update GLCI (warnings + docs) (#6586)

* adjust NOTE count

* silent compiler warning

* update flags

* remove wvla flag

* update CI docs

* update markdown highlighting

* add todos

* remove integration deployment

* update filepaths

* fix grammar

* Update .ci/README.md

Co-authored-by: Michael Chirico <[email protected]>

* mention when license needs to be renewed

---------

Co-authored-by: Michael Chirico <[email protected]>

Author: ben-schwen

.ci/README.md

@@ -1,6 +1,6 @@
 # data.table continuous integration and deployment
 
-On each Pull Request opened in GitHub we run GitHub Actions test jobs to provide prompt feedback about the status of PR. Our main CI pipeline runs on GitLab CI nightly. GitLab repository automatically mirrors our GitHub repository and runs pipeline on `master` branch every night. It tests more environments and different configurations. It publish variety of artifacts.
+On each Pull Request opened in GitHub we run GitHub Actions test jobs to provide prompt feedback about the status of PR. Our more thorough main CI pipeline runs nightly on GitLab CI. GitLab repository automatically mirrors our GitHub repository and runs pipeline on `master` branch every night. It tests more environments and different configurations. It publishes a variety of artifacts such as our [homepage](https://rdatatable.gitlab.io/data.table/) and [CRAN-like website for dev version](https://rdatatable.gitlab.io/data.table/web/packages/data.table/index.html), including windows binaries for the dev version.
 
 ## Environments
 
@@ -44,3 +44,22 @@ Base R implemented helper script, [originally proposed to base R](https://svn.r-
 ### [`publish.R`](./publish.R)
 
 Base R implemented helper script to orchestrate generation of most artifacts and to arrange them nicely. It is being used only in [_integration_ stage in GitLab CI pipeline](./../.gitlab-ci.yml).
+
+## GitLab Open Source Program
+
+We are currently part of the [GitLab for Open Source Program](https://about.gitlab.com/solutions/open-source/). This gives us 50,000 compute minutes per month for our GitLab CI. Our license needs to be renewed yearly (around July) and is currently managed by @ben-schwen.
+
+## Updating CI pipeline
+
+Basic CI checks are also run on every push to the GitLab repository. This can **and should** be used for PRs changing the CI pipeline before merging them to master.
+
+```shell
+# fetch changes from remote (GitHub) and push them to GitLab 
+git fetch [email protected]:Rdatatable/data.table.git new_branch:new_branch
+git push
+# after updating on GitHub, pull changes from remote and push to GitLab
+git pull [email protected]:Rdatatable/data.table.git new_branch
+git push
+```
+
+Make sure to include a link to the pipeline results in your PR. 

.ci/publish.R

@@ -27,7 +27,7 @@ format.bins <- function(ver, bin_ver, cran.home, os.type, pkg, version, repodir)
     plat.path = "windows"
   } else if (os.type=="macosx") {
     ext = "tgz"
-    plat.path = "macosx/el-capitan"
+    plat.path = "macosx/big-sur-arm64"
   } else stop("format.bins only valid for 'windows' or 'macosx' os.type")
   file = sprintf("bin/%s/contrib/%s/%s_%s.%s", plat.path, bin_ver, pkg, version, ext)
   fe = file.exists(file.path(repodir, file))

