date:20160311

Re: [Bioc-devel] Odd behavior by R CMD check

2016-03-11 Thread Henrik Bengtsson

If you have R-devel you can get those NOTEs using:

R CMD check --as-cran *.tar.gz

(It's been reported by --as-cran since Oct 2015 or so).

/Henrik

On Fri, Mar 11, 2016 at 2:45 PM, Hartley, Stephen (NIH/NHGRI) [F]
 wrote:
> Thanks.  I'll try that. I'm surprised, as my local R-Devel install isn't that 
> old.
>
> I used to have a few specific imports like this, but I was told to remove 
> them because BiocCheck did not like them (because these packages were not 
> declared in the "imports" line of the DESCRIPTION). I don't know if the 
> newest version of BiocCheck still complains about them now.
>
> -Steve
>
> -Original Message-
> From: Martin Morgan [mailto:martin.mor...@roswellpark.org]
> Sent: Friday, March 11, 2016 2:24 PM
> To: Hartley, Stephen (NIH/NHGRI) [F]; bioc-devel
> Subject: Re: [Bioc-devel] Odd behavior by R CMD check
>
>
>
> On 03/11/2016 02:17 PM, Hartley, Stephen (NIH/NHGRI) [F] wrote:
>> I'm seeing some odd behavior by the R CMD check command for my package, 
>> JunctionSeq.
>>
>> http://bioconductor.org/checkResults/3.3/bioc-LATEST/JunctionSeq/zin2-
>> checksrc.html
>>
>> It's not technically throwing warnings (just a "NOTE"), but it is claiming 
>> that there's no global definition for functions belonging to the default R 
>> packages (grDevices, utils, stats, and graphics).
>>
>> So I get lines like this:
>> drawGene: no visible global function definition for 'plot.new'
>>
>> drawGene: no visible global function definition for 'plot.window'
>>
>> drawGene: no visible global function definition for 'par'
>>
>> drawGene: no visible global function definition for 'strwidth'
>>
>> drawGene: no visible global function definition for 'lines'
>>
>> drawGene: no visible global function definition for 'rect'
>>
>> drawGene: no visible global function definition for 'segments'
>>
>> drawGene: no visible global function definition for 'strheight'
>>
>> Since it's still able to compile the vignette and everything it's clearly 
>> not actually having a problem finding these functions at runtime, but I 
>> can't figure out what would cause it to throw these notes. I don't get these 
>> notes when I run R CMD check locally on any of my test machines (windows, 
>> CentOS5 linux and scientific linux 6). And I've had it build with no issues 
>> before. I can't see how my recent changes could possibly have caused this ...
>>
>> Has anyone ever seen this before?
>
> This is the behavior with a recent version of R-devel; likely you are using 
> an older version or R-3.2.*. Things 'work' because the relevant packages are 
> on the search path, but would fail if for instance the user or another 
> package were to define a 'strheight' function that did something different 
> from graphics::strheight.
>
> The solution is to import the relevant functions, as indicated in the build 
> report.
>
>importFrom("grDevices", "cairo_ps", "col2rgb", "colorRamp", "dev.off",
>   "png", "rgb", "svg", "tiff", "x11")
>importFrom("graphics", "abline", "axis", "box", "hist", "layout",
>   "legend", "lines", "par", "plot", "plot.new", "plot.window",
>   "points", "rect", "segments", "smoothScatter", "strheight",
>   "strwidth", "text", "title")
>importFrom("stats", "Gamma", "as.formula", "coef", "coefficients",
>   "deviance", "dnbinom", "fitted.values", "formula", "glm",
>   "loess", "model.matrix", "optimize", "p.adjust", "pchisq",
>   "predict", "qf", "rchisq", "rnorm", "runif", "terms",
>   "weighted.mean")
>importFrom("utils", "object.size", "packageVersion", "read.delim",
>   "read.table", "write.table")
>
> Martin
>
>>
>> Regards,
>> Steve Hartley
>>
>>   [[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.
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] Odd behavior by R CMD check

2016-03-11 Thread Martin Morgan




On 03/11/2016 05:45 PM, Hartley, Stephen (NIH/NHGRI) [F] wrote:

Thanks.  I'll try that. I'm surprised, as my local R-Devel install
isn't that old.

I used to have a few specific imports like this, but I was told to
remove them because BiocCheck did not like them (because these
packages were not declared in the "imports" line of the DESCRIPTION).
I don't know if the newest version of BiocCheck still complains about
them now.


