Built site for gh-pages

.nojekyll

@@ -1 +1 @@
-d98fb0f9
+820ef537

search.json

@@ -263,7 +263,7 @@
     "href": "index.html#may-not-be-the-latest-2",
     "title": "personal radmin",
     "section": "may not be the latest",
-    "text": "may not be the latest\n> install.packages(\"parallelly\", repos = \"https://cran.rstudio.com\")\n\nInstalling package into ‘C:/Users/WDAGUtilityAccount/Documents/R/win-library/4.0’\n(as ‘lib’ is unspecified)\n\n  There is a binary version available but the source version is later:\n           binary source needs_compilation\nparallelly 1.31.0 1.32.1             FALSE\n\ninstalling the source package ‘parallelly’\n\ntrying URL 'https://cran.rstudio.com/src/contrib/parallelly_1.32.1.tar.gz'\nContent type 'application/x-gzip' length 124853 bytes (121 KB)\ndownloaded 121 KB\n\n* installing *source* package 'parallelly' ...\n** package 'parallelly' successfully unpacked and MD5 sums checked\n** using staged installation\n** R\n** inst\n** byte-compile and prepare package for lazy loading\n** help\n*** installing help indices\n  converting help for package 'parallelly'\n    finding HTML links ... done\n    as.cluster                              html  \n    autoStopCluster                         html  \n    availableConnections                    html  \n    availableCores                          html  \n    availableWorkers                        html  \n    canPortBeUsed                           html  \n    cpuLoad                                 html  \n    find_rshcmd                             html  \n    freeCores                               html  \n    freePort                                html  \n    getOption2                              html  \n    isConnectionValid                       html  \n    isForkedChild                           html  \n    isForkedNode                            html  \n    isLocalhostNode                         html  \n    isNodeAlive                             html  \n    makeClusterMPI                          html  \n    makeClusterPSOCK                        html  \n    parallelly.options                      html  \n    pid_exists                              html  \n    supportsMulticore                       html  \n*** copying figures\n** building package indices\n** testing if installed package can be loaded from temporary location\n*** arch - i386\n*** arch - x64\n** testing if installed package can be loaded from final location\n*** arch - i386\n*** arch - x64\n** testing if installed package keeps a record of temporary installation path\n* DONE (parallelly)"
+    "text": "may not be the latest\n> install.packages(\"parallelly\", repos = \"https://cran.r-project.org\")\n\nInstalling package into ‘C:/Users/WDAGUtilityAccount/Documents/R/win-library/4.0’\n(as ‘lib’ is unspecified)\n\n  There is a binary version available but the source version is later:\n           binary source needs_compilation\nparallelly 1.31.0 1.32.1             FALSE\n\ninstalling the source package ‘parallelly’\n\ntrying URL 'https://cran.r-project.org/src/contrib/parallelly_1.32.1.tar.gz'\nContent type 'application/x-gzip' length 124853 bytes (121 KB)\ndownloaded 121 KB\n\n* installing *source* package 'parallelly' ...\n** package 'parallelly' successfully unpacked and MD5 sums checked\n** using staged installation\n** R\n** inst\n** byte-compile and prepare package for lazy loading\n** help\n*** installing help indices\n  converting help for package 'parallelly'\n    finding HTML links ... done\n    as.cluster                              html  \n    autoStopCluster                         html  \n    availableConnections                    html  \n    availableCores                          html  \n    availableWorkers                        html  \n    canPortBeUsed                           html  \n    cpuLoad                                 html  \n    find_rshcmd                             html  \n    freeCores                               html  \n    freePort                                html  \n    getOption2                              html  \n    isConnectionValid                       html  \n    isForkedChild                           html  \n    isForkedNode                            html  \n    isLocalhostNode                         html  \n    isNodeAlive                             html  \n    makeClusterMPI                          html  \n    makeClusterPSOCK                        html  \n    parallelly.options                      html  \n    pid_exists                              html  \n    supportsMulticore                       html  \n*** copying figures\n** building package indices\n** testing if installed package can be loaded from temporary location\n*** arch - i386\n*** arch - x64\n** testing if installed package can be loaded from final location\n*** arch - i386\n*** arch - x64\n** testing if installed package keeps a record of temporary installation path\n* DONE (parallelly)"
