[Rd] Experimental package for asan-usan checks

[Tim Keitt]

I've been trying to replicate Brian's excellent work on sanity checks so we
can get that information before submitting. I've put together an
experimental package here: https://github.com/thk686/sanitycheckr

It uses a modified rocker r-devel-san image and attempts to install all
dependencies before running a check.

This would probably be better integrated into TravisCI, et al. It was
nonetheless a good opportunity to learn a bit about docker + asan/usan.
Happy to have people kick the tires, make suggestions or make pull requests.

THK

http://www.keittlab.org/

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Re: [Rd] strange warning: data() error?

[David Winsemius]

> On Apr 16, 2018, at 3:20 PM, David Winsemius  wrote:
> 
>> 
>> On Apr 16, 2018, at 2:58 PM, Therneau, Terry M., Ph.D. via R-devel 
>>  wrote:
>> 
>> A user asked me about this and I can't figure it out.
>> 
>> tmt% R
>> R Under development (unstable) (2018-04-09 r74565) -- "Unsuffered 
>> Consequences"
>> Copyright (C) 2018 The R Foundation for Statistical Computing
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> 
>>> library(survival)
>>> data(cgd0)
>> Warning message:
>> In data(cgd0) : data set ‘cgd0’ not found
>> 
>> 
>> 
>> The data set is present and can be manipulated: data() is not required.  
>> Other data sets in the survival package don't generate this message.
> 
> On a Mac the Data Manager panel lists that dataset as "cgd0 (cgd)" and I get 
> the same warning with any dataset that has a similar appearance of  paren-name-paren> , even the `state.abb` vector that is displayed "state.abb 
> (state)" (without the quotes.)
> 
>> data('state.abb')
> Warning message:
> In data("state.abb") : data set ‘state.abb’ not found
>> str(state.abb)
> chr [1:50] "AL" "AK" "AZ" "AR" "CA" "CO" "CT" "DE" "FL" "GA" "HI" "ID" "IL" 
> "IN" "IA" "KS" "KY" "LA" "ME" "MD" "MA" ...
>> data(stack.loss)
> Warning message:
> In data(stack.loss) : data set ‘stack.loss’ not found
> 
> So I guess the message is don't feel picked upon. It seems to be an 
> infelicity shared by many other datasets even those in the canonical 
> 'datasets' package.

> survival_Rdata <- 
> readRDS("/Library/Frameworks/R.framework/Versions/3.4/Resources/library/survival/data/Rdata.rds")
> survival_Rdata
$bladder
[1] "bladder"  "bladder1" "bladder2"

$cancer
[1] "cancer"

$cgd
[1] "cgd"  "cgd0"

$colon
[1] "colon"

$flchain
[1] "flchain"

$genfan
[1] "genfan"

$heart
[1] "heart" "jasa"  "jasa1"

--- snip 

data(bladder2)
# Warning message:
# In data(bladder2) : data set ‘bladder2’ not found

data(mgus1)
# Warning message:
# In data(mgus1) : data set ‘mgus1’ not found

>  data(mgus1)
Warning message:
In data(mgus1) : data set ‘mgus1’ not found

> data("survexp.mn")
Warning message:
In data("survexp.mn") : data set ‘survexp.mn’ not found



Hypothesis:   datasets in a ..library/data/Rdata.rds file whose listing does 
not match the name of the dataset from which it is derived will cause the 
behavior in question.

And Terry; After executing `data(package-"survival")` I must mention that the 
spelling of "Granulomatous" is not "Granulotomous", and neither is the spelling 
of "gammapathy", "gammapothy".


-- 

David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law

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Re: [Rd] strange warning: data() error?

[William Dunlap via R-devel]

data(package="survival") gives, in part,

cgd Chronic Granulotomous Disease data
cgd0 (cgd)  Chronic Granulotomous Disease data
colon   Chemotherapy for Stage B/C colon cancer
flchain Assay of serum free light chain for 7874
subjects.
genfan  Generator fans
heart   Stanford Heart Transplant data
jasa (heart)Stanford Heart Transplant data
jasa1 (heart)   Stanford Heart Transplant data

The 'name1 (name2)' entries indicate that 'name'; is in the file
labelled name2.  If you run data(cgd) you get both cgd and cdg0
in .GlobalEnv;  if you run data(heart) you get heart, jasa, and jasa1.
I don't think this has changed recently, although it might be nice
if the names were handled more symmetrically, like alias entries
in help files.


Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Mon, Apr 16, 2018 at 2:58 PM, Therneau, Terry M., Ph.D. via R-devel <
r-devel@r-project.org> wrote:

> A user asked me about this and I can't figure it out.
>
> tmt% R
> R Under development (unstable) (2018-04-09 r74565) -- "Unsuffered
> Consequences"
> Copyright (C) 2018 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> > library(survival)
> > data(cgd0)
> Warning message:
> In data(cgd0) : data set ‘cgd0’ not found
>
> 
>
> The data set is present and can be manipulated: data() is not required.
> Other data sets in the survival package don't generate this message.
>
> Terry T.
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

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Re: [Rd] strange warning: data() error?

[David Winsemius]

> On Apr 16, 2018, at 2:58 PM, Therneau, Terry M., Ph.D. via R-devel 
>  wrote:
> 
> A user asked me about this and I can't figure it out.
> 
> tmt% R
> R Under development (unstable) (2018-04-09 r74565) -- "Unsuffered 
> Consequences"
> Copyright (C) 2018 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
> 
> > library(survival)
> > data(cgd0)
> Warning message:
> In data(cgd0) : data set ‘cgd0’ not found
> 
> 
> 
> The data set is present and can be manipulated: data() is not required.  
> Other data sets in the survival package don't generate this message.

On a Mac the Data Manager panel lists that dataset as "cgd0 (cgd)" and I get 
the same warning with any dataset that has a similar appearance of  , even the `state.abb` vector that is displayed "state.abb 
(state)" (without the quotes.)

> data('state.abb')
Warning message:
In data("state.abb") : data set ‘state.abb’ not found
> str(state.abb)
 chr [1:50] "AL" "AK" "AZ" "AR" "CA" "CO" "CT" "DE" "FL" "GA" "HI" "ID" "IL" 
"IN" "IA" "KS" "KY" "LA" "ME" "MD" "MA" ...
> data(stack.loss)
Warning message:
In data(stack.loss) : data set ‘stack.loss’ not found

So I guess the message is don't feel picked upon. It seems to be an infelicity 
shared by many other datasets even those in the canonical 'datasets' package.


> 
> Terry T.
> 
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law

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[Rd] strange warning: data() error?

[Therneau, Terry M., Ph.D. via R-devel]

A user asked me about this and I can't figure it out.

tmt% R
R Under development (unstable) (2018-04-09 r74565) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

> library(survival)
> data(cgd0)
Warning message:
In data(cgd0) : data set ‘cgd0’ not found



The data set is present and can be manipulated: data() is not required.  Other data sets 
in the survival package don't generate this message.


Terry T.

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Re: [Rd] alpha transparency doesn't work for lines when xpd=TRUE

[William Dunlap via R-devel]

The problem occurs in the Windows GUI with the 'windows()' graphics device.
In the following example the red diagonal line appears in 3 plots but not
in the one
with xpd=TRUE and alpha.f=0.9.

> par(mfrow=c(2,2))
> for(xpd in c(FALSE, TRUE)) for(alpha.f in c(.9, 1))
plot(0:1,xpd=xpd,type="l",col=adjustcolor("red",alpha.f=alpha.f),main=paste0("xpd=",xpd,",
alpha.f=",alpha.f))
> dev.cur()
windows
  2
> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 16299)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C

[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_3.4.4


Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Mon, Apr 16, 2018 at 12:14 PM, David Winsemius 
wrote:

>
> > On Apr 16, 2018, at 10:41 AM, Jiaxuan Chen 
> wrote:
> >
> > Dear R-devel,
> >
> > I think I've found a bug - the alpha transparency doesn't work when
> plotting lines with xpd = TRUE.
> >
> > #works
> > plot(1:20, col="#1874CD", xpd=T, type="l")
> >
> > #works
> > plot(1:20, col="#1874CD50", xpd=F, type="l")
> >
> > #doesn't work
> > plot(1:20, col="#1874CD50", xpd=T, type="l")
>
> It's behaving as expected (last two lines light blue) on a Mac (El
> Capitan) and R 3.4.3. (I did check to see if T and F were still TRUE and
> FALSE at the time. It's possible that they were not in your session. Only
> TRUE and FALSE are reserved words.)
> >
> > Thank you.
> >
> > Jim
> >
> >
> >   [[alternative HTML version deleted]]
>
> All the R mailing lists are plain text.
>
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
> David Winsemius
> Alameda, CA, USA
>
> 'Any technology distinguishable from magic is insufficiently advanced.'
>  -Gehm's Corollary to Clarke's Third Law
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

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Re: [Rd] alpha transparency doesn't work for lines when xpd=TRUE

[David Winsemius]

> On Apr 16, 2018, at 10:41 AM, Jiaxuan Chen  
> wrote:
> 
> Dear R-devel,
> 
> I think I've found a bug - the alpha transparency doesn't work when plotting 
> lines with xpd = TRUE.
> 
> #works
> plot(1:20, col="#1874CD", xpd=T, type="l")
> 
> #works
> plot(1:20, col="#1874CD50", xpd=F, type="l")
> 
> #doesn't work
> plot(1:20, col="#1874CD50", xpd=T, type="l")

It's behaving as expected (last two lines light blue) on a Mac (El Capitan) and 
R 3.4.3. (I did check to see if T and F were still TRUE and FALSE at the time. 
It's possible that they were not in your session. Only TRUE and FALSE are 
reserved words.)
> 
> Thank you.
> 
> Jim
> 
> 
>   [[alternative HTML version deleted]]

All the R mailing lists are plain text.

> 
> __
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David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law

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[Bioc-devel] " Error in serialize(data, node$con, xdr = FALSE)" during Vignette build (ChIC)

[Carmen M. Livi]

Hi all,

my package recently got accepted and moved to the Bioconductor repository.

Suddenly I get an error during the package build for Linux and OS (the 
INSTALL is working). The error occurs during the creation of the 
vignette in a chunk. The error was not there before and I can't 
reproduce it on my local machine:


" Error in serialize(data, node$con, xdr = FALSE) :
error writing to connection
Execution halted "

Interestingly I get the same error in totally different points for Linux 
and OS.


I am using BiocParallel with BPPARAM = 
BiocParallel::MulticoreParam(workers = 5) and requested 5 CPUs.
Can it be that I am not supposed to use that many CPUs? Did anyone 
encounter a similar issue?
Should I avoid parallelization in the vignette or should I just reduce 
the number?
The dataset I use in the vignette is a small one, so I suppose it is not 
a memory issue.


Thanks for any suggestion,

Carmen

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Re: [Bioc-devel] Can not push to bioconductor! please help me!

[Shepherd, Lori]

Dear BioMedR maintainer,

Unfortunately BioMedR was removed from Bioconductor as of Release 3.6 (last
Oct).  We reached out several times before the 3.6 release as your package had
been failing since early July 2017. Part of the Bioconductor guidelines require
that packages are actively maintained and fixed in a timely manner. Packages are
built daily indicating if there are ERROR's or WARNING's and should be
occasionally checked:

http://bioconductor.org/checkResults/

Besides emailing you privately several times,  it was also posted before the
release on the support site and devel mailing list (bioc-devel@r-project.org)
links given below - giving time to respond before officially being
deprecated. And you would have recieved email notifications from
bbs-nore...@bioconductor.org indicating build failures.

https://support.bioconductor.org/p/100984/
https://support.bioconductor.org/p/100199/

https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011522.html

As you remained unresponsive and the package remained broken it began the
deprecation and end-of-life process.

If you would like to revive the package, it would need to go through
the package review process again and at this point is too late to be included in
the Bioc 3.7 release.  You can have it reviewed and accepted to be re-included 
in
Bioc 3.8 later this year.



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 Zhu MF 

Sent: Monday, April 16, 2018 12:32:10 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Can not push to bioconductor! please help me!

dear sir:


contents in GitHub and that in bioconductor are not the same. I want to update 
the package to follow the contents in github, but falied:


git remote -v
origin  g...@github.com:wind22zhu/BioMedR.git (fetch)
origin  g...@github.com:wind22zhu/BioMedR.git (push)
upstream  g...@git.bioconductor.org:packages/BioMedR.git (fetch)
upstream  g...@git.bioconductor.org:packages/BioMedR.git (push)




$ git push upstream master
Enter passphrase for key '/c/Users/ifyoung/.ssh/id_rsa':
FATAL: W any packages/BioMedR wind22zhu DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.






$ ssh -T g...@git.bioconductor.org




 R  packages/BioMedR


No WRITE(W) permissions?
Why?
Can you help me ? I have been stucked here  for several days!
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[Rd] alpha transparency doesn't work for lines when xpd=TRUE

[Jiaxuan Chen]

Dear R-devel,

I think I've found a bug - the alpha transparency doesn't work when plotting 
lines with xpd = TRUE.

#works
plot(1:20, col="#1874CD", xpd=T, type="l")

#works
plot(1:20, col="#1874CD50", xpd=F, type="l")

#doesn't work
plot(1:20, col="#1874CD50", xpd=T, type="l")

Thank you.

Jim


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Re: [Bioc-devel] Can not push to bioconductor! please help me!

[Turaga, Nitesh]

Hi Zhu,

You submitted your keys with the wrong username. Please use your SVN ID “m.zhu” 
and resubmit

Best,

Nitesh 
> On Apr 16, 2018, at 12:32 PM, Zhu MF  wrote:
> 
> dear sir:
> 
> 
> contents in GitHub and that in bioconductor are not the same. I want to 
> update the package to follow the contents in github, but falied:
> 
> 
> git remote -v
> origin  g...@github.com:wind22zhu/BioMedR.git (fetch)
> origin  g...@github.com:wind22zhu/BioMedR.git (push)
> upstream  g...@git.bioconductor.org:packages/BioMedR.git (fetch) 
> upstream  g...@git.bioconductor.org:packages/BioMedR.git (push)
> 
> 
> 
> 
> $ git push upstream master
> Enter passphrase for key '/c/Users/ifyoung/.ssh/id_rsa':
> FATAL: W any packages/BioMedR wind22zhu DENIED by fallthru
> (or you mis-spelled the reponame)
> fatal: Could not read from remote repository.
> Please make sure you have the correct access rights
> and the repository exists.
> 
> 
> 
> 
> 
> 
> $ ssh -T g...@git.bioconductor.org
> 
> 
> 
> 
> R  packages/BioMedR
> 
> 
> No WRITE(W) permissions?
> Why?
> Can you help me ? I have been stucked here  for several days!
>   [[alternative HTML version deleted]]
> 
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Re: [R-pkg-devel] Rd files: using \link[pkg]{foo} when file names differ between OSs

[Duncan Murdoch]

On 16/04/2018 1:06 PM, Martin Morgan wrote:



On 04/16/2018 12:31 PM, Duncan Murdoch wrote:

On 16/04/2018 12:06 PM, Martin Maechler wrote:

Duncan Murdoch 
  on Mon, 16 Apr 2018 11:52:10 -0400 writes:


  > On 16/04/2018 11:35 AM, Ramon Diaz-Uriarte wrote:
  >> Dear All,
  >>
  >> Two recent threads in the bioconductor devel mailing list
  >> (https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
  >> and
  >> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013259.html)
  >> are related to packages that have different names of html
  >> files in different operating systems.
  >>
  >> For example, parallel has a file called mclapply in
  >> Linux. So using, from the Rd file of another package,
  >> \link[parallel]{mclapply} works fine under Linux, but
  >> does not under Windows, because there is no mclapply.html
  >> file in Windows (there is a mcdummies file).
  >>
  >>
  >> Is there any recommended way to proceed in these cases?
  >>
  >>
  >> Yes, section 2.5 of Writing R Extensions indicates that
  >> \link[pkg]{foo} and \link[pkg:bar]{foo} are rarely
  >> needed; so the simplest way to proceed would be to avoid
  >> \link[pkg]{foo} and \link[pkg:bar]{foo}. I am asking for
  >> the cases where, as noted in 2.5, "more than one package
  >> offers help on a topic".