The right solution is to declare them in the Imports: line, too.

Martin



-Steve

-Original Message- From: Martin Morgan
[mailto:martin.mor...@roswellpark.org] Sent: Friday, March 11, 2016
2:24 PM To: Hartley, Stephen (NIH/NHGRI) [F]; bioc-devel Subject: Re:
[Bioc-devel] Odd behavior by R CMD check



On 03/11/2016 02:17 PM, Hartley, Stephen (NIH/NHGRI) [F] wrote:

I'm seeing some odd behavior by the R CMD check command for my
package, JunctionSeq.

http://bioconductor.org/checkResults/3.3/bioc-LATEST/JunctionSeq/zin2-



checksrc.html


It's not technically throwing warnings (just a "NOTE"), but it is
claiming that there's no global definition for functions belonging
to the default R packages (grDevices, utils, stats, and graphics).

So I get lines like this: drawGene: no visible global function
definition for 'plot.new'

drawGene: no visible global function definition for 'plot.window'

drawGene: no visible global function definition for 'par'

drawGene: no visible global function definition for 'strwidth'

drawGene: no visible global function definition for 'lines'

drawGene: no visible global function definition for 'rect'

drawGene: no visible global function definition for 'segments'

drawGene: no visible global function definition for 'strheight'

Since it's still able to compile the vignette and everything it's
clearly not actually having a problem finding these functions at
runtime, but I can't figure out what would cause it to throw these
notes. I don't get these notes when I run R CMD check locally on
any of my test machines (windows, CentOS5 linux and scientific
linux 6). And I've had it build with no issues before. I can't see
how my recent changes could possibly have caused this ...

Has anyone ever seen this before?


This is the behavior with a recent version of R-devel; likely you are
using an older version or R-3.2.*. Things 'work' because the relevant
packages are on the search path, but would fail if for instance the
user or another package were to define a 'strheight' function that
did something different from graphics::strheight.

The solution is to import the relevant functions, as indicated in the
build report.

importFrom("grDevices", "cairo_ps", "col2rgb", "colorRamp",
"dev.off", "png", "rgb", "svg", "tiff", "x11") importFrom("graphics",
"abline", "axis", "box", "hist", "layout", "legend", "lines", "par",
"plot", "plot.new", "plot.window", "points", "rect", "segments",
"smoothScatter", "strheight", "strwidth", "text", "title")
importFrom("stats", "Gamma", "as.formula", "coef", "coefficients",
"deviance", "dnbinom", "fitted.values", "formula", "glm", "loess",
"model.matrix", "optimize", "p.adjust", "pchisq", "predict", "qf",
"rchisq", "rnorm", "runif", "terms", "weighted.mean")
importFrom("utils", "object.size", "packageVersion", "read.delim",
"read.table", "write.table")

Martin



Regards, Steve Hartley

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Odd behavior by R CMD check

2016-03-11 Thread Hartley, Stephen (NIH/NHGRI) [F]

Thanks.  I'll try that. I'm surprised, as my local R-Devel install isn't that 
old.

I used to have a few specific imports like this, but I was told to remove them 
because BiocCheck did not like them (because these packages were not declared 
in the "imports" line of the DESCRIPTION). I don't know if the newest version 
of BiocCheck still complains about them now.

-Steve

-Original Message-
From: Martin Morgan [mailto:martin.mor...@roswellpark.org] 
Sent: Friday, March 11, 2016 2:24 PM
To: Hartley, Stephen (NIH/NHGRI) [F]; bioc-devel
Subject: Re: [Bioc-devel] Odd behavior by R CMD check

On 03/11/2016 02:17 PM, Hartley, Stephen (NIH/NHGRI) [F] wrote:
> I'm seeing some odd behavior by the R CMD check command for my package, 
> JunctionSeq.
>
> http://bioconductor.org/checkResults/3.3/bioc-LATEST/JunctionSeq/zin2-
> checksrc.html
>
> It's not technically throwing warnings (just a "NOTE"), but it is claiming 
> that there's no global definition for functions belonging to the default R 
> packages (grDevices, utils, stats, and graphics).
>
> So I get lines like this:
> drawGene: no visible global function definition for 'plot.new'
>
> drawGene: no visible global function definition for 'plot.window'
>
> drawGene: no visible global function definition for 'par'
>
> drawGene: no visible global function definition for 'strwidth'
>
> drawGene: no visible global function definition for 'lines'
>
> drawGene: no visible global function definition for 'rect'
>
> drawGene: no visible global function definition for 'segments'
>
> drawGene: no visible global function definition for 'strheight'
>
> Since it's still able to compile the vignette and everything it's clearly not 
> actually having a problem finding these functions at runtime, but I can't 
> figure out what would cause it to throw these notes. I don't get these notes 
> when I run R CMD check locally on any of my test machines (windows, CentOS5 
> linux and scientific linux 6). And I've had it build with no issues before. I 
> can't see how my recent changes could possibly have caused this ...
>
> Has anyone ever seen this before?

