Help understanding warning messages: Upon Updating Packages

AISYNC · November 29, 2018, 3:00am

Here is a truncated output of the long list of output messages I get upon:

update.packages(ask = FALSE)

This is managed by Anaconda on MacOS and I'll include the Pastebin with the entire warning message I was able to copy inside Terminal.

https://pastebin.com/M7znyY8k

-I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/readstat_io_unistd.c -o readstat/readstat_io_unistd.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/readstat_metadata.c -o readstat/readstat_metadata.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/readstat_bits.c -o readstat/readstat_bits.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/readstat_parser.c -o readstat/readstat_parser.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/sas/readstat_sas7bdat_read.c -o readstat/sas/readstat_sas7bdat_read.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/sas/readstat_xport.c -o readstat/sas/readstat_xport.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/sas/readstat_sas_rle.c -o readstat/sas/readstat_sas_rle.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/sas/readstat_sas.c -o readstat/sas/readstat_sas.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/sas/readstat_xport_read.c -o readstat/sas/readstat_xport_read.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/sas/ieee.c -o readstat/sas/ieee.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/sas/readstat_sas7bcat_write.c -o readstat/sas/readstat_sas7bcat_write.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/sas/readstat_sas7bdat_write.c -o readstat/sas/readstat_sas7bdat_write.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/sas/readstat_sas7bcat_read.c -o readstat/sas/readstat_sas7bcat_read.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/sas/readstat_xport_write.c -o readstat/sas/readstat_xport_write.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/spss/readstat_por_parse.c -o readstat/spss/readstat_por_parse.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/spss/readstat_sav_parse.c -o readstat/spss/readstat_sav_parse.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/spss/readstat_zsav_write.c -o readstat/spss/readstat_zsav_write.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/spss/readstat_por.c -o readstat/spss/readstat_por.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/spss/readstat_spss.c -o readstat/spss/readstat_spss.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/spss/readstat_por_write.c -o readstat/spss/readstat_por_write.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/spss/readstat_sav_write.c -o readstat/spss/readstat_sav_write.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/spss/readstat_zsav_read.c -o readstat/spss/readstat_zsav_read.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/spss/readstat_sav_parse_timestamp.c -o readstat/spss/readstat_sav_parse_timestamp.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/spss/readstat_zsav_compress.c -o readstat/spss/readstat_zsav_compress.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/spss/readstat_sav.c -o readstat/spss/readstat_sav.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/spss/readstat_por_read.c -o readstat/spss/readstat_por_read.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/spss/readstat_sav_read.c -o readstat/spss/readstat_sav_read.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/spss/readstat_spss_parse.c -o readstat/spss/readstat_spss_parse.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/spss/readstat_sav_compress.c -o readstat/spss/readstat_sav_compress.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/stata/readstat_dta_write.c -o readstat/stata/readstat_dta_write.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/stata/readstat_dta_parse_timestamp.c -o readstat/stata/readstat_dta_parse_timestamp.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/stata/readstat_dta.c -o readstat/stata/readstat_dta.o
x86_64-apple-darwin13.4.0-clang -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c readstat/stata/readstat_dta_read.c -o readstat/stata/readstat_dta_read.o
x86_64-apple-darwin13.4.0-clang++ -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o
x86_64-apple-darwin13.4.0-clang++ -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c haven_types.cpp -o haven_types.o
x86_64-apple-darwin13.4.0-clang++ -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c DfWriter.cpp -o DfWriter.o
x86_64-apple-darwin13.4.0-clang++ -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -Ireadstat -DHAVE_ZLIB -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c DfReader.cpp -o DfReader.o
x86_64-apple-darwin13.4.0-clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Users/{username}/anaconda3/lib/R/lib -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/{username}/anaconda3/lib -L/Users/{username}/anaconda3/lib -o haven.so tagged_na.o readstat/readstat_value.o readstat/readstat_malloc.o readstat/CKHashTable.o readstat/readstat_convert.o readstat/readstat_error.o readstat/readstat_writer.o readstat/readstat_variable.o readstat/readstat_io_unistd.o readstat/readstat_metadata.o readstat/readstat_bits.o readstat/readstat_parser.o readstat/sas/readstat_sas7bdat_read.o readstat/sas/readstat_xport.o readstat/sas/readstat_sas_rle.o readstat/sas/readstat_sas.o readstat/sas/readstat_xport_read.o readstat/sas/ieee.o readstat/sas/readstat_sas7bcat_write.o readstat/sas/readstat_sas7bdat_write.o readstat/sas/readstat_sas7bcat_read.o readstat/sas/readstat_xport_write.o readstat/spss/readstat_por_parse.o readstat/spss/readstat_sav_parse.o readstat/spss/readstat_zsav_write.o readstat/spss/readstat_por.o readstat/spss/readstat_spss.o readstat/spss/readstat_por_write.o readstat/spss/readstat_sav_write.o readstat/spss/readstat_zsav_read.o readstat/spss/readstat_sav_parse_timestamp.o readstat/spss/readstat_zsav_compress.o readstat/spss/readstat_sav.o readstat/spss/readstat_por_read.o readstat/spss/readstat_sav_read.o readstat/spss/readstat_spss_parse.o readstat/spss/readstat_sav_compress.o readstat/stata/readstat_dta_write.o readstat/stata/readstat_dta_parse_timestamp.o readstat/stata/readstat_dta.o readstat/stata/readstat_dta_read.o RcppExports.o haven_types.o DfWriter.o DfReader.o -lz -L/Users/{username}/anaconda3/lib/R/lib -lR -Wl,-framework -Wl,CoreFoundation
ld: warning: -pie being ignored. It is only used when linking a main executable
ld: warning: ignoring file /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd
ld: warning: ignoring file /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd
installing to /Users/{username}/anaconda3/lib/R/library/haven/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded

Goodbye at Wed Nov 28 18:45:04 2018

DONE (haven)

Goodbye at Wed Nov 28 18:45:04 2018

installing source package ‘shiny’ ...
** package ‘shiny’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

Goodbye at Wed Nov 28 18:45:16 2018

DONE (shiny)

Goodbye at Wed Nov 28 18:45:17 2018
ERROR: dependency ‘callr’ is not available for package ‘pkgbuild’

removing ‘/Users/{username}/anaconda3/lib/R/library/pkgbuild’

installing source package ‘tidyr’ ...
** package ‘tidyr’ successfully unpacked and MD5 sums checked
** libs
x86_64-apple-darwin13.4.0-clang++ -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o
x86_64-apple-darwin13.4.0-clang++ -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c fill.cpp -o fill.o
x86_64-apple-darwin13.4.0-clang++ -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c melt.cpp -o melt.o
x86_64-apple-darwin13.4.0-clang++ -I"/Users/{username}/anaconda3/lib/R/include" -DNDEBUG -I"/Users/{username}/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/{username}/anaconda3/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -I/Users/{username}/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c simplifyPieces.cpp -o simplifyPieces.o
x86_64-apple-darwin13.4.0-clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Users/{username}/anaconda3/lib/R/lib -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/{username}/anaconda3/lib -L/Users/{username}/anaconda3/lib -o tidyr.so RcppExports.o fill.o melt.o simplifyPieces.o -L/Users/{username}/anaconda3/lib/R/lib -lR -Wl,-framework -Wl,CoreFoundation
ld: warning: -pie being ignored. It is only used when linking a main executable
ld: warning: ignoring file /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd
ld: warning: ignoring file /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd
installing to /Users/{username}/anaconda3/lib/R/library/tidyr/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded

Goodbye at Wed Nov 28 18:45:29 2018

DONE (tidyr)

Goodbye at Wed Nov 28 18:45:29 2018
ERROR: dependency ‘pkgbuild’ is not available for package ‘pkgload’

removing ‘/Users/{username}/anaconda3/lib/R/library/pkgload’
ERROR: dependencies ‘callr’, ‘pkgbuild’, ‘xopen’ are not available for package ‘rcmdcheck’

removing ‘/Users/{username}/anaconda3/lib/R/library/rcmdcheck’

installing source package ‘sparklyr’ ...
** package ‘sparklyr’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

Goodbye at Wed Nov 28 18:45:41 2018

DONE (sparklyr)

Goodbye at Wed Nov 28 18:45:41 2018
ERROR: dependencies ‘callr’, ‘pkgbuild’, ‘pkgload’, ‘rcmdcheck’, ‘usethis’ are not available for package ‘devtools’

removing ‘/Users/{username}/anaconda3/lib/R/library/devtools’

