Odd ld warning from rstan

Interfaces RStan
1

Can anyone tell me what this is about, and if it’s something I should be concerned about?

ld: warning: text-based stub file 
/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd and library file 
/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation are out of sync. Falling back to 
library file for linking.

I get the above warning when calling stan_model on a Stan program.

Operating System: MacOS High Sierra (10.13.6)
RStan Version: 2.17.3

Output of writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars"))):
CXXFLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function
CC=clang
CXX=clang++ -arch x86_64 -ftemplate-depth-256

Output of devtools::session_info("rstan"):
Session info ---------------------------------------------------------------------------------------------------------------------------------------------------------
setting value
version R version 3.4.3 (2017-11-30)
system x86_64, darwin15.6.0
ui RStudio (1.1.383)
language (EN)
collate en_US.UTF-8
tz America/Denver
date 2018-10-04

Packages -------------------------------------------------------------------------------------------------------------------------------------------------------------
package * version date source
assertthat 0.2.0 2017-04-11 CRAN (R 3.4.0)
BH 1.66.0-1 2018-02-13 cran (@1.66.0-)
cli 1.0.0 2017-11-05 CRAN (R 3.4.2)
colorspace 1.3-2 2016-12-14 CRAN (R 3.4.0)
crayon 1.3.4 2017-09-16 CRAN (R 3.4.1)
dichromat 2.0-0 2013-01-24 CRAN (R 3.4.0)
digest 0.6.15 2018-01-28 cran (@0.6.15)
ggplot2 * 2.2.1 2016-12-30 CRAN (R 3.4.0)
glue 1.2.0 2017-10-29 CRAN (R 3.4.2)
graphics * 3.4.3 2017-12-07 local
grDevices * 3.4.3 2017-12-07 local
grid 3.4.3 2017-12-07 local
gridExtra 2.3 2017-09-09 CRAN (R 3.4.1)
gtable 0.2.0 2016-02-26 CRAN (R 3.4.0)
inline 0.3.14 2015-04-13 CRAN (R 3.4.0)
labeling 0.3 2014-08-23 CRAN (R 3.4.0)
lattice 0.20-35 2017-03-25 CRAN (R 3.4.3)
lazyeval 0.2.1 2017-10-29 CRAN (R 3.4.2)
magrittr 1.5 2014-11-22 CRAN (R 3.4.0)
MASS 7.3-50 2018-04-30 CRAN (R 3.4.4)
Matrix 1.2-12 2017-11-20 CRAN (R 3.4.3)
methods * 3.4.3 2017-12-07 local
munsell 0.4.3 2016-02-13 CRAN (R 3.4.0)
pillar 1.1.0 2018-01-14 CRAN (R 3.4.3)
plyr 1.8.4 2016-06-08 CRAN (R 3.4.0)
R6 2.2.2 2017-06-17 CRAN (R 3.4.0)
RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.4.0)
Rcpp 0.12.17 2018-05-18 cran (@0.12.17)
RcppEigen 0.3.3.3.1 2017-11-20 CRAN (R 3.4.3)
reshape2 1.4.3 2017-12-11 CRAN (R 3.4.3)
rlang 0.2.1 2018-05-30 cran (@0.2.1)
rstan * 2.17.3 2018-01-20 CRAN (R 3.4.3)
scales 0.5.0 2017-08-24 CRAN (R 3.4.1)
StanHeaders * 2.17.2 2018-01-20 CRAN (R 3.4.3)
stats * 3.4.3 2017-12-07 local
stats4 3.4.3 2017-12-07 local
stringi 1.2.2 2018-05-02 cran (@1.2.2)
stringr 1.3.1 2018-05-10 cran (@1.3.1)
tibble 1.4.2 2018-01-22 CRAN (R 3.4.3)
tools 3.4.3 2017-12-07 local
utf8 1.1.3 2018-01-03 CRAN (R 3.4.3)
utils * 3.4.3 2017-12-07 local
viridisLite 0.2.0 2017-03-24 CRAN (R 3.4.0)

2

I have never seen that before. What is the output of R CMD config LDFLAGS?

3

-L/usr/local/lib

4

I’m running from RStudio, though, and “which R” prints /usr/local/R, which may not have anything to do with the R installation used by RStudio…

The odd thing is that I haven’t changed my R installation in months, and I just now started seeing this warning.

5

Did you update your OS in the meantime?

6

Not very recently. However, I did update the Command Line Tools for XCode three days ago.

7

Sigh… Seems to be an issue with Xcode 10:

https://forums.developer.apple.com/thread/97850

8

I have a ctsem user getting these errors in the last couple of weeks when trying to compile stan models. Hasn’t upgraded to catalina. Did this ever get resolved / does someone have ideas?