Re: [Bioc-devel] Request R code this paper

[Joris Meys]

Dear,

you mailed the developers mailing list of Bioconductor, i.e. the list for 
people who develop packages for the Bioconductor suite. Please mail the authors 
of the paper instead. If you know the package they used, the source code of 
each package can be found on the bioconductor website.

Kind regards
Joris

--
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
--

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From: Bioc-devel  on behalf of Salwa El-Aty 

Sent: Tuesday, January 7, 2020 3:49 AM
To: Bioc-devel@r-project.org
Subject: [Bioc-devel] Request  R code  this paper

Dear Sir
I want to help me about to send  the  R Codes of   paper which title
  "Generalized  endpoint -inflated  binomial model" .COMPUTATION STATISTICS AND 
DATA ANALYSIS .89  , 2015
Best Regards
Salwa. A.Mousa

Sent from my Samsung device

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[Bioc-devel] Submitting a package with heavy data and vignette

[Joris Meys]

Dear,


we're planning on submitting a new package to Bioconductor. Due to the fact 
that this package revolves around simulation methods for massive datasets, the 
vignette necessarily need about 10 Mb of data and way more than 5 minutes to 
build. We were wondering how we would proceed best to submit this package. 
Downsizing the data and build time is alas not possible, as it would make the 
example in the vignette totally irrelevant.


I was thinking about the following construct:

- a main software package with the actual simulation functionality

- a "data" package depending on the main software package with only the example 
data and vignette.


We would love to hear your view on this, as we'd like to limit the amount of 
issues for both you and us once we submit the package(s). Other suggestions are 
more than welcome too.


Thank you in advance

Joris


--
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
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[Bioc-devel] SSH keys for the newly accepted package RCM

[Joris Meys]

Dear,

I'm the maintainer of the new package RCM, written by Stijn Hawinkel. In
the issue on github Stijn was asked to submit a SSH key to Bioconductor (
https://github.com/Bioconductor/Contributions/issues/949#issuecomment-451232446
).

I am also the maintainer of the unifiedWMWqPCR package and my SSH key has
been registered by Bioconductor before. Is it necessary for the author to
submit one as well, or is my key as a maintainer enough?

Cheers
Joris

-- 
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
<https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium=gmail=g>

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Re: [Bioc-devel] Installation procedure on website outdated

[Joris Meys]

Thank you for the information. I've linked our IT to the vignette of
BiocManager for the time being.

Cheers
Joris

On Fri, Sep 21, 2018 at 3:10 PM Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> The old installation is still valid for the current release 3.7.   We
> planned to update this page as it got closer to the next release 3.8.  As
> the release 3.8 is fast approaching (end of Oct) we will most likely be
> updating this page in the very near future.
>
>
> Thank you for bringing it to our attention.
>
> Cheers,
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Bioc-devel  on behalf of Joris
> Meys 
> *Sent:* Friday, September 21, 2018 7:22:18 AM
> *To:* bioc-devel
> *Subject:* [Bioc-devel] Installation procedure on website outdated
>
> Dear all,
>
> I wanted to point our IT departement to the new installation procedure of
> Bioconductor, and to my astonishment that information starts with
>
> source("https://bioconductor.org/biocLite.R;)
>
> No mention of BiocManager there. This information really needs updating
> imho, or is there a reason why the old installation procedure is still
> mentioned there?
>
> https://www.bioconductor.org/install/
>
> Cheers
> Joris
>
> --
> Joris Meys
> Statistical consultant
>
> Department of Data Analysis and Mathematical Modelling
> Ghent University
> Coupure Links 653, B-9000 Gent (Belgium)
> <
> https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium=gmail=g
> >
>
> tel: +32 (0)9 264 61 79
> ---
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> http://www.biowiskundedagen.ugent.be/
>
> ---
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>
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>
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>
> 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
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> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
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-- 
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
<https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium=gmail=g>

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[Bioc-devel] Installation procedure on website outdated

[Joris Meys]

Dear all,

I wanted to point our IT departement to the new installation procedure of
Bioconductor, and to my astonishment that information starts with

source("https://bioconductor.org/biocLite.R;)

No mention of BiocManager there. This information really needs updating
imho, or is there a reason why the old installation procedure is still
mentioned there?

https://www.bioconductor.org/install/

Cheers
Joris

-- 
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
<https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium=gmail=g>

tel: +32 (0)9 264 61 79
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Re: [Bioc-devel] BiocManager now on CRAN

[Joris Meys]

Dear Marcel,

A big thanks to you and the entire bioconductor team. I will spread the
word among my colleagues. I also noticed that the installation instructions
aren't adapted yet on the bioconductor site (
https://www.bioconductor.org/install/). Probably I'm just rushing here and
you are working on it, but I thought to inform you anyway as our courses
link to that website for official installation instructions.

