Re: [O] [BABEL] BUG Re: Omitting try/catch blocks from tangled R code?

[Eric Schulte]

Rainer M Krug <address@hidden> writes:

> Eric Schulte <address@hidden> writes:
>
>> Rainer M Krug <address@hidden> writes:
>>
>>> Eric Schulte <address@hidden> writes:
>>>
>>>> Rainer M Krug <address@hidden> writes:
>>>>
>>>>> Eric Schulte <address@hidden> writes:
>>>>>
>>>>>> Charles Berry <address@hidden> writes:
>>>>>>
>>>>>>> John Hendy <jw.hendy <at> gmail.com> writes:
>>>>>>>
>>>>>>> [deleted]
>>>>>>>> >
>>>>>>>> > I think the default behavior should be reverted, as tangling and
>>>>>>>> > exporting are two different things. When I tangle, I want to see the
>>>>>>>> > code blocks as they are in the org document (with possible variables 
>>>>>>>> > and
>>>>>>>> > expansions) but not to create files where I do not put it explicitly
>>>>>>>> > into a code block. These wrappers have nothing to do with the code, 
>>>>>>>> > and
>>>>>>>> > are only there for the exported engine. So I would either revert to 
>>>>>>>> > the
>>>>>>>> > original behavior, or, introduce a new header argument,
>>>>>>>> > e.g. :include-wrappers, which would, if set to t, include the export
>>>>>>>> > wrappers in the tangled file. This might be useful for debugging
>>>>>>>> > exporting of code block results, but not for general tangling.
>>>>>>>> 
>>>>>>>> Thanks for chiming in. This was my gut reaction to the default
>>>>>>>> behavior. I guess we're still only a sample size of 2, but
>>>>>>>> intuitively, I would think that tangling would be a separate beast in
>>>>>>>> most cases from exporting. Just to have it on the record, if I tangle,
>>>>>>>> it's usually to take the code I've used in something like a Beamer
>>>>>>>> presentation or document and combine it into a single .R file so
>>>>>>>> someone can run it without needing Org-mode.
>>>>>>>
>>>>>>> [deleted]
>>>>>>>
>>>>>>> Sorry to be late to add my $0.02...
>>>>>>>
>>>>>>> I never want the try/catch wrappers.
>>>>>>>
>>>>>>> But noweb is indispensable.
>>>>>>>
>>>>>>> I use noweb a lot to organize and collect blocks. In some cases, I 
>>>>>>> export
>>>>>>> them and in others I just tangle them.
>>>>>>>
>>>>>>> I hope that the revised code will allow me to turn off try/catch 
>>>>>>> wrapping
>>>>>>> and still be able to use noweb when tangling or exporting.
>>>>>>>
>>>>>>
>>>>>> In addition to noweb, there are cases where variable expansion is useful
>>>>>> in tangled code.
>>>>>>
>>>>>> The simplest option is to move things like try/catch blocks out of the
>>>>>> code block expansion function, and into the execution function.  Then if
>>>>>> other language present similar constructs (which we want to add to
>>>>>> execution by default but never want to tangle), we can think about
>>>>>> abstracting this out into some new level of code block expansion.
>>>>>>
>>>>>> Thoughts?
>>>>>
>>>>> Makes perfect sense to me, and would definitely be the better place to
>>>>> add them.
>>>>>
>>>>> If one wants enclosing code in the tangling, there is always
>>>>> the :epilogue and :prologue header arguments, and the try/catch should
>>>>> be considered as internal to the execution.
>>>>>
>>>>
>>>> Great, how's this patch work?  If it looks good I'll apply it.
>>>
>>> Git still puzzles me a lot... If you tell me how I can apply this patch
>>> (from emacs?) I will try it out.
>>>
>>
>> Here are some instructions from the command line.
>>
>> 1. write the patch out to a file on disk, say /tmp/0001-etc...patch
>>
>> 2. cd into the org-mode directory
>>
>> 3. make sure you're up to date with the latest
>>
>>      git pull
>>
>> 4. apply the patch
>>
>>      git am /tmp/0001-etc...patch
>>
>> and that should do it.
>
> OK - managed to apply the patch.
>
> Using 
>
> Org-mode version 8.2.5h (release_8.2.5h-846-geb806d @ 
> /Users/rainerkrug/.emacs.d/org-mode/lisp/)
>
> updated this morning, I get the following error:
>

Could you provide a minimal example file generating this error?

