Re: [Bioc-devel] Odd behavior by R CMD check
- Original Message -
> From: "Hartley, Stephen (NIH/NHGRI) [F]" <stephen.hart...@nih.gov>
> To: "Henrik Bengtsson" <henrik.bengts...@gmail.com>
> Cc: "bioc-devel" <bioc-devel@r-project.org>
> Sent: Monday, March 14, 2016 6:58:04 AM
> Subject: Re: [Bioc-devel] Odd behavior by R CMD check
> Why didn't this show up before in the SPB reports until recently? Is
> "--as-cran"
> a new addition to the SPB?
>
No. SPB does not use "--as-cran". As was pointed out earlier in this thread,
R-devel is now emitting this information by default (i.e. with or without the
--as-cran flag).
Dan
> -Original Message-
> From: Henrik Bengtsson [mailto:henrik.bengts...@gmail.com]
> Sent: Friday, March 11, 2016 6:06 PM
> To: Hartley, Stephen (NIH/NHGRI) [F]
> Cc: Martin Morgan; bioc-devel
> Subject: Re: [Bioc-devel] Odd behavior by R CMD check
>
> 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]
> <stephen.hart...@nih.gov> 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&qu
Re: [Bioc-devel] Odd behavior by R CMD check
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]
<stephen.hart...@nih.gov> 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
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
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
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]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