Cheers
Joris

On Wed, Jun 20, 2018 at 6:23 PM, Marcel Ramos 
wrote:

> Dear bioc-devs,
>
>
> A month ago we notified you about our "next generation" changes to
> BiocInstaller.
>
> Thanks to all beta testers and those who provided feedback and
> suggestions for a new package name.
>
>
> I am pleased to inform you that BiocManager is now on CRAN:
> https://cran.r-project.org/web/packages/BiocManager/index.html
>
>
> As mentioned in our last email, you can now install BiocManager using:
>
> ```
> install.packages("BiocManager")
> BiocManager::install("YourPackageNameHere")
> ```
>
> Action Item:
>
>-   Please modify the vignettes in your bioc-devel packages to
> reflect the use of BiocManager
>
>
> After the next couple of weeks or so, we will be identifying packages in
> bioc-devel (3.8) that still
> mention BiocInstaller / biocLite.
>
>
> Best regards,
> Marcel
>
> Bioconductor Core Team
> Roswell Park Cancer Institute
> Dept. of Biostatistics & Bioinformatics
> Elm & Carlton Streets
> Buffalo, New York 14263
>
>
> On 05/09/2018 06:11 PM, Martin Morgan wrote:
> > Developers --
> >
> > A preliminary heads-up and request for comments.
> >
> > Almost since project inception, we've used the commands
> >
> >   source("https://bioconductor.org/biocLite.R;)
> >   biocLite(pkgs)
> >
> > to install packages. This poses security risks (e.g., typos in the
> > url) and deviates from standard R package installation procedures.
> >
> >
> > We'd like to move to a different system where a base package, call it
> > 'BiocManager', is installed from CRAN and used to install Bioconductor
> > packages
> >
> >   if (!"BiocManager" %in% rownames(installed.packages()))
> >   install.packages("BiocManager")
> >   BiocManager::install(pkgs)
> >
> > This establishes a secure chain from user R session to Bioconductor
> > package installation. It is also more consistent with base R package
> > installation procedures.
> >
> > BiocManager exposes four functions
> >
> >   - install() or update packages
> >
> >   - version() version of Bioconductor in use
> >
> >   - valid() are all Bioconductor packages from the same Bioconductor
> > version?
> >
> >   - repositories() url location for Bioconductor version-specific
> > repositories
> >
> > install() behaves like biocLite(), using the most current version of
> > Bioconductor for the version of R in use. It stores this state using a
> > Bioconductor package 'BiocVersion', which is nothing more than a
> > sentinel for the version in use. One can also 'use devel' or a
> > particular version of Bioconductor (consistent with the version of R)
> > with
> >
> >   BiocManager::install(version = "3.8")   # or the synonym "devel"
> >
> >
> > We intend to phase this in over several release cycles, and to
> > continue to support the traditional biocLite() route for versions
> > before BiocManager becomes available.
> >
> > We also intend to change the overall versioning of 'Bioconductor'
> > itself, where releases are always even (3.8, 3.10, 3.12, ...) and
> > 'devel' always odd.
> >
> > Obviously this is a large change, eventually requiring updates to many
> > locations on our web site and individual vignettes.
> >
> >
> > Of course the key question is the name of the 'BiocManager' package.
> > It cannot easily be 'BiocInstaller', because of the differences in way
> > CRAN and Bioconductor version packages. Some possible names are
> > '
> > BiocInstall::install()
> > BiocPackages::install()
> > BiocManager
> > BiocMaestro
> >
> >
> > Your comments are welcome...
> >
> > Martin
> >
> >
> > This email message may contain legally privileged and/or...{{dropped:2}}
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> This email message may contain legally privileged and/or...{{dropped:4}}
&g

[Bioc-devel] eval() and evalq() of BiocGenerics used in Rcpp causes segfault in some cases

[Joris Meys]

Dear all,

the following issue drew my attention. The new package "conflicted"
manipulates the search path and by doing so, highlighted that Rcpp is using
the BiocGenerics version of evalq() in case BiocGenerics is loaded.
Otherwise it uses the base version.

This is easily fixed in Rcpp by using base::evalq() - ( which will require
all packages based on Rcpp to be recompiled. )

I wondered whether there is code that expects Rcpp to use the dispatching
of the BiocGenerics version of eval() and that would fail after the fix is
applied. Honestly, imho it shouldn't, but better safe than sorry. If you
have pointers, I can check the patch in these contexts and hopefully
prevent possible problems before they arise.

Reference to the issue :
https://github.com/RcppCore/Rcpp/issues/861#issuecomment-395199660

Cheers

-- 
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
<https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium=gmail=g>

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Re: [Bioc-devel] Package download when using functions from affy and oligo

[Joris Meys]

Dear all,

sorry for the delayed response, due to some unfortunate events I had to
prioritize my family the past week.

You find an RStudio project in a zipped folder on this link :
https://jorismeys.stackstorage.com/s/3ik0vMwsvueuT5a

It contains a script called testOligo.R that can be sourced and nukes my R
session in the second step of the rma() function. It also contains the
faulty .gz files. If you need more information, don't hesitate to contact
me.

Regarding improving general maintainability, I'm willing to help out on
that. Problem is that I'm rather behind with my own work, so I'm short on
time for the moment. I'll fork affy tomorrow (need to give class now) and
let's start from there then?

Cheers
Joris



On Sat, May 5, 2018 at 5:17 PM, Vincent Carey <st...@channing.harvard.edu>
wrote:

> How about a google drive?  This problem of autodownloading should be
> addressed directly.
> These facilities are still important but their maintenance is clearly a
> lower priority as the
> technologies handled have diminished use in the field.  I think we should
> be able to team up and remove autoinstallation elements of these packages,
> and
> perhaps improve general maintainability -- Joris, can you pick
> one, make a github repo that we can collaborate on revising, and then
> we can start?  It will involve a deprecation process.
>
> On Sat, May 5, 2018 at 10:54 AM, Joris Meys <jorism...@gmail.com> wrote:
>
>> Thank you for the answer.
>>
>> I was trying to create a reproducible example before I vented maybe a bit
>> too much in my previous mail.
>>
>> I managed to get closer to the problem and it is related to data that was
>> corrupted at download. I can send you a reproducible example that bombs R,
>> but I will have to send the specific data files as well. How do I send
>> them
>> best?
>>
>> Cheers
>> Joris
>>
>> On Sat, 5 May 2018, 00:09 James W. MacDonald, <jmac...@uw.edu> wrote:
>>
>> > I think there are multiple complaints here, so I'll take them one at a
>> > time.
>> >
>> > On Fri, May 4, 2018 at 3:56 PM, Obenchain, Valerie <
>> > valerie.obench...@roswellpark.org> wrote:
>> >
>> >> Joris,
>> >>
>> >> Sorry I don't have much to offer here. I've cc'd the authors of oligo
>> and
>> >> affy who may have some insight.
>> >>
>> >> Valerie
>> >>
>> >>
>> >> On 05/02/2018 11:35 AM, Joris Meys wrote:
>> >>
>> >> Dear,
>> >>
>> >> I've noticed that using certain functions in affy and oligo (eg
>> >> oligo::read.celfiles and affy::bg.correct) start with downloading
>> another
>> >> package and end with either R crashing or a warning that -after
>> >> installation succeeded- the package is not available.
>> >
>> >
>> > This is true for oligo, and perhaps a bit annoying. If you don't have
>> the
>> > package installed already, it gets the package, installs it, and then
>> says
>> > it's not available. This is an easy enough fix.
>> >
>> >
>> > After which using
>> >> some functions of both packages still crash R.
>> >>
>> >
>> > I don't know what to do with that. What functions?
>> >
>> >
>> >>
>> >> The warning I get when trying oligo::read.celfiles() on a single CEL
>> file
>> >> right after installing it about the pd.hugene.1.0.st.v1 package. The
>> even
>> >> more annoying thing is that on my machine it insists on building from
>> >> source, whereas on another Windows machine without Rtools, it
>> downloads a
>> >> binary.
>> >>
>> >
>> > That is an options setting that gets changed when you install Rtools.
>> The
>> > 'pkgType' option gets set to 'both' because you can now install both
>> kinds.
>> > And in install.packages it ends up getting switched from 'both' to
>> > 'source'. I haven't dug any further into that because I am not sure I
>> see
>> > why it's a problem. In the end there isn't a difference between
>> installing
>> > a source or a binary pdInfoPackage, and trying to get it to 'do the
>> right
>> > thing' might have some unforeseen consequences that I would rather not
>> have
>> > to worry about. This is really an 'if it ain't broke, don't fix it'
>> > scenario, IMO.
>> >
>> >
>> >
>> >>
>> >> Reason it frustrates the heck out of me, is that both affy and olig

Re: [Bioc-devel] CRAN R 3.5 binary - where is it?

[Joris Meys]

As Herve also indicated already, your best shot is the R-SIG-Debian list
for questions on debian like systems. That said, the maintainer Michael
Rutter announced the 3.5 binaries for all supported Ubuntu distros a few
weeks ago, but they're not on CRAN. For some reason not completely clear to
me, they reside at a launchpad now:

https://launchpad.net/~marutter/+archive/ubuntu/rrutter3.5

So you have to add that repo to the repolist using apt add-repository as
explained on the link above, and then the installation procedure is the
same as explained on the CRAN page Herve linked you to :

https://cran.r-project.org/bin/linux/ubuntu/

Cheers
Joris

On Thu, May 10, 2018 at 9:13 PM, Kenneth Condon <roonysga...@gmail.com>
wrote:

> Hi all,
>
> It sounds like the best thing to do is go back to the original binary and
> remove the source installation.
>
> Clarice, you know I can't even remember if I did that - I think I might try
> fix the current dependency issue tomorrow, but if any more come up, Ill go
> back to the begining do as you suggested with the binary again.
>
> Herve, the link I provided has R3.4.4 .deb binaries from 2018 - not sure
> where you are getting the 2014 from.
>
> Thanks,
> Kenneth
>
> On Thu, May 10, 2018 at 7:43 PM, Clarice Groeneveld <
> clari.groenev...@gmail.com> wrote:
>
> > Hi Kenneth,
> >
> > I see you're on Ubuntu 14.04. Have you tried in Terminal:
> > sudo apt-get update
> > sudo apt-get upgrade
> >
> > to upgrade your R version?
> >
> > Best,
> > Clarice.
> >
> > Em qui, 10 de mai de 2018 às 14:20, Kenneth Condon <
> roonysga...@gmail.com>
> > escreveu:
> >
> >> Hi all,
> >>
> >> I want to submit a package to bioconductor this week but first I want to
> >> build it on the latest R 3.5 release (with bioconductor 3.7). However,
> >> CRAN
> >> only has 3.4 binaries
> >> <https://cran.r-project.org/bin/linux/ubuntu/trusty/?C=N;O=A> so I've
> had
> >> to build 3.5 from source which has unfortunately sent me to dependency
> >> hell.
> >>
> >> Rather than spending the next 3 days fixing all dependencies, does
> anyone
> >> know when the 3.5 dependency is likely to surface?
> >>
> >> I think bioconductor 3.7 cannot be installed on R 3.4 so any advice
> would
> >> be appreciated.
> >>
> >> Thanks,
> >> Kenneth.
> >>
> >> [[alternative HTML version deleted]]
> >>
> >> ___
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> >>
> >
>
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-- 
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
<https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium=gmail=g>

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Re: [Bioc-devel] Package download when using functions from affy and oligo

[Joris Meys]

Thank you for the answer.

I was trying to create a reproducible example before I vented maybe a bit
too much in my previous mail.

I managed to get closer to the problem and it is related to data that was
corrupted at download. I can send you a reproducible example that bombs R,
but I will have to send the specific data files as well. How do I send them
best?

Cheers
Joris

On Sat, 5 May 2018, 00:09 James W. MacDonald, <jmac...@uw.edu> wrote:

> I think there are multiple complaints here, so I'll take them one at a
> time.
>
> On Fri, May 4, 2018 at 3:56 PM, Obenchain, Valerie <
> valerie.obench...@roswellpark.org> wrote:
>
>> Joris,
>>
>> Sorry I don't have much to offer here. I've cc'd the authors of oligo and
>> affy who may have some insight.
>>
>> Valerie
>>
>>
>> On 05/02/2018 11:35 AM, Joris Meys wrote:
>>
>> Dear,
>>
>> I've noticed that using certain functions in affy and oligo (eg
>> oligo::read.celfiles and affy::bg.correct) start with downloading another
>> package and end with either R crashing or a warning that -after
>> installation succeeded- the package is not available.
>
>
> This is true for oligo, and perhaps a bit annoying. If you don't have the
> package installed already, it gets the package, installs it, and then says
> it's not available. This is an easy enough fix.
>
>
> After which using
>> some functions of both packages still crash R.
>>
>
> I don't know what to do with that. What functions?
>
>
>>
>> The warning I get when trying oligo::read.celfiles() on a single CEL file
>> right after installing it about the pd.hugene.1.0.st.v1 package. The even
>> more annoying thing is that on my machine it insists on building from
>> source, whereas on another Windows machine without Rtools, it downloads a
>> binary.
>>
>
> That is an options setting that gets changed when you install Rtools. The
> 'pkgType' option gets set to 'both' because you can now install both kinds.
> And in install.packages it ends up getting switched from 'both' to
> 'source'. I haven't dug any further into that because I am not sure I see
> why it's a problem. In the end there isn't a difference between installing
> a source or a binary pdInfoPackage, and trying to get it to 'do the right
> thing' might have some unforeseen consequences that I would rather not have
> to worry about. This is really an 'if it ain't broke, don't fix it'
> scenario, IMO.
>
>
>
>>
>> Reason it frustrates the heck out of me, is that both affy and oligo
>> crashed the R session in different ways. During installation of a package,
>> during use of a function, and at different points when comparing my
>> machine
>> with the one of our students. The culprit seems to be in one of the
>> underlying packages, but I wasn't even able to detect which package is the
>> culprit, let alone which function crashes everything.
>>
>
> I understand your frustration, but that's not enough to go on. I have
> never, in like 18 years, had either oligo or affy randomly segfault on me.
> I understand that it is happening for you, but unless you can come up with
> a reproducible example, it's not possible for anybody to help.
>
>
>>
>> Is there a way around this so I can ensure that at least I have the same
>> setup as they have and I can try to come up with a reproducible example to
>> report this critical bug?
>>
>
> Again, I am not sure what to do with that. I am not sure what 'a way
> around this' pertains to, and ensuring you have the same setup as 'they
> have' seems to be something only you can accomplish. Is there some reason
> you cannot ensure that you have the same setup on two different computers?
>
> Best,
>
> Jim
>
>
>>
>> Thank you in advance
>> Joris
>>
>>
>>
>>
>>
>> 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,
>> distribution, or use of this email message is prohibited.  If you have
>> received this message in error, please notify the sender immediately by
>> e-mail and delete this email message from your computer. Thank you.
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>
>
>
> --
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Re: [Bioc-devel] Strange error for windows build

