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