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 >> ‘/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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel