Update packages file for version 21670

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

Makefile.common

@@ -4,8 +4,8 @@ all: build
 
 TOPLVL = ../..
 
-include $(TOPLVL)/projects/common/Makefile.functions
 include $(TOPLVL)/projects/common/Makefile.config
+include $(TOPLVL)/projects/common/Makefile.shared
 
 SHELL  = /bin/bash
 
@@ -19,7 +19,9 @@ RPMS ?= $(LATEST_RPMS)
 
 WITH_SUDO = $(shell cmp /usr/bin/mock /usr/sbin/mock &> /dev/null && echo sudo )
 
-MOCK     ?= $(WITH_SUDO) /usr/bin/mock -r clear
+# MOCK_CONFIG_VAL is set in Makefile.shared
+MOCK ?= $(WITH_SUDO) /usr/bin/mock -r $(MOCK_CONFIG_VAL)
+
 
 ifneq ($(wildcard upstream),)
 __allsources := $(notdir $(strip $(shell cat upstream)))
@@ -113,21 +115,29 @@ shell:
 
 # Always rebuild the source rpm
 .PHONY: $(SRPMFILE)
-$(SRPMFILE): $(SPECFILE) $(__allsources)
+$(SRPMFILE): $(SPECFILE) $(__allsources) localreponotice
 	@$(MAKE) spdxcheck
 	$(MOCK) --buildsrpm --source=./ --spec=$(SPECFILE) --result=results/ --no-cleanup-after --uniqueext=$(PKG_NAME)
 
-# Do a git fetch and a git rebase rather than a git pull so aborting
-# the git pull at a password prompt doesn't leave local changes stashed
-# Do the the git status dance so we only apply a stash we create
+# Do a git fetch and a git rebase to apply local commits on top of latest
+# commits from the remote. A git fetch/rebase is used rather than a git pull so
+# aborting the git pull at a password prompt doesn't leave local changes
+# stashed. Do the git status dance so we only apply a stash we create. Note
+# that a fetch/rebase is not attempted if the remote 'origin' is not
+# initialized locally, or if the remote contains no commits.
 pullrebase:
-	if [ -z "$$SKIP_GIT" ] && [ -e .git ]; then \
-		set -x ; \
+	@if [ -z "$$SKIP_GIT" ] && [ -e .git ]; then \
+		if ! git rev-parse --verify --quiet origin/master > /dev/null; then \
+			echo "Remote not yet initialized. Continuing."; \
+			exit 0; \
+		fi; \
+		echo "Fetching origin"; \
 		git fetch; \
 		if ! git rev-parse --verify --quiet FETCH_HEAD > /dev/null; then \
 			echo "No commits exist in remote. Continuing."; \
 			exit 0; \
 		fi; \
+		echo "Rebasing to origin/master"; \
 		if git status --porcelain | grep -q '^.[^?]'; \
 		then \
 			git stash save; \
@@ -142,17 +152,23 @@ pullrebase:
 #help already a specfile, it will be overwritten. Several files used by
 #help autospec will be created in the process. For more information, see
 #help the project at https://github.com/clearlinux/autospec
-autospec: pullrebase
+autospec: pullrebase localreponotice
 	rm -f results/*src.rpm
 	@if [ -e $(SPECFILE) ] && ! grep -q "# Generated by: autospec.py" $(SPECFILE) ; then \
 		echo "Specfile already exists and was not created by autospec.py! Aborting."; \
 		exit 1; \
 	fi
 	@printf 'PKG_NAME := %s\nURL = %s\nARCHIVES = %s\n\ninclude ../common/Makefile.common\n' $(PKG_NAME) '$(firstword $(value NEWURL) $(value URL))' '$(value ARCHIVES)' > Makefile
-	python3 $(TOPLVL)/projects/autospec/autospec/autospec.py -t . --integrity \
-		${NON_INTERACTIVE} --config "$(AUTOSPEC_CONF)" ${SKIP_GIT} \
-		$(firstword $(NEWURL) $(URL)) --name $(PKG_NAME) ${CLEANUP} \
-		$${SETVERSION:+ -v $${SETVERSION}} -a $(ARCHIVES)
+	python3 $(TOPLVL)/projects/autospec/autospec/autospec.py \
+		--target . \
+		--integrity \
+		--config "$(AUTOSPEC_CONF)" \
+		--name $(PKG_NAME) \
+		--archives $(ARCHIVES) \
+		--mock-config $(MOCK_CONFIG_VAL) \
+		$${SETVERSION:+ --version $${SETVERSION}} \
+		${NON_INTERACTIVE} ${SKIP_GIT} ${CLEANUP} \
+		$(firstword $(NEWURL) $(URL));
 	@$(MAKE) spdxcheck
 	@$(MAKE) checkblacklist
 	@if [ -e update_changelog.sh ] && [ -z "$$SKIP_GIT" ] ; then \
@@ -275,8 +291,11 @@ logcheck:
 $(TOPLVL)/repo:
 	@echo "Creating local RPM repository $(TOPLVL)/repo"
 	mkdir $(TOPLVL)/repo
+	$(MAKE) localrepocreate
 