  > You could make the links conditional on the OS.  For example,

  > #ifdef windows
  > See \link[parallel]{mcdummies}.
  > #endif
  > #ifdef unix
  > See \link[parallel]{mclapply}.
  > #endif

  > The other possibility (useful if there are major differences
between the
  > platforms) is to have two copies of the help file, one in
man/unix, one
  > in man/windows, but that doesn't seem appropriate from your
description.

  > Duncan Murdoch

and mid-term, I really think R and (CRAN, Bioc, ...) packages
should not do what we (R core) did here.
Rather,  \alias{mclapply}  should exist both for windows and
non-windows, and hence \link{mclapply}  would just work.


\alias{mclapply} does exist...



I forget whether that would work here:  parallel being a base package
(used by the package in question?) might mean it would be found without
the [parallel] in the link.  But in general, links to other packages
using [pkg] go to the *filename*, not to the alias.  This oddity happens
because we want the links to work even if the referenced package is
installed later than the Rd file is processed.


People are quite concerned about fixing the 'WARNING' this generates.
However from the text

file link 'mclapply' in package 'parallel' does not exist and so has
been  treated as a topic

the help pages are actually constructed correctly, finding the page on
which the topic (aka alias) 'mclapply' is defined. This contrasts with a
completely incorrect link (e.g., \link[stats]{mclapply}) generating a
warning

missing file link

and unable to link to the mclapply topic.

Perhaps the WARNING from \link[parallel]{mclapply} should be a NOTE?

There are other oddities in the threads that Ramon indicates

- WARNINGs from \link[foo]{bar} that should really be
\link[foo:baz]{bar} often only appear on Windows (parallel's use of
mcdummies is a special case here). Shouldn't they be
platform-independent? An example is

  
http://bioconductor.org/checkResults/3.7/bioc-LATEST/ADaCGH2/tokay2-checksrc.html


where as.MAList is defined in a file called asmalist.Rd so
\link[limma]{as.MAList} is incorrect. It generates a warning only on our
Windows machine (tokay2) not Linux or Mac. I had some recollection of
Windows-specific help system behavior, but I think this dates back to
the .chm days...


Yes, that looks like an issue in the Linux checks.



- There were a spate of independent posts about this, suggesting that
this is relatively new phenomenon (though it could also be that
maintainers have been busy preparing their packages for the next
release, so are now noticing the problem...)


The fact that cross-package links go to files rather than aliases is 
very old, but the checks may be newer.




- It doesn't seem like good practice to link to the file name, which
seems an internal aspect of a package, rather than to the alias, which
seems at least for symbols to be a user-facing public aspect of the package.


I agree, but as I said, this is very old.  It was old when I wrote the 
Rd parser.  I vaguely recall that the possibility of a change was 
considered and rejected, but I'm not sure about that.


Changing it to use only topics would likely cause problems for people 
who are not getting warnings now.  Perhaps it would be sensible to 
switch from filename to topic without a warning if the referenced 
package is available for checking, only issuing the warning if the check 
machine can't verify that the link is good.


Duncan Murdoch



- And finally I 

Re: [R-pkg-devel] Rd files: using \link[pkg]{foo} when file names differ between OSs

[Martin Morgan]

On 04/16/2018 12:31 PM, Duncan Murdoch wrote:

On 16/04/2018 12:06 PM, Martin Maechler wrote:

Duncan Murdoch 
 on Mon, 16 Apr 2018 11:52:10 -0400 writes:


 > On 16/04/2018 11:35 AM, Ramon Diaz-Uriarte wrote:
 >> Dear All,
 >>
 >> Two recent threads in the bioconductor devel mailing list
 >> (https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
 >> and
 >> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013259.html)
 >> are related to packages that have different names of html
 >> files in different operating systems.
 >>
 >> For example, parallel has a file called mclapply in
 >> Linux. So using, from the Rd file of another package,
 >> \link[parallel]{mclapply} works fine under Linux, but
 >> does not under Windows, because there is no mclapply.html
 >> file in Windows (there is a mcdummies file).
 >>
 >>
 >> Is there any recommended way to proceed in these cases?
 >>
 >>
 >> Yes, section 2.5 of Writing R Extensions indicates that
 >> \link[pkg]{foo} and \link[pkg:bar]{foo} are rarely
 >> needed; so the simplest way to proceed would be to avoid
 >> \link[pkg]{foo} and \link[pkg:bar]{foo}. I am asking for
 >> the cases where, as noted in 2.5, "more than one package
 >> offers help on a topic".

 > You could make the links conditional on the OS.  For example,

 > #ifdef windows
 > See \link[parallel]{mcdummies}.
 > #endif
 > #ifdef unix
 > See \link[parallel]{mclapply}.
 > #endif

 > The other possibility (useful if there are major differences 
between the
 > platforms) is to have two copies of the help file, one in 
man/unix, one
 > in man/windows, but that doesn't seem appropriate from your 
description.


 > Duncan Murdoch

and mid-term, I really think R and (CRAN, Bioc, ...) packages
should not do what we (R core) did here.
Rather,  \alias{mclapply}  should exist both for windows and
non-windows, and hence \link{mclapply}  would just work.


\alias{mclapply} does exist...



I forget whether that would work here:  parallel being a base package 
(used by the package in question?) might mean it would be found without 
the [parallel] in the link.  But in general, links to other packages 
using [pkg] go to the *filename*, not to the alias.  This oddity happens 
because we want the links to work even if the referenced package is 
installed later than the Rd file is processed.


People are quite concerned about fixing the 'WARNING' this generates. 
However from the text


  file link 'mclapply' in package 'parallel' does not exist and so has 
been  treated as a topic


the help pages are actually constructed correctly, finding the page on 
which the topic (aka alias) 'mclapply' is defined. This contrasts with a 
completely incorrect link (e.g., \link[stats]{mclapply}) generating a 
warning


  missing file link

and unable to link to the mclapply topic.

Perhaps the WARNING from \link[parallel]{mclapply} should be a NOTE?

There are other oddities in the threads that Ramon indicates

  - WARNINGs from \link[foo]{bar} that should really be 
\link[foo:baz]{bar} often only appear on Windows (parallel's use of 
mcdummies is a special case here). Shouldn't they be 
platform-independent? An example is



http://bioconductor.org/checkResults/3.7/bioc-LATEST/ADaCGH2/tokay2-checksrc.html

where as.MAList is defined in a file called asmalist.Rd so 
\link[limma]{as.MAList} is incorrect. It generates a warning only on our 
Windows machine (tokay2) not Linux or Mac. I had some recollection of 
Windows-specific help system behavior, but I think this dates back to 
the .chm days...


  - There were a spate of independent posts about this, suggesting that 
this is relatively new phenomenon (though it could also be that 
maintainers have been busy preparing their packages for the next 
release, so are now noticing the problem...)


  - It doesn't seem like good practice to link to the file name, which 
seems an internal aspect of a package, rather than to the alias, which 
seems at least for symbols to be a user-facing public aspect of the package.


