##### ## 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 <dtene...@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" <kmezh...@gmail.com>
> > To: "Dan Tenenbaum" <dtene...@fredhutch.org>
> > Cc: "Lihua Zhu" <julie....@umassmed.edu>, "Michael Lawrence" <
> lawrence.mich...@gene.com>, "bioc-devel"
> > <bioc-devel@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 <dtene...@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" <kmezh...@gmail.com>
> >> > To: "Lihua Zhu" <julie....@umassmed.edu>
> >> > Cc: "Dan Tenenbaum" <dtene...@fredhutch.org>, "Michael Lawrence" <
> >> lawrence.mich...@gene.com>, "bioc-devel"
> >> > <bioc-devel@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....@umassmed.edu>
> >> > wrote:
> >> >
> >> >> Thanks, Dan!
> >> >>
> >> >> Best,
> >> >>
> >> >> Julie
> >> >>
> >> >> On 4/11/16 12:22 PM, "Dan Tenenbaum" <dtene...@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....@umassmed.edu>
> >> >> >> To: "bioc-devel" <bioc-devel@r-project.org>
> >> >> >> Cc: "Michael Lawrence" <lawrence.mich...@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@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@r-project.org mailing list
> >> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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