[Joris Meys]

These functions all come from the stringi package. My first thought wpuld
be a namespace conflict.
Cheers
Joris

On Thu, 3 May 2018, 18:58 Christopher John, 
wrote:

> Dear Bioconductor
>
> I am getting a new weird error from today I think with my M3C package:
>
> http://bioconductor.org/packages/3.7/bioc/html/M3C.html
>
> Error in namespaceExport(ns, exports) :
>   undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%,
> %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%,
> %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-,
> stri_sub<-, stri_subset<-, stri_subset_charclass<-,
> stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c,
> stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge,
> stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv,
> stri_compare, stri_conv, stri_count, stri_count_boundaries,
> stri_count_charclass, stri_count_coll, stri_count_fixed,
> stri_count_regex, stri_count_words, stri_datetime_add,
> stri_datetime_create, stri_datetime_fields, stri_datetime_format,
> stri_datetime_fstr, stri_datetime_now, stri_datetime_parse,
> stri_datetime_symbols, stri_detect, stri_detect_charclass,
> stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup,
> stri_duplicated, stri_duplicated_any, stri_enc_detect,
> stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_info,
> stri_enc_isascii, stri_enc_isutf16be, stri_enc_isutf16le,
> stri_enc_isutf32be, stri_enc_isutf32le, stri_enc_isutf8,
> stri_enc_list, stri_enc_mark, stri_enc_set, stri_enc_toascii,
> stri_enc_tonative, stri_enc_toutf32, stri_enc_toutf8, stri_encode,
> stri_endswith, stri_endswith_charclass, stri_endswith_coll,
> stri_endswith_fixed, stri_escape_unicode, stri_extract,
> stri_extract_all, stri_extract_all_boundaries,
> stri_extract_all_charclass, stri_extract_all_coll,
> stri_extract_all_fixed, stri_extract_all_regex,
> stri_extract_all_words, stri_extract_first,
> stri_extract_first_boundaries, stri_extract_first_charclass,
> stri_extract_first_coll, stri_extract_first_fixed,
> stri_extract_first_regex, stri_extract_first_words, stri_extract_last,
> stri_extract_last_boundaries, stri_extract_last_charclass,
> stri_extract_last_coll, stri_extract_last_fixed,
> stri_extract_last_regex, stri_extract_last_words, stri_flatten,
> stri_info, stri_isempty, stri_join, stri_join_list, stri_length,
> stri_list2matrix, stri_locale_get, stri_locale_info, stri_locale_list,
> stri_locale_set, stri_locate, stri_locate_all,
> stri_locate_all_boundaries, stri_locate_all_charclass,
> stri_locate_all_coll, stri_locate_all_fixed, stri_locate_all_regex,
> stri_locate_all_words, stri_locate_first,
> stri_locate_first_boundaries, stri_locate_first_charclass,
> stri_locate_first_coll, stri_locate_first_fixed,
> stri_locate_first_regex, stri_locate_first_words, stri_locate_last,
> stri_locate_last_boundaries, stri_locate_last_charclass,
> stri_locate_last_coll, stri_locate_last_fixed, stri_locate_last_regex,
> stri_locate_last_words, stri_match, stri_match_all,
> stri_match_all_regex, stri_match_first, stri_match_first_regex,
> stri_match_last, stri_match_last_regex, stri_na2empty, stri_numbytes,
> stri_opts_brkiter, stri_opts_collator, stri_opts_fixed,
> stri_opts_regex, stri_order, stri_pad, stri_pad_both, stri_pad_left,
> stri_pad_right, stri_paste, stri_paste_list, stri_rand_lipsum,
> stri_rand_shuffle, stri_rand_strings, stri_read_lines, stri_read_raw,
> stri_remove_empty, stri_replace, stri_replace_all,
> stri_replace_all_charclass, stri_replace_all_coll,
> stri_replace_all_fixed, stri_replace_all_regex, stri_replace_first,
> stri_replace_first_charclass, stri_replace_first_coll,
> stri_replace_first_fixed, stri_replace_first_regex, stri_replace_last,
> stri_replace_last_charclass, stri_replace_last_coll,
> stri_replace_last_fixed, stri_replace_last_regex, stri_replace_na,
> stri_reverse, stri_sort, stri_split, stri_split_boundaries,
> stri_split_charclass, stri_split_coll, stri_split_fixed,
> stri_split_lines, stri_split_lines1, stri_split_regex,
> stri_startswith, stri_startswith_charclass, stri_startswith_coll,
> stri_startswith_fixed, stri_stats_general, stri_stats_latex, stri_sub,
> stri_subset, stri_subset_charclass, stri_subset_coll,
> stri_subset_fixed, stri_subset_regex, stri_timezone_get,
> stri_timezone_info, stri_timezone_list, stri_timezone_set,
> stri_trans_char, stri_trans_general, stri_trans_isnfc,
> stri_trans_isnfd, stri_trans_isnfkc, stri_trans_isnfkc_casefold,
> stri_trans_isnfkd, stri_trans_list, stri_trans_nfc, stri_trans_nfd,
> stri_trans_nfkc, stri_trans_nfkc_casefold, stri_trans_nfkd,
> stri_trans_tolower, stri_trans_totitle, stri_trans_toupper, stri_trim,
> stri_trim_both, stri_trim_left, stri_trim_right,
> stri_unescape_unicode, stri_unique, stri_width, stri_wrap,
> stri_write_lines
> ERROR: lazy loading failed for package 'M3C'
> * removing
> 

