[Bioc-devel] import except on Window Machine

Zhu, Lihua (Julie) Julie.Zhu at umassmed.edu
Mon Apr 11 22:36:49 CEST 2016 

Michael,

Thanks for confirming!

Best,

Julie

On 4/11/16 4:23 PM, "Michael Lawrence" <lawrence.michael at gene.com> wrote:

>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/bioCa
>>>>>>nc
>>>>>>er¹
>>>>>> >> > * restoring previous
>>>>>> >> >
>>>>>> >>
>>>>>>
>>>>>>Œ/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCa
>>>>>>nc
>>>>>>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-yoIQpGZOKgd4i
>>>>>>>>2b
>>>>>>>>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_mai
>>>>>>lm
>>>>>>an
>>>>>> >> >>
>>>>>> >>
>>>>>>
>>>>>>>>_listinfo_bioc-2Ddevel&d=BQICaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w
>>>>>>>>4D
>>>>>>>>erPl
>>>>>> >> >>
>>>>>> >>
>>>>>>
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>>>>>> >> >>
>>>>>> >>
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>>>>>> >> >>
>>>>>> >> >> _______________________________________________
>>>>>> >> >> Bioc-devel at r-project.org mailing list
>>>>>> >> >>
>>>>>>https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mai
>>>>>>lm
>>>>>>an_listinfo_bioc-2Ddevel&d=BQIFaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w
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