[Bioc-devel] namespace question

unfortunately,

Bioconductor version 3.3 (BiocInstaller 1.21.4), ?biocLite for help
Bioconductor does not yet support R version 3.4.0

On Tue, Apr 5, 2016 at 9:17 PM, Michael Lawrence <lawrence.michael at gene.com>
wrote:

You need R 3.4 for right now.

On Tue, Apr 5, 2016 at 1:16 PM, Karim Mezhoud <kmezhoud at gmail.com> wrote:

==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer

* installing to library
?/Library/Frameworks/R.framework/Versions/3.3/Resources/library?
* installing *source* package ?bioCancer? ...
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck =

vI[[i]]) :

   there is no package called ?c("dataTableOutput", "renderDataTable")?
ERROR: lazy loading failed for package ?bioCancer?
* removing

?/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCancer?

* restoring previous

?/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCancer?

Exited with status 1

On Tue, Apr 5, 2016 at 8:58 PM, Michael Lawrence <

lawrence.michael at gene.com>

wrote:

Yea, with the closing )

On Tue, Apr 5, 2016 at 12:37 PM, Karim Mezhoud <kmezhoud at gmail.com>

wrote:

If I include manually the exception, I hve to write this?

import(shiny, except=c('dataTableOutput','renderDataTable')
Thanks
Karim

On Tue, Apr 5, 2016 at 7:28 PM, Michael Lawrence
<lawrence.michael at gene.com>
wrote:

Roxygen does not yet support the feature. For now you'll have to live
with the warning or just importFrom(shiny, ...). Maybe there is some
way to manually patch the NAMESPACE with Roxygen?

Honestly, I would recommend against using Roxygen to manage your
NAMESPACE. Just write the thing...



On Tue, Apr 5, 2016 at 11:07 AM, Karim Mezhoud <kmezhoud at gmail.com>
wrote:

Hi,
Actually I have conflict between DT and shiny
  Warning: replacing previous import ?shiny::dataTableOutput? by
?DT::dataTableOutput? when loading ?bioCancer?
   Warning: replacing previous import ?shiny::renderDataTable? by
?DT::renderDataTable? when loading ?bioCancer?

I would like to import shiny except dataTableOutput and
renderDataTable.

#'@import shiny except dataTableOutput renderDataTable
I am using roxygen2
R Under development (unstable) (2016-03-11 r70310)
Which package Can I update to get the new import argument.
Thanks
Karim


On Tue, Apr 5, 2016 at 6:50 PM, Michael Lawrence
<lawrence.michael at gene.com>
wrote:

I will try to sneak that in since it seems to work and it would be
nice to use it before this Fall.

On Tue, Apr 5, 2016 at 10:32 AM, Dan Tenenbaum
<dtenenba at fredhutch.org>
wrote:

Michael, do you know if this change will be (or has already

been)

backported into R-3.3.0?

Thanks.
Dan


----- Original Message -----

From: "Lihua Zhu" <Julie.Zhu at umassmed.edu>
To: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "Michael

Lawrence"

<lawrence.michael at gene.com>
Cc: "bioc-devel" <bioc-devel at r-project.org>
Sent: Tuesday, April 5, 2016 9:49:26 AM
Subject: Re: [Bioc-devel] namespace question

Dan,

That is great! Thanks for letting us know!

Michael, thank for making it happen so quickly! It works like a
charm!

Best,

Julie

On 4/2/16 1:58 PM, "Bioc-devel on behalf of Dan Tenenbaum"
<bioc-devel-bounces at r-project.org on behalf of
dtenenba at fredhutch.org>
wrote:

BTW, looks like the change has been made to R-devel:

#### CHANGES IN R-devel NEW FEATURES

  * The ?import()? namespace directive now accepts an argument
?except?
which names symbols to exclude from the imports. The ?except?
expression
should evaluate to a character vector (after substituting

symbols

for
strings). See Writing R Extensions.