The downloaded source packages are in
‘/private/var/folders/l4/m8jt3zsx6yx4wh6vyr96gr480000gn/T/Rtmpc4XzJ1/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
There were 11 warnings (use warnings() to see them)
R> warnings()
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘ps’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘RJSONIO’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘processx’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘fs’ had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘xopen’ had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘callr’ had non-zero exit status
7: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘usethis’ had non-zero exit status
8: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘pkgbuild’ had non-zero exit status
9: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘pkgload’ had non-zero exit status
10: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘rcmdcheck’ had non-zero exit status
11: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘devtools’ had non-zero exit status
R>

Thanks. All help is appreciated.

technocrat · November 29, 2018, 6:48am

I don't use anaconda on my Mojave, so if you don't wish to use pre-compiled vanilla R (https://goo.gl/alZYVs) and pre-compiled vanilla RStudio (https://goo.gl/0kEJpc), all I can offer are generic comments.

The important warnings are at the bottom "non-zero exit status" means failure to install. Warnings that you see during the compilation process you can ignore. "Errors" also signify failure.

Unless you are into debugging in a big way, the autobahn to R is to go with the precompiled binaries. When downloading a package that is only available in source, make sure you have the latest X Code app from the App Store, and everytime you update it, open a terminal and

xcode-select --install

mfherman · November 29, 2018, 11:58am

In addition to installing Xcode you could try running the installer mentioned in step 2 in this post. When I upgraded to Mojave I needed to do this to compile packages successfully.

AISYNC · November 29, 2018, 1:38pm

@technocrat thanks for the help I'll keep that mind. I have X-Code updated and the license accepted / interface command line installed but ran it again to make sure. No change.

--It was really bugging me on my laptop so I removed Anaconda completely and just installed the binaries. I have it still running on my iMac and will try going through this in hopes to get a clean output.

Thanks again

technocrat · November 29, 2018, 4:34pm

Glad that works. I misspoke about Anaconda. I do have it for Python, and like it a lot. I just never use it for R. The fact that I don't have any of the problems you went through may just be luck in my $PATH.

AISYNC · November 29, 2018, 11:02pm

That sounds like an ideal setup. I'm far more familiar with R than Python. So I had R/RStudio installed long before needing to install Anaconda for Python. I tried setting up them up separately at first installing Anaconda. But after the binary install Anaconda takes over the terminal PATH and started conflicted with some files and packages in R or Atom/Sublime Text. So I opted to just try and use Anaconda alone for consistency but that clearly wasn't the case. Is there something you do in particular to keep R as separate as possible from any possible conflicts with Conda? (ex. is it installed through CRAN binary or homebrew?)

Interestingly enough I realized while command-line-tools was installed already upon running xcode-select --install in Terminal. The path below doesn't exist.

/Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg

I wasn't sure if that's an issue or not, but I installed the Command-Line-Tools.dmg from the Apple Developer portal and ran the command as specified by @mfherman. I can't be sure it fixed anything quite yet.

AISYNC · November 29, 2018, 11:06pm

I mentioned below:

/Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg

didn't exist on my system while xcode-select --install didn't prompt anything other than being already installed. Don't know if this could've been the problem? I've since gone through the post suggestions and am looking to see if I get any similar warning/error messages

technocrat · November 29, 2018, 11:27pm

Here's what I have

 $ 505:  xcode-select -v
xcode-select version 2354.

As far as Anaconda it does mess with your path, but it tells you in your .bashrc or .bash_profile.

  $ 504:  echo $PATH
/usr/local/opt/llvm/bin:/usr/local/ActiveGo-1.8.3/bin:/Users/rc/go/bin:/usr/local/ActiveGo-1.8.3/gopath/bin:/Users/rc/anaconda3/bin:/Users/rc/go/bin:/Users/rc/Library/Haskell/bin:/Users/rc/anaconda/bin:/Users/rc/.local/bin:/Users/rc/anaconda/bin:/usr/local/opt/ruby/bin:/usr/local/lib://Users/rc/go/bin:/usr/local/bin:/usr/local/mysql/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/usr/local/go/bin:/opt/X11/bin:/Users/rc/bin

will tell you the search order and where the system stops looking. Whenever I run into a conflict, I move up the desired path to the front and wait until the next conflict! Gettin' lazy.

system · December 20, 2018, 11:27pm

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