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....@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.mich...@gene.com> wrote: > >>On Mon, Apr 11, 2016 at 10:28 AM, Dan Tenenbaum <dtene...@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" <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 10:21:42 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 <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 >>>>> >> > 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/bioCanc >>>>>er¹ >>>>> >> > * restoring previous >>>>> >> > >>>>> >> >>>>> >>>>>Œ/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCanc >>>>>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....@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_ch >>>>>ec >>>>> >> >> >>>>> >> >>>>> >>>>>>>kResults_devel_bioc-2DLATEST_CRISPRseek_moscato2-2Dbuildsrc.html&d=BQ >>>>>>>ICaQ >>>>> >> >> >>>>> >> >>>>> >>>>>>>&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2b >>>>>>>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@r-project.org mailing list >>>>> >> >> >> >>>>> >> >> >> >>>>> >> >> >>>>> >> >>>>> >>>>>https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailm >>>>>an >>>>> >> >> >>>>> >> >>>>> >>>>>>>_listinfo_bioc-2Ddevel&d=BQICaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4D >>>>>>>erPl >>>>> >> >> >>>>> >> >>>>> >>>>>>>OmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=t9rR8WHE_O0PrI0B >>>>>>>-0yS >>>>> >> >> >>>>> >> >>>>> >>>>>>>t37UGJMdDhnwk0JFoVzS5Cw&s=3ZMFBJ4XMwlGXkfXcB5spcBnnzqBDeqk05sf_TSi88g >>>>>>>&e= >>>>> >> >> >>>>> >> >> _______________________________________________ >>>>> >> >> Bioc-devel@r-project.org mailing list >>>>> >> >> >>>>>https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailm >>>>>an_listinfo_bioc-2Ddevel&d=BQIFaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4D >>>>>erPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=p3WrsvoaEWYRGX >>>>>1hHvBYdHyfl3qSnDlhimrlUmhWc78&s=3y16NmxUwgAm1KDxESsjtgLdg1qSZ5EWMfbHqPx >>>>>x7Go&e= > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel