[Bioc-devel] import except on Window Machine

[Dan Tenenbaum]

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
>> > ‘/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
>> >
>> > 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_chec
>> >>
>> >>kResults_devel_bioc-2DLATEST_CRISPRseek_moscato2-2Dbuildsrc.html&d=BQICaQ
>> >>
>> >>&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPH
>> >>
>> >>hwHHF5gJMlij5cC5bLU&m=t9rR8WHE_O0PrI0B-0ySt37UGJMdDhnwk0JFoVzS5Cw&s=lEJWy
>> >> >>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_mailman
>> >>
>> >>_listinfo_bioc-2Ddevel&d=BQICaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPl
>> >>
>> >>OmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=t9rR8WHE_O0PrI0B-0yS
>> >>
>> >>t37UGJMdDhnwk0JFoVzS5Cw&s=3ZMFBJ4XMwlGXkfXcB5spcBnnzqBDeqk05sf_TSi88g&e=
>> >>
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