-#help repoadd: Creates a local Yum repository in the $(TOPLVL)/repo directory.
+#help repoadd: Adds locally-built RPMs for this package to the local RPM
+#help repository. If this repository does not yet exist, it is created and
+#help enabled.
 repoadd: results/build.log $(TOPLVL)/repo
 	@if [ -z "`grep '^Wrote: .*$(shell basename $(SRPMFILE))$$' results/build.log`" ]; then \
 		echo "You have not yet succesfully built this release yet"; exit 1; \
@@ -285,17 +304,16 @@ repoadd: results/build.log $(TOPLVL)/repo
 		echo "Cleaning old rpms:"; \
 		for r in `cat .repo-index`; do \
 			echo "-$$r"; \
-			rm $(TOPLVL)/repo/$$r; \
+			rm -f $(TOPLVL)/repo/$$r; \
 		done; \
 		rm .repo-index; \
 	fi
 	for r in $(LATEST_RPMS); do echo "+$$r"; echo $$(basename $$r) >> .repo-index; cp $$r $(TOPLVL)/repo; done
-	( cd $(TOPLVL)/repo ; if type createrepo_c 1>/dev/null 2>&1; then createrepo_c .; else createrepo .; fi );
-	@cp $(TOPLVL)/projects/common/image-creator/yum.conf $(TOPLVL)/repo/.yum.conf
-	@printf "\n\n[local]\nname=Local\nfailovermethod=priority\nenabled=1\ngpgcheck=0\n" >> $(TOPLVL)/repo/.yum.conf
-	@printf "baseurl=file://$$(realpath $(TOPLVL))/repo/\n\n" >> $(TOPLVL)/repo/.yum.conf
+	$(MAKE) localrepocreate
+	$(call localrepoenable,${PM_CONF},${MOCK_CONF})
 
-#help repodel: Removes package from local Yum repository.
+#help repodel: Removes RPMs from the local RPM repository that were
+#help previously added by 'make repoadd' for this package.
 repodel:
 	@if [ -f .repo-index ]; then \
 		echo "Cleaning old rpms:"; \
@@ -304,8 +322,19 @@ repodel:
 			rm -f $(TOPLVL)/repo/$$r; \
 		done; \
 		rm .repo-index; \
+		$(MAKE) localrepocreate; \
 	fi
 
+#help repoenable: Enables the local RPM repository for use with Yum/DNF and
+#help Mock. If this repository does not yet exist, it is created.
+repoenable: $(TOPLVL)/repo ; $(call localrepoenable,${PM_CONF},${MOCK_CONF})
+
+#help repodisable: Disables the local RPM repository.
+repodisable: localrepodisable ;
+
+#help repostatus: Summarizes the local RPM repository status.
+repostatus: localrepostatus ;
+
 loop-up:
 	$(loopup)
 

Makefile.config

@@ -54,6 +54,13 @@ AUTOSPEC_CONF = $(TOPLVL)/projects/common/autospec.conf
 # in "pkg-mapping" for cloning/pulling package repos.
 USE_PACKAGE_MAPPING = yes
 
+# Package manager config file. Default to the in-tree copy.
+PM_CONF = $(TOPLVL)/projects/common/image-creator/yum.conf
+
+# Mock configuration file. Default to the in-tree copy.
+MOCK_CONF = $(TOPLVL)/projects/common/koji-client-files/clear.cfg
+
+
 # Include any site local configuration variables. These variables may override
 # the definitions given above.
 -include $(TOPLVL)/projects/common/Makefile.config.site_local

Makefile.shared

@@ -62,6 +62,82 @@ define remotepkgname
 $(if $(USE_PACKAGE_MAPPING),$$(awk -v P="$(1)" '$$1 == P { res=$$2 } END { print res ? res : P }' $(TOPLVL)/projects/common/pkg-mapping),$(1))
 endef
 
