Todo: --- check new NaNs in SWI --- deal with y <- '$NaN'. --- sort(colSums(mds_drivers), decreasing=true) % true not recognised as boolean --- consider returning the numeric '$NaN' rather than the atomic '$NaN' from R to (swi?) Prolog --- define nan/1 & infinity/1 ? --- add support for infinity- there is already something there but Swi does not deal well with it --- just change c(...) vectors to use the standard vectors (ala matrices) --- when encountering an integer in atoms Data, cast it to atom, rather than exception --- fix frames, Mt <- mtcars. (segs faults right now) --- test on Yap --- interactions <- sapply(1:ncol(genomic_data), function(i) sapply(1:ncol(genomic_data), function(j) {f<- try(fisher.test(genomic_data[,i], genomic_data[,j]), silent=TRUE); if(class(f)=="try-error") 0 else ifelse(f$estimate>1, -log10(f$p.val),log10(f$p.val))} ))

2:2 @ 22.06.23 22.06.21 fixed binaries for x64-win64 and added i386-win32/ 2:2 @ 22.06.21 2022/06/21 new binaries for: aarch64-linux/ x64-win64/ x86_64-darwin/ x86_64-linux/ 2022/01/17 patches for src/real.c from Jan Wielemaker: The type warnings will cause issues on some platforms (read: crash).

• Lacking the return value check for PL_put_term() can also cause a crash if this runs out of stack.

2022/01/17 Fixed, -.. -> --dump-runtime-variables 2020/09/05 explicit loading of library(apply)

2:1 @ 20.05.29 2020/5/29 recompiled for SWI-Prolog 8.2.0 2017/11/22 disabled bindRIO() on my work linux this mangles names of packages when they are loaded 2017/11/22 added PROTECT around R_tryEval()

2:0 2016/9/5 IJAR publication

1:5 2016/1/23 (j_review) New op( 700, fx, ~ ) New =< -> <= Fix - Expr was cut too soon in atom conversion term transformation. Fix new fix of a$b[c] <-d (test atomic rather than compound/3) Fix a$b[c] <- d (add example) New @~@ -> %in% (maybe add example) New R negation, !, operator. New \= prolog -> != R New support for expressions in array indices: hmrn_pass <- hmrn[ hmrn$'Contamination' == "PASS", *]

1:4 2015/5/24 (configurable) Many changes from Samer Abdallah. Particularly supporting threaded deployment for web services.

1:3 2015/5/3 (collaborative) Changed is_rvar/1,2 to r_is_var/1,2. Changed start_r/0 and end_r/0 to r_start/0 and r_end/0 respectively. Changed devoff/0 and devoff_all/0 to r_devoff/0 and r_devoff_all/0. Deleted real_debug/0 and real_nodebug/0. Added a bit of documentation to intro section and r_citation/2. Added r_new/1. Added <<- as a shorthand for r_new(Rvar), Rvar <- Expr with error handling.

This is probably going to be a quick release, the following is quite interesting Added [Rexpr] <- Fun ++ Opts and related r_call(Fun,[rvar(Rexpr)|Opts] ).

Added support for $R_LIB_REAL in r_library, which allows to replace public libs with local source files. Added r_remove/1 to interface. Updated arity/3 and compound/3. % not tested on Yap yet Fixed devoff_all.

1:2:0 2015/1/2 (regardless) Pack real.pl now reads 1.2 rather than 1.2.0. Fixes, (3rd part) are reserved for developement. Further structure added to real.c. Changes to C-interface to modularly & backward-compatibly support SWI-7 endogenous lists. Changed current_prolog_flag(real,none) to real_started(false). Changed prefs:start_r_auto(false) to current_prolog_flag(real_start,false). Added NaN examples. Fixed NaN in beginning of matrices and matrix rows. Silent loading of <- library(Lib) and added ?- r_library(Lib) Added support for NaN in matrices and vector shifting. ('$NaN' bi- and '' uni-directional (Prolog -> R) ). Support for x <- [row(1,2,3),r(4,5,6)]. Fixed x <- list(). on Swi 7. Cushioned Yap use by wrapping thread_self/1 to real_thread_self/1.

1:1:0 2014/02/15 (thankless_task) Added support for threaded execution. We need to look into environments to make deployment easier.

1:0:4 2014/12/25 Fixed passing unamed R lists to Prolog pairs. Missing name is the number position. Added example for that.

0:1:2 2013 November 3 (the_stoic) Added support for a[x,y] and a(). Corrected some branch variables, thanks to new Swi warnings. Jan, added some stuff on strings support.

0:1:1 2013 January 17 (cross_compiled) swipl-win.exe doesnot use the std I/O streams. So <-print/1 doesnot display on console. Added message that only displays when Prolog was started with swipl-win.exe and only once. The windows dlls are now cross compiled. There are now also shared (.so) libs for linux i386 and x86_64. Added Makefile.swi to the sources.

0:1:0 2012 December 26 [oliebollen] First release with updated syntax, documentation and Windows binaries. Reflects state of affairs for the PADL 2013 related publication. Great work by Vitor on passing c() via C and on utf support.

0:0:5 2012 September 12 ?fixed? * in array indicators (tut5) broken (why ?). Moved real_ex.pl to examples/for_real.pl Fixed ' x <- list(.), x$a <- 3. '. Added to examples (composite_list). In readme.txt autoconfig -> autoconf. Support $ as term. Expand the cases understood as printable to include ^ and $. Added r_wait/0.

0:0:4 2012 May 24 Fixed translation of P <- (v1-v2)^2, (report: Michiel Hildebrand) Added a (v1-v2)^2 example to real_ex.pl .

0:0:3 2012 Feb ?? Complete re-writing of the C-code for SWI interface. (80% done by Jan Wielimeker.) Added examples/pagerank.pl (Vitor Santos Costa).

0:0:2 2011 Dec ?? 0:0:1 2011 Dec ??

First two releases only shown to Vitor and Jan.