Changeset: 08dec86bd606 for MonetDB URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=08dec86bd606 Added Files: clients/R/Tests/install.timeout Removed Files: clients/R/MonetDB.R/DESCRIPTION clients/R/MonetDB.R/NAMESPACE clients/R/MonetDB.R/NEWS clients/R/MonetDB.R/R/control.R clients/R/MonetDB.R/R/dbapply.R clients/R/MonetDB.R/R/dbi.R clients/R/MonetDB.R/R/dplyr.R clients/R/MonetDB.R/R/mapi.R clients/R/MonetDB.R/man/MonetDB.R.Rd clients/R/MonetDB.R/man/MonetDBLite.Rd clients/R/MonetDB.R/man/control.Rd clients/R/MonetDB.R/man/dbApply.Rd clients/R/MonetDB.R/man/dbSendUpdate.Rd clients/R/MonetDB.R/man/dbTransaction.Rd clients/R/MonetDB.R/man/mc.Rd clients/R/MonetDB.R/man/monetdb.read.csv.Rd clients/R/MonetDB.R/man/monetdbRtype.Rd clients/R/MonetDB.R/man/monetdb_queryinfo.Rd clients/R/MonetDB.R/man/monetdbd.liststatus.Rd clients/R/MonetDB.R/man/mq.Rd clients/R/MonetDB.R/man/sqlitecompat.Rd clients/R/MonetDB.R/man/src_monetdb.Rd clients/R/MonetDB.R/src/mapisplit-r.c clients/R/MonetDB.R/src/mapisplit.c clients/R/MonetDB.R/src/mapisplit.h clients/R/Tests/survey.R clients/R/Tests/survey.reqtests clients/R/Tests/survey.stable.err clients/R/Tests/survey.stable.out clients/R/build-for-cran.sh tools/embedded/Makefile.ag tools/embedded/Tests/All tools/embedded/Tests/dbi.R tools/embedded/Tests/dbi.reqtests tools/embedded/Tests/dbi.stable.err tools/embedded/Tests/dbi.stable.out tools/embedded/Tests/deps-test.R tools/embedded/Tests/deps-test.stable.err tools/embedded/Tests/deps-test.stable.out tools/embedded/Tests/deps-test.timeout tools/embedded/Tests/dplyr.R tools/embedded/Tests/install-binary.R tools/embedded/Tests/install-binary.stable.err tools/embedded/Tests/install-binary.stable.out tools/embedded/Tests/install-source.R tools/embedded/Tests/install-source.stable.err tools/embedded/Tests/install-source.stable.out tools/embedded/Tests/install-source.timeout tools/embedded/Tests/install.reqtests tools/embedded/Tests/lowlevel.R tools/embedded/Tests/lowlevel.reqtests tools/embedded/Tests/lowlevel.stable.err tools/embedded/Tests/lowlevel.stable.out tools/embedded/build-on-windows.bat tools/embedded/build-rpkg.sh tools/embedded/demo.c tools/embedded/embedded.c tools/embedded/embedded.h tools/embedded/embeddedr.c tools/embedded/embeddedr.h tools/embedded/inlined_scripts.c tools/embedded/inlined_scripts.py tools/embedded/inlined_scripts.sh tools/embedded/pcre-for-osx.h tools/embedded/pkg-excludes tools/embedded/rcheck.sh tools/embedded/rpackage/DESCRIPTION tools/embedded/rpackage/NAMESPACE tools/embedded/rpackage/R/monetdb.R tools/embedded/rpackage/configure tools/embedded/rpackage/configure.win tools/embedded/rpackage/man/embedded.Rd tools/embedded/undef.h tools/embedded/windows/libtool.sh tools/embedded/windows/pmc.sh tools/embedded/windows/sedscript.tpl Modified Files: clients/Makefile.ag clients/R/Tests/All clients/R/Tests/dbapply.R clients/R/Tests/dbi.R clients/R/Tests/dbi.stable.err clients/R/Tests/deps-install.R clients/R/Tests/deps-test.R clients/R/Tests/dplyr-flights.R clients/R/Tests/dplyr.R clients/R/Tests/install.R clients/R/Tests/install.stable.out clients/R/Tests/testrandom.R sql/test/Users/Tests/copyinto.SQL.py tools/Makefile.ag Branch: default Log Message:
