Comments (7)
I wish I could help, but I don't have access to a Mac, except to look at the travis-ci builds, which aren't running Mojave.
The blog post at https://nistara.net/post/compile-issues-r/ seems to suggest that preventing clang from compiling the code might help, i.e. stick to using gcc only.
from uwot.
Don't have a Mac either, but did you notice that in your command line there is in fact the string All my packages loaded Tue Aug 27 23:05:12 2019
which has no meaning for the compiler? I don't know where it came from, but it's funny.
from uwot.
It did compile in another Mac with the similar set-up but not sure what is causing this. I have seen this before with R loading some sort of package info during completion.
Anyway could you tell me the way to manually compile and generate binary of uwot without using R ?
Thanks.
from uwot.
I'm using a Mac, and it works fine for me.
$ clang --version
Apple LLVM version 10.0.0 (clang-1000.11.45.5)
Target: x86_64-apple-darwin17.7.0
Thread model: posix
$ sw_vers
ProductName: Mac OS X
ProductVersion: 10.13.6
BuildVersion: 17G8030
As @SamGG mentioned, the error message is very unusual. Can you clone the repo and post the full output of R CMD INSTALL --preclean path/to/uwot/directory
?
from uwot.
So I did R CMD check
and here is an output;
%more 00check.log
* using log directory ‘/Volumes/Documents/Users/akihoji/uwot-master.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin18.6.0 (64-bit)
* using session charset: UTF-8
* checking for file ‘uwot-master/DESCRIPTION’ ... ERROR
Required fields missing or empty:
‘Author’ ‘Maintainer’
* DONE
Status: 1 ERROR
OK then I tried R CMD INSTALL -fake and
% R CMD INSTALL --fake Downloads/uwot-master
Loading required package: usethis
Attaching package: ‘BiocManager’
The following object is masked from ‘package:devtools’:
install
All my packages loaded Thu Aug 29 20:00:12 2019* installing to library ‘/Volumes/Documents/Users/akihoji/Library/R/3.x/library’
* installing *source* package ‘uwot’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Loading required package: usethis
Attaching package: ‘BiocManager’
The following object is masked from ‘package:devtools’:
install
All my packages loaded Thu Aug 29 20:00:14 2019
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Loading required package: usethis
Attaching package: ‘BiocManager’
The following object is masked from ‘package:devtools’:
install
All my packages loaded Thu Aug 29 20:00:18 2019
** testing if installed package can be loaded from final location
Loading required package: usethis
Attaching package: ‘BiocManager’
The following object is masked from ‘package:devtools’:
install
All my packages loaded Thu Aug 29 20:00:20 2019
** testing if installed package keeps a record of temporary installation path
* DONE (uwot)
This installed uwot but missing full functionalities as expected.
R CMD INSTALL failed and the output is ;
% R CMD INSTALL --preclean Downloads/uwot-master
Loading required package: usethis
Attaching package: ‘BiocManager’
The following object is masked from ‘package:devtools’:
install
All my packages loaded Thu Aug 29 20:41:43 2019* installing to library ‘/Volumes/Documents/Users/akihoji/Library/R/3.x/library’
* installing *source* package ‘uwot’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.1_1/lib/R/include" -DNDEBUG -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/Rcpp/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppProgress/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppParallel/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppAnnoy/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/dqrng/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include -DRCPP_PARALLEL_USE_TBB=1 -DSTRICT_R_HEADERS -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.1_1/lib/R/include" -DNDEBUG -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/Rcpp/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppProgress/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppParallel/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppAnnoy/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/dqrng/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include -DRCPP_PARALLEL_USE_TBB=1 -DSTRICT_R_HEADERS -fPIC -g -O2 -c connected_components.cpp -o connected_components.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.1_1/lib/R/include" -DNDEBUG -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/Rcpp/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppProgress/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppParallel/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppAnnoy/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/dqrng/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include -DRCPP_PARALLEL_USE_TBB=1 -DSTRICT_R_HEADERS -fPIC -g -O2 -c gradient.cpp -o gradient.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.1_1/lib/R/include" -DNDEBUG -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/Rcpp/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppProgress/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppParallel/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppAnnoy/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/dqrng/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include -DRCPP_PARALLEL_USE_TBB=1 -DSTRICT_R_HEADERS -fPIC -g -O2 -c nn_parallel.cpp -o nn_parallel.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.1_1/lib/R/include" -DNDEBUG -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/Rcpp/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppProgress/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppParallel/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppAnnoy/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/dqrng/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include -DRCPP_PARALLEL_USE_TBB=1 -DSTRICT_R_HEADERS -fPIC -g -O2 -c optimize.cpp -o optimize.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.1_1/lib/R/include" -DNDEBUG -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/Rcpp/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppProgress/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppParallel/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppAnnoy/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/dqrng/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include -DRCPP_PARALLEL_USE_TBB=1 -DSTRICT_R_HEADERS -fPIC -g -O2 -c perplexity.cpp -o perplexity.