Update packages file for version 36280

Signed-off-by: clrbuilder <clrbuilder@intel.com>

Makefile.common

@@ -74,7 +74,7 @@ mockproper:
 	$(MOCK) --clean --uniqueext=$(PKG_NAME)
 
 configemail:
-	@test -d .git || git init
+	@test -d .git || git init -b main
 	@$(call subjectprefix,$(PKG_NAME))
 	@echo -n "Subject prefix email configured to: "
 	@git config --get format.subjectPrefix
@@ -132,7 +132,7 @@ $(SRPMFILE): $(SPECFILE) $(__allsources) localreponotice clean-old-content
 # initialized locally, or if the remote contains no commits.
 pullrebase:
 	@if [ -z "$$SKIP_GIT" ] && [ -e .git ]; then \
-		if ! git rev-parse --verify --quiet origin/master > /dev/null; then \
+		if ! git rev-parse --verify --quiet origin/main > /dev/null; then \
 			echo "Remote not yet initialized. Continuing."; \
 			exit 0; \
 		fi; \
@@ -146,7 +146,7 @@ pullrebase:
 			echo "Current branch up-to-date. Continuing."; \
 			exit 0; \
 		fi; \
-		echo "Rebasing to origin/master"; \
+		echo "Rebasing to origin/main"; \
 		if git status --porcelain | grep -q '^.[^?]'; \
 		then \
 			git stash save; \
@@ -310,8 +310,8 @@ prekoji-checks:
 koji: prekoji-checks kojidef
 	@$(MAKE) spdxcheck
 	@$(MAKE) checkblacklist
-	@if [ "$(CURRENT_BRANCH)" != "master" ] && [ "$(CURRENT_BRANCH)" != "main" ]; then \
-		echo "Error: Must be on the \"master\" or \"main\" branch to submit to koji" >&2; \
+	@if [ "$(CURRENT_BRANCH)" != "main" ]; then \
+		echo "Error: Must be on the \"main\" branch to submit to koji" >&2; \
 		exit 1; \
 	fi; \
 	if ! git diff --quiet HEAD -- ${SPECFILE}; then \
@@ -319,7 +319,7 @@ koji: prekoji-checks kojidef
 		exit 1; \
 	fi; \
 	git fetch; \
-	if git rev-parse --verify --quiet origin/master >/dev/null; then \
+	if git rev-parse --verify --quiet origin/main >/dev/null; then \
 		git pull --rebase; \
 	fi; \
 	if git ls-remote --tags --exit-code origin $(SRPMVERS) >/dev/null; then \
@@ -327,7 +327,7 @@ koji: prekoji-checks kojidef
 		exit 1; \
 	fi
 	git tag $(SRPMVERS)
-	git push origin $(CURRENT_BRANCH):master refs/tags/$(SRPMVERS)
+	git push origin $(CURRENT_BRANCH):main refs/tags/$(SRPMVERS)
 	$(KOJI_CMD) build $$KOJI_NOWAIT $(KOJI_TAG) $(PKG_BASE_URL)/$(PKG_NAME)?#$(SRPMVERS)
 