This is the behavior with a recent version of R-devel; likely you are using an 
older version or R-3.2.*. Things 'work' because the relevant packages are on 
the search path, but would fail if for instance the user or another package 
were to define a 'strheight' function that did something different from 
graphics::strheight.

The solution is to import the relevant functions, as indicated in the build 
report.

   importFrom("grDevices", "cairo_ps", "col2rgb", "colorRamp", "dev.off",
  "png", "rgb", "svg", "tiff", "x11")
   importFrom("graphics", "abline", "axis", "box", "hist", "layout",
  "legend", "lines", "par", "plot", "plot.new", "plot.window",
  "points", "rect", "segments", "smoothScatter", "strheight",
  "strwidth", "text", "title")
   importFrom("stats", "Gamma", "as.formula", "coef", "coefficients",
  "deviance", "dnbinom", "fitted.values", "formula", "glm",
  "loess", "model.matrix", "optimize", "p.adjust", "pchisq",
  "predict", "qf", "rchisq", "rnorm", "runif", "terms",
  "weighted.mean")
   importFrom("utils", "object.size", "packageVersion", "read.delim",
  "read.table", "write.table")

Martin

>
> Regards,
> Steve Hartley
>
>   [[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.

___
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[Bioc-devel] Odd behavior by R CMD check

2016-03-11 Thread Hartley, Stephen (NIH/NHGRI) [F]

I'm seeing some odd behavior by the R CMD check command for my package, 
JunctionSeq.

http://bioconductor.org/checkResults/3.3/bioc-LATEST/JunctionSeq/zin2-checksrc.html

It's not technically throwing warnings (just a "NOTE"), but it is claiming that 
there's no global definition for functions belonging to the default R packages 
(grDevices, utils, stats, and graphics).

So I get lines like this:
drawGene: no visible global function definition for 'plot.new'

drawGene: no visible global function definition for 'plot.window'

drawGene: no visible global function definition for 'par'

drawGene: no visible global function definition for 'strwidth'

drawGene: no visible global function definition for 'lines'

drawGene: no visible global function definition for 'rect'

drawGene: no visible global function definition for 'segments'

drawGene: no visible global function definition for 'strheight'

Since it's still able to compile the vignette and everything it's clearly not 
actually having a problem finding these functions at runtime, but I can't 
figure out what would cause it to throw these notes. I don't get these notes 
when I run R CMD check locally on any of my test machines (windows, CentOS5 
linux and scientific linux 6). And I've had it build with no issues before. I 
can't see how my recent changes could possibly have caused this ...

Has anyone ever seen this before?

Regards,
Steve Hartley

[[alternative HTML version deleted]]

___
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Re: [Bioc-devel] Your branch and 'bioc/master' have diverged

2016-03-11 Thread Luca De Sano

But, after the what you suggest, git and svn be will synchronized?


--
Luca De Sano
Research Associate

Department of Informatics, Systems and Communication
University of Milan Bicocca

Institute of Biomembranes and Bioenergetics of the Italian National
Research Council (IBBE-CNR)

email: l.des...@campus.unimib.it
PEC: luca.des...@pec.it

On 10 March 2016 at 19:47, Dan Tenenbaum  wrote:

>
>
> - Original Message -
> > From: "Luca De Sano" 
> > To: "Dan Tenenbaum" 
> > Cc: "bioc-devel" 
> > Sent: Thursday, March 10, 2016 10:21:38 AM
> > Subject: Re: [Bioc-devel] Your branch and 'bioc/master' have diverged
>
> > On 10 March 2016 at 18:17, Dan Tenenbaum  wrote:
> >
> >>
> >>
> >> - Original Message -
> >> > From: "Luca De Sano" 
> >> > To: "bioc-devel" 
> >> > Sent: Thursday, March 10, 2016 3:22:14 AM
> >> > Subject: [Bioc-devel] Your branch and 'bioc/master' have diverged
> >>
> >> > Hi all,
> >> > I'm trying to update the devel branch of my package following the
> >> > instruction found in
> >> https://bioconductor.org/developers/how-to/git-mirrors/
> >> > .
> >> >
> >> > The repo of my project is: https://github.com/BIMIB-DISCo/TRONCO
> >> >
> >> >>From devel I've first tried to do a git merge master, with no results.
> >> I've
> >> > then tried the cherry-pick method and all seemed to work well.
> However,
> >> > during the git-svn dcommit, I've obtained a:
> >> >
> >> > svn: Commit blocked by pre-commit hook (exit code 1) with output:
> >> > The y in the x.y.z version number should be even in release
> >> > in file branches/RELEASE_3_2/madman/Rpacks/VegaMC/DESCRIPTION.
> >> > See http://bioconductor.org/developers/how-to/version-numbering/
> >> >
> >>
> >>
> >> Did you really get this commit error message about trying to commit to
> the
> >> devel branch of TRONCO? The message refers to the _release_ branch of
> >> _VegaMC_. If you did get that error message in response to a commit of
> >> TRONCO, then something is very wrong with that pre-commit hook.
> >>
> >
> > No. Sorry was just a cut error, I was searching the mailing list
> for
> > similar errors ... The message was like:
> >
> > svn: Commit blocked by pre-commit hook (exit code 1) with output:
> > The y in the x.y.z version number should be even in release
> > in file [some path which I don't remember at the
> > moment]/madman/Rpacks/TRONCO/DESCRIPTION.
> > See http://bioconductor.org/developers/how-to/version-numbering/
> >
> >
> >
> >>
> >>
> >>
> >> > There has been a problem with a commit (a wrong version update which
> was
> >> > rejected from svn).
> >> >
> >> > I've fixed this problem on my master removing the wrong commit as
> >> described
> >> > here http://www.clock.co.uk/blog/deleting-a-git-commit . I've then
> >> tried to
> >> > bring those changes on devel doing this:
> >> >
> >>
> >> Which commit was 'wrong'?
> >>
> >
> > The problem was a wrong version update in a commit made one month ago.
> This
> > commit triggered the pre-commit hook and, even If I've fixed it with a
> new
> > commit, the problem has remained. So, following the instructions
> mentioned
> > above, I've removed the commit from the history tree.
> >
> >
> >
> >>
> >>
> >> >   - git reset --hard on devel to the last right commit
> >> >   - git cherry-pick on the others commit from my master branch
> >> >
> >> > After the cherry-pick, on git, all worked well. The resul of git log
> is:
> >> >
> >> > dex@darthvader ~/project/TRONCO $ git log --graph --decorate
> >> > --pretty=oneline --abbrev-commit --all
> >> > *   2e27604 (HEAD, origin/master, origin/development, origin/HEAD,
> >> master,
> >> > development, devel) Merge pull request #47 from
> BIMIB-DISCo/development
> >> >|\
> >> >| * 340c809 date update
> >> >|/
> >> > * 4700191 dependencies update
> >> > * 31c2cab regex problems
> >> > [...]
> >> >
> >> > I've then tried to commit to svn, but the git svn dcommit
> >> --add-author-from
> >> > now isn't workig...
> >> >
> >> > dex@darthvader ~/project/TRONCO $ git svn dcommit --add-author-from
> >> > Unable to determine upstream SVN information from HEAD history.
> >> > Perhaps the repository is empty. at /usr/lib/git-core/git-svn line
> 856.
> >> >
> >> > And the result of a git status is:
> >> >
> >> > dex@darthvader ~/project/TRONCO $ git status
> >> > On branch devel
> >> > Your branch and 'bioc/master' have diverged,
> >> > and have 615 and 25 different commits each, respectively.
> >> >  (use "git pull" to merge the remote branch into yours)
> >> >
> >> > nothing to commit, working directory clean
> >> >
> >> >
> >> > The situation at the moment is:
> >> >
> >> >
> >> >   -
> >> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TRONCO/R/
> >> >   is a mix of old and new version... I don't know why. Some files are
> up
> >> to
> >> >   date with my master

Re: [Bioc-devel] Odd behavior by R CMD check

Re: [Bioc-devel] Odd behavior by R CMD check

Re: [Bioc-devel] Odd behavior by R CMD check

[Bioc-devel] Odd behavior by R CMD check

Re: [Bioc-devel] Your branch and 'bioc/master' have diverged

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