+# Enables the local RPM repo by installing package manager and Mock configs.
+# First argument is the path to the package manager config, and the second
+# argument is the path to the mock config. Each of these config files is
+# augmented for local repo support.
+define localrepoenable
+	@cp $(1) $(TOPLVL)/repo/yum.conf
+	@printf "\n\n[local]\nname=Local\nfailovermethod=priority\nenabled=1\ngpgcheck=0\n" >> $(TOPLVL)/repo/yum.conf
+	@printf "baseurl=file://$$(realpath $(TOPLVL))/repo/\n\n" >> $(TOPLVL)/repo/yum.conf
+	@cp $(2) $(TOPLVL)/repo/clear.cfg
+	@printf "\n\n[localrepo]\nname=Local repo\nfailovermethod=priority\nenabled=1\ngpgcheck=0\n" >> $(TOPLVL)/repo/clear.cfg
+	@printf "baseurl=file://$$(realpath $(TOPLVL))/repo/\n\n" >> $(TOPLVL)/repo/clear.cfg
+	@sed -i '/^"""/d; $$a"""' $(TOPLVL)/repo/clear.cfg
+endef
+
+# Disables the local RPM repo by removing the installed package manager and
+# Mock configuration files.
+localrepodisable:
+	@rm -f $(TOPLVL)/repo/yum.conf
+	@rm -f $(TOPLVL)/repo/clear.cfg
+
+# Runs createrepo_c (or createrepo) for the local RPM repo
+localrepocreate:
+	( cd $(TOPLVL)/repo ; if type createrepo_c 1>/dev/null 2>&1; then createrepo_c .; else createrepo .; fi );
+
+# Remove all RPMs from the local RPM repo
+localrepoclean:
+	@find $(TOPLVL)/repo -maxdepth 1 -name '*.rpm' -delete
+
+# Summarizes the local RPM repo status
+localrepostatus:
+	@if [ ! -d $(TOPLVL)/repo ]; then \
+		echo '** Local repo not found'; \
+		exit 0; \
+	fi; \
+	if [ -f $(TOPLVL)/repo/yum.conf ]; then \
+		echo '** Local repo enabled for Yum/DNF.'; \
+	else \
+		echo '** Local repo not enabled for Yum/DNF.'; \
+	fi; \
+	if [ -f $(TOPLVL)/repo/clear.cfg ]; then \
+		echo '** Local repo enabled for Mock.'; \
+	else \
+		echo '** Local repo not enabled for Mock.'; \
+	fi; \
+	echo -n '** Local repo package list: '; \
+	( \
+		cd "$(TOPLVL)/repo"; \
+		LC_COLLATE="C"; \
+		shopt -s nullglob; \
+		set -- *.rpm; \
+		if [ -n "$$1" ]; then \
+			printf '\n'; printf '%q\n' "$$@"; \
+		else \
+			printf 'none found\n'; \
+		fi; \
+	)
+
+# Detection of whether to use the local RPM repo occurs on-the-fly. Normally,
+# variable definitions appear in Makefile.config, but these variables are not
+# intended to be user-modifiable.
+ifeq ($(wildcard $(TOPLVL)/repo/clear.cfg),)
+MOCK_CONFIG_VAL = $(realpath $(MOCK_CONF))
+else
+MOCK_CONFIG_VAL = $(realpath $(TOPLVL)/repo/clear.cfg)
+USE_LOCAL_REPO = 1
+endif
+
+localreponotice:
+	@if [ -n "${USE_LOCAL_REPO}" ]; then \
+		printf '\n\n** NOTICE: Using local repo for the build. Continuing after 3 seconds.\n'; \
+		printf '** If this is not desired, run `make repodisable`.\n'; \
+		printf '** The repo can be re-enabled later with `make repoenable`.\n'; \
+		printf '** Run `touch $(TOPLVL)/repo/opt-in-build` to prevent the 3 second delay.\n\n\n'; \
+		[ -f $(TOPLVL)/repo/opt-in-build ] || sleep 3; \
+	fi >&2
+
 .PHONY: help
 ##### Code
 # Make sure that HELPSPACE has exactly HELPLEN spaces in it

Makefile.toplevel

@@ -4,8 +4,8 @@ all: clone
 
 TOPLVL  = .
 
