When pak is enabled restore fails to remove unused dependencies

My renv.lock only lists renv as a dependency: ``` "Packages": { "renv": { ... ``` My renv library contains tidyverse, drc and all their dependencies (a lot). In my project neither tidyverse nor drc are used anymore at this point. ``` r$> renv::status() No issues found -- the project is in a consistent state. ``` This seems already wrong to me, there are tons of installed dependencies that are unrequired: ``` r$> renv::dependencies() Finding R package dependencies ... Done! Source Package Require Version Dev 1 /Users/carlos/Desktop/Scratch/renv.lock renv FALSE ``` Now I add to some file: ``` library(tidyverse) library(drc) ``` so that: ``` r$> renv::status() The following package(s) are in an inconsistent state: package installed recorded used abind y n y askpass y n y backports y n y base64enc y n y bit y n y bit64 y n y ... ``` At this point `renv::restore(clean = TRUE)` does nothing at all. Perhaps I'm misunderstanding how all this should work but AFAIU: - Before adding the `library(...)` lines `status` should have said that there were installed and unused dependencies and `restore(clean = TRUE)` should have removed them. - After adding the `library(...)` lines the output of `status` is fine but `restore(clean = TRUE)` still does nothing. Both behaviors seem wrong to me, according to the lock file all the installed dependencies has to be removed. More so in the first scenario where even the inferred dependencies were nil. The documentation of `restore` clearly states: > If clean = TRUE, restore() will additionally delete any packages in the project library that don't appear in the lockfile. <details> <summary>Diagnostics</summary> ``` Diagnostics Report [renv 1.2.2] =============================== # Session Info --------------------------------------------------------------- R version 4.5.3 (2026-03-11) Platform: aarch64-apple-darwin20 Running under: macOS Tahoe 26.4.1 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 time zone: America/Argentina/Buenos_Aires tzcode source: internal attached base packages: [1] stats graphics grDevices datasets utils methods base loaded via a namespace (and not attached): [1] compiler_4.5.3 tools_4.5.3 yaml_2.3.12 renv_1.2.2 pak_0.9.4 # Project -------------------------------------------------------------------- Project path: "~/Desktop/Scratch" # Status --------------------------------------------------------------------- The following package(s) are in an inconsistent state: package installed recorded used abind y n y askpass y n y backports y n y base64enc y n y bit y n y bit64 y n y blob y n y boot y n y broom y n y bslib y n y cachem y n y callr y n y car y n y carData y n y cellranger y n y cli y n y clipr y n y codetools y n y colorspace y n y conflicted y n y cowplot y n y cpp11 y n y crayon y n y curl y n y data.table y n y DBI y n y dbplyr y n y Deriv y n y digest y n y doBy y n y dplyr y n y drc y n y dtplyr y n y evaluate y n y farver y n y fastmap y n y fontawesome y n y forcats y n y forecast y n y Formula y n y fracdiff y n y fs y n y gargle y n y generics y n