 #help rekoji: In case a previous 'make koji' failed, trigger a rebuild for the

Makefile.toplevel

@@ -68,13 +68,18 @@ ${PULL_PKGS}:
 	if [ ! -d "$$p/.git" ]; then echo "Nothing to pull for $$p - $$p/.git missing"; exit 0; fi; \
 	cd "$$p" ; \
 	if git remote | grep origin >/dev/null 2>&1; then \
-		O=$$(git rev-parse origin/master 2>/dev/null); \
+		case "$$p" in \
+			("projects/"*) BRANCH=master ;; \
+			("packages/"*) BRANCH=main ;; \
+			(*) BRANCH=master ;; \
+		esac; \
+		O=$$(git rev-parse origin/"$$BRANCH" 2>/dev/null); \
 		git fetch --tags origin >/dev/null 2>&1; \
-		N=$$(git rev-parse origin/master); \
+		N=$$(git rev-parse origin/"$$BRANCH"); \
 		if [ "$$O" != "$$N" ]; then \
 			echo "Updating: $$p"; \
-			if ! git merge --ff-only origin/master 2>/dev/null; then \
-				echo "$$p: Cannot fast-forward $$(git rev-parse --abbrev-ref HEAD) to origin/master" ; \
+			if ! git merge --ff-only origin/"$$BRANCH" 2>/dev/null; then \
+				echo "$$p: Cannot fast-forward $$(git rev-parse --abbrev-ref HEAD) to origin/$$BRANCH" ; \
 			fi ; \
 			git --no-pager log --graph --pretty=format:'%Cred%h%Creset -%C(yellow)%d%Creset %s %Cgreen(%cr) %C(bold blue)<%an>%Creset' --abbrev-commit $$O..$$N; echo; \
 		fi ; \
@@ -159,19 +164,19 @@ status: $(PACKAGES_FILE) $(addprefix packages/,$(PKGS_LOCAL))
 	if [ -d "$$p/.git" ] &&  [ -n "$$(git -C $$p status -uno --porcelain)" ]; then echo "Uncommitted changes in $$p:"; git -C "$$p" status --short; fi ;\
 	done
 
-#help diff: Runs git diff for all package repos and displays the output using
-#help diffstat. Requires that diffstat is installed.
+#help diff: Runs git diff for all package repos and displays the diffstat using
+#help the --stat flag.
 diff: $(PACKAGES_FILE) $(addprefix packages/,$(PKGS_LOCAL))
 	@for p in projects/common $(addprefix packages/,$(PKGS_LOCAL)); do \
-		(cd $$p; git status --porcelain | grep -vq '^?? ' && (echo "Uncommitted changes in: $$p"; git diff | diffstat -p1); :) ;\
+		(cd $$p; git status --porcelain | grep -vq '^?? ' && (echo "Uncommitted changes in: $$p"; git diff --stat); :) ;\
 	done
 
-#help log: Run git log origin/master..HEAD for all package repos, thus
+#help log: Run git log origin/main..HEAD for all package repos, thus
 #help displaying any committed but unpushed changes.
 log: $(PACKAGES_FILE) $(addprefix packages/,$(PKGS_LOCAL))
 	@for p in projects/common $(addprefix packages/,$(PKGS_LOCAL)); do \
-		( cd $$p; if [ -n "$$(git rev-list origin/master..HEAD)" ] ; then \
-		echo $$p ; git --no-pager log --pretty="format:%s" origin/master..HEAD ; echo ; echo;\
+		( cd $$p; if [ -n "$$(git rev-list origin/main..HEAD)" ] ; then \
+		echo $$p ; git --no-pager log --pretty="format:%s" origin/main..HEAD ; echo ; echo;\
 		fi ; ) \
 	done
 
@@ -211,7 +216,7 @@ autospecnew: preautospecnew-checks localreponotice
 		mkdir -p $(TOPLVL)/packages/$(NAME); \
 		( \
 			cd $(TOPLVL)/packages/$(NAME); \
-			git init; \
+			git init -b main; \
 			git remote add origin $(PKG_BASE_URL)/$(NAME); \
 			$(call gitoliteurl,packages/$(NAME)); \
 			$(call subjectprefix,$(NAME)); \
@@ -262,7 +267,7 @@ autospecnewgo: preautospecnew-checks localreponotice
 		mkdir -p $(TOPLVL)/packages/$(NAME); \
 		( \
 			cd $(TOPLVL)/packages/$(NAME); \
-			git init; \
+			git init -b main; \
 			git remote add origin $(PKG_BASE_URL)/$(NAME); \
 			$(call gitoliteurl,packages/$(NAME)); \
 			$(call subjectprefix,$(NAME)); \