-include $(TOPLVL)/projects/common/Makefile.functions
 include $(TOPLVL)/projects/common/Makefile.config
+include $(TOPLVL)/projects/common/Makefile.shared
 
 SHELL   = /bin/bash
 
@@ -80,7 +80,11 @@ ${PULL_PKGS}:
 			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 ; \
-		$(call gitoliteurl,$$p); \
+		if [ "$$p" = "projects/autospec" ] ; then \
+			git remote set-url --push origin https://github.com/clearlinux/autospec.git; \
+		else \
+			$(call gitoliteurl,$$p); \
+		fi ; \
 	else \
 		echo "$$p: no such remote 'origin'"; \
 	fi ; \
@@ -188,22 +192,56 @@ provides:
 #help autospecnew: Creates a new autospec package with for a given URL=$(URL)
 #help with NAME=$(NAME). Several files used by autospec will be created in the
 #help process. For more information about autospec, see the project page on Github https://github.com/clearlinux/autospec
-autospecnew:
+autospecnew: localreponotice
 	@if [ -z $(NAME) ] || [ -z $(URL) ]; then \
 		echo "Please specify NAME and URL. The ARCHIVES variable is optional."; \
 		exit 1; \
 	fi
-	@git clone $(PKG_BASE_URL)/$(NAME) $(TOPLVL)/packages/$(NAME) &> /dev/null || true
 	@if [ ! -d $(TOPLVL)/packages/$(NAME)/.git ]; then \
 		echo "no remote repository found, creating new package repository and running autospec"; \
 		mkdir -p $(TOPLVL)/packages/$(NAME); \
+		( \
+			cd $(TOPLVL)/packages/$(NAME); \
+			git init; \
+			git remote add origin $(PKG_BASE_URL)/$(NAME); \
+			$(call gitoliteurl,packages/$(NAME)); \
+			$(call subjectprefix,$(NAME)); \
+		); \
 		printf 'PKG_NAME := %s\nURL = %s\nARCHIVES = %s\n\ninclude ../common/Makefile.common\n' $(NAME) '$(value URL)' '$(value ARCHIVES)' > $(TOPLVL)/packages/$(NAME)/Makefile; \
-		python3 $(TOPLVL)/projects/autospec/autospec/autospec.py --integrity -t packages/$(NAME) --config $(AUTOSPEC_CONF) $(URL) --name $(NAME); \
+		python3 $(TOPLVL)/projects/autospec/autospec/autospec.py \
+			--target packages/$(NAME) \
+			--integrity \
+			--config "$(AUTOSPEC_CONF)" \
+			--name $(NAME) \
+			--archives $(ARCHIVES) \
+			--mock-config $(MOCK_CONFIG_VAL) \
+			$${SETVERSION:+ --version $${SETVERSION}} \
+			${NON_INTERACTIVE} ${SKIP_GIT} ${CLEANUP} \
+			$(URL); \
 		$(TOPLVL)/projects/common/checkblacklist.sh $(TOPLVL)/projects/common/blacklist $(TOPLVL)/packages/${NAME}/results/*.rpm; \
 	else \
 		echo "$(NAME) already exists at $(TOPLVL)/packages/$(NAME)"; \
 		exit 1; \
 	fi
 
+$(TOPLVL)/repo:
+	@echo "Creating local RPM repository $(TOPLVL)/repo"
+	mkdir $(TOPLVL)/repo
+	$(MAKE) localrepocreate
+
+#help repoenable: Enables the local RPM repository for use with Yum/DNF and
+#help Mock. If this repository does not yet exist, it is created.
+repoenable: $(TOPLVL)/repo ; $(call localrepoenable,${PM_CONF},${MOCK_CONF})
+
+#help repodisable: Disables the local RPM repository.
+repodisable: localrepodisable ;
+
+#help repoclean: Removes all RPMs from the local RPM repository.
+repoclean: localrepoclean localrepocreate ;
+
+#help repostatus: Summarizes the local RPM repository status.
+repostatus: localrepostatus ;
+
+
 # Define site local toplevel targets in a separate makefile
 -include $(TOPLVL)/projects/common/Makefile.toplevel.site_local

packages

@@ -9,6 +9,7 @@ Jinja2
 Keras
 LS_COLORS
 LVM2
+LibRaw
 LibVNCServer
 Linux-PAM
 LuaJIT
@@ -24,124 +25,456 @@ OpenSP
 Paste
 PasteDeploy
 Pillow
-PyQt5
 PyWavelets
 PyYAML
 Pygments
 QtAwesome
 QtPy
 R
+R-AER
 R-BH
+R-Brobdingnag
+R-CVST
 R-Cairo
+R-CircStats
+R-ClustVarLV
+R-Cubist
 R-DBI
+R-DBItest
+R-DEoptim
+R-DEoptimR
+R-DRR
+R-DT
+R-DendSer
+R-DistributionUtils
+R-Ecdat
+R-Ecfun
+R-EnvStats
+R-FNN
+R-Formula
+R-GGally
+R-GPArotation
+R-GeneralizedHyperbolic
+R-GlobalOptions
+R-Hmisc
+R-ICS
+R-ICSNP
 R-IRdisplay
 R-IRkernel
+R-ISwR
+R-Lahman
+R-LearnBayes
+R-Matching
 R-MatrixModels
+R-ModelMetrics
+R-NLP
+R-NMF
+R-NMOF
+R-PKI
+R-R.methodsS3
+R-R.oo
+R-R.utils
+R-R2Cuba
+R-R2HTML
 R-R6
+R-RANN
 R-RColorBrewer
 R-RCurl
+R-RJSONIO
+R-ROCR
+R-RSQLite
+R-RSclient
+R-RUnit
+R-RandomFields
+R-RandomFieldsUtils
 R-Rcpp
+R-RcppArmadillo
 R-RcppEigen
+R-RcppProgress
+R-RcppRoll
+R-Rmpfr
+R-Rmpi
+R-Rtsne
+R-SDMTools
+R-SQUAREM
+R-Sleuth2
+R-SnowballC
 R-SparseM
+R-StanHeaders
+R-SuppDists
 R-TH.data
+R-TRAMPR
+R-TSP
 R-TTR
+R-TeachingDemos
+R-VGAM
+R-VGAMdata
+R-VIM
 R-XML
+R-abind
+R-acepack
+R-actuar
+R-ade4
+R-analogue
+R-ape
+R-argparse
+R-arm
 R-assertthat
 R-backports
 R-base64enc
+R-bayesm
+R-bayesplot
+R-bdsmatrix
+R-betareg
+R-bibtex
+R-bindr
+R-bindrcpp
+R-bipartite
+R-bit
+R-bit64
 R-bitops
+R-blob
 R-brew
+R-brglm
+R-bridgesampling
+R-brms
+R-broom
+R-caTools
+R-callr
 R-car
+R-carData
+R-caret
+R-cclust
+R-cellranger
+R-checkmate
 R-chron
+R-circlize
+R-classInt
+R-cli
+R-clue
+R-clustMixType
+R-coda
+R-coin
 R-colorspace
+R-colourpicker
+R-combinat
 R-commonmark
+R-compositions
+R-corpcor
+R-corrplot
+R-cowplot
 R-crayon
+R-crosstalk
 R-curl
+R-cvTools
+R-data.table
+R-dbarts
+R-dbplyr
+R-ddalpha
+R-deSolve
+R-debugme
 R-deepnet
+R-deldir
+R-dendextend
 R-desc
 R-devtools
+R-dfoptim
 R-dichromat
+R-diffusionMap
 R-digest
+R-dimRed
+R-diptest
+R-dlm
+R-doMC
+R-doMPI
+R-doParallel
+R-doRNG
+R-doSNOW
+R-dotCall64
+R-dplyr
+R-drc
+R-dtw
+R-dygraphs
 R-dynlm
 R-e1071
+R-earth
+R-ellipse
+R-energy
 R-evaluate
+R-expint
+R-expm
+R-fastICA
+R-fastcluster
+R-fastmatch
+R-fda
+R-ff
+R-fields
+R-findpython
+R-fitdistrplus
+R-flashClust
+R-flexmix
+R-forcats
 R-foreach
 R-formatR
+R-fpc
+R-futile.logger
+R-futile.options
+R-gam
+R-gamm4
+R-gbm
+R-gclus
+R-gdata
+R-geometry
+R-getopt
+R-ggjoy
 R-ggplot2
+R-ggplot2movies
+R-ggridges
 R-git2r
 R-glmnet
+R-glue
+R-gmodels
+R-gmp
+R-goftest
+R-gower
+R-gplots
+R-gridBase
+R-gridExtra
 R-gtable
 R-gtools
+R-haven
+R-hexbin
 R-highr
 R-hms
+R-htmlTable
 R-htmltools
+R-htmlwidgets
 R-httpuv
 R-httr
+R-ica
+R-igraph
+R-inline
+R-inum
+R-ipred
+R-irlba
 R-iterators
+R-jpeg
 R-jsonlite
+R-kernlab
+R-klaR
 R-knitr
 R-labeling
+R-labelled
+R-laeken
+R-lambda.r
+R-lars
+R-latticeExtra
+R-lava
 R-lazyeval
+R-lda
+R-leaps
+R-lfe
+R-libcoin
+R-lle
 R-lme4
 R-lmtest
+R-locfit
+R-loo
+R-lpSolve
 R-lubridate
+R-magic
 R-magrittr
 R-manipulate
 R-mapproj
 R-maps
 R-maptools
 R-markdown
+R-matrixStats
+R-matrixcalc
+R-maxLik
+R-mclust
+R-mda
+R-memisc
 R-memoise
+R-mi
 R-microbenchmark
 R-mime
+R-miniUI
+R-minpack.lm
 R-minqa
+R-miscTools
+R-mixtools
+R-mlbench
+R-mnormt
 R-mockery
+R-modelr
+R-modeltools
 R-mondate
 R-multcomp
+R-multiwayvcov
 R-munsell
+R-mvoutlier
 R-mvtnorm
+R-network
 R-neuralnet
+R-nleqslv
 R-nloptr
+R-nortest
+R-numDeriv
+R-nycflights13
 R-openssl
+R-openxlsx
+R-optparse
+R-packrat
+R-pamr
+R-party
+R-partykit
+R-pbapply
 R-pbdZMQ
 R-pbkrtest
+R-pcaPP
+R-pdfCluster
+R-permute
+R-phylogram
 R-pillar
 R-pkgconfig
+R-pkgmaker
+R-plm
+R-plogr
+R-plotly
+R-plotmo
+R-plotrix
+R-pls
 R-plyr
+R-pmml
 R-png
+R-polspline
+R-polyclip
+R-polycor
+R-prabclus
+R-pracma
 R-praise
+R-prettyunits
+R-princurve
+R-prodlim
+R-profileModel
+R-progress
 R-proto
+R-proxy
 R-pryr
+R-psych
+R-purrr
+R-pxweb
+R-qap
 R-quadprog
 R-quantmod
 R-quantreg
+R-questionr
 R-randomForest
+R-ranger
+R-raster
+R-rasterVis
+R-readr
+R-readxl
+R-recipes
+R-registry
+R-rematch
 R-repr
+R-reprex
+R-reshape
 R-reshape2
+R-reticulate
+R-rgenoud
+R-rgl
+R-rio
 R-rlang
 R-rmarkdown
+R-rms
+R-rngtools
+R-robCompositions
+R-robustbase
+R-rootSolve
 R-roxygen2
 R-rprojroot
+R-rrcov
+R-rsconnect
+R-rstan
+R-rstanarm
+R-rstantools
 R-rstudioapi
 R-rversions
+R-rvest
+R-sROC
+R-sampling
 R-sandwich
 R-scales
+R-scatterplot3d
+R-segmented
+R-selectr
+R-sem
+R-seriation
+R-setRNG
+R-sfsmisc
+R-sgeostat
+R-shape
 R-shiny
+R-shinyjs
+R-shinystan
+R-shinythemes
+R-slam
+R-sm
+R-smoother
+R-sn
+R-sna
+R-snow
+R-snowfall
+R-som
 R-sourcetools
 R-sp
+R-spData
+R-spam
+R-spatstat
+R-spatstat.data
+R-spatstat.utils
+R-spdep
+R-spls
 R-statmod
+R-statnet.common
 R-stringi
 R-stringr
+R-strucchange
+R-subselect
+R-superpc
+R-survey
+R-systemfit
 R-tau
+R-tclust
+R-tensor
+R-tensorA
 R-testit
 R-testthat
+R-threejs
 R-tibble
+R-tidyr
+R-tidyselect
+R-tidyverse
 R-timeDate
 R-tis
+R-tm
+R-topicmodels
+R-treatSens
 R-tree
+R-trimcluster
+R-truncnorm
 R-tseries
+R-tsne
+R-utf8
 R-uuid
+R-vcd
+R-vegan
+R-viridis
 R-viridisLite
+R-visNetwork
 R-whisker
 R-withr
 R-xml2
@@ -176,12 +509,15 @@ WebOb
 WebTest
 Werkzeug
 Whoosh
+Z3
 abireport
 absl-py
 accountsservice
 acl
 acme
 acpica-unix2
+acrn-devicemodel
+acrn-hypervisor
 adwaita-icon-theme
 aeon
 alabaster
@@ -208,7 +544,9 @@ asio
 asn1crypto
 aspell
 aspell-en
+astor
 astroid
+astunparse
 at
 at-spi2-atk
 at-spi2-core
@@ -223,6 +561,7 @@ augeas
 authconfig
 autoconf
 autoconf-archive
+autoconf213
 autofs
 autogen
 automake
@@ -230,9 +569,11 @@ awscli
 azure-configs
 babeltrace
 babl
+backcall
 backports.functools_lru_cache
 backports.ssl_match_hostname
 backports.weakref
+baobab
 bash
 bash-completion
 bash_kernel
@@ -255,10 +596,12 @@ bluez
 bndl-lamp-basic
 bokeh
 boost
+borgbackup
 boto
 boto3
 botocore
 bridge-utils
+brotli
 bsdiff
 btrfs-progs
 bundle-chroot-builder
@@ -269,8 +612,10 @@ c_rehash
 ca-certs
 ca-certs-static
 cabextract
+cached-property