URL:

https://urldefense.proofpoint.com/v2/url?u=http-3A__developer.r-2Dproject.

org_blosxom.cgi_R-2Ddevel_NEWS_2016_04_02-23n2016-2D04-2D02&d=BQIGaQ&c=WJB

j9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5g

JMlij5cC5bLU&m=HCJuUKMo50mOyjfD0AtQzV69c0SnACXTGdX_iHcWRfo&s=MbBj5lNGwkIfP

hrHI2clfQd1aq1yPyROa3utKrCP4ug&e=



----- Original Message -----

From: "Michael Lawrence" <lawrence.michael at gene.com>
To: "Herv? Pag?s" <hpages at fredhutch.org>
Cc: "Michael Lawrence" <lawrence.michael at gene.com>,
"bioc-devel"
<bioc-devel at r-project.org>
Sent: Saturday, April 2, 2016 4:10:10 AM
Subject: Re: [Bioc-devel] namespace question

Also, just btw, there are two other places where arbitrary R
code
can
be evaluated in the NAMESPACE, but no one has abused them

yet.

as
far
as I know. The first argument to if() and the .fixes argument
to
useDynLib(). The latter sets the precedent for the except=
behavior.
Although someone forgot to document it, you can do
.fixes=c("prefix",
"suffix") to both prefix and suffix incoming native symbols.
Currently, the documentation only mentions prefixing. Not

sure

when
suffixing would be desirable.


On Fri, Apr 1, 2016 at 4:14 PM, Herv? Pag?s
<hpages at fredhutch.org>
wrote:

On 04/01/2016 01:39 PM, Michael Lawrence wrote:

Yes, it's arbitrary R code that is evaluated, so paste0()
would
work.
You're right that it's a big door and could let people do
weird
things. Do you foresee a problem with that?

Opening such a big door raises many questions. In addition

to

allowing
people do weird/crazy things (like putting calls to

library()

or requireNamespace() etc... in them), NAMESPACE files with
arbitrary
R code in them become more complicated to maintain and the
tools
for
parsing/processing them also become more complicated to

write

and
maintain.

Now we have a new category of errors that can happen at
package
installation time: errors triggered by the evaluation of

the R

expressions embedded in the NAMESPACE file. Hopefully 'R CMD
INSTALL'
will report something that can be understood by mere mortals
when
this
happens.

Once you create the feeling that a NAMESPACE file is just a
file
that contains arbitrary R code then people expect import(),
export()
etc.. to be ordinary R functions with a man page (being able
to
do
?import would not hurt actually) and they'll naturally try

to

do
things like

   unwanted_foo_symbols <- ... long and complicated

expression

                               eventually calling

user-defined

helper
                               functions located in the
NAMESPACE
file
...
   import(foo, except=unwanted_foo_symbols)

Can't blame them for that. But is this the kind of things

that

we're
ready to see in NAMESPACE files?

Also once you've open that door, people will naturally

wonder

why
they
can use an R expression in the 'except' part of import( ,
except=)
but
not elsewhere e.g. in

   import(foo, only=paste0("bar", 1:10))

as a more elegant way of doing importFrom(foo, bar1, bar2,
...,
bar10).
This dissymmetry between the syntax of "import only this"

and

"import
all except this" feels very arbitrary. If you don't support
the
import( , only=) syntax, people might legitimately ask

things

like

   do.call(importFrom, c(list("foo"), as.list(paste0("bar",
1:10))))

to work. Again, can't blame them for that. But do we want

this

kind
of
things to work? I'm worried debugging NAMESPACE files would
become a
full-time job...

I guess one could have implemented NAMESPACE parsing by
evaluating
the
code in an environment (inheriting from the base namespace)
where
import(), export(), etc, were defined. Maybe there's a good
reason
why
it was not implemented that way.

I'm sure there is ;-)

H.

On Fri, Apr 1, 2016 at 12:55 PM, Herv? Pag?s
<hpages at fredhutch.org>
wrote:

On 03/31/2016 04:07 PM, Michael Lawrence wrote:

I agree. The importExcept idea also works that way:
importExcept(foo,
bar,
baz)

But import(foo, except=c(bar, baz)) reads better.

mmh... so R expressions with calls to base functions like
base::c()
are
making their way in the NAMESPACE file. That's opening a

big

door.
Does
that mean that we'll be able to do things like:

import(foo, except=paste0("bar", 1:10))

Or maybe c(bar, baz) in your above example is just an
arbitrary
syntax
that just happens to look like an R expression but won't

be

evaluated
as such?


H.

On Thu, Mar 31, 2016 at 4:00 PM,  <

luke-tierney at uiowa.edu>

wrote:

I don't think you want to separate it from the import.
Better
to
allow
something like

import(foo, exclude=bar)

or

import(foo, exclude=c("bar", "baz"))

This seems reasonably natural and shouldn't be too hard

to

implement. (But is has been a while since I've worked on
this
code).

Best,

luke


On Thu, 31 Mar 2016, Karim Mezhoud wrote:

I think "From" is needed to specify which package we

want

to
exlude
functions.