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@@ -284,7 +284,7 @@
     "href": "index.html#how-do-i-know-i-got-a-binary",
     "title": "personal radmin",
     "section": "how do I know I got a binary?",
-    "text": "how do I know I got a binary?\n\nCRAN CRAN PPMrenv\n\n\n> install.packages(\"parallelly\", repos = \"https://cran.rstudio.com\")\nInstalling package into ‘C:/Users/edavi/Documents/R/win-library/4.1’\n(as ‘lib’ is unspecified)\ntrying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/parallelly_1.32.1.zip'\nContent type 'application/zip' length 306137 bytes (298 KB)\ndownloaded 298 KB\n\npackage ‘parallelly’ successfully unpacked and MD5 sums checked\n\nThe downloaded binary packages are in\n    C:\\Users\\edavi\\AppData\\Local\\Temp\\Rtmpa2s3e8\\downloaded_packages\n\n\n> install.packages(\"renv\", repos=\"https://cran.rstudio.com\")\nInstalling package into ‘/Users/edavidaja/Library/R/x86_64/4.1/library’\n(as ‘lib’ is unspecified)\ntrying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/renv_0.15.5.tgz'\nContent type 'application/x-gzip' length 1866760 bytes (1.8 MB)\n==================================================\ndownloaded 1.8 MB\n\n\nThe downloaded binary packages are in\n /var/folders/b5/fl4ff68d23s148tg1_1gnflc0000gn/T//RtmpMk69B0/downloaded_packages\n\n\n> install.packages(\"remotes\")\nInstalling package into ‘C:/Users/WDAGUtilityAccount/AppData/Local/R/win-library/4.2’\n(as ‘lib’ is unspecified)\ntrying URL 'https://packagemanager.rstudio.com/all/latest/bin/windows/contrib/4.2/remotes_2.4.2.zip'\nContent type 'binary/octet-stream' length 399930 bytes (390 KB)\ndownloaded 390 KB\n\npackage ‘remotes’ successfully unpacked and MD5 sums checked\n\nThe downloaded binary packages are in\n  C:\\Users\\WDAGUtilityAccount\\AppData\\Local\\Temp\\RtmpA1edRi\\downloaded_packages\n\n\n> renv::install(\"fs\")\nRetrieving 'https://packagemanager.rstudio.com/all/latest/bin/windows/contrib/4.2/fs_1.5.2.zip' ...\n  OK [downloaded 380.9 Kb in 0.5 secs]\nInstalling fs [1.5.2] ...\n  OK [installed binary]\nMoving fs [1.5.2] into the cache ...\n  OK [moved to cache in 7.4 milliseconds]"
+    "text": "how do I know I got a binary?\n\nCRAN CRAN p3mrenv\n\n\n> install.packages(\"parallelly\", repos = \"https://cran.r-project.org\")\nInstalling package into ‘C:/Users/edavi/Documents/R/win-library/4.1’\n(as ‘lib’ is unspecified)\ntrying URL 'https://cran.r-project.org/bin/windows/contrib/4.1/parallelly_1.32.1.zip'\nContent type 'application/zip' length 306137 bytes (298 KB)\ndownloaded 298 KB\n\npackage ‘parallelly’ successfully unpacked and MD5 sums checked\n\nThe downloaded binary packages are in\n    C:\\Users\\edavi\\AppData\\Local\\Temp\\Rtmpa2s3e8\\downloaded_packages\n\n\n> install.packages(\"renv\", repos=\"https://cran.r-project.org\")\nInstalling package into ‘/Users/edavidaja/Library/R/x86_64/4.1/library’\n(as ‘lib’ is unspecified)\ntrying URL 'https://cran.r-project.org/bin/macosx/contrib/4.1/renv_0.15.5.tgz'\nContent type 'application/x-gzip' length 1866760 bytes (1.8 MB)\n==================================================\ndownloaded 1.8 MB\n\n\nThe downloaded binary packages are in\n /var/folders/b5/fl4ff68d23s148tg1_1gnflc0000gn/T//RtmpMk69B0/downloaded_packages\n\n\n> install.packages(\"remotes\")\nInstalling package into ‘C:/Users/WDAGUtilityAccount/AppData/Local/R/win-library/4.2’\n(as ‘lib’ is unspecified)\ntrying URL 'https://p3m.dev/cran/latest/bin/windows/contrib/4.2/remotes_2.4.2.zip'\nContent type 'binary/octet-stream' length 399930 bytes (390 KB)\ndownloaded 390 KB\n\npackage ‘remotes’ successfully unpacked and MD5 sums checked\n\nThe downloaded binary packages are in\n  C:\\Users\\WDAGUtilityAccount\\AppData\\Local\\Temp\\RtmpA1edRi\\downloaded_packages\n\n\n> renv::install(\"fs\")\nRetrieving 'https://p3m.dev/cran/latest/bin/windows/contrib/4.2/fs_1.5.2.zip' ...\n  OK [downloaded 380.9 Kb in 0.5 secs]\nInstalling fs [1.5.2] ...\n  OK [installed binary]\nMoving fs [1.5.2] into the cache ...\n  OK [moved to cache in 7.4 milliseconds]"
   },
   {
     "objectID": "index.html#pop-quiz-hotshot",
@@ -321,12 +321,33 @@
     "section": "got tools?",
     "text": "got tools?\n\ndevtools::has_devel()\n\n\n## Your system is ready to build packages!"