.gitlab-ci.yml

@@ -143,15 +143,14 @@ test-lin-rel-cran:
   <<: *test-lin
   image: registry.gitlab.com/jangorecki/dockerfiles/r-base
   variables:
-    _R_CHECK_COMPILATION_FLAGS_KNOWN_: "-Wvla"
     _R_CHECK_CRAN_INCOMING_: "TRUE"           ## stricter --as-cran checks should run in dev pipelines continuously (not sure what they are though)
     _R_CHECK_CRAN_INCOMING_REMOTE_: "FALSE"   ## Other than no URL checking (takes many minutes) or 'Days since last update 0' NOTEs needed, #3284
     _R_CHECK_CRAN_INCOMING_TARBALL_THRESHOLD_: "7500000" ## bytes
-    _R_CHECK_PKG_SIZES_THRESHOLD_: "7"        ## MB 'checking installed package size' NOTE
+    _R_CHECK_PKG_SIZES_THRESHOLD_: "10"        ## MB 'checking installed package size' NOTE increased due to po
   script:
     - *install-deps
-    - echo 'CFLAGS=-g -O2 -fopenmp -Wall -Wvla -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2' > ~/.R/Makevars
-    - echo 'CXXFLAGS=-g -O2 -fopenmp -Wall -Wvla -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2' >> ~/.R/Makevars
+    - echo 'CFLAGS=-g -O2 -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2' > ~/.R/Makevars
+    - echo 'CXXFLAGS=-g -O2 -fopenmp -Wall -pedantic -fstack-protector-strong -D_FORTIFY_SOURCE=2' >> ~/.R/Makevars
     - R CMD check --as-cran $(ls -1t data.table_*.tar.gz | head -n 1)
     - >-
         Rscript -e 'l=tail(readLines("data.table.Rcheck/00check.log"), 1L); if (!identical(l, "Status: OK")) stop("Last line of ", shQuote("00check.log"), " is not ", shQuote("Status: OK"), " but ", shQuote(l)) else q("no")'
@@ -198,7 +197,7 @@ test-lin-dev-clang-cran:
     - R CMD check --as-cran $(ls -1t data.table_*.tar.gz | head -n 1)
     - (! grep "warning:" data.table.Rcheck/00install.out)
     - >-
-        Rscript -e 'l=tail(readLines("data.table.Rcheck/00check.log"), 1L); notes<-"Status: 3 NOTEs"; if (!identical(l, notes)) stop("Last line of ", shQuote("00check.log"), " is not ", shQuote(notes), " (size of tarball, installed package size, non-API calls) but ", shQuote(l)) else q("no")'
+        Rscript -e 'l=tail(readLines("data.table.Rcheck/00check.log"), 1L); notes<-"Status: 2 NOTEs"; if (!identical(l, notes)) stop("Last line of ", shQuote("00check.log"), " is not ", shQuote(notes), " (size of tarball, non-API calls) but ", shQuote(l)) else q("no")'
 
 # stated dependency on R
 test-lin-ancient-cran:
@@ -311,7 +310,6 @@ integration:
     - saas-linux-medium-amd64
   only:
     - master
-    - macos_binaries
   needs: ["mirror-packages","build","test-lin-rel","test-lin-rel-cran","test-lin-dev-gcc-strict-cran","test-lin-dev-clang-cran","test-lin-rel-vanilla","test-lin-ancient-cran","test-win-rel","test-win-dev" ,"test-win-old","test-mac-rel","test-mac-old"]
   script:
     - R --version
@@ -333,9 +331,6 @@ integration:
     - rm -f bus/mirror-packages/cran/bin/macosx/big-sur-arm64/contrib/$R_REL_VERSION/data.table_*.tgz
     # - rm -f bus/mirror-packages/cran/bin/macosx/big-sur-arm64/contrib/$R_DEV_VERSION/data.table_*.tgz
     - rm -f bus/mirror-packages/cran/bin/macosx/big-sur-arm64/contrib/$R_OLD_VERSION/data.table_*.tgz
-    #- rm -f bus/mirror-packages/cran/bin/macosx/el-capitan/contrib/$R_REL_VERSION/data.table_*.tgz
-    #- rm -f bus/mirror-packages/cran/bin/macosx/el-capitan/contrib/$R_DEV_VERSION/data.table_*.tgz
-    #- rm -f bus/mirror-packages/cran/bin/macosx/el-capitan/contrib/$R_OLD_VERSION/data.table_*.tgz
     ## merge mirror-packages and R devel packages
     - mv bus/mirror-packages/cran bus/$CI_JOB_NAME/
     ## publish package sources

src/freadR.h

@@ -21,7 +21,7 @@
 // Where no halt is happening, we can just use raw Rprintf() or warning()
 void __halt(bool warn, const char *format, ...);   // see freadR.c
 #define STOP(...)   __halt(0, __VA_ARGS__)
-static char internal_error_buff[1001]; // match internalErrSize
+static char internal_error_buff[1001] __attribute__((unused)); // match internalErrSize // todo: fix imports such that compiler warns correctly #6468
 #define INTERNAL_STOP(...) do {snprintf(internal_error_buff, 1000, __VA_ARGS__); __halt(0, "%s %s: %s. %s", _("Internal error in"), __func__, internal_error_buff, _("Please report to the data.table issues tracker"));} while (0)
 #define DTPRINT     Rprintf
 #define DTWARN(...) warningsAreErrors ? __halt(1, __VA_ARGS__) : warning(__VA_ARGS__)

src/fwrite.h

@@ -9,7 +9,7 @@
   #include "po.h"
   #define STOP     error
   #define DTPRINT  Rprintf
-  static char internal_error_buff[256];
+  static char internal_error_buff[256] __attribute__((unused)); // todo: fix imports such that compiler warns correctly #6468
   #define INTERNAL_STOP(...) do {snprintf(internal_error_buff, 255, __VA_ARGS__); error("%s %s: %s. %s", _("Internal error in"), __func__, internal_error_buff, _("Please report to the data.table issues tracker"));} while (0)
 #endif