y ggplot2 y n y glue y n y googledrive y n y googlesheets4 y n y gtable y n y gtools y n y haven y n y highr y n y hms y n y htmltools y n y httr y n y ids y n y isoband y n y jquerylib y n y jsonlite y n y knitr y n y labeling y n y lattice y n y lifecycle y n y lme4 y n y lmtest y n y lubridate y n y magrittr y n y MASS y n y Matrix y n y MatrixModels y n y memoise y n y mgcv y n y microbenchmark y n y mime y n y minqa y n y modelr y n y multcomp y n y mvtnorm y n y nlme y n y nloptr y n y nnet y n y numDeriv y n y openssl y n y pbkrtest y n y pillar y n y pkgconfig y n y plotrix y n y processx y n y progress n n y ps y n y purrr y n y quantreg y n y R6 y n y ragg y n y rappdirs y n y rbibutils y n y RColorBrewer y n y Rcpp y n y RcppArmadillo n n y RcppEigen n n y Rdpack y n y readr y n y readxl y n y reformulas y n y rematch y n y rematch2 y n y reprex y n y rlang y n y rmarkdown y n y rstudioapi y n y rvest y n y S7 y n y sandwich y n y sass y n y scales y n y selectr y n y SparseM y n y stringi y n y stringr y n y survival y n y sys y n y systemfonts y n y textshaping y n y TH.data y n y tibble y n y tidyr y n y tidyselect y n y tidyverse y n y timechange y n y timeDate y n y tinytex y n y tzdb y n y urca y n y utf8 y n y uuid y n y vctrs y n y viridisLite y n y vroom y n y withr y n y xfun y n y xml2 y n y yaml y n y zoo y n y See `?renv::status` for advice on resolving these issues. # Packages ------------------------------------------------------------------- Library Source Lockfile Source Path Dependency DBI 1.3.0 CRAN <NA> <NA> [1] indirect Deriv 4.2.0 CRAN <NA> <NA> [1] indirect Formula 1.2-5 CRAN <NA> <NA> [1] indirect KernSmooth 2.23-26 CRAN <NA> <NA> [2] <NA> MASS 7.3-65 CRAN <NA> <NA> [2] indirect Matrix 1.7-5 CRAN <NA> <NA> [1] indirect MatrixModels 0.5-4 CRAN <NA> <NA> [1] indirect R6 2.6.1 CRAN <NA> <NA> [1] indirect RColorBrewer 1.1-3 CRAN <NA> <NA> [1] indirect Rcpp 1.1.1-1.1 CRAN <NA> <NA> [1] indirect RcppArmadillo <NA> <NA> <NA> <NA> <NA> indirect RcppEigen <NA> <NA> <NA> <NA> <NA> indirect Rdpack 2.6.6 CRAN <NA> <NA> [1] indirect S7 0.2.2 CRAN <NA> <NA> [1] 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<NA> <NA> [1] indirect xfun 0.57 CRAN <NA> <NA> [1] indirect xml2 1.5.2 CRAN <NA> <NA> [1] indirect yaml 2.3.12 CRAN <NA> <NA> [1] indirect zoo 1.8-15 CRAN <NA> <NA> [1] indirect [1]: /Users/carlos/Desktop/Scratch/.renv/library/macos/R-4.5/aarch64-apple-darwin20 [2]: /Users/carlos/Library/Caches/org.R-project.R/R/renv/sandbox/macos/R-4.5/aarch64-apple-darwin20/4cd76b74 # /Library/Frameworks/R.framework/Resources/etc/Makeconf --------------------- # etc/Makeconf. Generated from Makeconf.in by configure. -*- Makefile -*- # # ${R_HOME}/etc/Makeconf # # R was configured using the following call # (not including env. vars and site configuration) # configure 'FW_VERSION=4.5-arm64' 'CC=clang -arch arm64' 'CXX=clang++ -arch arm64' 'OBJC=clang -arch arm64' 'FC=/opt/gfortran/bin/gfortran -arch arm64' 'CFLAGS=-falign-functions=64 -Wall -g -O2' 'CXXFLAGS=-falign-functions=64 -Wall -g -O2' 'OBJCFLAGS=-falign-functions=64 -Wall -g -O2' 'FCFLAGS=-Wall -g -O2' 'F77FLAGS=-Wall -g -O2' 'LDFLAGS=-L/opt/R/arm64/lib' 'CPPFLAGS=-I/opt/R/arm64/include' '--enable-memory-profiling' '--enable-R-framework' '--with-tcl-config=/opt/R/arm64/lib/tclConfig.sh' '--with-tk-config=/opt/R/arm64/lib/tkConfig.sh' '--with-2025blas' '--build=aarch64-apple-darwin20' 'build_alias=aarch64-apple-darwin20' 'PKG_CONFIG_PATH=/usr/lib/pkgconfig:/opt/R/arm64/lib/pkgconfig:/opt/R/arm64/share/pkgconfig:/opt/X11/lib/pkgconfig:/opt/X11/share/pkgconfig' ## This fails if it contains spaces, or if it is quoted include $(R_SHARE_DIR)/make/vars.mk AR = ar BLAS_LIBS = -L"$(R_HOME)/lib$(R_ARCH)" -lRblas ## C compilers CC = clang -arch arm64 -std=gnu2x CFLAGS = -falign-functions=64 -Wall -g -O2 $(LTO) CC17 = clang -arch arm64 -std=gnu17 C17FLAGS = -falign-functions=64 -Wall -g -O2 $(LTO) CC23 = clang -arch arm64 -std=gnu2x C23FLAGS = -falign-functions=64 -Wall -g -O2 $(LTO) CC90 = clang -arch arm64 -std=gnu90 C90FLAGS = -falign-functions=64 -Wall -g -O2 $(LTO) CC99 = clang -arch arm64 -std=gnu99 C99FLAGS = -falign-functions=64 -Wall -g -O2 $(LTO) CPICFLAGS = -fPIC CPPFLAGS = -I/opt/R/arm64/include C_VISIBILITY = -fvisibility=hidden ## C++ compilers CXX = clang++ -arch arm64 -std=gnu++17 CXXFLAGS = -falign-functions=64 -Wall -g -O2 $(LTO) CXXPICFLAGS = -fPIC CXX11 = clang++ -arch arm64 CXX11FLAGS = -falign-functions=64 -Wall -g -O2 $(LTO) CXX11PICFLAGS = -fPIC CXX11STD = -std=gnu++11 CXX14 = clang++ -arch arm64 CXX14FLAGS = -falign-functions=64 -Wall -g -O2 $(LTO) CXX14PICFLAGS = -fPIC CXX14STD = -std=gnu++14 CXX17 = clang++ -arch arm64 CXX17FLAGS = -falign-functions=64 -Wall -g -O2 $(LTO) CXX17PICFLAGS = -fPIC CXX17STD = -std=gnu++17 CXX20 = clang++ -arch arm64 CXX20FLAGS = -falign-functions=64 -Wall -g -O2 $(LTO) CXX20PICFLAGS = -fPIC CXX20STD = -std=gnu++20 CXX23 = clang++ -arch arm64 CXX23FLAGS = -falign-functions=64 -Wall -g -O2 $(LTO) CXX23PICFLAGS = -fPIC CXX23STD = -std=gnu++23 CXX26 = clang++ -arch arm64 CXX26FLAGS = -falign-functions=64 -Wall -g -O2 $(LTO) CXX26PICFLAGS = -fPIC CXX26STD = -std=gnu++26 CXX_VISIBILITY = -fvisibility=hidden DYLIB_EXT = .dylib DYLIB_LD = $(CC) DYLIB_LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup# $(CFLAGS) $(CPICFLAGS) ## should be used by packages for dylibs, but at the time of writing was not DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS) ECHO = echo ECHO_C = \c ECHO_N = ECHO_T = ## Fortran FC = /opt/gfortran/bin/gfortran -arch arm64 FCFLAGS = -Wall -g -O2 $(LTO_FC) ## additional libs needed when linking with $(FC), e.g. on some Oracle compilers FCLIBS_XTRA = FFLAGS = -Wall -g -O2 $(LTO_FC) FLIBS = -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath FPICFLAGS = -fPIC FPIEFLAGS = -fPIE F_VISIBILITY = -fvisibility=hidden FOUNDATION_CPPFLAGS = FOUNDATION_LIBS = -framework Foundation JAR = /usr/bin/jar JAVA = /usr/bin/java JAVAC = /usr/bin/javac JAVAH = /usr/bin/javah ## JAVA_HOME might be used in the next three. ## They are for packages 'JavaGD' and 'rJava' JAVA_HOME = /Library/Java/JavaVirtualMachines/jdk-11.0.18+10/Contents/Home JAVA_CPPFLAGS = -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/darwin JAVA_LIBS = -L$(JAVA_HOME)/lib/server -ljvm JAVA_LD_LIBRARY_PATH = $(JAVA_HOME)/lib/server LAPACK_LIBS = -L"$(R_HOME)/lib$(R_ARCH)" -lRlapack LDFLAGS = -L/opt/R/arm64/lib ## We only need this is if it is external and not libc, as otherwise link to R ## Oo macOS, where libintl is static and so compiled in, can still link to R LIBINTL = LIBM = LIBR0 = -L"$(R_HOME)/lib$(R_ARCH)" LIBR1 = -lR LIBR = -F/Library/Frameworks/R.framework/.. -framework R LIBS = -lpcre2-8 -lbz2 -lz -licucore -ldl -lm -liconv ## needed by R CMD config LIBnn = lib LIBTOOL = $(SHELL) "$(R_HOME)/bin/libtool" ## set for --enable-lto, --enable-lto=check LTO = LTO_FC = LTO_LD = ## set for --enable-lto=R, used in INSTALL LTO_OPT = LTO_FC_OPT = ## needed to build applications linking to static libR MAIN_LD = $(CC) MAIN_LDFLAGS = MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LDFLAGS) MKINSTALLDIRS = "$(R_HOME)/bin/mkinstalldirs" NM = /usr/bin/nm -B OBJC = clang -arch arm64 OBJCFLAGS = -falign-functions=64 -Wall -g -O2 -fobjc-exceptions $(LTO) OBJC_LIBS = -lobjc OBJCXX = clang++ -arch arm64 -std=gnu++17 R_ARCH = RANLIB = ranlib SAFE_FFLAGS = -Wall -g -O2 ## A version of SHLIB_LIBADD not overridden in install.R. SAN_LIBS = SED = /usr/bin/sed SHELL = /bin/sh SHLIB_CFLAGS = SHLIB_CXXFLAGS = SHLIB_CXXLD = $(CXX) SHLIB_CXXLDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup# $(CXXFLAGS) $(CXXPICFLAGS) $(LTO_LD) SHLIB_CXX11LD = $(CXX11) $(CXX11STD) SHLIB_CXX11LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup# $(CXX11FLAGS) $(CXX11PICFLAGS) $(LTO_LD) SHLIB_CXX14LD = $(CXX14) $(CXX14STD) SHLIB_CXX14LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup# $(CXX14FLAGS) $(CXX14PICFLAGS) $(LTO_LD) SHLIB_CXX17LD = $(CXX17) $(CXX17STD) SHLIB_CXX17LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup# $(CXX17FLAGS) $(CXX17PICFLAGS) $(LTO_LD) SHLIB_CXX20LD = $(CXX20) $(CXX20STD) SHLIB_CXX20LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup# $(CXX20FLAGS) $(CXX20PICFLAGS) $(LTO_LD) SHLIB_CXX23LD = $(CXX23) $(CXX23STD) SHLIB_CXX23LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup# $(CXX23FLAGS) $(CXX23PICFLAGS) $(LTO_LD) SHLIB_CXX26LD = $(CXX26) $(CXX26STD) SHLIB_CXX26LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup# $(CXX26FLAGS) $(CXX26PICFLAGS) $(LTO_LD) SHLIB_EXT = .so SHLIB_FCLD = $(FC) SHLIB_FCLDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup# $(FCFLAGS) $(FPICFLAGS) SHLIB_FFLAGS = SHLIB_LD = $(CC) ## used for add-on packages linked by C SHLIB_LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup# $(CFLAGS) $(CPICFLAGS) $(LTO_LD) ## used for standard packages SHLIB_LDFLAGS_R = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup# $(CFLAGS) $(CPICFLAGS) $(LTO_LD) ## used in install.R to add OBJC_LIBS, FLIBS .... SHLIB_LIBADD = ## We want to ensure libR is picked up from $(R_HOME)/lib ## before e.g. /usr/local/lib if a version is already installed. SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LIBR0) $(LDFLAGS) SHLIB_OPENMP_CFLAGS = SHLIB_OPENMP_CXXFLAGS = SHLIB_OPENMP_FFLAGS = STRIP_STATIC_LIB = strip -S STRIP_SHARED_LIB = strip -x TCLTK_CPPFLAGS = -I/opt/R/arm64/include -I/opt/R/arm64/include -I/usr/X11R6/include TCLTK_LIBS = -L/opt/R/arm64/lib -ltcl8.6 -L/opt/R/arm64/lib -ltk8.6 -L/usr/X11R6/lib -lX11 -Wl,-weak-lXss -lXext YACC = bison -y ## for linking to libR.a STATIC_LIBR = # "$(R_HOME)/lib$(R_ARCH)/libR.a" $(BLAS_LIBS) $(FLIBS) $(LIBINTL) -lreadline -lncurses $(LIBS) ## These are recorded as macros for legacy use in packages ## set on AIX, formerly for old glibc (-D__NO_MATH_INLINES) R_XTRA_CFLAGS = ## was formerly set on HP-UX R_XTRA_CPPFLAGS = -I"$(R_INCLUDE_DIR)" -DNDEBUG ## currently unset R_XTRA_CXXFLAGS = ## used for gfortran >= 7 in R 3.6.1 - 4.2.x R_XTRA_FFLAGS = ## SHLIB_CFLAGS SHLIB_CXXFLAGS SHLIB_FFLAGS are apparently currently unused ## SHLIB_CXXFLAGS is undocumented, there is no SHLIB_FCFLAGS ALL_CFLAGS = $(PKG_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS) ## XDEFS was a temporary measure for use by R CMD INSTALL ALL_CPPFLAGS = -I"$(R_INCLUDE_DIR)" -DNDEBUG $(PKG_CPPFLAGS) $(CLINK_CPPFLAGS) $(CPPFLAGS) $(XDEFS) ## CXX_DEFS allows adding defines only for C++, e.g. -DR_NO_REMAP ALL_CXXFLAGS = $(PKG_CXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(CXXFLAGS) $(CXX_DEFS) ALL_OBJCFLAGS = $(PKG_OBJCFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(OBJCFLAGS) ALL_OBJCXXFLAGS = $(PKG_OBJCXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(OBJCXXFLAGS) ALL_FFLAGS = $(PKG_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS) ## can be overridden by R CMD SHLIB P_FCFLAGS = $(PKG_FFLAGS) ALL_FCFLAGS = $(P_FCFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FCFLAGS) ## LIBR here as a couple of packages use this without SHLIB_LINK ALL_LIBS = $(PKG_LIBS) $(SHLIB_LIBADD) $(SAN_LIBS) $(LIBR) $(LIBINTL) .SUFFIXES: .SUFFIXES: .c .cc .cpp .d .f .f90 .f95 .m .mm .M .o .c.o: $(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -c $< -o $@ .c.d: @echo "making $@ from $<" @$(CC) -MM $(ALL_CPPFLAGS) $< > $@ .cc.o: $(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@ .cpp.o: $(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@ .cc.d: @echo "making $@ from $<" @$(CXX) -M $(ALL_CPPFLAGS) $< > $@ .cpp.d: @echo "making $@ from $<" @$(CXX) -M $(ALL_CPPFLAGS) $< > $@ .m.o: $(OBJC) $(ALL_CPPFLAGS) $(ALL_OBJCFLAGS) -c $< -o $@ .m.d: @echo "making $@ from $<" @$(OBJC) -MM $(ALL_CPPFLAGS) $< > $@ .mm.o: $(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@ .M.o: $(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@ .f.o: $(FC) $(ALL_FFLAGS) -c $< -o $@ .f95.o: $(FC) $(ALL_FCFLAGS) -c $< -o $@ .f90.o: $(FC) $(ALL_FCFLAGS) -c $< -o $@ # R CMD config --all --------------------------------------------------------- CC = clang -arch arm64 -std=gnu2x CFLAGS = -falign-functions=64 -Wall -g -O2 CPICFLAGS = -fPIC CPPFLAGS = -I/opt/R/arm64/include CC17 = clang -arch arm64 -std=gnu17 C17FLAGS = -falign-functions=64 -Wall -g -O2 CC23 = clang -arch arm64 -std=gnu2x C23FLAGS = -falign-functions=64 -Wall -g -O2 CC90 = clang -arch arm64 -std=gnu90 C90FLAGS = -falign-functions=64 -Wall -g -O2 CC99 = clang -arch arm64 -std=gnu99 C99FLAGS = -falign-functions=64 -Wall -g -O2 CXX = clang++ -arch arm64 -std=gnu++17 CXXFLAGS = -falign-functions=64 -Wall -g -O2 CXXPICFLAGS = -fPIC CXX11 = clang++ -arch arm64 CXX11STD = -std=gnu++11 CXX11FLAGS = -falign-functions=64 -Wall -g -O2 CXX11PICFLAGS = -fPIC CXX14 = clang++ -arch arm64 CXX14STD = -std=gnu++14 CXX14FLAGS = -falign-functions=64 -Wall -g -O2 CXX14PICFLAGS = -fPIC CXX17 = clang++ -arch arm64 CXX17STD = -std=gnu++17 CXX17FLAGS = -falign-functions=64 -Wall -g -O2 CXX17PICFLAGS = -fPIC CXX20 = clang++ -arch arm64 CXX20STD = -std=gnu++20 CXX20FLAGS = -falign-functions=64 -Wall -g -O2 CXX20PICFLAGS = -fPIC CXX23 = clang++ -arch arm64 CXX23STD = -std=gnu++23 CXX23FLAGS = -falign-functions=64 -Wall -g -O2 CXX23PICFLAGS = -fPIC CXX26 = clang++ -arch arm64 CXX26STD = -std=gnu++26 CXX26FLAGS = -falign-functions=64 -Wall -g -O2 CXX26PICFLAGS = -fPIC DYLIB_EXT = .dylib DYLIB_LD = clang -arch arm64 -std=gnu2x DYLIB_LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup FC = /opt/gfortran/bin/gfortran -arch arm64 FFLAGS = -Wall -g -O2 FPICFLAGS = -fPIC FLIBS = -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath FCFLAGS = -Wall -g -O2 SAFE_FFLAGS = -Wall -g -O2 OBJC = clang -arch arm64 OBJCFLAGS = -falign-functions=64 -Wall -g -O2 -fobjc-exceptions JAVA = /usr/bin/java JAVAC = /usr/bin/javac JAVAH = /usr/bin/javah JAR = /usr/bin/jar JAVA_HOME = /Library/Java/JavaVirtualMachines/jdk-11.0.18+10/Contents/Home JAVA_LIBS = -L/Library/Java/JavaVirtualMachines/jdk-11.0.18+10/Contents/Home/lib/server -ljvm JAVA_CPPFLAGS = -I/Library/Java/JavaVirtualMachines/jdk-11.0.18+10/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk-11.0.18+10/Contents/Home/include/darwin LDFLAGS = -L/opt/R/arm64/lib SHLIB_CFLAGS = SHLIB_CXXFLAGS = SHLIB_CXXLD = clang++ -arch arm64 -std=gnu++17 SHLIB_CXXLDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup SHLIB_CXX11LD = clang++ -arch arm64 -std=gnu++11 SHLIB_CXX11LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup SHLIB_CXX14LD = clang++ -arch arm64 -std=gnu++14 SHLIB_CXX14LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup SHLIB_CXX17LD = clang++ -arch arm64 -std=gnu++17 SHLIB_CXX17LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup SHLIB_CXX20LD = clang++ -arch arm64 -std=gnu++20 SHLIB_CXX20LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup SHLIB_CXX23LD = clang++ -arch arm64 -std=gnu++23 SHLIB_CXX23LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup SHLIB_CXX26LD = clang++ -arch arm64 -std=gnu++26 SHLIB_CXX26LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup SHLIB_EXT = .so SHLIB_FFLAGS = SHLIB_LD = clang -arch arm64 -std=gnu2x SHLIB_LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup TCLTK_CPPFLAGS = -I/opt/R/arm64/include -I/opt/R/arm64/include -I/usr/X11R6/include TCLTK_LIBS = -L/opt/R/arm64/lib -ltcl8.6 -L/opt/R/arm64/lib -ltk8.6 -L/usr/X11R6/lib -lX11 -Wl,-weak-lXss -lXext BLAS_LIBS = -L/Library/Frameworks/R.framework/Resources/lib -lRblas LAPACK_LIBS = -L/Library/Frameworks/R.framework/Resources/lib -lRlapack MAKE = make LIBnn = lib AR = ar NM = /usr/bin/nm -B RANLIB = ranlib LTO = LTO_FC = LTO_LD = ## The following variables are defunct CPP CXXCPP # User Profile --------------------------------------------------------------- [no