[Bioc-devel] import except on Window Machine

Michael Lawrence lawrence.michael at gene.com
Mon Apr 11 22:23:39 CEST 2016 

Yes, you're right, sorry. I didn't realize that the generic is always
exported from a package defining methods on the generic. That can make
the exceptions more difficult to maintain. A better syntax for this
case might have been:

import(cranPackage, override=values)

But we have to live with except= for now.

Michael

On Mon, Apr 11, 2016 at 12:25 PM, Zhu, Lihua (Julie)
<Julie.Zhu at umassmed.edu> wrote:
> Thanks Michael!
>
> FYI, I would get a warning message if I did not use import(IRanges,
> except=values).
>
> Best,
>
> Julie
>
> On 4/11/16 2:40 PM, "Michael Lawrence" <lawrence.michael at gene.com> wrote:
>
>>On Mon, Apr 11, 2016 at 10:28 AM, Dan Tenenbaum <dtenenba at fredhutch.org>
>>wrote:
>>> In that output you sent me, it's still using roxygen (via devtools) to
>>>create the namespace. Try creating it manually and see if you still get
>>>the same error.
>>>
>>> What does your NAMESPACE look like anyway?
>>>
>>> Looking at the NAMESPACE for CRISPRseek, the instances of the 'except'
>>>syntax look like this:
>>>
>>> import(S4Vectors, except=c(fold, values))
>>> import(IRanges, except=values)
>>
>>Unrelated note: should be no need to exclude values from IRanges. It
>>is S4Vectors that exports the generic.
>>
>>>
>>> So maybe make sure the objects to be excepted are not quoted?
>>>
>>> Dan
>>>
>>>
>>>
>>> ----- Original Message -----
>>>> From: "Karim Mezhoud" <kmezhoud at gmail.com>
>>>> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
>>>> Cc: "Lihua Zhu" <Julie.Zhu at umassmed.edu>, "Michael Lawrence"
>>>><lawrence.michael at gene.com>, "bioc-devel"
>>>> <bioc-devel at r-project.org>
>>>> Sent: Monday, April 11, 2016 10:21:42 AM
>>>> Subject: Re: [Bioc-devel] import except on Window Machine
>>>
>>>> ##### ##    BUILT &   RELOAD
>>>> ==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer
>>>>
>>>> * installing to library
>>>> Œ/Library/Frameworks/R.framework/Versions/3.3/Resources/library¹
>>>> ERROR: failed to lock directory
>>>> Œ/Library/Frameworks/R.framework/Versions/3.3/Resources/library¹ for
>>>> modifying
>>>> Try removing
>>>>
>>>>Œ/Library/Frameworks/R.framework/Versions/3.3/Resources/library/00LOCK-b
>>>>ioCancer¹
>>>>
>>>> Exited with status 3.
>>>>
>>>> ######## BUILT SOURCE PACKAGE
>>>> ==> devtools::document(roclets=c('rd', 'collate', 'namespace'))
>>>>
>>>> Updating bioCancer documentation
>>>> Loading bioCancer
>>>> Documentation completed
>>>>
>>>> ==> devtools::build()
>>>>
>>>> '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file
>>>> --no-environ  \
>>>>  --no-save --no-restore CMD build '/Volumes/DATA/radiant/bioCancer'  \
>>>>  --no-resave-data --no-manual
>>>>
>>>> * checking for file Œ/Volumes/DATA/radiant/bioCancer/DESCRIPTION¹ ...
>>>>OK
>>>> * preparing ŒbioCancer¹:
>>>> * checking DESCRIPTION meta-information ... OK
>>>> * checking for LF line-endings in source and make files
>>>> * checking for empty or unneeded directories
>>>> * building ŒbioCancer_0.99.0.tar.gz¹
>>>>
>>>> [1] "/Volumes/DATA/radiant/bioCancer_0.99.0.tar.gz"
>>>>
>>>> Source package written to /Volumes/DATA/radiant
>>>>
>>>> On Mon, Apr 11, 2016 at 6:10 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
>>>> wrote:
>>>>
>>>>> roxygen2 does not support the new syntax. Do you still get the same
>>>>>error
>>>>> if you write your NAMESPACE manually?
>>>>>
>>>>> ----- Original Message -----
>>>>> > From: "Karim Mezhoud" <kmezhoud at gmail.com>
>>>>> > To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
>>>>> > Cc: "Lihua Zhu" <Julie.Zhu at umassmed.edu>, "Michael Lawrence" <
>>>>> lawrence.michael at gene.com>, "bioc-devel"
>>>>> > <bioc-devel at r-project.org>
>>>>> > Sent: Monday, April 11, 2016 10:08:15 AM
>>>>> > Subject: Re: [Bioc-devel] import except on Window Machine
>>>>>
>>>>> >> sessionInfo()
>>>>> > R version 3.3.0 beta (2016-04-06 r70435)
>>>>> > Platform: x86_64-apple-darwin13.4.0 (64-bit)
>>>>> > Running under: OS X 10.11.3 (El Capitan)
>>>>> >
>>>>> > locale:
>>>>> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>>> >
>>>>> >
>>>>> > On Mon, Apr 11, 2016 at 6:07 PM, Dan Tenenbaum
>>>>><dtenenba at fredhutch.org>
>>>>> > wrote:
>>>>> >
>>>>> >> Karim, What is the sessionInfo() in your R-3.3? It might be too
>>>>>old to
>>>>> >> have the new feature. It needs to be at svn rev r70426 or newer.
>>>>> >>
>>>>> >> Dan
>>>>> >>
>>>>> >>
>>>>> >> ----- Original Message -----
>>>>> >> > From: "Karim Mezhoud" <kmezhoud at gmail.com>
>>>>> >> > To: "Lihua Zhu" <Julie.Zhu at umassmed.edu>
>>>>> >> > Cc: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "Michael Lawrence"
>>>>><
>>>>> >> lawrence.michael at gene.com>, "bioc-devel"
>>>>> >> > <bioc-devel at r-project.org>
>>>>> >> > Sent: Monday, April 11, 2016 10:03:52 AM
>>>>> >> > Subject: Re: [Bioc-devel] import except on Window Machine
>>>>> >>
>>>>> >> > Dear Julie,
>>>>> >> > Are you using roxigen2 to edit NAMESPACE file?
>>>>> >> > Are you using R 3.4?
>>>>> >> > Thanks
>>>>> >> >
>>>>> >> > In my case, When I used R 3.3 I get this error:
>>>>> >> >
>>>>> >> >
>>>>> >> > ==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer
>>>>> >> >
>>>>> >> > * installing to library
>>>>> >> > Œ/Library/Frameworks/R.framework/Versions/3.3/Resources/library¹
>>>>> >> > * installing *source* package ŒbioCancer¹ ...
>>>>> >> > ** R
>>>>> >> > ** inst
>>>>> >> > ** preparing package for lazy loading
>>>>> >> > Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck =
>>>>> >> vI[[i]])
>>>>> >> > :
>>>>> >> >  there is no package called Œc("dataTableOutput",
>>>>>"renderDataTable")¹
>>>>> >> > ERROR: lazy loading failed for package ŒbioCancer¹
>>>>> >> > * removing
>>>>> >> >
>>>>> >>
>>>>>
>>>>>Œ/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCanc
>>>>>er¹
>>>>> >> > * restoring previous
>>>>> >> >
>>>>> >>
>>>>>
>>>>>Œ/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCanc
>>>>>er¹
>>>>> >> >
>>>>> >> > Exited with status 1
>>>>> >> >
>>>>> >> > When I used R 3.4, I get :
>>>>> >> >
>>>>> >> > unfortunately,
>>>>> >> >
>>>>> >> > Bioconductor version 3.3 (BiocInstaller 1.21.4), ?biocLite for
>>>>>help
>>>>> >> > Bioconductor does not yet support R version 3.4.0
>>>>> >> >
>>>>> >> >
>>>>> >> >