README.md

@@ -23,7 +23,7 @@ Download the [user setup](user-setup.sh) script and run it on your Clear Linux
 system as an unprivileged user.
 
 ```
-$ curl -O https://raw.githubusercontent.com/clearlinux/common/master/user-setup.sh
+$ curl -O https://raw.githubusercontent.com/clearlinux/common/main/user-setup.sh
 $ chmod +x user-setup.sh
 $ ./user-setup.sh
 ```

packages

@@ -49,6 +49,7 @@ QGIS
 R
 R-AER
 R-AMORE
+R-ATR
 R-Amelia
 R-AmesHousing
 R-BB
@@ -432,6 +433,9 @@ R-future
 R-future.apply
 R-g.data
 R-gam
+R-gamlss
+R-gamlss.data
+R-gamlss.dist
 R-gamm4
 R-gargle
 R-gbRd
@@ -588,6 +592,7 @@ R-mda
 R-measures
 R-memisc
 R-memoise
+R-metadat
 R-metafor
 R-mi
 R-mice
@@ -648,6 +653,7 @@ R-optextras
 R-optimx
 R-optparse
 R-ordinal
+R-ordinalCont
 R-orthopolynom
 R-pROC
 R-packrat
@@ -937,6 +943,7 @@ R-tm
 R-tmvnsim
 R-toOrdinal
 R-topicmodels
+R-tram
 R-tree
 R-triebeard
 R-trimcluster
@@ -1061,7 +1068,6 @@ analitza
 ansible
 ansible-core
 antlr4-python3-runtime
-anyio
 apache-ant
 applaunchservices
 appstream
@@ -1127,6 +1133,7 @@ bcache-tools
 bcc
 bcftools
 bdftopcf
+bemenu
 bijiben
 bind-utils
 binutils
@@ -1179,6 +1186,7 @@ byobu
 bz2file
 bzip2
 c-ares
+c-basic-meta
 cJSON
 c_rehash
 ca-certs
@@ -1202,7 +1210,6 @@ cdparanoia
 ceph
 ceph-deploy
 cereal
-certbot
 cfitsio
 cgdb
 cgit
@@ -1294,6 +1301,7 @@ compat-lua-53
 compat-nettle-soname7
 compat-pangomm-soname14
 compat-poppler-soname112
+compat-poppler-soname117
 compat-protobuf-soname23
 compat-readline-soname5
 compat-rest-soname07
@@ -1385,6 +1393,7 @@ docbook2X
 docker
 docker-cli
 dockerpty
+docutils
 dolphin
 dolphin-plugins
 dos2unix
@@ -1496,7 +1505,6 @@ fribidi
 fritzing-app
 fs
 fsearch
-funcparserlib
 fuse
 fwupd
 fwupd-efi
@@ -1505,6 +1513,7 @@ gawk
 gc
 gcab
 gcc
+gcc11
 gcc7
 gcc8
 gcc9
@@ -2012,6 +2021,7 @@ ledmon
 lensfun
 leptonica
 less
+level-zero
 leveldb
 lftp
 libArcus
@@ -2070,6 +2080,7 @@ libcomps
 libconfig
 libcroco
 libcryptui
+libcuckoo
 libcxx
 libdaemon
 libdatrie
@@ -2325,6 +2336,7 @@ lksctp-tools
 llvm
 llvm11
 llvm12
+llvm13
 lm-sensors
 lmdb
 logrotate
@@ -3598,14 +3610,17 @@ pypi-aiofiles
 pypi-aiohttp
 pypi-aiohttp_cors
 pypi-aiosignal
+pypi-aiosmtpd
 pypi-alabaster
 pypi-ansi2html
 pypi-ansible_compat
 pypi-ansible_pygments
+pypi-anyio
 pypi-apacheconfig
 pypi-apipkg
 pypi-appdirs
 pypi-applicationinsights
+pypi-appnope
 pypi-argcomplete
 pypi-argon2_cffi
 pypi-argon2_cffi_bindings
@@ -3622,6 +3637,7 @@ pypi-async_generator