Thanks,

>
> ,----
> | Debugger entered--Lisp error: (wrong-type-argument sequencep 67)
> |   mapconcat(identity "COLUMNS <-
> | 
> read.table(\"/var/folders/50/wcr5bjwn75q595n6x82gxj280000gn/T/babel-21363l1U/R-import-21363S9b\",\n
> | header=TRUE,\n row.names=1,\n sep=\"\\t\",\n
> | as.is=TRUE)\nCOLS_TO_EVAL <-
> | 
> read.table(\"/var/folders/50/wcr5bjwn75q595n6x82gxj280000gn/T/babel-21363l1U/R-import-21363fHi\",\n
> | header=TRUE,\n row.names=1,\n sep=\"\\t\",\n as.is=TRUE)\nALLSPECIES
> | <-
> | 
> read.table(\"/var/folders/50/wcr5bjwn75q595n6x82gxj280000gn/T/babel-21363l1U/R-import-21363sRo\",\n
> | header=TRUE,\n row.names=1,\n sep=\"\\t\",\n as.is=TRUE)\nSPECIES <-
> | 
> read.table(\"/var/folders/50/wcr5bjwn75q595n6x82gxj280000gn/T/babel-21363l1U/R-import-213635bu\",\n
> | header=TRUE,\n row.names=1,\n sep=\"\\t\",\n as.is=TRUE)\nYEARS <-
> | 
> read.table(\"/var/folders/50/wcr5bjwn75q595n6x82gxj280000gn/T/babel-21363l1U/R-import-21363Gm0\",\n
> | header=TRUE,\n row.names=1,\n sep=\"\\t\",\n as.is=TRUE)\nPRESENT <-
> | 2008\nMINEFFORT <- 3\nPROPTRAIN <- 0.6\nRNGSEED <- 13\nRNGKIND <-
> | \"Mersenne-Twister\"\nRNGNORMALKIND <- \"Inversion\"\nREFGRID <-
> | \"./refGrid_8km.rds\"\nIFN <-
> | \"./__BOX__/IFN/DB_IFN/rds/tabplot.rds\"\nIFNCOUNT <-
> | \"./__BOX__/IFN/DB_IFN/rdsRasterized/tabplot.count.8km.rds\"\nIFNMEAN
> | <-
> | \"./__BOX__/IFN/DB_IFN/rdsRasterized/tabplot.mean.8km.rds\"\nIFNPRES
> | <-
> | \"./__BOX__/IFN/DB_IFN/rdsRasterized/tabplot.pres.8km.rds\"\nIFNSD
> | <-
> | \"./__BOX__/IFN/DB_IFN/rdsRasterized/tabplot.sd.8km.rds\"\nIFNTABTREE
> | <- \"./__BOX__/IFN/DB_IFN/rds/tabtree.rds\"\ndata.sources <-
> | list.files(\"./data\", pattern=\"*.rda$\",
> | full.names=TRUE)\nR.sources <- list.files(\"./R\", pattern=\"*.R$\",
> | full.names=TRUE)\ncat(\"Loading Data\\n\")\nas.vector( sapply(
> | data.sources, load) )\ncat(\"\\nSourcing R files\\n\")\nsapply(
> | R.sources, source)" "\n")
> |   org-babel-execute:R("data.sources <- list.files(\"./data\",
> | pattern=\"*.rda$\", full.names=TRUE)\nR.sources <-
> | list.files(\"./R\", pattern=\"*.R$\",
> | full.names=TRUE)\ncat(\"Loading Data\\n\")\nas.vector( sapply(
> | data.sources, load) )\ncat(\"\\nSourcing R files\\n\")\nsapply(
> | R.sources, source)" ((:comments . "link") (:shebang . "") (:cache
> | . "no") (:padline . "yes") (:noweb . "no") (:tangle . "yes")
> | (:exports . "both") (:results . "replace output") (:var COLUMNS
> | ("annee" "Year of simulation") ("ipoints_Qdiv" "Point Number (also
> | refer to number of the climatic input file)") ("iespece" "species
> | number (4==>Beech; 3:Oak)") ("scenario" "Type of forest management
> | (no matter)") ("climat" "Type of climate (no matter)") ("RUsolinit"
> | "Soil water Holding Capacity of the point (mm)") ("PByC" "gross
> | photosynthesis (yearly, gC/m²/year)") ("PNyC" "Net photosynthesis,
> | (PByC - leaf Respiration) (gC/m²/year)") ("NPPyC" "Net primary
> | productivity, (gC/m²/year)") ("ETRy" "Evapotranspiration of stand
> | (mm/year)") ("age_peup" "Age at the end of the revolution") ("RVy"
> | "total respiration of living tissue") ("DBBVy" "aboveground annualm
> | growth (gC/m²/year)") ("RMTVy" "maintenance respiration of stems
> | (gC/m²/year)") ("RMBRy" "maintenance respiration of branches
> | (gC/m²/year)") ("Rtoty" "total heterotrophic respiration
> | (gC/m²/year) (SOIL)") ("levelstress_2" "indices of water stress
