you need to proceed when
> you don't use a fancy tool like roxygen2 to automatically generate
> the NAMESPACE and man pages in your package:
>
> 1) The real true way to not expose a function to the user is to not
>  export it. What one exports from a package is controlled via
>  the NAMESPACE file. So first you need to learn about how to use
>  the NAMESPACE file to control exactly what you want to expose to
>  the user. See "Writing R Extensions" manual for the details.
>
> 2) Every symbol that is exported needs to be documented, that is, there
>  must be a man page with an alias for this symbol. And of course
>  opening the man page at the R prompt with ? should display
>  useful information about that symbol.
>  'R CMD check' is the tool that will check that every exported
>  symbol is documented. It will also perform many checks on the
>  man pages to make sure that they are formatted properly.
>
> 3) As Dan said previously, any function that is exported also needs
>  to have runnable examples and a \value section in its man page.
>  Note that this is a

Re: [Bioc-devel] runnable examples for internal function ?

[Dan Tenenbaum]

- Original Message -
> From: "Hervé Pagès" 
> To: "Tiphaine Martin" , "Michael Lawrence" 
> , "Dan Tenenbaum"
> 
> Cc: bioc-devel@r-project.org
> Sent: Thursday, October 16, 2014 11:43:32 AM
> Subject: Re: [Bioc-devel] runnable examples for internal function ?
> 
> Hi Tiphaine,
> 
> On 10/15/2014 06:30 AM, Martin, Tiphaine wrote:
> >
> > Hi Herve,
> >
> > Thank you for your email. very useful.
> > But I updated my NAMESPACE in order to list only functions that I
> > want to export.
> > Even if I did that and if in addition, I keep different man files
> > for functions that I do not want to export, I have this error
> > message.
> > But if I removed them, I don't have error messages.
> > I kept different man files for functions that I do not want to
> > export to help my colleagues. It seems that currently, it is not
> > recommended in Bioconductor.
> 
> By "colleagues" I guess you mean "co-developers", not "users" of
> your package right?
> 
> Yes it seems reasonable to expect 'R CMD BiocCheck' to only check
> \value and \example for man pages that document exported things.
> We should fix that.
> 

I am looking at the build report for your latest upload:

http://bioconductor.org/spb_reports/coMET_0.99.2_buildreport_20141016031739.html#oaxaca_check_anchor

I do not see that BiocCheck is complaining about this. 

Are you running BiocCheck on your own machine against a newer version of the 
package? If so, can you send me the package (off-list)?

If BiocCheck really is doing the wrong thing, I need to be able to reproduce 
the problem in order to fix it. So I would appreciate it if you can send me a 
package that causes this problem.

Thanks,
Dan




> Note that it's questionable whether it's a good idea or not to keep
> around man pages for non exported things. IMO it's better to document
> internal helpers using in-source comments. And since you already
> have those in-source comments in place anyway (because you're
> using roxygen2), all you need to do is find a way to block
> roxygen2 from generating the man pages for these internal helpers.
> Co-developers of your package will still be able to see useful
> information and that information will be placed where developers
> expect it to be: in the source code itself.
> 
> My 2 cents.
> 
> Cheers,
> H.
> 
> >
> > thank you for your help,
> >
> > Tiphaine
> > 
> > From: Hervé Pagès 
> > Sent: 14 October 2014 03:02
> > To: Martin, Tiphaine; Michael Lawrence; Dan Tenenbaum
> > Cc: bioc-devel@r-project.org
> > Subject: Re: [Bioc-devel] runnable examples for internal function ?
> >
> > Hi Tiphaine,
> >
> > On 10/13/2014 04:31 PM, Martin, Tiphaine wrote:
> >> Hi,
> >>
> >>
> >> I wrote a list of functions used in my package called coMET. I
> >> decided with my colleagues to try to publish it in Bioconductor.
> >> Currently, it has not been yet submitted to bioconductor because
> >> I would like to be sure that it satisfies all your guidelines.
> >> A list of functions is useful only internally. I saw that there
> >> are two methods to remove the function from the package index and
> >> to disable some of their automated tests: the first method is to
> >> put a dot as first letter, the second method is to put the
> >> "internal" keyword
> >> (http://cran.r-project.org/web/packages/roxygen2/vignettes/rdkeywords.html).
> >
> > That link is to the documentation of the roxygen2 package. Are you
> > using roxygen2 to develop your package? You didn't say so.
> > You say that "you saw that prefixing the function name with a dot
> > or putting the 'internal' keyword in the man page will 'remove the
> > function from the package index and disable some of its automated
> > tests'". I guess that's something you saw in the roxygen2
> > documentation
> > right? I don't use roxygene2 myself so I don't know what's the
> > roxygen2
> > way to control what's exposed or not to the user. However I know
> > many
> > BioC developers use it for their package so maybe they'll be able
> > to
> > provide some good advice here.
> >
> > Keep in mind that using a tool like roxygen2 adds an extra layer of
> > convenience when developing your package but, unfortunately, it
> > doesn't
> > completely exempt you from learning and understanding some basic
> > concepts like NAMESPACE, man pages aliases, keywords, etc...
> > The ultimate reference for these things is still the "Writing R
> > Extensions" manual:
> >
> > http://cran.r-project.org/doc/manuals/r-release/R-exts.html
> >
> > So, and FWIW, below I'll describe quickly how you need to proceed
> > when
> > you don't use a fancy tool like roxygen2 to automatically generate
> > the NAMESPACE and man pages in your package:
> >
> > 1) The real true way to not expose a function to the user is to not
> >  export it. What one exports from a package is controlled via
> >  the NAMESPACE file. So first you need to learn about how to
> >  use
> >  the NAMESPACE file to control exact

Re: [Bioc-devel] error about Display environment/ biomart for the build of my package

[Dan Tenenbaum]

- Original Message -
> From: "Tiphaine Martin" 
> To: bioc-devel@r-project.org
> Sent: Thursday, October 16, 2014 10:56:48 AM
> Subject: [Bioc-devel] error about Display environment/ biomart for the build  
> of my package
> 
> Hi,
> 
> 
> I have a type of warning message by bioconductor package tracker on
> Linux and Mac that I don't have when I did that  on my computers. So
> I don't know to correct or to check it on my computers. I think that
> it is related to the package trackViewer, which need to have tcl/tk
> package.
> 
> 
> Error on Mac OS (check and BiocCheck steps)
> 
> ** testing if installed package can be loaded
> Warning in fun(libname, pkgname) :
>   no display name and no $DISPLAY environment variable
> 
> Error on Linus (BiocCheck step)
> 
> * Installing package...
> Warning in fun(libname, pkgname) :
>   no DISPLAY variable so Tk is not available
> 
> 

This package builder is _supposed_ to run under X11 (using Xvfb, the virtual 
frame buffer); the message you are seeing indicates that maybe this is not 
working properly. Anyway, as I look at 

http://bioconductor.org/spb_reports/coMET_0.99.2_buildreport_20141016031739.html#oaxaca_check_anchor

I see that the essage you see is just a warning that comes up when BioCheck 
tries to install the package, and that warning does not actually increment your 
RECOMMENDED count. So in other words, if you can fix the R CMD check warnings 
and the other BiocCheck issues, then you will get a green box for the "CHECK" 
phase.

> I have an error message on window to connect to Biomart. In my
> package, I create Gviz's annotation tracks that connect to UCSC and
> ENSEMBL via Biomart connection.
> 
> This connection worked on Linux and Mac. So I would like to know if
> other people observed the biomart connection more difficulty under
> windows than under Mac and Linux or if it is just unlucky event.
> 

Biomart is somewhat flaky and almost every day in the nightly build report 
there are packages that fail (usually on a single platform) because biomart 
couldn't be reached at that moment in time. The next time you build the 
package, this will probably not occur.

Dan


> 
> Regards,
> 
> Tiphaine
> 
> 
>   [[alternative HTML version deleted]]
> 
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>

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Re: [Bioc-devel] runnable examples for internal function ?

[Leonardo Collado Torres]