[Bioc-devel] Package download when using functions from affy and oligo

[Joris Meys]

Dear,

I've noticed that using certain functions in affy and oligo (eg
oligo::read.celfiles and affy::bg.correct) start with downloading another
package and end with either R crashing or a warning that -after
installation succeeded- the package is not available. After which using
some functions of both packages still crash R.

The warning I get when trying oligo::read.celfiles() on a single CEL file
right after installing it about the pd.hugene.1.0.st.v1 package. The even
more annoying thing is that on my machine it insists on building from
source, whereas on another Windows machine without Rtools, it downloads a
binary.

Reason it frustrates the heck out of me, is that both affy and oligo
crashed the R session in different ways. During installation of a package,
during use of a function, and at different points when comparing my machine
with the one of our students. The culprit seems to be in one of the
underlying packages, but I wasn't even able to detect which package is the
culprit, let alone which function crashes everything.

Is there a way around this so I can ensure that at least I have the same
setup as they have and I can try to come up with a reproducible example to
report this critical bug?

Thank you in advance
Joris

-- 
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
<https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium=gmail=g>

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Re: [Bioc-devel] Switch to SSH protocol for git clone instructions on package landing pages?

[Joris Meys]

Using SSH will only work when they have a public key on the git server
registered. Otherwise they will get the dreaded "Please make sure you have
the correct access rights and the repository exists" error message. The
same happens when I forget to add the correct key to my pageant. In my
humble opinion it doesn't pay off to make it more difficult for general
users to download the source code in order to make the process more simple
for your developers.

Cheers
Joris

On Sun, Apr 29, 2018 at 4:03 PM, Peter Hickey <peter.hic...@gmail.com>
wrote:

> The one-liner on the package landing page describing how to check out
> a package from the git repo uses HTTPS rather than ssh, e.g.:
>
> # From https://bioconductor.org/packages/bsseq/
> git clone https://git.bioconductor.org/packages/bsseq
>
> However, as a developer we should be using the SSH protocol
> (https://bioconductor.org/developers/how-to/git/faq/).
>
> Is there any reason not to use the SSH protocol (i.e. git clone
> g...@git.bioconductor.org:packages/bsseq) in the instructions given on
> the landing page? It seems to me an unnecessary source of friction,
> particularly for new developers who will end up with the dreaded
> "fatal: remote error: FATAL: W any packages/myPackage nobody DENIED by
> fallthru (or you mis-spelled the reponame)" error message if they
> don't know to switch protocols
> (https://bioconductor.org/developers/how-to/git/faq/)
>
> Cheers,
> Pete
>
> ___
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>



-- 
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
<https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium=gmail=g>

tel: +32 (0)9 264 61 79
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Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

[Joris Meys]

On Wed, Apr 25, 2018 at 11:52 PM, Rahmatallah, Yasir <yrahmatal...@uams.edu>
wrote:

> Dear all,
>
> Build report show that many packages still have check warnings due to
> missing file links (cross referencing pages from other packages) under
> windows. The issue happens because there are different man pages for
> different operating systems. My package (GSAR) shows the same warning under
> Windows in the build report, although it locally passes R CMD build and R
> CMD check without warnings. Although not a perfect solution, substituting
> the linking in the .Rd file \code{\link[pkg:bar]{foo}} with
> \code{\link{foo}} or \code{\link[pkg]{foo}} was suggested in a recent
> discussion
> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013315.html


Actually, that is the correct solution. As per "Writing R Extensions",
\link[pkg]{name} searches for a html file with the name name.html in
package pkg. In a number of cases the name of the html help file is not the
same as the function you want to point to. For example, ppois and qpois etc
are discussed in a page called Poisson. Also in "Writing R Extensions" they
mention that if you want to use another name as a link, you should do
\link[pkg:name]{foo}. In our example: \link[stats:Poisson]{ppois}

https://cran.r-project.org/doc/manuals/R-exts.html#Cross_002dreferences

>
> I understood that although a check warning is produced (under Windows
> only), it will be accepted (considered as advice) and packages that
> currently show it will proceed to Bioc release. Is that correct? There are
> still many packages showing this warning in yesterday's report
> http://bioconductor.org/checkResults/3.7/bioc-LATEST/#show=warnings
>

As this is the case for even recommended packages like the survival
package, I don't see how this would be a reason to reject a package. But it
still makes sense to adapt your links in the way it is specified in the
official R manual.

Cheers
Joris

-- 
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
<https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium=gmail=g>

tel: +32 (0)9 264 61 79
---
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Re: [Bioc-devel] Deadline for All Package Maintainers

[Joris Meys]

Just for the record: This is the deadline for getting everything solved
before the packages get incorporated into the 3.7 release, right? So we
should now push only to the master (as the release_3_7 branch apparently
doesn't exist yet)?

Cheers
Joris

On Mon, Apr 23, 2018 at 2:35 PM, Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> This is a reminder that the last day to pass R CMD build and R CMD check
> is this Wednesday April 25th.  Please update all package that are failing
> on the build reports by this time.
>
>
> Software Packages:
>
> http://bioconductor.org/checkResults/3.7/bioc-LATEST/
>
> Data Experiment Packages:
>
> http://bioconductor.org/checkResults/3.7/data-experiment-LATEST/
>
> Workflow Packages:
>
> http://bioconductor.org/checkResults/3.7/workflows-LATEST/
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
>
> 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,
> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
> [[alternative HTML version deleted]]
>
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>



-- 
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
<https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium=gmail=g>

tel: +32 (0)9 264 61 79
---
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http://www.biowiskundedagen.ugent.be/

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[Bioc-devel] Setup for pushing changes in unifiedWMWqPCR to bioconductor git.

[Joris Meys]

Hi all,

For the package unifiedWMWqPCR I want to push some updates on the
documentation, but apparently I don't have access to the bioconductor git
any longer. I had to completely reinstall my system here, so probably
either my key got lost, or I'm using the wrong account to push.

I tried to find out what key and user was registered, but couldn't find it.
Hence a few questions:

- Is there any way to find out how I am registered today (i.e. name and
public key)?
- I'm JoFAM on github, but the repo is in an organization called
CenterForStatistics-UGent. What github name do I use then for sending a new
public key?
- I use my work email for maintaining the package, but my account is set to
my personal email. Is that a problem and if so, how should I tackle that?

Thank you in advance.

-- 
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)
<https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium=gmail=g>

tel: +32 (0)9 264 61 79
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Re: [Bioc-devel] Trying to clone my repo but my key is not recognized.

[Joris Meys]

As said, this is what I got after

git fetch upstream

As per instructions here:
http://bioconductor.org/developers/how-to/git/maintain-github-bioc/ (I did
carry out the previous steps as well).

Cheers
Joris




On Tue, Aug 22, 2017 at 11:24 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:

> On 08/22/2017 04:59 AM, Joris Meys wrote:
>
>> Hi,
>>
>> I sent my public key as registered in my github account to you a while
>> ago,
>> but when I tried to clone my repository, I get the following error message
>> after git fetch upstream:
>>
>> -
>>
>> The authenticity of host 'git.bioconductor.org (34.192.48.227)' can't be
>> established.
>> ECDSA key fingerprint is SHA256:nXILc5fVCnDfOID8HgPi+mS
>> ufGtr2JMYgnRa1JAQj/Q.
>> Are you sure you want to continue connecting (yes/no)? yes
>>
>> Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA)
>> to
>> the list of known hosts.
>> Permission denied (publickey).
>> fatal: Could not read from remote repository.
>>
>> Please make sure you have the correct access rights and the repository
>> exists.
>>
>> -
>>
>> I've been googling and hurting my brain to figure out what I did wrong,
>> but
>> I honestly don't have a clue. Can anyone tell me how I can solve this?
>>
>
> can you show the command that you are using to (try to) clone your
> repository?
>
>
>
>> Cheers
>> Joris
>>
>>
>
> 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,
> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>



-- 
Joris Meys
Statistical consultant

Ghent University
Faculty of Bioscience Engineering
Department of Mathematical Modelling, Statistics and Bio-Informatics

tel : +32 9 264 59 87
joris.m...@ugent.be
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[Bioc-devel] Trying to clone my repo but my key is not recognized.

[Joris Meys]

Hi,

I sent my public key as registered in my github account to you a while ago,
but when I tried to clone my repository, I get the following error message
after git fetch upstream:

-

The authenticity of host 'git.bioconductor.org (34.192.48.227)' can't be
established.
ECDSA key fingerprint is SHA256:nXILc5fVCnDfOID8HgPi+mSufGtr2JMYgnRa1JAQj/Q.
Are you sure you want to continue connecting (yes/no)? yes

Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (ECDSA) to
the list of known hosts.
Permission denied (publickey).
fatal: Could not read from remote repository.

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

-

I've been googling and hurting my brain to figure out what I did wrong, but
I honestly don't have a clue. Can anyone tell me how I can solve this?

Cheers
Joris

-- 
Joris Meys
Statistical consultant

Ghent University
Faculty of Bioscience Engineering
Department of Mathematical Modelling, Statistics and Bio-Informatics

tel : +32 9 264 59 87
joris.m...@ugent.be
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Re: [Bioc-devel] BiocGenerics attaches when methods package is imported

[Joris Meys]

Hi Andreas,

for a good understanding: just mentioning the methods package in the
DESCRIPTION file isn't doing a thing if you don't also add

import(methods)

to the NAMESPACE file.

So it looks like the warning occurs when the package indicates that the
methods package is imported when it actually isn't. Do you still get that
warning if you update the NAMESPACE file?

Cheers
Joris

On Mon, Feb 15, 2016 at 4:52 PM, Andreas Kapouranis <
kapouranis.andr...@gmail.com> wrote:

> Hi,
>
> I am developing a package for Bioconductor, and I have a weird issue when
> importing the 'methods' package. Before I add the 'methods' package in
> Imoprts in the DESCRIPTION file, I pass the CMD check without any warnings.
>
> However, when I add the 'methods' package in the Imports field, I get a
> warning during CMD check. (I need the methods package since I use the
> methods::is() function, and if I call it just as is(), when running the
> package from Rscript will fail since by default it does not load the
> 'methods' package.)
>
> I read a similar issue here:
> https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008193.html
> and I updated all my packages from Bioconductor including IRanges and
> GenomicRanges.
>
> This is the warning that I get, which is exactly the same as the previous
> issue in Bioc-Devel, and I understand that for some reason the BiocGenerics
> is attached only when the 'methods' package is imported.
>
> * checking for missing documentation entries ... WARNING
>
> Attaching package: ‘BiocGenerics’
>
> The following objects are masked from ‘package:parallel’:
>
> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
> clusterExport, clusterMap, parApply, parCapply, parLapply,
> parLapplyLB, parRapply, parSapply, parSapplyLB
>
> The following objects are masked from ‘package:stats’:
>
> IQR, mad, xtabs
>
> The following objects are masked from ‘package:base’:
>
> Filter, Find, Map, Position, Reduce, anyDuplicated, append,
> as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
> eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
> lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
> pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
> tapply, union, unique, unlist, unsplit
>
> All user-level objects in a package should have documentation entries.
> See chapter ‘Writing R documentation files’ in the ‘Writing R
> Extensions’ manual.
>
>
>
> My DESCRIPTION file when I add the 'methods' package is the following:
> ...
> Depends: R (>= 3.2.0)
> LazyData: TRUE
> RoxygenNote: 5.0.1
> Imports: GenomicRanges,
> IRanges,
> assertthat,
> S4Vectors,
> graphics,
> data.table,
> methods
> Suggests: knitr,
> rmarkdown,
> testthat
> VignetteBuilder: knitr
>
>
>
> Regards,
> Andreas
>
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>
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-- 
Joris Meys
Statistical consultant

Ghent University
Faculty of Bioscience Engineering
Department of Mathematical Modelling, Statistics and Bio-Informatics

tel : +32 9 264 59 87
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