[R-pkg-devel] MacOS flat namespace
Bob Rudis
bob @end|ng |rom rud@|@
Wed May 6 17:55:58 CEST 2020
Can you provide a bit more context? I just grabbed the pkg source from CRAN and it builds fine.
$ clang --version
Apple clang version 11.0.3 (clang-1103.0.32.59)
Target: x86_64-apple-darwin19.5.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
─ Session info ───────────────────────────────────────────────────────────────────────────
setting value
version R version 4.0.0 RC (2020-04-21 r78267)
os macOS Catalina 10.15.5
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2020-05-06
─ Packages ───────────────────────────────────────────────────────────────────────────────
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
backports 1.1.6 2020-04-05 [1] CRAN (R 4.0.0)
bit * 1.1-15.2 2020-02-10 [1] CRAN (R 4.0.0)
bit64 * 0.9-7 2017-05-08 [1] CRAN (R 4.0.0)
callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
codetools 0.2-16 2018-12-24 [1] CRAN (R 4.0.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
devtools * 2.2.2 2020-02-17 [1] CRAN (R 4.0.0)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 4.0.0)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
fs 1.4.1 2020-04-04 [1] CRAN (R 4.0.0)
glue 1.4.0 2020-04-03 [1] CRAN (R 4.0.0)
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 4.0.0)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 4.0.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)
processx 3.4.2 2020-02-09 [1] CRAN (R 4.0.0)
ps 1.3.2 2020-02-13 [1] CRAN (R 4.0.0)
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
raster 3.1-5 2020-04-19 [1] CRAN (R 4.0.0)
Rcpp 1.0.4.6 2020-04-09 [1] CRAN (R 4.0.0)
remotes 2.1.1 2020-02-15 [1] CRAN (R 4.0.0)
rgdal 1.4-8 2019-11-27 [1] CRAN (R 4.0.0)
rlang 0.4.5 2020-03-01 [1] CRAN (R 4.0.0)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
sp 1.4-1 2020-02-28 [1] CRAN (R 4.0.0)
testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.0)
uFTIR * 0.1.1 2020-03-11 [1] CRAN (R 4.0.0)
usethis * 1.5.1 2019-07-04 [1] CRAN (R 4.0.0)
withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.0)
[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library
> On May 6, 2020, at 06:17, Fabio Corradini Santander <fabio.corradini using inia.cl> wrote:
>
> Hi,
> Two months ago I released a package I developed in Debian 9 GCC (
> https://CRAN.R-project.org/package=uFTIR). The package was accepted on
> CRAN, and it can be installed on Windows and Linux machines. However, it is
> not working on MacOS. I don't know why. The problem starts after the
> installation, as the OS cannot load the compiled code. Cutting the long
> paths of CRAN, the problem looks like (for r-oldrel-osx-x86_64):
>
> ...
> ** testing if installed package can be loaded from temporary location
> Error: package or namespace load failed for ‘uFTIR’ in dyn.load(file,
> DLLpath = DLLpath, ...):
> unable to load shared object '.../libs/uFTIR.so':
> dlopen(.../libs/uFTIR.so, 6): Symbol not found:
> _H5P_CLS_DATASET_CREATE_ID_g
> Referenced from: .../libs/uFTIR.so
> Expected in: flat namespace
> in .../libs/uFTIR.so
> Error: loading failed
> ...
> (The missing symbol for r-release-osx-x86_64 is a different
> one: _jpeg_resync_to_restart)
>
> I saw this thread (https://github.com/RcppCore/RcppArmadillo/issues/224)
> about Rcpp, but CRAN is not using gcc, but clang, so it is not really the
> same... although I was lost when they discussed about libc++ and libstdc++.
>
> I also saw this thread from stackoverflow (
> https://stackoverflow.com/questions/40922814/error-in-dyn-loaddllfile-unable-to-load-shared-object-expected-in-flat-na)
> but I don't have a mix between cpp and plain c.
>
> I think that probably has to do with my Makevars file (
> https://community.rstudio.com/t/error-during-the-installation-of-utf8-package/4005/2)...
> maybe I shouldn't use PKG_LIBS and LDLIBS instead? But if I change it, how
> will it affect the -already successful- installations on windows and linux?
>
> The Makevars for Mac and Linux is:
>
> CXX_STD = CXX11
> PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) `pkg-config --cflags gdal`
> PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
> `pkg-config --libs gdal`
>
> I will appreciate a hint,
>
> Fabio.
>
> --
>
>
> [[alternative HTML version deleted]]
>
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