On Thu, Oct 16, 2014 at 7:42 PM, Dan Tenenbaum  wrote:
>
>
>
> - Original Message -
> > From: "Hervé Pagès" 
> > To: "Tiphaine Martin" , "Michael Lawrence" 
> > , "Dan Tenenbaum"
> > 
> > Cc: bioc-devel@r-project.org
> > Sent: Thursday, October 16, 2014 11:43:32 AM
> > Subject: Re: [Bioc-devel] runnable examples for internal function ?
> >
> > Hi Tiphaine,
> >
> > On 10/15/2014 06:30 AM, Martin, Tiphaine wrote:
> > >
> > > Hi Herve,
> > >
> > > Thank you for your email. very useful.
> > > But I updated my NAMESPACE in order to list only functions that I
> > > want to export.
> > > Even if I did that and if in addition, I keep different man files
> > > for functions that I do not want to export, I have this error
> > > message.
> > > But if I removed them, I don't have error messages.
> > > I kept different man files for functions that I do not want to
> > > export to help my colleagues. It seems that currently, it is not
> > > recommended in Bioconductor.
> >
> > By "colleagues" I guess you mean "co-developers", not "users" of
> > your package right?
> >
> > Yes it seems reasonable to expect 'R CMD BiocCheck' to only check
> > \value and \example for man pages that document exported things.
> > We should fix that.
> >
>
> I am looking at the build report for your latest upload:
>
> http://bioconductor.org/spb_reports/coMET_0.99.2_buildreport_20141016031739.html#oaxaca_check_anchor
>
> I do not see that BiocCheck is complaining about this.
>
> Are you running BiocCheck on your own machine against a newer version of the 
> package? If so, can you send me the package (off-list)?
>
> If BiocCheck really is doing the wrong thing, I need to be able to reproduce 
> the problem in order to fix it. So I would appreciate it if you can send me a 
> package that causes this problem.
>
> Thanks,
> Dan
>
>
>
>
> > Note that it's questionable whether it's a good idea or not to keep
> > around man pages for non exported things. IMO it's better to document
> > internal helpers using in-source comments. And since you already
> > have those in-source comments in place anyway (because you're
> > using roxygen2), all you need to do is find a way to block
> > roxygen2 from generating the man pages for these internal helpers.



Just use a dot at the beginning of the name for your internal
function. Then `devtools` will ignore them. For example, using so with
my package skips the 5 internal functions that have roxygen2 in-source
documentation but that are not exported.

> library('devtools')
> document('derfinder')
Updating derfinder documentation
Loading derfinder
Skipping invalid path:  .getSegmentsRle.Rd
Skipping invalid path:  .clusterMakerRle.Rd
Skipping invalid path:  .advanced_argument.Rd
Skipping invalid path:  .define_cluster.Rd
Skipping invalid path:  .runFunFormal.Rd

> packageVersion('devtools')
[1] ‘1.6.1’
> packageVersion('roxygen2')
[1] ‘4.0.2’

Cheers,
Leo


>
> > Co-developers of your package will still be able to see useful
> > information and that information will be placed where developers
> > expect it to be: in the source code itself.
> >
> > My 2 cents.
> >
> > Cheers,
> > H.
> >
> > >
> > > thank you for your help,
> > >
> > > Tiphaine
> > > 
> > > From: Hervé Pagès 
> > > Sent: 14 October 2014 03:02
> > > To: Martin, Tiphaine; Michael Lawrence; Dan Tenenbaum
> > > Cc: bioc-devel@r-project.org
> > > Subject: Re: [Bioc-devel] runnable examples for internal function ?
> > >
> > > Hi Tiphaine,
> > >
> > > On 10/13/2014 04:31 PM, Martin, Tiphaine wrote:
> > >> Hi,
> > >>
> > >>
> > >> I wrote a list of functions used in my package called coMET. I
> > >> decided with my colleagues to try to publish it in Bioconductor.
> > >> Currently, it has not been yet submitted to bioconductor because
> > >> I would like to be sure that it satisfies all your guidelines.
> > >> A list of functions is useful only internally. I saw that there
> > >> are two methods to remove the function from the package index and
> > >> to disable some of their automated tests: the first method is to
> > >> put a dot as first letter, the second method is to put the
> > >> "internal" keyword
> > >> (http://cran.r-project.org/web/packages/roxygen2/vignettes/rdkeywords.html).
> > >
> > > That link is to the documentation of the roxygen2 package. Are you
> > > using roxygen2 to develop your package? You didn't say so.
> > > You say that "you saw that prefixing the function name with a dot
> > > or putting the 'internal' keyword in the man page will 'remove the
> > > function from the package index and disable some of its automated
> > > tests'". I guess that's something you saw in the roxygen2
> > > documentation
> > > right? I don't use roxygene2 myself so I don't know what's the
> > > roxygen2
> > > way to control what's exposed or not to the user. However I know
> > > many
> > > BioC developers use it for their package so maybe they'll be able
> > > to
> > > provide some good advice here.
> > >