user profile detected] # Settings ------------------------------------------------------------------- List of 15 $ bioconductor.version : NULL $ external.libraries : chr(0) $ ignored.packages : chr(0) $ lockfile.sanitize : logi TRUE $ package.dependency.fields: chr [1:3] "Imports" "Depends" "LinkingTo" $ ppm.enabled : NULL $ ppm.ignored.urls : chr(0) $ r.version : NULL $ snapshot.dev : logi FALSE $ snapshot.type : chr "implicit" $ use.cache : logi TRUE $ vcs.ignore.cellar : logi TRUE $ vcs.ignore.library : logi TRUE $ vcs.ignore.local : logi TRUE $ vcs.manage.ignores : logi TRUE # Options -------------------------------------------------------------------- List of 9 $ defaultPackages : chr [1:6] "datasets" "utils" "grDevices" "graphics" ... $ download.file.method : NULL $ download.file.extra : NULL $ install.packages.compile.from.source: chr "interactive" $ pkgType : chr "both" $ repos : Named chr "https://cloud.r-project.org" ..- attr(*, "names")= chr "CRAN" $ renv.consent : logi TRUE $ renv.project.path : chr "/Users/carlos/Desktop/Scratch" $ renv.verbose : logi TRUE # Environment Variables ------------------------------------------------------ CC = <NA> CFLAGS = <NA> CPPFLAGS = <NA> CXX = <NA> CXXFLAGS = <NA> HOME = /Users/carlos LANG = en_US.UTF-8 LDFLAGS = <NA> MAKE = make R_LIBS = .rlib:/Users/carlos/.rlib R_LIBS_SITE = /Library/Frameworks/R.framework/Resources/site-library R_LIBS_USER = /Users/carlos/Desktop/Scratch/.renv/library/macos/R-4.5/aarch64-apple-darwin20 RENV_CONFIG_PAK_ENABLED = TRUE RENV_CONFIG_PPM_DEFAULT = FALSE RENV_DEFAULT_R_ENVIRON = <NA> RENV_DEFAULT_R_ENVIRON_USER = <NA> RENV_DEFAULT_R_LIBS = .rlib:/Users/carlos/.rlib RENV_DEFAULT_R_LIBS_SITE = /Library/Frameworks/R.framework/Resources/site-library RENV_DEFAULT_R_LIBS_USER = /Users/carlos/Library/R/arm64/4.5/library RENV_DEFAULT_R_PROFILE = <NA> RENV_DEFAULT_R_PROFILE_USER = <NA> RENV_PATHS_RENV = .renv RENV_PROJECT = /Users/carlos/Desktop/Scratch # PATH ----------------------------------------------------------------------- - /Users/carlos/Desktop/Scratch/.venv/bin - /Users/carlos/.venv/lib/python3.13/site-packages/quarto_cli/bin - /Users/carlos/Documents/Util - /Users/carlos/.venv/bin - /Users/carlos/.local/bin - /opt/homebrew/bin - /opt/homebrew/sbin - /usr/local/bin - /System/Cryptexes/App/usr/bin - /usr/bin - /bin - /usr/sbin - /sbin - /var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin - /var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin - /var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin - /opt/pkg/env/active/bin - /opt/pmk/env/global/bin - /Users/carlos/.venv/lib/python3.13/site-packages/quarto_cli/bin - /Users/carlos/Documents/Util - /Users/carlos/.venv/bin - /Users/carlos/.local/bin - /Users/carlos/.vscode/extensions/ms-python.debugpy-2025.18.0-darwin-arm64/bundled/scripts/noConfigScripts # Cache ---------------------------------------------------------------------- There are a total of 1 package installed in the renv cache. Cache path: "~/Library/Caches/org.R-project.R/R/renv/cache/v5/macos/R-4.5/aarch64-apple-darwin20" ``` </details>