Check system dependencies using pkg manager (#117)

* #109 extend and document java check tolerance * #105 stub action Stub action as generated by github workflow starter * #105 WIP basic setup * #105 activate for current branch * #105 use more recent setup R version * #105 os matrix, javareconf * #105 javareconf as root * Install rJava from package manager * #105 nonroot javareconf * #105 java debugging * #105 more java debugging * #105 try r version 4 only * #105 debug PATH * #105 set vars for javareconf * #105 alternatives wrong flag syntax * #105 display javareconf output * #105 display javareconf output * #105 set vars before R install * #105 remove preinstalled JVMs * issue #105 check java home path * #105 pass java home explicitly to javareconf * #105 remove java check, too severe * #105 add tinytex to build vignettes * #105 no TeX, same check as travis * #105 add changes from full example * #105 param OS + version, skip vignettes * #105 skip vignettes in build * #105 upload if fail, check XLConnect pkg file * #105 debug check, pkg file not as expected * #105 more file debugging * #105 more debugging * #105 retry with tinytex install * #105 add LaTeX dependencies * #105 use R helper functions for TeX deps * #105 >_< * #105 R install tinytex to get helper fns * #105 conditionals, correct step order * #105 more TeX deps * #105 still need install tinytex * #105 typo * #105 compact vignettes * #105 test nodoc path * #105 typo build_args * #105 more lenient option for no doc check * #105 nodoc: ignore subdirectory issues * #105 ignore warnings in nodoc * issue #105 reduce size of upload, upload built pkg * #105 more combinations * #105 add windows + env vars * #105 no windows, show test output * #105 fallback to devtools if rcmdcheck not here * #105 try MRAN snapshot for 3.2.5 * #105 cache incl. repo, temp. only legacy * #105 avoid fallback on CRAN * #105 explicit repos * #105 use legacy-compatible sessionInfo() * #105 install rcmdcheck from CRAN if available * #105 no devtools fallback, all builds * #105 coverage information * #105 coverage -_- * #105 covr sys dependencies * #105 cover only if success, explicit checks * #105 disable full test suite flag * #105 effective TZ variation * #105 reactivate full test suite option * #105 remove commented out code * #105 run complete test suite * #105 install built package to run tests * #105 correct path to src package * #105 set RCMDCHECK var explicitly * #105 working dir for test suite * #105 correct path to test output * #105 clean after full tests * #105 Windows * #105 typo in conditional * #105 windows: use cmd shell * #105 Windows: no javareconf >_< * #105 windows: set pkg repo as quick fix * #105 Windows: check java version * #105 Java: both x64 and x86 * #105 java x86 exception * #105 restrict to java x64 on macOS * #105 abridged check witout multi archs * #105 single arch for full test suite * #105 temp: check windows only * #105 reactivate others, multiarch except on win * #105 typo in R conditional * fix copy paste error in dependency loading * Issues #103, #106 - add poi ooxml schemas * #103, #106 - test xlsx file * Check system packages - incl. debian names * Add available RPM package names * Javadeps: suppress warnings of pkg queries * Javadeps: suppress system check warnings * JavaDeps try suppressing pkg messages * JavaDeps: use capture.output for system calls * JavaDeps: check distro * trim immediately after capture.output * JavaDeps simplify, capture not needed * JavaDeps remove NOTEs * JavaDeps - ignore util function in codecov * JavaDeps fix rpm version check * JavaDeps - try latest R setup * JavaDeps - disable macOs not working * JavaDeps revert r setup to v1 * JavaDeps - patched action for macOs * Prepare cran comments for upcoming release * Upgrade java dependencies * check if non-legacy works * JavaDeps - PR was merged, set to master actions * JavaDeps keep previous POI version * JavaDeps - NEWS update * JavaDeps: update POI, off by 1 last row of empty * JavaDeps use backwards compatible XLConnect, revert tests * JavaDeps - java check before d/l pkg when installing * JavaDeps - check java version without .jinit * JavaDeps copyright headers * PR feedback: java version check message * PR Feedback: reword CRAN comment * PR feedback 2nd round of copyright headers * PR feedback remove wordpress references * PR feedback install instructions * JavaDeps final 1.0.2 JAR
miraisolutions · Feb 11, 2021 · 9515879 · 9515879
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diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
@@ -90,7 +90,7 @@ jobs:
           architecture: x64
 
       - name: Set up R ${{ matrix.config.r-version }}
-        uses: r-lib/actions/setup-r@v1
+        uses: r-lib/actions/setup-r@master
         with:
           r-version: ${{ matrix.config.r-version }}
 
@@ -217,7 +217,7 @@ jobs:
         if: success() && matrix.config.r-version == 'release' && matrix.config.os-name == 'ubuntu'
         run: |
           library(covr)
-          covr::codecov(function_exclusions=c("onLoad", "onAttach", "xlcEnsureDependencies"))
+          covr::codecov(function_exclusions=c("onLoad", "onAttach", "xlcEnsureDependencies", "checkSystemPackage"))
         shell: Rscript {0}
 