   },
+  {
+    "objectID": "index.html#system-dependencies",
+    "href": "index.html#system-dependencies",
+    "title": "personal radmin",
+    "section": "system dependencies",
+    "text": "system dependencies\n\nxml2opensslunitsgdal\n\n\n* installing *source* package ‘xml2’ ...\n** package ‘xml2’ successfully unpacked and MD5 sums checked\n** using staged installation\nPackage libxml-2.0 was not found in the pkg-config search path.\nPerhaps you should add the directory containing `libxml-2.0.pc'\nto the PKG_CONFIG_PATH environment variable\nPackage 'libxml-2.0', required by 'virtual:world', not found\nPackage libxml-2.0 was not found in the pkg-config search path.\nPerhaps you should add the directory containing `libxml-2.0.pc'\nto the PKG_CONFIG_PATH environment variable\nPackage 'libxml-2.0', required by 'virtual:world', not found\nUsing PKG_CFLAGS=\nUsing PKG_LIBS=-lxml2\n------------------------- ANTICONF ERROR ---------------------------\nConfiguration failed because libxml-2.0 was not found. Try installing:\n * deb: libxml2-dev (Debian, Ubuntu, etc)\n * rpm: libxml2-devel (Fedora, CentOS, RHEL)\n * csw: libxml2_dev (Solaris)\nIf libxml-2.0 is already installed, check that 'pkg-config' is in your\nPATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config\nis unavailable you can set INCLUDE_DIR and LIB_DIR manually via:\nR CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'\n--------------------------------------------------------------------\nERROR: configuration failed for package ‘xml2’\n* removing ‘/usr/local/lib/R/site-library/xml2’\n\nThe downloaded source packages are in\n    ‘/tmp/Rtmp9JMc7F/downloaded_packages’\nWarning message:\nIn install.packages(\"xml2\") :\n  installation of package ‘xml2’ had non-zero exit status\n\n\n* installing *source* package ‘s2’ ...\n** package ‘s2’ successfully unpacked and MD5 sums checked\n** using staged installation\nTesting compiler using PKG_CFLAGS=\n--------------------------- [ANTICONF] --------------------------------\nConfiguration failed because openssl was not found. Try installing:\n * deb: libssl-dev (Debian, Ubuntu, etc)\n * rpm: openssl-devel (Fedora, CentOS, RHEL)\n * csw: libssl_dev (Solaris)\n * brew: [email protected] (Mac OSX)\nIf openssl is already installed, check that 'pkg-config' is in your\nPATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config\nis unavailable you can set INCLUDE_DIR and LIB_DIR manually via:\nR CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'\n-------------------------- [ERROR MESSAGE] ---------------------------\ntools/version.c:1:10: fatal error: openssl/opensslv.h: No such file or directory\n    1 | #include <openssl/opensslv.h>\n      |          ^~~~~~~~~~~~~~~~~~~~\ncompilation terminated.\n--------------------------------------------------------------------\nERROR: configuration failed for package ‘s2’\n* removing ‘/usr/local/lib/R/site-library/s2’\n\n\n* installing *source* package ‘units’ ...\n** package ‘units’ successfully unpacked and MD5 sums checked\n** using staged installation\nconfigure: units: 0.8-5\n...\nconfigure: error:\n--------------------------------------------------------------------------------\n  Configuration failed because libudunits2.so was not found. Try installing:\n    * deb: libudunits2-dev (Debian, Ubuntu, ...)\n    * rpm: udunits2-devel (Fedora, EPEL, ...)\n    * brew: udunits (OSX)\n  If udunits2 is already installed in a non-standard location, use:\n    --configure-args='--with-udunits2-lib=/usr/local/lib'\n  if the library was not found, and/or:\n    --configure-args='--with-udunits2-include=/usr/include/udunits2'\n  if the header was not found, replacing paths with appropriate values.\n  You can alternatively set UDUNITS2_INCLUDE and UDUNITS2_LIBS manually.\n--------------------------------------------------------------------------------\n\nSee `config.log' for more details\nERROR: configuration failed for package ‘units’\n* removing ‘/usr/local/lib/R/site-library/units’\n\n\n* installing *source* package ‘sf’ ...\n** package ‘sf’ successfully unpacked and MD5 sums checked\n** using staged installation\nconfigure: CC: gcc\nconfigure: CXX: g++ -std=gnu++17\nchecking for gdal-config... no\nno\nconfigure: error: gdal-config not found or not executable.\nERROR: configuration failed for package ‘sf’\n* removing ‘/usr/local/lib/R/site-library/sf’\n\nThe downloaded source packages are in\n    ‘/tmp/Rtmp8bqjb0/downloaded_packages’\nWarning message:\nIn install.packages(\"sf\") :\n  installation of package ‘sf’ had non-zero exit status"
+  },
+  {
+    "objectID": "index.html#bonus-complication",
+    "href": "index.html#bonus-complication",
+    "title": "personal radmin",
+    "section": "bonus complication",
+    "text": "bonus complication\nruntime dependencies\n\n✅❌\n\n\n> library(sf)\nLinking to GEOS 3.12.2, GDAL 3.9.1, PROJ 9.4.1; sf_use_s2() is TRUE\n\n\nThe downloaded source packages are in\n    ‘/tmp/RtmpIvTerY/downloaded_packages’\n> library(sf)\nError: package or namespace load failed for ‘sf’ in dyn.load(file, DLLpath = DLLpath, ...):\n unable to load shared object '/usr/local/lib/R/site-library/units/libs/units.so':\n  libudunits2.so.0: cannot open shared object file: No such file or directory"
+  },
+  {
+    "objectID": "index.html#which-sysdeps",
+    "href": "index.html#which-sysdeps",
+    "title": "personal radmin",
+    "section": "which sysdeps?",
+    "text": "which sysdeps?"