 cairo
 cairomm
+cantarell-fonts
 cargo
 caribou
 catch2
@@ -317,6 +662,7 @@ clr-systemd-config
 clr-update-triggers
 clr-wallpapers
 clrtrust
+clucene-core
 clutter
 clutter-gst
 clutter-gtk
@@ -334,15 +680,18 @@ comedilib
 compat-SDL2-soname1
 compat-efivar-soname0
 compat-fuse-soname2
+compat-gegl
 compat-glew-soname1
 compat-guile-soname20
 compat-libical-soname2
 compat-libpng-soname12
 compat-libwebp-soname6
 compat-llvm-soname4
+compat-llvm-soname5
 compat-mpfr-soname4
 compat-opencv-soname32
 compat-opencv-soname33
+compat-protobuf-soname14
 compat-readline
 component
 compositeproto
@@ -365,6 +714,7 @@ cpuid
 cracklib
 crcmod
 createrepo_c
+cri-containerd
 cri-o
 cri-tools
 cryptography
@@ -389,6 +739,7 @@ dbus-glib
 dconf
 deap
 decorator
+defusedxml
 dejagnu
 desktop-file-utils
 dfc
@@ -409,6 +760,7 @@ docbook-xml
 docker
 docker-py
 docutils
+dogtail
 dos2unix
 dosfstools
 double-conversion
@@ -473,6 +825,7 @@ flex
 flmsg
 flnet
 fltk
+folks
 font-adobe-100dpi
 font-adobe-75dpi
 font-bitstream-type1
@@ -489,6 +842,7 @@ functools32
 fuse
 futures
 garcon
+gast
 gawk
 gc
 gcab
@@ -509,6 +863,8 @@ geoclue
 geocode-glib
 gettext
 gevent
+gexiv2
+gfbgraph
 gflags
 ghostscript
 gimp
@@ -537,6 +893,7 @@ gnome-bluetooth
 gnome-calculator
 gnome-calendar
 gnome-characters
+gnome-color-manager
 gnome-common
 gnome-control-center
 gnome-desktop
@@ -545,17 +902,26 @@ gnome-font-viewer
 gnome-icon-theme
 gnome-initial-setup
 gnome-keyring
+gnome-logs
+gnome-maps
 gnome-menus
+gnome-music
 gnome-online-accounts
 gnome-panel
+gnome-photos
 gnome-screenshot
 gnome-session
 gnome-settings-daemon
 gnome-shell
 gnome-shell-extensions
+gnome-system-monitor
 gnome-terminal
 gnome-themes-standard
+gnome-todo
 gnome-tweak-tool
+gnome-user-docs
+gnome-video-effects
+gnome-weather
 gnu-efi
 gnupg
 gnuplot
@@ -563,6 +929,7 @@ gnutls
 go
 gobject-introspection
 golang-github-cpuguy83-go-md2man
+gom
 goocanvas
 google-api-python-client
 google-apitools
@@ -575,6 +942,7 @@ gpredict
 gptfdisk
 gradle
 gradle-dep
+graphene
 graphviz
 greenlet
 grep
@@ -582,9 +950,11 @@ grig
 grilo
 grilo-plugins
 groff
+grpcio
 grub
 gsettings-desktop-schemas
 gsl
+gsound
 gspell
 gst-plugins-bad
 gst-plugins-base
@@ -626,6 +996,7 @@ httpretty
 hub
 hunspell
 hwloc
+hyperscan
 hyperstart
 hypothesis
 i2c-tools
@@ -637,6 +1008,7 @@ icon-naming-utils
 icu4c
 idna
 imagesize
+imapfilter
 indent
 infiniband-diags
 iniparse
@@ -644,6 +1016,7 @@ init-rdahead
 inotify-tools
 inputproto
 intltool
+invm-frameworks
 ioping
 iotop
 ipaddr
@@ -667,15 +1040,19 @@ irssi
 isa-l
 iso-codes
 iso8601
+isodate
 isort
 ister
 itstool
 iw
+ixpdimm_sw
+jansson
 jedi
 jedi-vim
 jemalloc
 jmespath
 joe
+josepy
 jq
 json-c
 json-glib
@@ -687,6 +1064,8 @@ jupyter-notebook-gist
 jupyter_client
 jupyter_console
 jupyter_core
+jupyterlab
+jupyterlab_launcher
 kafka-dep
 kbd
 kbproto
@@ -694,6 +1073,7 @@ kexec-tools
 keyring
 keyutils
 khal
+kiwisolver