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.1_1/lib/R/include" -DNDEBUG -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/Rcpp/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppProgress/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppParallel/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppAnnoy/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/dqrng/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include -DRCPP_PARALLEL_USE_TBB=1 -DSTRICT_R_HEADERS -fPIC -g -O2 -c sampler.cpp -o sampler.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.1_1/lib/R/include" -DNDEBUG -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/Rcpp/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppProgress/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppParallel/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppAnnoy/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/dqrng/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include -DRCPP_PARALLEL_USE_TBB=1 -DSTRICT_R_HEADERS -fPIC -g -O2 -c smooth_knn.cpp -o smooth_knn.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.1_1/lib/R/include" -DNDEBUG -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/Rcpp/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppProgress/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppParallel/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppAnnoy/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/dqrng/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include -DRCPP_PARALLEL_USE_TBB=1 -DSTRICT_R_HEADERS -fPIC -g -O2 -c supervised.cpp -o supervised.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.1_1/lib/R/include" -DNDEBUG -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/Rcpp/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppProgress/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppParallel/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/RcppAnnoy/include" -I"/Volumes/Documents/Users/akihoji/Library/R/3.x/library/dqrng/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include -DRCPP_PARALLEL_USE_TBB=1 -DSTRICT_R_HEADERS -fPIC -g -O2 -c transform.cpp -o transform.o
Loading required package: usethis
Attaching package: ‘BiocManager’
The following object is masked from ‘package:devtools’:
install
Loading required package: usethis
Attaching package: ‘BiocManager’
The following object is masked from ‘package:devtools’:
install
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/lib -L/usr/local/Cellar/r/3.6.1_1/lib/R/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/lib -o uwot.so RcppExports.o connected_components.o gradient.o nn_parallel.o optimize.o perplexity.o sampler.o smooth_knn.o supervised.o transform.o All my packages loaded Thu Aug 29 20:42:39 2019 -L/usr/local/Cellar/r/3.6.1_1/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
clang-8: error: no such file or directory: 'All'
clang-8: error: no such file or directory: 'my'
clang-8: error: no such file or directory: 'packages'
clang-8: error: no such file or directory: 'loaded'
clang-8: error: no such file or directory: 'Thu'
clang-8: error: no such file or directory: 'Aug'
clang-8: error: no such file or directory: '29'
clang-8: error: no such file or directory: '20:42:41'
clang-8: error: no such file or directory: '2019'
make: *** [uwot.so] Error 1
ERROR: compilation failed for package ‘uwot’
* removing ‘/Volumes/Documents/Users/akihoji/Library/R/3.x/library/uwot’
from uwot.
Probably should have mentioned to do R CMD build
, and then R CMD INSTALL
on the tarball.
But that's probably not the real problem. Your R installation seems to be doing strange things. Why is it giving out these messages:
Loading required package: usethis
Attaching package: ‘BiocManager’
The following object is masked from ‘package:devtools’:
install
All my packages loaded ...
You probably have an .Rprofile
file somewhere that is triggering these messages - you might consider getting rid of it. I don't understand how it would interfere with clang, but clearly it is doing so, so the first task is to simplify the problem.
from uwot.
I did look for .Rprofile eveywhere but could not find one that was causing the problem. As you mentioned, devtools' call for usethis pops up and appears to interfere with clang which I am not sure how.
So, I have two R libraries, system and my custom. My custom library has everything that I have installed including devtools and BiocManager and I though autoloading devtools and BIocManger invoked the call for "usethis." So I tried to install uwot in the system library and uwot installation went without a hitch.
I've installed a bunch of other packages (including singleR) from github without a hitch. There must be something in the code that is provoking the loading of "usethis".
Anyways, thanks for all the help.
from uwot.
Related Issues (20)
- Test failure an arm64, ppc64el and s390x HOT 8
- Add general_simplicial_set_intersection to the uwot API HOT 3
- umap_transform causes R Studio to abort (R encountered a fatal error.) HOT 4
- umap_transform can give odd results with dens_scale HOT 17
- umap transform fuzzy graph HOT 3
- Citing {uwot} HOT 1
- Weird looking UMAP for spectral flow data HOT 3
- What C++ version should CXX_STD have? HOT 14
- devtools can no longer build uwot on Windows HOT 5
- I can not load the saved model, an example from the help HOT 9
- Reproducibility issue with the same data and OS HOT 17
- umap_transform with seurat umap coordinate HOT 2
- dgCMatrix_colSums' not found error when using a binary matrix HOT 2
- irlba as_cholmod_sparse problems
- Does uwot need connecting internet? HOT 4
- retrieve umap parameters HOT 2
- `fuzzy_simplicial_set()` for BBKNN HOT 5
- Differences in model parameters when calling umap() causes umap_transform() to error HOT 3
- How to input similarity_graph back into umap parameters? HOT 3
- Range scale input before optimization HOT 2
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from uwot.