  - And finally I did make an svn commit related to this, so am 
sensitive to blundering here


R-devel/src/library/tools/R$ svn log -c74129

r74129 | morgan | 2018-01-17 16:52:53 -0500 (Wed, 17 Jan 2018) | 10 lines

correct warning when \link[base]{foo} is incorrect

- now "missing file link" rather than "file link 'foo' in package 'base'
  does not exist and will be treated as a topic" (foo is _not_ a topic
  in base; the link to foo.html is missing)
- vice-versa for \link[base]{rbind} (rbind _is_ a topic in base, 
documented in

  cbind.html, and will be resolved by the help system)
- see https://stat.ethz.ch/pipermail/r-devel/2009-October/055287.html and
  c50198

Re: [R-pkg-devel] vignette via devtools: sometimes found, sometimes not (same package)

[Alexandre Courtiol]

Re,

On 16 April 2018 at 17:35, Georgi Boshnakov <
georgi.boshna...@manchester.ac.uk> wrote:

> Hi,
>
> The problem is indeed difficult to debug but there are things that can be
> done to narrow it down.
>
> 1. Are there 1/3 unlucky computers fixed? (I.e does the problem occur
> always on the same computers) Also, do you really mean computer or user?
>

Yes, I mean computer, not user.

>
> 2. Are the students working under R studio? If so, does the same problem
> appear if the same procedure is run outside R studio.
>

I will try tomorrow (but from memory I think the answer will be yes).

>
> 3. Further to 2.,  You mention development mode - do (some) students also
> have a copy of your repository? This may be aproblem if they don't update
> it too.
>

No, only me has the devel version.

>
> 4. What happens if R is restarted?


I will try tomorrow (but I think the answer will be nothing).


> 5. It may be worth checking .Rprofle and similar for the concerned
> computers (or users, see 1.)
>

I will try as well but most had a fresh install and did not mess with
settings.

>
> Hope this is of some help.
>

I will look at all this and also gather the session infos as Ben suggested.
I think I know how to proceed to get to the bottom of that, but I was just
hoping that the problem was already well known and the answer as well...
If it is for anyone, please reply. Otherwise, I will investigate.
Thanks to everyone.
Alex


>
>
>  Georgi Boshnakov
>
>
> 
> From: R-package-devel [r-package-devel-boun...@r-project.org] on behalf
> of Alexandre Courtiol [alexandre.court...@gmail.com]
> Sent: 16 April 2018 14:40
> To: List r-package-devel
> Subject: [R-pkg-devel] vignette via devtools: sometimes found, sometimes
> not (same package)
>
> Dear all,
> I am teaching a class and for that I created a R package that mostly
> contains vignettes (the slides of the course).
> I host the package on GitHub because I want the students to download every
> day the latest version of the package.
> Building the vignettes takes a couple of hours so I pre-build the vignettes
> using devtools::build_vignettes before pushing my updates to GitHub.
> The student install the package using
> devtools::install_github("courtiol/LM2GLMM").
> Then, they do library(LM2GLMM) and browseVignettes(package = "LM2GLMM")...
>
> ... and that works on 2/3 of the computers, for the others it says
> vignettes not found.
>
> Any idea why and what can I do to make it 100% success?
> Of course on my laptop it works, so I cannot investigate.
> Also, since they all use different versions of R, devtools or OS... I would
> like to know the one thing that must be changed if it comes from that (but
> I am not sure it does).
>
> I have added a back up function that works for the 1/3 of unfortunate
> students:
>
> get_vignettes <- function() {
>   utils::browseURL(paste0(find.package("LM2GLMM"), "/doc/")) ## for
> installed
>   utils::browseURL(paste0(find.package("LM2GLMM"), "/inst/doc/")) ## for
> development
>   return(invisible(NULL))
> }
>
> This functions opens de vignette folder and that shows that all the
> students actually have the html files installed correctly. But it is ugly
> because then they have to find the good html file and so forth, so I would
> rather have a better solution.
>
> Many thanks,
>
> Alex
>
> --
> Alexandre Courtiol
>
> http://sites.google.com/site/alexandrecourtiol/home
>
> *"Science is the belief in the ignorance of experts"*, R. Feynman
>
> [[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>



-- 
Alexandre Courtiol

http://sites.google.com/site/alexandrecourtiol/home

*"Science is the belief in the ignorance of experts"*, R. Feynman

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[Bioc-devel] Can not push to bioconductor! please help me!

[Zhu MF]

dear sir:


contents in GitHub and that in bioconductor are not the same. I want to update 
the package to follow the contents in github, but falied:


git remote -v
origin  g...@github.com:wind22zhu/BioMedR.git (fetch)
origin  g...@github.com:wind22zhu/BioMedR.git (push)
upstream  g...@git.bioconductor.org:packages/BioMedR.git (fetch) 
upstream  g...@git.bioconductor.org:packages/BioMedR.git (push)




$ git push upstream master
Enter passphrase for key '/c/Users/ifyoung/.ssh/id_rsa':
FATAL: W any packages/BioMedR wind22zhu DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.






$ ssh -T g...@git.bioconductor.org




 R  packages/BioMedR


No WRITE(W) permissions?
Why?
Can you help me ? I have been stucked here  for several days!
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Re: [R-pkg-devel] Rd files: using \link[pkg]{foo} when file names differ between OSs

[Duncan Murdoch]

On 16/04/2018 12:06 PM, Martin Maechler wrote:

Duncan Murdoch 
 on Mon, 16 Apr 2018 11:52:10 -0400 writes:


 > On 16/04/2018 11:35 AM, Ramon Diaz-Uriarte wrote:
 >> Dear All,
 >>
 >> Two recent threads in the bioconductor devel mailing list
 >> (https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
 >> and
 >> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013259.html)
 >> are related to packages that have different names of html
 >> files in different operating systems.
 >>
 >> For example, parallel has a file called mclapply in
 >> Linux. So using, from the Rd file of another package,
 >> \link[parallel]{mclapply} works fine under Linux, but
 >> does not under Windows, because there is no mclapply.html
 >> file in Windows (there is a mcdummies file).
 >>
 >>
 >> Is there any recommended way to proceed in these cases?
 >>
 >>
 >> Yes, section 2.5 of Writing R Extensions indicates that
 >> \link[pkg]{foo} and \link[pkg:bar]{foo} are rarely
 >> needed; so the simplest way to proceed would be to avoid
 >> \link[pkg]{foo} and \link[pkg:bar]{foo}. I am asking for
 >> the cases where, as noted in 2.5, "more than one package
 >> offers help on a topic".

 > You could make the links conditional on the OS.  For example,

 > #ifdef windows
 > See \link[parallel]{mcdummies}.
 > #endif
 > #ifdef unix
 > See \link[parallel]{mclapply}.
 > #endif

 > The other possibility (useful if there are major differences between the
 > platforms) is to have two copies of the help file, one in man/unix, one
 > in man/windows, but that doesn't seem appropriate from your description.

 > Duncan Murdoch

and mid-term, I really think R and (CRAN, Bioc, ...) packages
should not do what we (R core) did here.
Rather,  \alias{mclapply}  should exist both for windows and
non-windows, and hence \link{mclapply}  would just work.


I forget whether that would work here:  parallel being a base package 
(used by the package in question?) might mean it would be found without 
the [parallel] in the link.  But in general, links to other packages 
using [pkg] go to the *filename*, not to the alias.  This oddity happens 
because we want the links to work even if the referenced package is 
installed later than the Rd file is processed.


The reason the file was named "mclapply" in man/unix but "mcdummies" in 
man/windows was likely to save some time:  there are several aliases 
documented in that one file on Windows, but they are in separate files 
on Unix.


Duncan Murdoch



Martin Maechler


 >> Thanks,
 >> R.