>>>>> >> > On Mon, Apr 11, 2016 at 5:30 PM, Zhu, Lihua (Julie) <
>>>>> >> Julie.Zhu at umassmed.edu>
>>>>> >> > wrote:
>>>>> >> >
>>>>> >> >> Thanks, Dan!
>>>>> >> >>
>>>>> >> >> Best,
>>>>> >> >>
>>>>> >> >> Julie
>>>>> >> >>
>>>>> >> >> On 4/11/16 12:22 PM, "Dan Tenenbaum" <dtenenba at fredhutch.org>
>>>>>wrote:
>>>>> >> >>
>>>>> >> >> >The windows machine is still running an older version of R
>>>>>that does
>>>>> >> not
>>>>> >> >> >support this NAMESPACE syntax. I will update it this week.
>>>>> >> >> >Dan
>>>>> >> >> >
>>>>> >> >> >
>>>>> >> >> >----- Original Message -----
>>>>> >> >> >> From: "Lihua Zhu" <Julie.Zhu at umassmed.edu>
>>>>> >> >> >> To: "bioc-devel" <bioc-devel at r-project.org>
>>>>> >> >> >> Cc: "Michael Lawrence" <lawrence.michael at gene.com>
>>>>> >> >> >> Sent: Monday, April 11, 2016 9:18:31 AM
>>>>> >> >> >> Subject: [Bioc-devel] import except on Window Machine
>>>>> >> >> >
>>>>> >> >> >> Michael,
>>>>> >> >> >>
>>>>> >> >> >> For some reason,  adding except clause in import in the
>>>>>NAMESPACE
>>>>> >> file
>>>>> >> >> >>gives
>>>>> >> >> >> error on window server, although it runs fine on Linux and
>>>>>Mac OS
>>>>> X.
>>>>> >> >> >>
>>>>> >> >> >>
>>>>> >> >>
>>>>> >>
>>>>>
>>>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_ch
>>>>>ec
>>>>> >> >>
>>>>> >>
>>>>>
>>>>>>>kResults_devel_bioc-2DLATEST_CRISPRseek_moscato2-2Dbuildsrc.html&d=BQ
>>>>>>>ICaQ
>>>>> >> >>
>>>>> >>
>>>>>
>>>>>>>&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2b
>>>>>>>gmPH
>>>>> >> >>
>>>>> >>
>>>>>
>>>>>>>hwHHF5gJMlij5cC5bLU&m=t9rR8WHE_O0PrI0B-0ySt37UGJMdDhnwk0JFoVzS5Cw&s=l
>>>>>>>EJWy
>>>>> >> >> >>zN3zY_O2V1X3QmOZcPD25KidcjhIQMAky52xsA&e=
>>>>> >> >> >>
>>>>> >> >> >> Here is the line that gives error.
>>>>> >> >> >> import(S4Vectors, except=c(fold, values))
>>>>> >> >> >>
>>>>> >> >> >> Did I miss something? Thank!
>>>>> >> >> >>
>>>>> >> >> >> Best regards,
>>>>> >> >> >>
>>>>> >> >> >> Julie
>>>>> >> >> >>
>>>>> >> >> >>
>>>>> >> >> >>
>>>>> >> >> >>      [[alternative HTML version deleted]]
>>>>> >> >> >>
>>>>> >> >> >> _______________________________________________
>>>>> >> >> >> Bioc-devel at r-project.org mailing list
>>>>> >> >> >>
>>>>> >> >> >>
>>>>> >> >>
>>>>> >>
>>>>>
>>>>>https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailm
>>>>>an
>>>>> >> >>
>>>>> >>
>>>>>
>>>>>>>_listinfo_bioc-2Ddevel&d=BQICaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4D
>>>>>>>erPl
>>>>> >> >>
>>>>> >>
>>>>>
>>>>>>>OmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=t9rR8WHE_O0PrI0B
>>>>>>>-0yS
>>>>> >> >>
>>>>> >>
>>>>>
>>>>>>>t37UGJMdDhnwk0JFoVzS5Cw&s=3ZMFBJ4XMwlGXkfXcB5spcBnnzqBDeqk05sf_TSi88g
>>>>>>>&e=
>>>>> >> >>
>>>>> >> >> _______________________________________________
>>>>> >> >> Bioc-devel at r-project.org mailing list
>>>>> >> >>
>>>>>https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailm
>>>>>an_listinfo_bioc-2Ddevel&d=BQIFaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4D
>>>>>erPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=p3WrsvoaEWYRGX
>>>>>1hHvBYdHyfl3qSnDlhimrlUmhWc78&s=3y16NmxUwgAm1KDxESsjtgLdg1qSZ5EWMfbHqPx
>>>>>x7Go&e=
>

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