 kmod
 koji
 krb5
@@ -748,6 +1128,7 @@ libcap
 libcap-ng
 libcdio
 libcgroup
+libchamplain
 libcomps
 libconfig
 libcroco
@@ -766,6 +1147,7 @@ libgcrypt
 libgd
 libgdata
 libgee
+libgepub
 libgfortran-avx
 libgfortran-compat-soname3
 libgit2
@@ -813,7 +1195,9 @@ libpthread-stubs
 libpwquality
 librepo
 librsvg
+librtlsdr
 libsamplerate
+libsass
 libseccomp
 libsecret
 libsigc++
@@ -821,6 +1205,7 @@ libsndfile
 libsolv
 libsoup
 libspectre
+libsrtp
 libssh
 libssh2
 libstoragemgmt
@@ -925,9 +1310,11 @@ motd-update
 motif
 mozjs
 mozjs38
+mozjs52
 mpc
 mpfr
 mpg123
+msgpack-python
 msmtp
 msr-tools
 mstflint
@@ -945,8 +1332,8 @@ nasm
 nautilus
 nbconvert
 nbformat
+nbsphinx
 ncurses
-ncurses-compat
 ndctl
 ndg_httpsclient
 neofetch
@@ -1017,6 +1404,7 @@ opusfile
 orc
 ordereddict
 ostree
+ovirt-guest-agent
 p11-kit
 p7zip
 packaging
@@ -1185,6 +1573,7 @@ pyOpenSSL
 pyaml
 pyasn1
 pyasn1-modules
+pyatspi
 pycairo
 pycodestyle
 pycparser
@@ -1229,6 +1618,7 @@ python-systemd
 python-tappy
 python-toml
 python-urwid
+python-zeep
 python3
 pytz
 pyudev
@@ -1238,10 +1628,37 @@ pyzmq
 qemu
 qemu-lite
 qpdf
-qt-everywhere-opensource-src
+qt3d
+qtbase
+qtcanvas3d
+qtcharts
+qtconnectivity
 qtconsole
+qtdeclarative
+qtgraphicaleffects
+qtimageformats
+qtlocation
+qtmultimedia
+qtquickcontrols
+qtquickcontrols2
+qtremoteobjects
+qtscript
+qtscxml
+qtsensors
+qtserialbus
+qtserialport
+qtsvg
+qttools
+qttranslations
+qtvirtualkeyboard
+qtwayland
+qtwebchannel
+qtwebsockets
+qtx11extras
+qtxmlpatterns
 quagga
 quilt
+ragel
 randrproto
 rdma-core
 re2c
@@ -1270,6 +1687,7 @@ rxvt-unicode
 s2tc
 s3transfer
 samba
+sassc
 satyr
 sbc
 sbsigntools
@@ -1284,6 +1702,7 @@ screen
 scripttest
 scrnsaverproto
 seaborn
+seahorse
 secretstorage
 sed
 setproctitle
@@ -1313,13 +1732,13 @@ sox
 spark-dep
 speex
 speexdsp
+sphinx_rtd_theme
 sphinxcontrib-newsfeed
 sphinxcontrib-websupport
 spi-tools
 spice
 spice-gtk
 spice-protocol
-spyder
 spyder-notebook
 sqlite-autoconf
 sqlparse
@@ -1331,6 +1750,7 @@ strace
 subunit
 sudo
 sure
+suricata
 swig
 swupd-client
 swupd-overdue
@@ -1376,6 +1796,7 @@ tiptop
 tk
 tmux
 tokyocabinet
+toolbelt
 tornado
 totem
 totem-pl-parser
@@ -1384,6 +1805,7 @@ tqdm
 traceback2
 traceroute
 tracker
+tracker-miners
 traitlets
 tree
 typed-ast
@@ -1415,6 +1837,7 @@ videoproto
 vim
 vim-go
 vinagre
+vino
 virt-manager
 virt-viewer
 virtualenv
@@ -1432,11 +1855,13 @@ webencodings
 webkitgtk
 websocket_client
 websockify
+weechat
 weston
 wget
 wheel
 which
 widgetsnbextension
+woff2
 wol
 wpa_supplicant
 wrapt
@@ -1495,6 +1920,7 @@ xkbcomp
 xkeyboard-config
 xlog
 xmlsec1
+xmlstarlet
 xmlto
 xorg-server
 xorriso

user-setup.sh

@@ -149,4 +149,4 @@ fi
 echo -en "\n************************\n"
 
 echo 'Workspace has been set up in the "clearlinux" directory'
-echo 'NOTE: logout and log back in or run "newgrp kvm" to finalize the setup process'
+echo 'NOTE: logout and log back in to finalize the setup process'