 >> --
 >> Ramon Diaz-Uriarte
 >> Department of Biochemistry, Lab B-25
 >> Facultad de Medicina
 >> Universidad Autónoma de Madrid
 >> Arzobispo Morcillo, 4
 >> 28029 Madrid
 >> Spain



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Re: [R-pkg-devel] Rd files: using \link[pkg]{foo} when file names differ between OSs

[Martin Maechler]

> Duncan Murdoch 
> on Mon, 16 Apr 2018 11:52:10 -0400 writes:

> On 16/04/2018 11:35 AM, Ramon Diaz-Uriarte wrote:
>> Dear All,
>> 
>> Two recent threads in the bioconductor devel mailing list
>> (https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
>> and
>> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013259.html)
>> are related to packages that have different names of html
>> files in different operating systems.
>> 
>> For example, parallel has a file called mclapply in
>> Linux. So using, from the Rd file of another package,
>> \link[parallel]{mclapply} works fine under Linux, but
>> does not under Windows, because there is no mclapply.html
>> file in Windows (there is a mcdummies file).
>> 
>> 
>> Is there any recommended way to proceed in these cases?
>> 
>> 
>> Yes, section 2.5 of Writing R Extensions indicates that
>> \link[pkg]{foo} and \link[pkg:bar]{foo} are rarely
>> needed; so the simplest way to proceed would be to avoid
>> \link[pkg]{foo} and \link[pkg:bar]{foo}. I am asking for
>> the cases where, as noted in 2.5, "more than one package
>> offers help on a topic".

> You could make the links conditional on the OS.  For example,

> #ifdef windows
> See \link[parallel]{mcdummies}.
> #endif
> #ifdef unix
> See \link[parallel]{mclapply}.
> #endif

> The other possibility (useful if there are major differences between the 
> platforms) is to have two copies of the help file, one in man/unix, one 
> in man/windows, but that doesn't seem appropriate from your description.

> Duncan Murdoch

and mid-term, I really think R and (CRAN, Bioc, ...) packages
should not do what we (R core) did here.
Rather,  \alias{mclapply}  should exist both for windows and
non-windows, and hence \link{mclapply}  would just work.

Martin Maechler


>> Thanks,
>> R.

>> --
>> Ramon Diaz-Uriarte
>> Department of Biochemistry, Lab B-25
>> Facultad de Medicina
>> Universidad Autónoma de Madrid
>> Arzobispo Morcillo, 4
>> 28029 Madrid
>> Spain

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Re: [Bioc-devel] Windows

[Ramon Diaz-Uriarte]

And I have now asked this in R-pkg-devel
(https://stat.ethz.ch/pipermail/r-package-devel/2018q2/002617.html), as
suggested by Martin Maechler
(https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013169.html) in the
thread linked by Lori.

But if you can use \link{foo} (instead of \link[pkg]{foo} and
\link[pkg:bar]{foo}), as also suggested by Håkon Tjeldnes, then you should
have no problems.


Best,

R.

On Mon, 16-April-2018, at 13:16:54, Shepherd, Lori 
 wrote:
> This was also discussed in this thread a few weeks ago
>
> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
>
>
>
> 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 Mike Smith 
> 
> Sent: Monday, April 16, 2018 6:13:38 AM
> To: Rainer Johannes; bioc-devel
> Subject: Re: [Bioc-devel] Windows  on Tokay2>
>
> Martin mentioned that he changed the wording in
> https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e
> , so more recently than your version of R-devel.
>
> Mike
>
> On 16 April 2018 at 11:57, Rainer Johannes 
> wrote:
>
>> Thanks Mike,
>>
>> I somehow missed the discussion you mentioned. I would really not like to
>> include the name of the Rd file I want to link to. The *default* way that
>> works on Linux and macOS should also work on Windows - otherwise what's the
>> matter of the alias? Interestingly, on my Windows test machine (Windows 7)
>> I don't get these warnings (R-devel from 2018-01-07 r74091).
>>
>> jo
>>
>> > On 16 Apr 2018, at 10:49, Mike Smith  wrote:
>> >
>> > Hi Johannes,
>> >
>> > xcms is certainly not alone with the warning, and it was discussed in
>> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
>> >
>> > I think you should be able to get round it by including the name of Rd
>> file you're linking to e.g.  
>> \code{\link[MSnbase:pickpeaks-method]{pickPeaks}}
>> (I haven't actually tested this though).
>> >
>> > Mike
>> >
>> > On 16 April 2018 at 09:06, Rainer Johannes 
>> wrote:
>> > Dear all,
>> >
>> > we're experiencing WARNINGS in xcms on Tokay2 that are all related to
>> links in Rd files to functions and methods in other packages.
>> > Example:
>> > we have \code{\link[MSnbase]{pickPeaks}} in
>> XCMSnExp-inherited-methods.Rd that links to the method in MSnbase, that
>> works nicely on Linux and macOS build machines, but on tokay2 we get:
>> >
>> >   Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.
>> INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link
>> 'pickPeaks' in package 'MSnbase' does not exist and so has been treated as
>> a topic
>> >
>> > is there any other solution to removing all links to external packages?
>> >
>> > thanks, jo
>> >
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>>
>>
>
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>
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--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
   ramon.d...@iib.uam.es

http://ligarto.org/rdiaz

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Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

[Ramon Diaz-Uriarte]

Dear Martin,


On Mon, 09-April-2018, at 17:35:47, Martin Maechler 
 wrote:
>> Ramon Diaz-Uriarte 
>> on Mon, 9 Apr 2018 16:51:38 +0200 writes:
>
> > Dear Martin,
>
> > On Fri, 06-April-2018, at 18:59:00, Martin Morgan
> >  wrote:
> >> On 04/06/2018 10:44 AM, Lluís Revilla wrote:
> >>> I have recently faced a similar warning.  This is when a
> >>> link to a help page of another package is broken (there
> >>> is not such help page). Although those could be false
> >>> positives: mclapply help page does exists in parallel
> >>> package.  as.MAList does exists in devel limma
> >> 
> >> when \link-ing to another package, from
> >> RShowDoc("R-exts") section 2.5 the [] has to name the
> >> html help page, not the name of the function. For
> >> instance, `mclapply` is documented on a man page called
> >> mcdummies.Rd (!), so '\link[parallel:mcdummies]{nearest}
> >> would presumably not
>
> > I am confused here: as far as I can tell, there is an
> > mclapply.html file:
>
> > http://stat.ethz.ch/R-manual/R-devel/library/parallel/html/mclapply.html
>
> > In addition, when I use the \link[parallel:mcdummies] I
> > get a warning when testing under Linux.
>
>
> > On rereading section 2.5, I think \link[pkg]{foo} should
> > work too (if there is a foo.html file.)
>
> > Nevertheless, section 2.5 indicates that \link[pkg]{foo}
> > and \link[pkg:bar]{foo} are rarely needed, so I'll try to
> > remove them (except in those cases, covered in section
> > 2.5, where "more than one package offers help on a topic")
>
> Only on Windows, indeed,
> mclapply() is just a dummy function, calling lapply() IIRC.
>
> It is unfortunate that given the above you would be lead to use
> different \link{}s if you are on Windows than on non-Win...
>
> This would be a good question on the   R-package-devel   mailing
> list.
>

Done (https://stat.ethz.ch/pipermail/r-package-devel/2018q2/002617.html).

Thanks,

R.


