[Bioc-devel] import except on Window Machine

[Dan Tenenbaum]

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)

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