chore: Replace Rcpp by cpp11 #419

Antonov548 · 2023-01-22T11:43:21Z

No description provided.

…cpp11

krlmlr

Thanks. What does the C stack overflow on macOS mean?

DESCRIPTION

krlmlr · 2023-01-28T11:54:38Z

DESCRIPTION

@@ -48,13 +49,13 @@ LazyLoad: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 SystemRequirements: libpq >= 9.0: libpq-dev (deb) or postgresql-devel
-    (rpm)
+    (rpm), C++17


Do we really need C++17?

There was warning in CI about default c++17 standard in DESCRIPTION file on the latest Ubuntu as I understood

krlmlr · 2023-01-28T11:55:41Z

src/DbColumnStorage.cpp

  }
 }

-Rcpp::RObject DbColumnStorage::class_from_datatype(DATA_TYPE dt) {
+cpp11::sexp DbColumnStorage::class_from_datatype(DATA_TYPE dt) {


Can a cpp11 vector object contain R_NilValue ?

cpp11::r_vector which is used for cpp11::strings, cpp11::integers etc., can not be assigned to R_NilValue, only cpp11::sexp which in general make sense.

src/connection.cpp

Antonov548 · 2023-01-28T12:17:17Z

Thanks. What does the C stack overflow on macOS mean?

It's seems known problem, I will take a look. The same problem on Mac was with cpp11.

use cpp11 and cpp11 only

pachadotdev · 2023-01-31T18:20:30Z

Thanks. What does the C stack overflow on macOS mean?

It's seems known problem, I will take a look. The same problem on Mac was with cpp11.

I've been testing this PR and it works well

also, it solves #400

krlmlr · 2023-02-01T04:34:48Z

Thanks. We need to fix the stack overflow on macOS.

krlmlr · 2023-02-01T04:36:31Z

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RPostgres
 Title: Rcpp Interface to PostgreSQL
-Version: 1.4.5.9002
+Version: 1.4.5.9003


Please don't change this in PRs.

krlmlr · 2023-02-01T04:37:53Z

DESCRIPTION

+SystemRequirements: 
+    libpq >= 9.0: libpq-dev (deb) or postgresql-devel (rpm),
+    C++11


C++11 can no longer be mentioned due to recent changes in R-devel. Will the checks succeed if we leave it out?

Suggested change

SystemRequirements:

libpq >= 9.0: libpq-dev (deb) or postgresql-devel (rpm),

C++11

SystemRequirements:

libpq >= 9.0: libpq-dev (deb) or postgresql-devel (rpm)

pachadotdev · 2023-02-06T19:59:21Z

@Antonov548 I tested locally and it works. The CI shows a problem with CRAN links, I googled and I found this r-lib/actions#697. Lmk how can I help to fix this.

pachadotdev · 2023-02-07T21:49:18Z

@Antonov548 it seems to be ok now r-lib/actions#697 (comment)

all the checks here are passing

so far, I am using this PR wih my usual data analysis and it works

krlmlr

Thanks. I have tweaked one test, looks great otherwise.

Some tests now output Error: Disconnected . I have tracked this down to a failure in DbConnection::check_connection() when a result set is invalid (?). The commit 373c7a5 succeeds in the main branch, but after merging the main branch here, the tests now fail. Can you please take a look?

Antonov548 · 2023-02-08T09:47:03Z

@krlmlr Fixed 👍

pachadotdev · 2023-02-08T19:38:12Z

@krlmlr @Antonov548 I pulled the last changes. It works well with Ubuntu 20.04.

Here's the full check

> check()
ℹ Updating RPostgres documentation
ℹ Loading RPostgres
ℹ 26 functions decorated with [[cpp11::register]]
✔ generated file cpp11.R
✔ generated file cpp11.cpp
ℹ Re-compiling RPostgres (debug build)
── R CMD INSTALL ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────
─  installing *source* package ‘RPostgres’ ...
   ** using staged installation
   Found pkg-config cflags and libs (libpq 15.1)!
   Using PKG_CFLAGS=-I/usr/include/postgresql
   Using PKG_LIBS=-lpq
   Using PKG_PLOGR=
   ** libs
   g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/postgresql -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR  -I'/usr/lib/R/site-library/cpp11/include' -I'/usr/lib/R/site-library/plogr/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -UNDEBUG -Wall -pedantic -g -O0 -fdiagnostics-color=always -c connection.cpp -o connection.o
   g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/postgresql -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR  -I'/usr/lib/R/site-library/cpp11/include' -I'/usr/lib/R/site-library/plogr/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -UNDEBUG -Wall -pedantic -g -O0 -fdiagnostics-color=always -c cpp11.cpp -o cpp11.o
   g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o RPostgres.so DbColumn.o DbColumnDataSource.o DbColumnDataSourceFactory.o DbColumnStorage.o DbConnection.o DbDataFrame.o DbResult.o PqColumnDataSource.o PqColumnDataSourceFactory.o PqDataFrame.o PqResult.o PqResultImpl.o PqResultSource.o PqUtils.o RPostgres-init.o connection.o cpp11.o encode.o encrypt.o logging.o result.o -lpq -L/usr/lib/R/lib -lR
   installing to /tmp/RtmpkE2Ned/devtools_install_1be4a5bff7354/00LOCK-RPostgres/00new/RPostgres/libs
   ** checking absolute paths in shared objects and dynamic libraries
─  DONE (RPostgres)
── Building ───────────────────────────────────────────────────────────────────────────────────────────────────────── RPostgres ──
Setting env vars:
• CFLAGS    : -Wall -pedantic -fdiagnostics-color=always
• CXXFLAGS  : -Wall -pedantic -fdiagnostics-color=always
• CXX11FLAGS: -Wall -pedantic -fdiagnostics-color=always
• CXX14FLAGS: -Wall -pedantic -fdiagnostics-color=always
• CXX17FLAGS: -Wall -pedantic -fdiagnostics-color=always
• CXX20FLAGS: -Wall -pedantic -fdiagnostics-color=always
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
── R CMD build ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/home/pacha/github/RPostgres/DESCRIPTION’ ...
─  preparing ‘RPostgres’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  installing the package to build vignettes
✔  creating vignettes (19.6s)
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘RPostgres_1.4.5.9003.tar.gz’
   
── Checking ─────────────────────────────────────────────────────────────────────── RPostgres ──
Setting env vars:
• _R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE
• _R_CHECK_CRAN_INCOMING_REMOTE_    : FALSE
• _R_CHECK_CRAN_INCOMING_           : FALSE
• _R_CHECK_FORCE_SUGGESTS_          : FALSE
• NOT_CRAN                          : true
── R CMD check ─────────────────────────────────────────────────────────────────────────────────
─  using log directory ‘/tmp/RtmpkE2Ned/RPostgres.Rcheck’
─  using R version 4.2.2 Patched (2022-11-10 r83330)
─  using platform: x86_64-pc-linux-gnu (64-bit)
─  using session charset: UTF-8
─  using options ‘--no-manual --as-cran’ (842ms)
✔  checking for file ‘RPostgres/DESCRIPTION’
─  this is package ‘RPostgres’ version ‘1.4.5.9003’
─  package encoding: UTF-8
✔  checking package namespace information
✔  checking package dependencies (989ms)
✔  checking if this is a source package ...
✔  checking if there is a namespace
✔  checking for executable files (1.5s)
✔  checking for hidden files and directories ...
✔  checking for portable file names ...
✔  checking for sufficient/correct file permissions ...
✔  checking serialization versions
─  checking whether package ‘RPostgres’ can be installed ... [25s/25s] OK (25s)
N  checking installed package size ...
     installed size is  5.8Mb
     sub-directories of 1Mb or more:
       libs   5.3Mb
✔  checking package directory
✔  checking for future file timestamps ...
✔  checking ‘build’ directory ...
✔  checking DESCRIPTION meta-information ...
N  checking top-level files ...
     possible bashism in configure line 21 ('command' with option other than -p):
     if [ `uname` = "Darwin" ] && [ `command -v pkg-config` ]; then
     possible bashism in configure line 38 ('command' with option other than -p):
     if [ -z "$FORCE_AUTOBREW" ] && [ `command -v pkg-config` ]; then
     possible bashism in configure line 58 ('command' with option other than -p):
     if [ -z "$FORCE_AUTOBREW" ] && [ `command -v pg_config` ]; then
✔  checking for left-over files ...
✔  checking index information ...
✔  checking package subdirectories ...
✔  checking R files for non-ASCII characters ...
✔  checking R files for syntax errors ...
✔  checking whether the package can be loaded (396ms)
✔  checking whether the package can be loaded with stated dependencies ...
✔  checking whether the package can be unloaded cleanly ...
✔  checking whether the namespace can be loaded with stated dependencies ...
✔  checking whether the namespace can be unloaded cleanly (413ms)
✔  checking loading without being on the library search path (405ms)
✔  checking dependencies in R code (588ms)
✔  checking S3 generic/method consistency (741ms)
✔  checking replacement functions (352ms)
✔  checking foreign function calls (422ms)
✔  checking R code for possible problems (3.9s)
✔  checking Rd files ...
✔  checking Rd metadata ...
✔  checking Rd line widths ...
✔  checking Rd cross-references ...
✔  checking for missing documentation entries (431ms)
✔  checking for code/documentation mismatches (1.2s)
✔  checking Rd \usage sections (893ms)
✔  checking Rd contents ...
✔  checking for unstated dependencies in examples ...
✔  checking line endings in shell scripts
✔  checking line endings in C/C++/Fortran sources/headers ...
✔  checking line endings in Makefiles
✔  checking compilation flags in Makevars ...
✔  checking for GNU extensions in Makefiles ...
✔  checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS)
✔  checking use of PKG_*FLAGS in Makefiles ...
✔  checking use of SHLIB_OPENMP_*FLAGS in Makefiles ...
✔  checking pragmas in C/C++ headers and code ...
✔  checking compilation flags used ...
✔  checking compiled code ...
✔  checking installed files from ‘inst/doc’ ...
✔  checking files in ‘vignettes’
✔  checking examples (991ms)
✔  checking for unstated dependencies in ‘tests’ ...
─  checking tests ...
✔  Running ‘testthat.R’ (1.2s)
✔  checking for unstated dependencies in vignettes ...
✔  checking package vignettes in ‘inst/doc’ ...
✔  checking re-building of vignette outputs (1s)
✔  checking for non-standard things in the check directory ...
✔  checking for detritus in the temp directory
   
   See
     ‘/tmp/RtmpkE2Ned/RPostgres.Rcheck/00check.log’
   for details.
   
   
── R CMD check results ───────────────────────────────────────────────────────────────────────────────── RPostgres 1.4.5.9003 ────
Duration: 46.5s

❯ checking installed package size ... NOTE
    installed size is  5.8Mb
    sub-directories of 1Mb or more:
      libs   5.3Mb

❯ checking top-level files ... NOTE
    possible bashism in configure line 21 ('command' with option other than -p):
    if [ `uname` = "Darwin" ] && [ `command -v pkg-config` ]; then
    possible bashism in configure line 38 ('command' with option other than -p):
    if [ -z "$FORCE_AUTOBREW" ] && [ `command -v pkg-config` ]; then
    possible bashism in configure line 58 ('command' with option other than -p):
    if [ -z "$FORCE_AUTOBREW" ] && [ `command -v pg_config` ]; then

0 errors ✔ | 0 warnings ✔ | 2 notes ✖

pachadotdev · 2023-02-08T20:31:24Z

@krlmlr @Antonov548 I send a PR to fix the notes about bashisms

krlmlr

Let's do one last pass.

src/encrypt.cpp

src/connection.cpp

This reverts commit 44c1918.

krlmlr · 2023-02-13T19:02:29Z

Thanks!

Antonov548 and others added 12 commits January 22, 2023 12:08

init cpp11

93ae2e8

encrypt.cpp fix

ded1f0d

connection cpp11::external_pointer

b50174b

result cpp11::external_pointer

aa71b44

encode.cpp cpp11

3b6b881

connection.cpp cpp11

88639d1

DbConnection cpp11

d44c3fe

update external_pointer release to reset

6f712d4

Merge branch 'main' into cpp11

bfda2ed

remove error message

6b35f3a

update wait_for_notify

39b48f3

return empty list instead of NULL

a720ae6

Antonov548 marked this pull request as draft January 26, 2023 14:54

Antonov548 added 8 commits January 26, 2023 15:54

Merge branch 'main' into cpp11

4c7cf8b

result cpp11::list

22398b7

Merge branch 'cpp11' of https://github.com/Antonov548/RPostgres into …

867b5d3

…cpp11

data frame cpp11

76ecec5

column storage

1dc6bde

remove strings

e20f8ea

warning/stop/package

ad948f9

remove Rcpp

4db227f

Antonov548 marked this pull request as ready for review January 28, 2023 11:30

undo DESCRIPTION

ae7a9d4

Antonov548 changed the title ~~Replace Rcpp by cpp11~~ chore: Replace Rcpp by cpp11 Jan 28, 2023

krlmlr reviewed Jan 28, 2023

View reviewed changes

fix new line

435f97d

pachadotdev added 2 commits January 30, 2023 02:30

use cpp11 and cpp11 only

e60c573

re roxygenize with newer roxygen installed version (7.2.3)

92c27a5

pachadotdev mentioned this pull request Jan 30, 2023

Converting RPostgres backend to cpp11 #400

Closed

Antonov548 added 3 commits January 30, 2023 15:12

use std::string for warning/stop

a67c4c2

Merge pull request #1 from pachadotdev/cpp11

718db2c

use cpp11 and cpp11 only

remove import Rcpp

37bc3fe

krlmlr reviewed Feb 1, 2023

View reviewed changes

Antonov548 added 4 commits February 1, 2023 11:01

update DESCRIPTION

56de452

remove cxx11 from Makevars

57c7b91

string for cpp11::warning

4b68109

Merge branch 'r-dbi:main' into cpp11

3a8d2e0

krlmlr added 2 commits February 8, 2023 05:44

Tweak test

6533d54

Merge branch 'main' into cpp11

ac129e5

krlmlr reviewed Feb 8, 2023

View reviewed changes

fix: release connection with result

44c1918

krlmlr reviewed Feb 9, 2023

View reviewed changes

src/encrypt.cpp Outdated Show resolved Hide resolved

src/connection.cpp Outdated Show resolved Hide resolved

Antonov548 and others added 3 commits February 9, 2023 12:09

retrun std::string instead of r_string

7ca870b

Revert "fix: release connection with result"

4a1ac62

This reverts commit 44c1918.

Early return if connection closed already

87def43

krlmlr merged commit 0069b89 into r-dbi:main Feb 13, 2023

Antonov548 deleted the cpp11 branch February 14, 2023 18:37

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chore: Replace Rcpp by cpp11 #419

chore: Replace Rcpp by cpp11 #419

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chore: Replace Rcpp by cpp11 #419

chore: Replace Rcpp by cpp11 #419

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