 pypi-async_timeout
 pypi-asynctest
 pypi-atomicwrites
+pypi-atpublic
 pypi-attrs
 pypi-awesomeversion
 pypi-awscrt
@@ -3640,6 +3656,7 @@ pypi-backcall
 pypi-backports.cached_property
 pypi-backports.entry_points_selectable
 pypi-backports.functools_lru_cache
+pypi-backports.shutil_get_terminal_size
 pypi-backports.ssl_match_hostname
 pypi-backports.weakref
 pypi-bash_kernel
@@ -3671,8 +3688,11 @@ pypi-cached_property
 pypi-cachetools
 pypi-cachy
 pypi-capturer
+pypi-cattrs
 pypi-cchardet
 pypi-cerberus
+pypi-certbot
+pypi-certbot_dns_google
 pypi-certifi
 pypi-cffi
 pypi-cffsubr
@@ -3766,6 +3786,7 @@ pypi-envs
 pypi-eternalegypt
 pypi-etuples
 pypi-evdev
+pypi-exceptiongroup
 pypi-exdir
 pypi-execnet
 pypi-executing
@@ -3787,10 +3808,12 @@ pypi-flask
 pypi-flatten_json
 pypi-flit
 pypi-flit_core
+pypi-flit_scm
 pypi-fontmath
 pypi-freezegun
 pypi-frozenlist
 pypi-fsspec
+pypi-funcparserlib
 pypi-future
 pypi-gast
 pypi-gcs_oauth2_boto_plugin
@@ -3824,6 +3847,7 @@ pypi-h11
 pypi-h2
 pypi-h5py
 pypi-hammock
+pypi-hatch_vcs
 pypi-hatchling
 pypi-heapdict
 pypi-hkp4py
@@ -3951,6 +3975,7 @@ pypi-mkdocs_material
 pypi-mkdocs_material_extensions
 pypi-mock
 pypi-molecule
+pypi-molecule_docker
 pypi-monotonic
 pypi-more_itertools
 pypi-moreorless
@@ -3983,12 +4008,14 @@ pypi-netdisco
 pypi-netifaces
 pypi-networkx
 pypi-nibabel
+pypi-nltk
 pypi-nocasedict
 pypi-nocaselist
 pypi-nodeenv
 pypi-nose
 pypi-nose_timer
 pypi-notebook
+pypi-notebook_shim
 pypi-numpoly
 pypi-numpy
 pypi-numpydoc
@@ -4016,6 +4043,7 @@ pypi-pathlib
 pypi-pathspec
 pypi-patsy
 pypi-pbr
+pypi-pdm_pep517
 pypi-pdocs
 pypi-pecan
 pypi-ped
@@ -4097,6 +4125,7 @@ pypi-pylint
 pypi-pyls_black
 pypi-pymdown_extensions
 pypi-pynacl
+pypi-pynetbox
 pypi-pynsist
 pypi-pyopengl
 pypi-pyopenssl
@@ -4255,6 +4284,7 @@ pypi-sphinx_last_updated_by_git
 pypi-sphinx_notfound_page
 pypi-sphinx_rtd_theme
 pypi-sphinx_thebe
+pypi-sphinx_theme_builder
 pypi-sphinx_togglebutton
 pypi-sphinxcontrib_apidoc
 pypi-sphinxcontrib_applehelp
@@ -4342,6 +4372,7 @@ pypi-ua_parser
 pypi-uamqp
 pypi-uc_micro_py
 pypi-ufolib2
+pypi-uharfbuzz
 pypi-ujson
 pypi-uncertainpy
 pypi-unicodedata2
@@ -4367,6 +4398,7 @@ pypi-webcolors
 pypi-webencodings
 pypi-webob
 pypi-websocket_client
+pypi-websockets
 pypi-webtest
 pypi-werkzeug
 pypi-wheel
@@ -4723,6 +4755,7 @@ usrbinjava
 usrbinpython
 usrbinvi
 utf8cpp
+utf8proc
 util-linux
 util-macros
 uwsgi
@@ -4878,3 +4911,4 @@ zopfli
 zsh
 zstd
 zstd-bin
+zxing