I think  excludeFrom (package, function)  seems to be
intuitive.

thanks,
Karim



On Thu, Mar 31, 2016 at 9:54 PM, Herv? Pag?s
<hpages at fredhutch.org>
wrote:

On 03/31/2016 12:55 PM, Michael Lawrence wrote:

Probably should just stick to exact symbols for now.

If

there
is a
case where a pattern is actually useful, rather than
just
an
obfuscation, we can extend the feature set.

Fair enough. Not really intuitive that excludeImport
uses
the
same
syntax as (but does the opposite of) importFrom

though.

Maybe
having
the name of the directive start with "import" would

help

e.g.

importExcept(hash, values)  # opposite of
importFrom(hash,
values)

Thanks,
H.

On Thu, Mar 31, 2016 at 12:11 PM, Zhu, Lihua (Julie)
<Julie.Zhu at umassmed.edu> wrote:

Herve,

That is a very interesting idea and works for me!
Thanks!

importPatternFrom(IRanges, "^values$")


Best,

Julie

On 3/31/16 2:51 PM, "Bioc-devel on behalf of Herv?
Pag?s"
<bioc-devel-bounces at r-project.org on behalf of
hpages at fredhutch.org>
wrote:

On 03/30/2016 08:35 PM, Michael Lawrence wrote:

That would work, but R is not going to be happy
about
redundant
imports. Interactively, users would balk at symbol
qualification.

There are two classes of conflict:
1) Same semantics, where a common generic would
arbitrate,
or one
package could depend on the other, and
2) Different semantics, in which case one of the
functions
should
probably be renamed, although that might not be
practical
or
easy
to
agree upon.

When those approaches fail, qualification is the
only
recourse.

I will think about adding an excludeImport() or
importAs().

What about having something like an
importPatternFrom()
directive
similar to the exportPattern() directive and have
these
directives
support some of the grep() toggles like
'ignore.case',
'fixed',
'invert' etc... ?

Then Julie could just do:

importPatternFrom(hash, "^values$", invert=TRUE)

H.

On Wed, Mar 30, 2016 at 8:20 PM, Robert M. Flight
<rflight79 at gmail.com

wrote:

In the cases of having conflicting names, is it

not

appropriate
then
to use
the "package::function" form for calling a
particular
function?

On Wed, Mar 30, 2016 at 11:14 PM Michael Lawrence
<lawrence.michael at gene.com>
wrote:

I can't find the hash function in IRanges. Are

you

sure
it
has
one?

On Wed, Mar 30, 2016 at 8:07 PM, Zhu, Lihua
(Julie)
<Julie.Zhu at umassmed.edu> wrote:

Michael,

I have the same user case as Kasper. Another
example
is
that
both
IRanges
and hash packages have hash. I need to use the
hash
from
the
hash
package
instead of the one from IRanges.

Best,

Julie

On Mar 30, 2016, at 7:57 PM, Kasper Daniel

Hansen

<kasperdanielhansen at gmail.com> wrote:

My usecase is when I import() two packages who
has a
conflict
in
a
name.
For example, both Biobase and matrixStats has
both
anyMissing
and
rowMedians. I am happy to get all of these two
packages,
but I
need
to
resolve the conflict.  Since I want to keep the
ones
from
matrixStats I

know

need to figure out how to import Biobase
selectively.
Which I
can,
using
the tools from codetoolsBioC, but I would also

be

happy
with
an
importFromExcept(), which would make my life

much

easier.

Best,
Kasper

On Wed, Mar 30, 2016 at 4:47 PM, Michael

Lawrence

<lawrence.michael at gene.com> wrote:

I'm curious about which symbols you wouldn't
want
to
import,
and
why.

On Wed, Mar 30, 2016 at 12:19 PM, Zhu, Lihua
(Julie)
<Julie.Zhu at umassmed.edu> wrote:

Hi,

Is there a function to import all the

exported

objects
from
a
package
except a few named ones in NAMESPACE file?

For example, I would like to import all the
functions
in
S4Vectors
except fold. Is there a way to  specify this
without
listing
all
other
functions using importFrom?

Many thanks for your help!

Best regards,

Julie

********************************************
Lihua Julie Zhu, Ph.D
Research Professor
Department of Molecular, Cell and Cancer
Biology
(MCCB)
Head of MCCB Bioinformatics Core
Program in Molecular Medicine
Program in Bioinformatics and Integrative
Biology
University of Massachusetts Medical School
364 Plantation Street, Room 613
Worcester, MA 01605
508-856-5256 phone
(508) 856 5460 fax

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