Merge with Jun2016 branch. diffs (truncated from 7880 to 300 lines): diff --git a/clients/Makefile.ag b/clients/Makefile.ag --- a/clients/Makefile.ag +++ b/clients/Makefile.ag @@ -6,4 +6,4 @@ SUBDIRS = HAVE_MAPI?mapilib HAVE_MAPI?mapiclient HAVE_ODBC?odbc HAVE_PERL?perl php examples HAVE_PYTHON2?python2 HAVE_PYTHON3?python3 NATIVE_WIN32?NT -EXTRA_DIST_DIR = Tests R ruby +EXTRA_DIST_DIR = Tests ruby diff --git a/clients/R/MonetDB.R/DESCRIPTION b/clients/R/MonetDB.R/DESCRIPTION deleted file mode 100644 --- a/clients/R/MonetDB.R/DESCRIPTION +++ /dev/null @@ -1,15 +0,0 @@ -Package: MonetDB.R -Version: 1.0.2 -Title: Connect MonetDB to R -Authors@R: c(person("Hannes Muehleisen", role = c("aut", "cre"),email = "han...@cwi.nl"), - person("Anthony Damico", role = "aut"), - person("Thomas Lumley", role = "ctb")) -Author: Hannes Muehleisen [aut, cre], Anthony Damico [aut], Thomas Lumley [ctb] -Maintainer: Hannes Muehleisen <han...@cwi.nl> -Imports: DBI (>= 0.3.1), digest (>= 0.6.4), methods, codetools -Enhances: dplyr (>= 0.3.0), MonetDBLite -Description: Allows to pull data from MonetDB into R. Includes a DBI implementation and a dplyr backend. -License: MPL (== 2.0) -URL: http://www.monetdb.org -SystemRequirements: MonetDB, available from http://www.monetdb.org or MonetDBLite R package -Collate: mapi.R dbi.R dbapply.R dplyr.R control.R diff --git a/clients/R/MonetDB.R/NAMESPACE b/clients/R/MonetDB.R/NAMESPACE deleted file mode 100644 --- a/clients/R/MonetDB.R/NAMESPACE +++ /dev/null @@ -1,24 +0,0 @@ -import(DBI,digest,methods,codetools,utils) - -# export only driver constructor, everything else is DBI stuff.. -export(MonetDB,MonetR,MonetDBR,MonetDB.R) -export(MonetDBLite,monetdblite,RMonetDBLite,rmonetdblite) -export(monet.read.csv,monetdb.read.csv) -# those are not in the DBI -exportMethods(dbSendUpdate,dbSendUpdateAsync,dbTransaction,mdbapply,isIdCurrent,initExtension) -# shorthands -export(mc,mq) -useDynLib(MonetDB.R) - -# control.R -export(monetdb.server.setup) -export(monetdb.server.start) -export(monetdb.server.stop) -export(monetdbd.liststatus) -export(monetdb.liststatus) -export(monetdb.server.shutdown) -export(monetdb.server.getpid) - -# dplyr.R -export(src_monetdb) -# rest of dplyr.R exported via hack in src_monetdb diff --git a/clients/R/MonetDB.R/NEWS b/clients/R/MonetDB.R/NEWS deleted file mode 100644 --- a/clients/R/MonetDB.R/NEWS +++ /dev/null @@ -1,211 +0,0 @@ -1.0.1 -- added isIdCurrent for improved compatibility with RSQLite -- new option monetdb.log.query allows export of dbSendQuery statements to file -- no longer depends on DBI but imports it. Preferred way of constructing connections: library(DBI); con <- dbConnect(MonetDB.R::MonetDB(), ...) - -1.0.0 -- Added support for esoteric data types such as MONTH_INTERVAL (Thanks, Roman) -- Cleaned up SQL to R type mapping (we had this twice) -- Now creating actual R integers if data fits -- dbWriteTable now quotes table/column names if necessary, and outputs warnings if it did -- New mdbapply function to automatically create and run embedded R functions in MonetDB -- Fixes for dplyr backend -- Fix for case when query only returns a prompt (CALL ..., Thanks, Roman) -- Fix for empty result set on dbGetQuery(), no longer returning NULL (Thanks, Fabian) -- Fix for dbConnect(), it ignored the url parameter somehow, which broke some sqlsurvey -- Added lower.case.names argument to monet.read.csv() in case users want to avoid quoting (a bit) -- Fix for dbConnect() that should be more robust to invalid connections -- Cleaned up quoting behavior in dbListTables(), dbRemoveTable() etc. -- Now re-establishing connection if interrupt (CMD-C or ESC) occurs -- Fixed a bug in monetdb.read.csv for multiple CSV files without headers -- Added transactions to monetdb.read.csv so no empty tables are left over -- Removed nrows parameter to monetdb.read.csv -- Added col.names argument to monetdb.read.csv -- dplyr src_monetdb now has a con parameter to pass an existing DBI connection -- Fixed a bug when running in a non-UTF8 locale (Thanks, Marcis) -- Fixed a bug when dbWriteTable would not adhere to transactional semantics -- Fixed != comparisions in dplyr (Thanks, David) -- Support for running MonetDB in embedded mode (MonetDBLite) -- Support for monetdblite:/some/path URLs in dbConnect() -- Fixed an off-by-one error in type conversion (Thanks, Kirill) -- Wait support for monetdb.server.stop on Windows -- dbWriteTable now invokes monetdb.read.csv when called with a character vector as value argument - -0.9.7 -- Fixed crash on Windows (Sorry, everyone) - -0.9.6 -- monetdb.read.csv new create= parameter (Thanks, Duncan) -- deprecated nrows parameter to monetdb.read.csv, not neccessary any more because of changes to MonetDB -- Fixed non-ASCII character handling (Thanks, Roman) -- Fully removed C-based socket code -- support for dplyr verbs sample_n() and sample_frac() - -0.9.5 -- Removed package date (Thanks, Dimitar) -- Added sys. schema name to internal queries, so SET SCHEMA xx would not break things (Thanks again, Dimitar) -- Fixed monetdb:// URL handling on newer R versions (Thanks, Alex) -- DBI 0.3 compatibility (isValid etc.) -- deprecated dbTransaction() (DBI has standardized dbBegin()) -- Back to R socket code for peace of mind -- Code cleanup -- dplyr integration moved to MonetDB.R package - -0.9.4 -- dbWriteTable overhaul (thanks, Anthony) -- Fix for dbListTables for MonetDB versions after Jan2014 - -0.9.3 -- Remove trailing slashes for monetdb.program.path parameter for monetdb.server.setup (Thanks, Anthony!) -- fixed monetdbd.liststatus (Thanks, Bart) - -0.9.2 -- monetdb_queryinfo method to find out things about an arbitrary query cheaply -- new options monetdb.sequential, monetdb.debug.query and monetdb.debug.mapi -- debug output now uses the message() function -- source code cleanup -- dbListTables() now hides system tables per default, also got options to include the - schema name and quoting in the result (sys_tables, schema_names and quote) -- fixed various TODO's in the code to get closer to 1.0 (exciting) -- fixed a bug when the error identifier sent by MonetDB was non-numeric -- IPv6 addresses in dbConnect() should now work (another long-standing TODO) - -0.9.1 -- dbGetInfo() now supported on MonetDBConnection (dplyr compatibility) -- dbTransaction(), dbCommit() and dbRollback() support -- fixed leaking of socket variable in dbConnect() -- fixed monetdb.server.setup for UNIX-like systems (Thanks, Enzo) -- fixed issue in dbClearResult() which produced a protocol error - -0.9 -- various extensions to monetdb.read.csv -- removed monet.frame from this package, moved to github - -0.8.5 -- added parameters newline and quote to monetdb.write.csv - -0.8.4 -- fixed bug when reading empty table (Thanks, Anthony) -- removed assertion in mapisplit.c that triggered sometimes for unclear reasons - -0.8.3 -- fixed a problem where integer SEXPs turned to double somehow - -0.8.2 -- fixed bug in dbConnect() where port and timeout were not always integer values - -0.8.1 -- fixed bug in dbWriteTable() where VARCHAR(255) was used for character data instead of STRING - -0.8 -- New All-C socket code (Thanks, Windows) -- new dbConnect() parameter organization (!) -- new mc() shorthand method for db connections - -0.7.10 -- More tip-toeing around in dbConnect() -- More error-tolerant MAPI parsing - -0.7.9 -- Changes in dbConnect() error handling - -0.7.8 -- fix for [, large offsets are not translated to SQL correctly - -0.7.7 -- fix for aggregatef(), formula arguments were not evaluated in the right direction -- support for mathematical operations on boolean columns - -0.7.6 -- fix for C implementation for line splitting - -0.7.5 -- more fetch() fixes - -0.7.4 -- string to line splitting to c, NA handling to C as well - -0.7.3 -- c implementation of very expensive function - -0.7.2 -- fetch() performance enhancements and bug fixes - -0.7.1 -- minor fixes to fetch() function from basic DBI - -0.7 -- some cran compatibility changes - -0.6.4 -- tabulate() support -- unique() support -- bugfix in subset() - -0.6.3 -- Quieter startup -- dbSendQuery() now fails if the query is bogus -- implemented dbGetException() - -0.6.2 -- subset() is back! - -0.6 -- merge() support from Anthony -- CRAN cleanup -- MonetDB control code for UNIX-like systems - -0.5.16 -- bugfixes in monet.frame - -0.5.15 -- rbind() support on monet.frame from Anthony - -0.5.14 -- sample() support on monet.frame - -0.5.13 -- bugfix in server control code from Anthony - -0.5.12 -- integrated formula-based aggregation from Anthony - -0.5.11 -- fixed a bug in aggregate() to allow count-aggregation on non-numeric columns - -0.5.10 -- MonetDB server control code (Windows) from Anthony Damico - -0.5.9 -- Increased default socket timeout to 24h. Rationale: Import jobs may take this long, and all operations can always be cancelled with CTRL-C - -0.5.8 -- aggregate() support in DB - -0.5.5 -- Column name, type and dimension hints for monet.frame, makes it faster - -0.5.4 -- Initial support for sort(), head(), tail(), summary(), var(), sd(), quantile() and median() in monet.frame -- Changed str() implementation to not show sample data but column names/types instead - -0.5 -- first release aimed at CRAN publication -- monet.frame virtual data object -- various bugfixes -- documentation -- port in monetdb:// URI now optional, defaults to 50000 - -0.4 -- make dbColumnInfo return the R-side data type as well as the Monet-side one. - -0.3 -- write support in dbSendQuery, new functions dbWriteTable and dbSendUpdate - -0.2 -- fixed handling of boolean values, now have proper R types -- new parameter to dbConnect to specify connection timeout -- check for empty responses in .mapiRead, now stop()s with a warning and some help - -0.1 -- initial version, basic read support diff --git a/clients/R/MonetDB.R/R/control.R b/clients/R/MonetDB.R/R/control.R deleted file mode 100644 --- a/clients/R/MonetDB.R/R/control.R +++ /dev/null @@ -1,250 +0,0 @@ -monetdb.server.start <- - function( bat.file ){ - .Deprecated("Consider using MonetDBLite") - if ( .Platform$OS.type == "unix" ) { - if( !file.exists( bat.file ) ) stop( paste( bat.file , "does not exist. Run monetdb.server.setup() to create a batch file." ) ) - - # uugly, find path of pid file again by parsing shell script. - sc <- utils::read.table(bat.file,sep="\n",stringsAsFactors=F) - pidfile <- substring(sc[[2,1]],11) - - # run script - system(bat.file,wait=T) - - # read pid from file - pid <- scan(pidfile,what=integer(),n=1) - return(pid) - } - if ( .Platform$OS.type == "windows" ) { - - # capture the result of a `tasklist` system call - before.win.tasklist <- system2( 'tasklist' , stdout = TRUE ) _______________________________________________ checkin-list mailing list checkin-list@monetdb.org https://www.monetdb.org/mailman/listinfo/checkin-list