+  },
   {
     "objectID": "index.html#activity-1",
     "href": "index.html#activity-1",
     "title": "personal radmin",
     "section": "activity",
-    "text": "activity\n\ninstall a package from r-universe\n\n\n\nopen the personal-radmin project\ninstall.packages(\"gitcellar\") # not on cran!\nupdate your project .Rprofile:\nusethis::edit_r_profile(scope = \"project\")\noptions(repos = c(\n  ropensci = \"https://ropensci.r-universe.dev\",\n  CRAN = \"https://cloud.r-project.org\", # macOS\n  RSPM = \"https://packagemanager.rstudio.com/cran/latest\" # windows\n))\nsave .Rprofile and restart R\ninstall.packages(\"gitcellar\")\n\n\n\n  \n    −\n    +\n \n 05:00"
+    "text": "activity\n\ninstall a package from r-universe\n\n\n\nopen the personal-radmin project\ninstall.packages(\"gitcellar\") # not on cran!\nupdate your project .Rprofile:\nusethis::edit_r_profile(scope = \"project\")\noptions(repos = c(\n  ropensci = \"https://ropensci.r-universe.dev\",\n  CRAN = \"https://cloud.r-project.org\", # macOS\n  RSPM = \"https://p3m.dev/cran/latest\" # windows\n))\nsave .Rprofile and restart R\ninstall.packages(\"gitcellar\")\n\n\n\n  \n    −\n    +\n \n 05:00"
   },
   {
     "objectID": "index.html#discussion",
@@ -371,8 +392,8 @@
     "text": "tools\n\n\nppm\n\n\n\n\nrenv\n\n\n\n\n\nrenv has a number of tools that are helpful for adopting a project-based workflow: - lockfile records what packages you use and where you instaled them from - renv::install() can handle installation from remote sources, local sources, package versions, bioconductor, rspm - per-project library isolation with global package cache - makes it easy to install experimental versions of packages and then roll back to a stable release if it doesn’t work out"
   },
   {
-    "objectID": "index.html#ppm-3",
-    "href": "index.html#ppm-3",
+    "objectID": "index.html#ppm-2",
+    "href": "index.html#ppm-2",
     "title": "personal radmin",
     "section": "ppm",
     "text": "ppm"
@@ -490,8 +511,8 @@
     "text": "package managers\nsoftware whose job it is to install other software\n🙉 not the same kinds of packages as PPM\n\n\n\n\npackage manager\n\n\n\n\n windows\nscoop, chocolatey, winget\n\n\n macOS\nhomebrew\n\n\n linux\nhomebrew, apt, yum, zypper"
   },
   {
-    "objectID": "index.html#section",
-    "href": "index.html#section",
+    "objectID": "index.html#section-2",
+    "href": "index.html#section-2",
     "title": "personal radmin",
     "section": "⚠️",
     "text": "⚠️\nAvoid installing your language with a package manager\n\nYou want to avoid having the language version your projects are using changed out from you unexpectedly Tools for freezing installations with your package manager are not consistently effective Other software that you install with your package manager may expect that package manager to be running the latest Idiosyncracies of your language will be better understood by a dedicated tool"

sitemap.xml

@@ -2,6 +2,6 @@
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     <loc>https://rstats-wtf.github.io/wtf-personal-radmin-slides/index.html</loc>
-    <lastmod>2024-08-03T17:24:11.844Z</lastmod>
+    <lastmod>2024-08-03T19:00:21.181Z</lastmod>
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