Thorsten Jolitz writes: > Rainer M Krug writes: > >> Rainer M Krug writes: >> >>> Thorsten Jolitz writes: >>> >>>> Rainer M Krug writes: >>>> >>>> Hi Rainer, >>>> >>>> sorry for the late reply, I was offline some time. >>> >>> No problem. >>> >>>> >>>>> I have modified the variable transfer in ob-R.el so that the variable >>>>> transfer code is enclosed as can be seen below. >>>>> >>>>> My idea is that I can fold the R output so that the variable >>>>> transfer is >>>>> collapsed. I understand that I can use one of the org-outside-org minor >>>>> modes [1] (presumibly utshine?) - but I can't figure out how. >>>>> >>>>> My questions are: >>>>> >>>>> 1) which enclosing should I use to fold the transfer code away? >>>> >>>> Outshine is like Org, no enclosing, but file structuring with >>>> (outcommented) headlines. >>> >>> So everything after the outcommented headline will be folded - so if I >>> only want to fold one part, I have to use >>> >>> ,---- >>> | ## * If this is folded >>> | SOME R CODE >>> | ## * This not anymore >>> | SOME R CODE >>> `---- >>> >>> which I could fold to >>> >>> ,---- >>> | ## * If this is folded [...] >>> | ## * This not anymore >>> | SOME R CODE >>> `---- >>> >>> correct? >> >> I just tried it, and get the following: >> >> Unfolded: >> >> ,---- >> | > >> | + . + ## * Variable Transfer from org >> | ########################################################## >> | ## org:variables environment created and in search path >> | ########################################################## >> | >> | ## * Back to normal code >> | here it is @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ >> | > > >> `---- >> >> where "here it is @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@" is output >> From normal R code in a source block evaluated. >> >> Folded: >> >> ,---- >> | > >> | + . + ## * Variable Transfer from org >> | ##########################################################... >> | here it is @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ >> | > > >> `---- >> >> Is this what is expected? > > no, it should look just like a folded subtree in Org-mode. > The problem is probably this > > ,-------------------------------------- > | + . + ## * Variable Transfer from org > `-------------------------------------- > > because in outshine, just like in Org, a header must (!) start at the > beginning of line to be recognized. I changed it in the buffer, so that it now reads: ,---- | > | ## * Variable Transfer from org | ########################################################## | ## org:variables environment created and in search path | ########################################################## | | ## * Back to normal code | here it is @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ | > > `---- but the folding still results in ,---- | > | ## * Variable Transfer from org | ##########################################################... | here it is @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ | > > `---- If it helps, here is the buffer: ,---- | R version 3.1.0 (2014-04-10) -- "Spring Dance" | Copyright (C) 2014 The R Foundation for Statistical Computing | Platform: x86_64-apple-darwin13.1.0 (64-bit) | | R is free software and comes with ABSOLUTELY NO WARRANTY. | You are welcome to redistribute it under certain conditions. | Type 'license()' or 'licence()' for distribution details. | | Natural language support but running in an English locale | | R is a collaborative project with many contributors. | Type 'contributors()' for more information and | 'citation()' on how to cite R or R packages in publications. | | Type 'demo()' for some demos, 'help()' for on-line help, or | 'help.start()' for an HTML browser interface to help. | Type 'q()' to quit R. | | During startup - Warning messages: | 1: Setting LC_CTYPE failed, using "C" | 2: Setting LC_COLLATE failed, using "C" | 3: Setting LC_TIME failed, using "C" | 4: Setting LC_MESSAGES failed, using "C" | 5: Setting LC_MONETARY failed, using "C" | > > options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient', show.error.locations=TRUE) | > | ## * Variable Transfer from org | ########################################################## | ## org:variables environment created and in search path | ########################################################## | | ## * Back to normal code | here it is @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ | > > `---- I figured it out: The problems are the comment lines - if I delete these, it is working. I can work around this. Cheers and thanks, Rainer > > Or is the comment syntax wrong for R-mode? Is it only > > ,------------- > | # * Level 1 > `------------- > > ? I can't check right now, you can try it out by writing an Org header in an > R buffer and then call M-x comment-region on the marked line. Maybe I > got confused because PicoLisp uses ## for comments ... > >>>>> 2) which minor mode should I use for this and how can I configure it? >>>> >>>> I'm not sure if I understand. When you use ob-R.el, you work in Org >>>> files with R source blocks, right? >>> >>> Correct. >>> >>>> When