chore: Replace Rcpp by cpp11

Antonov548 commented 1 year ago

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.

pachadotdev commented 1 year ago

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 https://github.com/r-dbi/RPostgres/issues/400

krlmlr commented 1 year ago

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

pachadotdev commented 1 year ago

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

pachadotdev commented 1 year ago

@Antonov548 it seems to be ok now https://github.com/r-lib/actions/issues/697#issuecomment-1420383340

all the checks here are passing

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

Antonov548 commented 1 year ago

@krlmlr Fixed 👍

pachadotdev commented 1 year ago

@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 commented 1 year ago

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

krlmlr commented 1 year ago

Thanks!

r-dbi / RPostgres

chore: Replace Rcpp by cpp11 #419