> Martin
>
>
> >> generate the warning. Similarly
> >> \link[limma:asmalist]{as.MAList}.
> >> 
> >> There are several things that still need exploration.
> >> 
> >> - platform-specific (I have a vague understanding that
> >> Windows is special, but that might be outdated... [at
> >> least in this context...])
> >> 
>
> > I am only getting the warnings under Windows (which lead
> > me to think it was windows misbehaving).
>
>
> >> - recent. I have to admit to changing the text of the
> >> warning with this commit
> >> 
> >> 
> >> 
> https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e
> >> 
> >> but what I was intending to do was to change what it
> >> says, from the warning in release ('missing file link')
> >> to what it says, correctly, in devel 'file link ... does
> >> not exist and so has been treated as a topic'.  The old
> >> text appears in release, and the new in devel, as
> >> anticipated.  If I messed up somehow please let me
> >> know...
> >> 
> >> - even with the warning, the link isn't broken in the
> >> dynamic help system (it might have been broken prior to
> >> my commit...).
>
> > OK, thanks.
>
> > Best,
>
>
> > R.
>
>
> >> 
> >> Martin
> >> 
> >>> 
> >>> HTH
> >>> 
> >>> On 6 April 2018 at 16:35, Vincent Carey
> >>>  wrote:
> >>> 
>  ive seen this too apropos bigrquery on windows
>  
>  On Fri, Apr 6, 2018 at 10:22 AM Ramon Diaz-Uriarte
>   wrote:
>  
> > 
> > Dear All,
> > 
> > Two packages I maintain are showing, in Windows, a
> > warning during check with messages like
> > 
> > Rd warning:
> > 
> C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp21WlQD/R.INSTALL23343f935731/
>  OncoSimulR/man/oncoSimulIndiv.Rd:570:
> > file link 'mclapply' in package 'parallel' does not
> > exist and so has been treated as a topic
> > 
> > or
> > 
> > Rd warning:
> > C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQfQaA1/R.
>  INSTALL1ec81d5b6233/ADaCGH2/man/inputToADaCGH.Rd:45:
> > file link 'as.MAList' in package 'limma' does not
> > exist and so has been treated as a topic
> > 
> > 
> > 
> > that I cannot reproduce under Linux and that I think
> > are false positives. Is there a way to avoid this
> > warning? As far as I can tell, those links really
> > exist.
> > 
> > Best,
> > 
> > 
> > R.
> > 
> > --
> > Ramon Diaz-Uriarte Department of Biochemistry, Lab
> > B-25 Facultad de Medicina Universidad 

Re: [R-pkg-devel] vignette via devtools: sometimes found, sometimes not (same package)

[Ben Bolker]

I don't have a good solution but wonder if you could narrow down the
problem by getting them to send you sessionInfo() (or
devtools::session_info()) from a clean R session with just devtools
loaded.

  system.file() might be an alternative to paste0 + find.package()
(won't help much with the fundamental problem)



On Mon, Apr 16, 2018 at 9:40 AM, Alexandre Courtiol
 wrote:
> Dear all,
> I am teaching a class and for that I created a R package that mostly
> contains vignettes (the slides of the course).
> I host the package on GitHub because I want the students to download every
> day the latest version of the package.
> Building the vignettes takes a couple of hours so I pre-build the vignettes
> using devtools::build_vignettes before pushing my updates to GitHub.
> The student install the package using
> devtools::install_github("courtiol/LM2GLMM").
> Then, they do library(LM2GLMM) and browseVignettes(package = "LM2GLMM")...
>
> ... and that works on 2/3 of the computers, for the others it says
> vignettes not found.
>
> Any idea why and what can I do to make it 100% success?
> Of course on my laptop it works, so I cannot investigate.
> Also, since they all use different versions of R, devtools or OS... I would
> like to know the one thing that must be changed if it comes from that (but
> I am not sure it does).
>
> I have added a back up function that works for the 1/3 of unfortunate
> students:
>
> get_vignettes <- function() {
>   utils::browseURL(paste0(find.package("LM2GLMM"), "/doc/")) ## for
> installed
>   utils::browseURL(paste0(find.package("LM2GLMM"), "/inst/doc/")) ## for
> development
>   return(invisible(NULL))
> }
>
> This functions opens de vignette folder and that shows that all the
> students actually have the html files installed correctly. But it is ugly
> because then they have to find the good html file and so forth, so I would
> rather have a better solution.
>
> Many thanks,
>
> Alex
>
> --
> Alexandre Courtiol
>
> http://sites.google.com/site/alexandrecourtiol/home
>
> *"Science is the belief in the ignorance of experts"*, R. Feynman
>
> [[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

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Re: [Rd] packageDate() segfaults, if used without argument

[Rainer Hurling]

Hi Martin,

Am 16.04.2018 um 09:03 schrieb Martin Maechler:

Rainer Hurling 
 on Sun, 15 Apr 2018 11:01:59 +0200 writes:


 > Out of curiosity, I played a bit with the new function
 > packageDate() from April, 4th. All works fine, except
 > using it without any argument.  In this case, it
 > segfaults:

Thank you, Rainer, for the report -- about the *development* version of R


Yupp.



Note that the segfault would not have happened in  'R 3.5.0 beta'
(today turning to be 'R 3.5.0 RC'  : RC := Release Candidate )
which we'd be very happy if you used extensively.


Ah, interesting news, that this does not occur with beta and RC.



 > #> packageDate() Error in packageDescription(pkg, lib.loc
 > = lib.loc, fields = date.fields) : argument "pkg" is
 > missing, with no default

 >  *** caught segfault *** address 0x77bc3c0, cause 'memory
 > not mapped' Segmentation fault (core dumped)

 > My system is FreeBSD 12.0-CURRENT amd64 with R-devel
 > (r74601).

It was a lapsus -- of mine -- not at all related to packageDate(),
corrected yesterday (svn r 74604).


Nice to here. Thanks for the fast response and greetings,
Rainer



Martin



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[R-pkg-devel] vignette via devtools: sometimes found, sometimes not (same package)

[Alexandre Courtiol]

Dear all,
I am teaching a class and for that I created a R package that mostly
contains vignettes (the slides of the course).
I host the package on GitHub because I want the students to download every
day the latest version of the package.
Building the vignettes takes a couple of hours so I pre-build the vignettes
using devtools::build_vignettes before pushing my updates to GitHub.
The student install the package using
devtools::install_github("courtiol/LM2GLMM").
Then, they do library(LM2GLMM) and browseVignettes(package = "LM2GLMM")...

... and that works on 2/3 of the computers, for the others it says
vignettes not found.

Any idea why and what can I do to make it 100% success?
Of course on my laptop it works, so I cannot investigate.
Also, since they all use different versions of R, devtools or OS... I would
like to know the one thing that must be changed if it comes from that (but
I am not sure it does).

I have added a back up function that works for the 1/3 of unfortunate
students:

get_vignettes <- function() {
  utils::browseURL(paste0(find.package("LM2GLMM"), "/doc/")) ## for
installed
  utils::browseURL(paste0(find.package("LM2GLMM"), "/inst/doc/")) ## for
development
  return(invisible(NULL))
}

This functions opens de vignette folder and that shows that all the
students actually have the html files installed correctly. But it is ugly
because then they have to find the good html file and so forth, so I would
rather have a better solution.

Many thanks,

Alex

-- 
Alexandre Courtiol

http://sites.google.com/site/alexandrecourtiol/home

*"Science is the belief in the ignorance of experts"*, R. Feynman

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Re: [Bioc-devel] repository change after package acceptance

[Shepherd, Lori]

Yes Bioconductor utilizes the copy on 
git.bioconductor.org:packages/PowerExplorer.git  so as long as changes are 
pushed there - your github repository doesn't matter -


You may have to submit additional ssh-keys to Bioconductor for access; by 
default we use ssh keys from the github account that it was submitted under.



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 Xu Qiao 

Sent: Monday, April 16, 2018 7:55:40 AM
To: Llu�s Revilla
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] repository change after package acceptance

Thanks for your help, Llu�s.