do you want to fold the R output below? When you are in org-mode >>>> or when editing source blocks in R-mode? >>> >>> The evaluated code - not in the source code. >>> >>>> >>>> In the former case, Org-mode is in charge and you don't need >>>> outshine. >>> >>> True. >>> >>>> In the latter case, you could install outshine as described in the >>>> docs and then add outline-minor-mode to the ESS/R mode hook, i.e. >>> >>> That's it. >>> >>>> >>>> ,------------------------------------------------------------------------------- >>>> | ;; outline >>>> | (when (require 'outline nil t) >>>> | (add-hook 'ess-mode-hook 'outline-minor-mode)) ; is that the >>>> | hook for R-mode? >>>> | >>>> | ;; outshine >>>> | (when (require 'outshine nil t) >>>> | (add-hook 'outline-minor-mode-hook 'outshine-hook-function) >>>> | (setq outshine-use-speed-commands t)) >>>> `------------------------------------------------------------------------------- >>>> >>>> Outshine headlines are outcommented Org headlines, i.e. >>>> >>>> ,---------------------------------- >>>> | * Beginning org variable transfer >>>> `---------------------------------- >>>> >>>> becomes >>>> >>>> ,---------- >>>> | ## * Beginning org variable transfer >>>> `---------- >>>> >>>> in R-mode. >>>> >>>> The R output would become an outshine-subtree with the header above, >>>> just like in Org-mode, possibly surrounded by other subtrees. >>> >>> Sounds great - thanks a lot. I will try it out, >>> >>> Rainer >>> >>>> >>>>> --8<---------------cut here---------------start------------->8--- >>>>>> ###################################################################### >>>>> ## Beginning org variable transfer >>>>> try(detach(.org_variables_), silent=TRUE) >>>>> .org_variables_ <- new.env() >>>>> assign( 'COLUMNS', read.table("/var/folders/50/wcr5bjwn75q595n6x82gxj280000gn/T/babel-74428N93/R-import-74428U4A", header=TRUE, row.names=1, sep="\t", as.is=TRUE ), envir = .org_variables_ ); lockBinding('COLUMNS', .org_variables_) >>>>> assign( 'COLS_TO_EVAL', read.table("/var/folders/50/wcr5bjwn75q595n6x82gxj280000gn/T/babel-74428N93/R-import-74428hCH", header=TRUE, row.names=1, sep="\t", as.is=TRUE ), envir = .org_variables_ ); lockBinding('COLS_TO_EVAL', .org_variables_) >>>>> assign( 'ALLSPECIES', read.table("/var/folders/50/wcr5bjwn75q595n6x82gxj280000gn/T/babel-74428N93/R-import-74428uMN", header=TRUE, row.names=1, sep="\t", as.is=TRUE ), envir = .org_variables_ ); lockBinding('ALLSPECIES', .org_variables_) >>>>> assign( 'SPECIES', read.table("/var/folders/50/wcr5bjwn75q595n6x82gxj280000gn/T/babel-74428N93/R-import-744287WT", header=TRUE, row.names=1, sep="\t", as.is=TRUE ), envir = .org_variables_ ); lockBinding('SPECIES', .org_variables_) >>>>> assign( 'YEARS', read.table("/var/folders/50/wcr5bjwn75q595n6x82gxj280000gn/T/babel-74428N93/R-import-74428IhZ", header=TRUE, row.names=1, sep="\t", as.is=TRUE ), envir = .org_variables_ ); lockBinding('YEARS', .org_variables_) >>>>> assign('PRESENT', 2008, envir = .org_variables_); lockBinding('PRESENT', .org_variables_) >>>>> assign('MINEFFORT', 3, envir = .org_variables_); lockBinding('MINEFFORT', .org_variables_) >>>>> assign('PROPTRAIN', 0.6, envir = .org_variables_); lockBinding('PROPTRAIN', .org_variables_) >>>>> assign('RNGSEED', 13, envir = .org_variables_); lockBinding('RNGSEED', .org_variables_) >>>>> assign('RNGKIND', "Mersenne-Twister", envir = .org_variables_); lockBinding('RNGKIND', .org_variables_) >>>>> assign('RNGNORMALKIND', "Inversion", envir = .org_variables_); lockBinding('RNGNORMALKIND', .org_variables_) >>>>> assign('REFGRID', "./refGrid_8km.rds", envir = .org_variables_); lockBinding('REFGRID', .org_variables_) >>>>> assign('IFN', "./__BOX__/IFN/DB_IFN/rds/tabplot.rds", envir = .org_variables_); lockBinding('IFN', .org_variables_) >>>>> assign('IFNCOUNT', "./__BOX__/IFN/DB_IFN/rdsRasterized/tabplot.count.8km.rds", envir = .org_variables_); lockBinding('IFNCOUNT', .org_variables_) >>>>> assign('IFNMEAN', "./__BOX__/IFN/DB_IFN/rdsRasterized/tabplot.mean.8km.rds", envir = .org_variables_); lockBinding('IFNMEAN', .org_variables_) >>>>> assign('IFNPRES', "./__BOX__/IFN/DB_IFN/rdsRasterized/tabplot.pres.8km.rds", envir = .org_variables_); lockBinding('IFNPRES', .org_variables_) >>>>> assign('IFNSD', "./__BOX__/IFN/DB_IFN/rdsRasterized/tabplot.sd.8km.rds", envir = .org_variables_); lockBinding('IFNSD', .org_variables_) >>>>> assign('IFNTABTREE', "./__BOX__/IFN/DB_IFN/rds/tabtree.rds", envir = .org_variables_); lockBinding('IFNTABTREE', .org_variables_) >>>>> lockEnvironment(.org_variables_) >>>>> attach(.org_variables_) >>>>> save(.org_variables_, file='org_variables.RData') >>>>> ## end org variable transfer >>>>> ###################################################################### >>>>> --8<---------------cut here---------------end--------------->8--- >>>>> >>>>> >>>>> Footnotes: >>>>> [1] http://orgmode.org/worg/org-tutorials/org-outside-org.html -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D): +49 - (0)3 21 21 25 22 44 email: Rainer@krugs.de Skype: RMkrug PGP: 0x0F52F982