[Bioc-devel] import except on Window Machine

Michael Lawrence lawrence.michael at gene.com
Mon Apr 11 20:40:06 CEST 2016 

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
>> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
>> ERROR: failed to lock directory
>> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’ for
>> modifying
>> Try removing
>> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/00LOCK-bioCancer’
>>
>> 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 ‘/Volumes/DATA/radiant/bioCancer/DESCRIPTION’ ... OK
>> * preparing ‘bioCancer’:
>> * checking DESCRIPTION meta-information ... OK
>> * checking for LF line-endings in source and make files
>> * checking for empty or unneeded directories
>> * building ‘bioCancer_0.99.0.tar.gz’
>>
>> [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
>>> >> > ‘/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=
>>> >> >>
>>> >> >> _______________________________________________
>>> >> >> Bioc-devel at r-project.org mailing list
>>> >> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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