-Xu

From: Llu�s Revilla [mailto:lluis.revi...@gmail.com]
Sent: maanantai 16. huhtikuuta 2018 13.48
To: Xu Qiao 
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] repository change after package acceptance

Dear Xu,

While you, with your ssh key, keep pushing to the 
git.bioconductor.org it doesn't matter where else 
is stored.
To move a repository within github you need to follow this tutorial: 
https://help.github.com/articles/transferring-a-repository-owned-by-your-personal-account/#transferring-to-an-organization
Regards,
Llu�s


On 16 April 2018 at 12:05, Xu Qiao > 
wrote:
Hi everyone,

I am the developer of package "PowerExplorer",  it has been accepted last week, 
and now it is visible on Bioconductor git server. However, the package was 
developed in my own personal GitHub repository, now I need to move it into our 
lab repository. Does anyone have any idea how to do this smoothly? Since the 
Bioconductor is expecting to be associated with my original GitHub-id.

Kind regards,
Xu
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Re: [Bioc-devel] repository change after package acceptance

[Xu Qiao]

Thanks for your help, Lluís.

-Xu

From: Lluís Revilla [mailto:lluis.revi...@gmail.com]
Sent: maanantai 16. huhtikuuta 2018 13.48
To: Xu Qiao 
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] repository change after package acceptance

Dear Xu,

While you, with your ssh key, keep pushing to the 
git.bioconductor.org it doesn't matter where else 
is stored.
To move a repository within github you need to follow this tutorial: 
https://help.github.com/articles/transferring-a-repository-owned-by-your-personal-account/#transferring-to-an-organization
Regards,
Lluís


On 16 April 2018 at 12:05, Xu Qiao > 
wrote:
Hi everyone,

I am the developer of package "PowerExplorer",  it has been accepted last week, 
and now it is visible on Bioconductor git server. However, the package was 
developed in my own personal GitHub repository, now I need to move it into our 
lab repository. Does anyone have any idea how to do this smoothly? Since the 
Bioconductor is expecting to be associated with my original GitHub-id.

Kind regards,
Xu
___
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Re: [Bioc-devel] Need some help to submit a R package.

[Martin Morgan]

If you are still having problems understanding warnings, it is probably 
better to use the github issue -- it may take some time to get an 
answer, because the reviewers have many responsibilities.


It looks like your 'webhook' is not correct, and that you are not 
changing the version of your package (from 0.99.0 to 0.99.1, 0.99.2, 
...) when you wish to generate another build report. @grimbough 
indicated in the github issue how to address these problems.


Martin

On 04/16/2018 03:58 AM, Pijush Das wrote:

Dear  Ruqian,


Yes sir, I have opened the build report which is a link to an HTML page
with details.
But I unable to understand why the WARNING massages are showing.

Three days before the other reviewers had made some comments and asked me
to address
those issues and also told me to solve the NOTEs produced by BioCheck.

Presently I am working on the sigFeature package to address those issues.
I shall communicate soon after solving those issues.


Thank you


Regards
Pijush



On Mon, Apr 16, 2018 at 4:06 AM, Ruqian Lyu 
wrote:


Hi Pijush,

Did you open the build report which is a link to an HTML page with details
of the warning?


Regards,
Ruqian



On Fri, Apr 13, 2018 at 4:54 PM, Pijush Das  wrote:


Dear Sir,


I have submitted an R package named "sigFeature" in Github and also
Bioconductor 9 days before.
The reviewers only said that there is some WARNING problem in the package
in different platform.

But after that they are not communicating any thing regarding the package.
I have checked the package
windows and Ubuntu it is working fine.

I unable to understand what actually the problem is ?
And the reviewers are not communicating about the problem. Though I am
getting lots of email from bioc-devel dealing with others package
problem .

Please suggest me what should I do now ?




Thank you



Regards
Pijush




On Mon, Apr 2, 2018 at 4:26 PM, Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:


Hi,

Please read through this documentation.

http://bioconductor.org/developers/package-submission/


Nitesh


On Apr 2, 2018, at 2:00 AM, Pijush Das  wrote:

Dear Sir,



I have developed an R package. I want to submit this package in
Bioconductor.
Please help me to submit the R package.









regards
Pijush Das

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Re: [Bioc-devel] Windows

[Shepherd, Lori]

This was also discussed in this thread a few weeks ago

https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html



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 Mike Smith 

Sent: Monday, April 16, 2018 6:13:38 AM
To: Rainer Johannes; bioc-devel
Subject: Re: [Bioc-devel] Windows 

Martin mentioned that he changed the wording in
https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e
, so more recently than your version of R-devel.

Mike

On 16 April 2018 at 11:57, Rainer Johannes 
wrote:

> Thanks Mike,
>
> I somehow missed the discussion you mentioned. I would really not like to
> include the name of the Rd file I want to link to. The *default* way that
> works on Linux and macOS should also work on Windows - otherwise what's the
> matter of the alias? Interestingly, on my Windows test machine (Windows 7)
> I don't get these warnings (R-devel from 2018-01-07 r74091).
>
> jo
>
> > On 16 Apr 2018, at 10:49, Mike Smith  wrote:
> >
> > Hi Johannes,
> >
> > xcms is certainly not alone with the warning, and it was discussed in
> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
> >
> > I think you should be able to get round it by including the name of Rd
> file you're linking to e.g.  \code{\link[MSnbase:pickpeaks-method]{pickPeaks}}
> (I haven't actually tested this though).
> >
> > Mike
> >
> > On 16 April 2018 at 09:06, Rainer Johannes 
> wrote:
> > Dear all,
> >
> > we're experiencing WARNINGS in xcms on Tokay2 that are all related to
> links in Rd files to functions and methods in other packages.
> > Example:
> > we have \code{\link[MSnbase]{pickPeaks}} in
> XCMSnExp-inherited-methods.Rd that links to the method in MSnbase, that
> works nicely on Linux and macOS build machines, but on tokay2 we get:
> >
> >   Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.
> INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link
> 'pickPeaks' in package 'MSnbase' does not exist and so has been treated as
> a topic
> >
> > is there any other solution to removing all links to external packages?
> >
> > thanks, jo
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>

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Re: [Bioc-devel] repository change after package acceptance

[Lluís Revilla]

Dear Xu,

While you, with your ssh key, keep pushing to the git.bioconductor.org it
doesn't matter where else is stored.
To move a repository within github you need to follow this tutorial:
https://help.github.com/articles/transferring-a-repository-owned-by-your-personal-account/#transferring-to-an-organization

Regards,

Lluís


On 16 April 2018 at 12:05, Xu Qiao  wrote:

> Hi everyone,
>
> I am the developer of package "PowerExplorer",  it has been accepted last
> week, and now it is visible on Bioconductor git server. However, the
> package was developed in my own personal GitHub repository, now I need to
> move it into our lab repository. Does anyone have any idea how to do this
> smoothly? Since the Bioconductor is expecting to be associated with my
> original GitHub-id.
>
> Kind regards,
> Xu
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] Windows

[Mike Smith]

Martin mentioned that he changed the wording in
https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e
, so more recently than your version of R-devel.

Mike

On 16 April 2018 at 11:57, Rainer Johannes 
wrote:

> Thanks Mike,
>
> I somehow missed the discussion you mentioned. I would really not like to
> include the name of the Rd file I want to link to. The *default* way that
> works on Linux and macOS should also work on Windows - otherwise what's the
> matter of the alias? Interestingly, on my Windows test machine (Windows 7)
> I don't get these warnings (R-devel from 2018-01-07 r74091).
>
> jo
>
> > On 16 Apr 2018, at 10:49, Mike Smith  wrote:
> >
> > Hi Johannes,
> >
> > xcms is certainly not alone with the warning, and it was discussed in
> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
> >
> > I think you should be able to get round it by including the name of Rd
> file you're linking to e.g.  \code{\link[MSnbase:pickpeaks-method]{pickPeaks}}
> (I haven't actually tested this though).
> >
> > Mike
> >
> > On 16 April 2018 at 09:06, Rainer Johannes 
> wrote:
> > Dear all,
> >
> > we're experiencing WARNINGS in xcms on Tokay2 that are all related to
> links in Rd files to functions and methods in other packages.
> > Example:
> > we have \code{\link[MSnbase]{pickPeaks}} in
> XCMSnExp-inherited-methods.Rd that links to the method in MSnbase, that
> works nicely on Linux and macOS build machines, but on tokay2 we get:
> >
> >   Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.
> INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link
> 'pickPeaks' in package 'MSnbase' does not exist and so has been treated as
> a topic
> >
> > is there any other solution to removing all links to external packages?
> >
> > thanks, jo
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>

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[Bioc-devel] repository change after package acceptance

[Xu Qiao]

Hi everyone,

I am the developer of package "PowerExplorer",  it has been accepted last week, 
and now it is visible on Bioconductor git server. However, the package was 
developed in my own personal GitHub repository, now I need to move it into our 
lab repository. Does anyone have any idea how to do this smoothly? Since the 
Bioconductor is expecting to be associated with my original GitHub-id.