> | based on stomatal conductance") ("Ta" "Annual Temperature (°C) (do
> | not use problem)") ("PRI" "Rain (mm) (do not use problem)") ("LMAX"
> | "Leaf Area Index") ("RVCy" "Growth respiration of living tissue")
> | ("RVMy" "Maintenance respiration of all living tissue") ("DBSSy"
> | "annual storage growth (gc/m²/year)") ("DBRFy" "annual fine roots
> | growth (gC/m²/year)") ("LambX" "X co,ordinates in Lamberts Zone II
> | (EPSG 27572)") ("LambY" "Y co,ordinates in Lamberts Zone II (EPSG
> | 27572)") ("Altitude" "Elevation(m)") ("coupebb" "exported biomass
> | through cutting (gC/m²)") ("bbois" "wood biomass of the stand
> | (gC/m²)")) (:var COLS_TO_EVAL ("NPPyC" "FALSE") ("DBBVy" "TRUE")
> | ("DBRFy" "FALSE") ("DBSSy" "FALSE") ("levelstress_2" "TRUE")) (:var
> | ALLSPECIES ("Quercus robur" 1 "quercus_robur" "") ("Quercus peatrea"
> | 2 "quercus_peatrea" "") ("Quercus pubescens" 3 "quercus_pubescens"
> | "") ("Fagus sylvatica" 4 "fagus_sylvatica" "") ("Carpinus betulus" 5
> | "carpinus_betulus" "") ("Other broadleaf species" 6
> | "other_broadleaf_species" "") ("Picae abies" 7 "picae_abies" "")
> | ("Abies alba" 8 "abies_alba" "") ("Pinus maritima" 9
> | "pinus_maritima" "") ("Pinus sylvestris" 10 "pinus_sylvestris" "")
> | ("pseudotsuga meniezi" 11 "pseudotsuga_meniezi" "") ("Other
> | coniferous species" 12 "other_coniferous_species" "")) (:var SPECIES
> | ("Fagus sylvatica" "fagus" 4 "fagus_sylvatica" "red") ("Quercus
> | robur" "quercus" 3 "quercus_robur" "green")) (:var YEARS (1990)
> | (2000)) (:var PRESENT . 2008) (:var MINEFFORT . 3) (:var PROPTRAIN
> | . 0.6) (:var RNGSEED . 13) (:var RNGKIND . "Mersenne-Twister") (:var
> | RNGNORMALKIND . "Inversion") (:var REFGRID . "./refGrid_8km.rds")
> | (:var IFN . "./__BOX__/IFN/DB_IFN/rds/tabplot.rds") (:var IFNCOUNT
> | . "./__BOX__/IFN/DB_IFN/rdsRasterized/tabplot.count.8km.rds") (:var
> | IFNMEAN . "./__BOX__/IFN/DB_IFN/rdsRasterized/tabplot.mean.8km.rds")
> | (:var IFNPRES
> | . "./__BOX__/IFN/DB_IFN/rdsRasterized/tabplot.pres.8km.rds") (:var
> | IFNSD . "./__BOX__/IFN/DB_IFN/rdsRasterized/tabplot.sd.8km.rds")
> | (:var IFNTABTREE . "./__BOX__/IFN/DB_IFN/rds/tabtree.rds") (:hlines
> | . "no") (:colnames . "yes") (:mkdirp . "yes") (:no-expand . "TRUE")
> | (:rownames . "yes") (:session . "*R_MOBILIS*") (:tangle-mode . 292)
> | (:result-type . output) (:result-params "output" "replace")
> | (:rowname-names (COLUMNS "annee" "ipoints_Qdiv" "iespece" "scenario"
> | "climat" "RUsolinit" "PByC" "PNyC" "NPPyC" "ETRy" "age_peup" "RVy"
> | "DBBVy" "RMTVy" "RMBRy" "Rtoty" "levelstress_2" "Ta" "PRI" "LMAX"
> | "RVCy" "RVMy" "DBSSy" "DBRFy" "LambX" "LambY" "Altitude" "coupebb"
> | "bbois") (COLS_TO_EVAL 1 2 3 4 5) (ALLSPECIES 1 2 3 4 5 6 7 8 9 10
> | 11 12) (SPECIES "fagus" "quercus") (YEARS 1 2)) (:colname-names
> | (COLUMNS "" "name" "description") (COLS_TO_EVAL "" "name" "usable")
> | (ALLSPECIES "" "fullName" "iespece" "IFNName" "color") (SPECIES ""
> | "fullName" "shortName" "iespece" "IFNName" "color") (YEARS ""
> | "year"))))
> |   org-babel-execute-src-block(nil)
> |   org-babel-execute-buffer(nil)
> |   org-babel-execute-subtree(nil)
> |   call-interactively(org-babel-execute-subtree nil nil)
> `----
>
> Cheers,
>
> Rainer
>
>>
>> Best,
>>
p>>>
>>> Thanks,
>>>
>>> Rainer
>>>
>>>>
>>>> Thanks,

-- 
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D