       - name: Upload check results

diff --git a/NEWS b/NEWS
@@ -1,5 +1,11 @@
 XLConnect News
 --------------
+1.0.2 2021-02-??
+  * Increase compatibility up to java 15
+  * fix missing jar dependency: poi-ooxml-schemas.jar
+  * resolve existing shared jars via package manager instead of via the file system
+  * upgrade java dependencies: commons compress (1.20) and commons codec (1.15)
+
 1.0.1 2020-03-20
   * Add java version check
 1.0.0 2020-03-19

diff --git a/R/XLConnectSettings.R b/R/XLConnectSettings.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/aref.R b/R/aref.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/aref2idx.R b/R/aref2idx.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/cellstyle.R b/R/cellstyle.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/cellstyle.operators.R b/R/cellstyle.operators.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/cellstyle.setBorder.R b/R/cellstyle.setBorder.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/cellstyle.setDataFormat.R b/R/cellstyle.setDataFormat.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/cellstyle.setFillBackgroundColor.R b/R/cellstyle.setFillBackgroundColor.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/cellstyle.setFillForegroundColor.R b/R/cellstyle.setFillForegroundColor.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/cellstyle.setFillPattern.R b/R/cellstyle.setFillPattern.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/cellstyle.setWrapText.R b/R/cellstyle.setWrapText.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/checkSystemPackage.R b/R/checkSystemPackage.R
@@ -0,0 +1,63 @@
+#############################################################################
+#
+# XLConnect
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+#############################################################################
+
+#############################################################################
+#
+# XLConnect Package Installation: find system packages by name, including
+# installed files, using Debian or Red Hat package managers
+#
+# Author: Simon Poltier, Mirai Solutions GmbH
+#
+#############################################################################
+
+ checkSystemPackage <- function (debianpkgname, rpmpkgname, versionpattern) {
+  dpkg <- function(args) {
+    suppressWarnings(system2("dpkg", args, stdout = TRUE, stderr = TRUE))
+  }
+  rpm <- function(args) {
+    suppressWarnings(system2("rpm", args, stdout = TRUE, stderr = TRUE))
+  }
+  distro <- function(distroName) {
+    releaseLines <- suppressWarnings(system2("cat",c("/etc/*-release"), stdout = TRUE, stderr = TRUE))
+    sum(grepl(pattern = paste0("ID.*",distroName), x = releaseLines, ignore.case = TRUE), na.rm = TRUE) > 0
+  }
+  if (!is.null(rpmpkgname) && distro("rhel")) {
+    pkgInfo <- rpm(c("-qi", rpmpkgname))
+    versionStr <- pkgInfo[which(grepl('Version', pkgInfo))]
+    if(length(versionStr) != 0) {
+      foundVersion <- strsplit(versionStr, " +: +")[[1]][2]
+      if(grepl(versionpattern, foundVersion)) {
+        allFiles <- rpm(c("-ql", rpmpkgname))
+        allFiles[which(grepl(".*/java.*jar", allFiles))]
+      } else { c() }
+    } else { c() }
+  }
+  else if(!is.null(debianpkgname) && distro("debian")) {
+    pkgList <- dpkg(c("-l", debianpkgname))
+    pkgLine <- pkgList[which(grepl(debianpkgname, pkgList))][1]
+    foundVersion <- strsplit(pkgLine, " +")[[1]][3]
+    if(grepl(versionpattern, foundVersion)) {
+      allFiles <- dpkg(c("--listfiles", debianpkgname))
+      allFiles[which(grepl(".*/java.*jar", allFiles))]
+    } else { c() }
+  }
+  else { c() }
+ }
+
diff --git a/R/classToXlcType.R b/R/classToXlcType.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/col2idx.R b/R/col2idx.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/constants.R b/R/constants.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/cref2idx.R b/R/cref2idx.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/dataframeFromJava.R b/R/dataframeFromJava.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/dataframeToJava.R b/R/dataframeToJava.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/extractRownames.R b/R/extractRownames.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/extractSheetName.R b/R/extractSheetName.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/getColSubset.R b/R/getColSubset.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -99,4 +99,4 @@ getColSubset <- function(object, sheet, startRow, endRow, startCol, endCol, head
 	}
 
 	globalSubset
-}
+}
diff --git a/R/idx2aref.R b/R/idx2aref.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/idx2col.R b/R/idx2col.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/idx2cref.R b/R/idx2cref.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/includeRownames.R b/R/includeRownames.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/jTryCatch.R b/R/jTryCatch.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/jseq.R b/R/jseq.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/jsle.R b/R/jsle.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/loadWorkbook.R b/R/loadWorkbook.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/mirai.R b/R/mirai.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/normalizeDataframe.R b/R/normalizeDataframe.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by

diff --git a/R/onAttach.R b/R/onAttach.R
@@ -1,7 +1,7 @@
 #############################################################################
 #
 # XLConnect
-# Copyright (C) 2010-2018 Mirai Solutions GmbH
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by