Kind regards,
Xu
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Re: [Bioc-devel] Windows

[Rainer Johannes]

Thanks Mike,

I somehow missed the discussion you mentioned. I would really not like to 
include the name of the Rd file I want to link to. The *default* way that works 
on Linux and macOS should also work on Windows - otherwise what's the matter of 
the alias? Interestingly, on my Windows test machine (Windows 7) I don't get 
these warnings (R-devel from 2018-01-07 r74091).

jo

> On 16 Apr 2018, at 10:49, Mike Smith  wrote:
> 
> Hi Johannes,
> 
> xcms is certainly not alone with the warning, and it was discussed in 
> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
> 
> I think you should be able to get round it by including the name of Rd file 
> you're linking to e.g.  \code{\link[MSnbase:pickpeaks-method]{pickPeaks}} (I 
> haven't actually tested this though).
> 
> Mike
> 
> On 16 April 2018 at 09:06, Rainer Johannes  wrote:
> Dear all,
> 
> we're experiencing WARNINGS in xcms on Tokay2 that are all related to links 
> in Rd files to functions and methods in other packages.
> Example:
> we have \code{\link[MSnbase]{pickPeaks}} in XCMSnExp-inherited-methods.Rd 
> that links to the method in MSnbase, that works nicely on Linux and macOS 
> build machines, but on tokay2 we get:
> 
>   Rd warning: 
> C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59:
>  file link 'pickPeaks' in package 'MSnbase' does not exist and so has been 
> treated as a topic
> 
> is there any other solution to removing all links to external packages?
> 
> thanks, jo
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 

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Re: [Bioc-devel] Windows

[Mike Smith]

Hi Johannes,

xcms is certainly not alone with the warning, and it was discussed in
https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html

I think you should be able to get round it by including the name of Rd file
you're linking to e.g.  \code{\link[MSnbase:pickpeaks-method]{pickPeaks}}
(I haven't actually tested this though).

Mike

On 16 April 2018 at 09:06, Rainer Johannes 
wrote:

> Dear all,
>
> we're experiencing WARNINGS in xcms on Tokay2 that are all related to
> links in Rd files to functions and methods in other packages.
> Example:
> we have \code{\link[MSnbase]{pickPeaks}} in XCMSnExp-inherited-methods.Rd
> that links to the method in MSnbase, that works nicely on Linux and macOS
> build machines, but on tokay2 we get:
>
>   Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.
> INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link
> 'pickPeaks' in package 'MSnbase' does not exist and so has been treated as
> a topic
>
> is there any other solution to removing all links to external packages?
>
> thanks, jo
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] Need some help to submit a R package.

[Pijush Das]

Dear  Ruqian,


Yes sir, I have opened the build report which is a link to an HTML page
with details.
But I unable to understand why the WARNING massages are showing.

Three days before the other reviewers had made some comments and asked me
to address
those issues and also told me to solve the NOTEs produced by BioCheck.

Presently I am working on the sigFeature package to address those issues.
I shall communicate soon after solving those issues.


Thank you


Regards
Pijush



On Mon, Apr 16, 2018 at 4:06 AM, Ruqian Lyu 
wrote:

> Hi Pijush,
>
> Did you open the build report which is a link to an HTML page with details
> of the warning?
>
>
> Regards,
> Ruqian
>
>
>
> On Fri, Apr 13, 2018 at 4:54 PM, Pijush Das  wrote:
>
>> Dear Sir,
>>
>>
>> I have submitted an R package named "sigFeature" in Github and also
>> Bioconductor 9 days before.
>> The reviewers only said that there is some WARNING problem in the package
>> in different platform.
>>
>> But after that they are not communicating any thing regarding the package.
>> I have checked the package
>> windows and Ubuntu it is working fine.
>>
>> I unable to understand what actually the problem is ?
>> And the reviewers are not communicating about the problem. Though I am
>> getting lots of email from bioc-devel dealing with others package
>> problem .
>>
>> Please suggest me what should I do now ?
>>
>>
>>
>>
>> Thank you
>>
>>
>>
>> Regards
>> Pijush
>>
>>
>>
>>
>> On Mon, Apr 2, 2018 at 4:26 PM, Turaga, Nitesh <
>> nitesh.tur...@roswellpark.org> wrote:
>>
>> > Hi,
>> >
>> > Please read through this documentation.
>> >
>> > http://bioconductor.org/developers/package-submission/
>> >
>> >
>> > Nitesh
>> >
>> > > On Apr 2, 2018, at 2:00 AM, Pijush Das  wrote:
>> > >
>> > > Dear Sir,
>> > >
>> > >
>> > >
>> > > I have developed an R package. I want to submit this package in
>> > > Bioconductor.
>> > > Please help me to submit the R package.
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > > regards
>> > > Pijush Das
>> > >
>> > >   [[alternative HTML version deleted]]
>> > >
>> > > ___
>> > > Bioc-devel@r-project.org mailing list
>> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>> >
>> >
>> > This email message may contain legally privileged and/or confidential
>> > information.  If you are not the intended recipient(s), or the employee
>> or
>> > agent responsible for the delivery of this message to the intended
>> > recipient(s), you are hereby notified that any disclosure, copying,
>> > 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]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>

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[Bioc-devel] Windows

[Rainer Johannes]

Dear all,

we're experiencing WARNINGS in xcms on Tokay2 that are all related to links in 
Rd files to functions and methods in other packages.
Example:
we have \code{\link[MSnbase]{pickPeaks}} in XCMSnExp-inherited-methods.Rd that 
links to the method in MSnbase, that works nicely on Linux and macOS build 
machines, but on tokay2 we get:

  Rd warning: 
C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59:
 file link 'pickPeaks' in package 'MSnbase' does not exist and so has been 
treated as a topic

is there any other solution to removing all links to external packages?

thanks, jo

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Re: [Rd] packageDate() segfaults, if used without argument

[Martin Maechler]

> Rainer Hurling 
> on Sun, 15 Apr 2018 11:01:59 +0200 writes:

> Out of curiosity, I played a bit with the new function
> packageDate() from April, 4th. All works fine, except
> using it without any argument.  In this case, it
> segfaults:

Thank you, Rainer, for the report -- about the *development* version of R

Note that the segfault would not have happened in  'R 3.5.0 beta'
(today turning to be 'R 3.5.0 RC'  : RC := Release Candidate )
which we'd be very happy if you used extensively.

> #> packageDate() Error in packageDescription(pkg, lib.loc
> = lib.loc, fields = date.fields) : argument "pkg" is
> missing, with no default

>  *** caught segfault *** address 0x77bc3c0, cause 'memory
> not mapped' Segmentation fault (core dumped)

> My system is FreeBSD 12.0-CURRENT amd64 with R-devel
> (r74601).

It was a lapsus -- of mine -- not at all related to packageDate(),
corrected yesterday (svn r 74604).

Martin

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