Error Loading #1
Comments
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I failed to correctly configure RcppParallel and was getting away with it on Windows when building the package via devtools. I think I've fixed the underlying issue. Could you please try again with the latest build and let me know? I have added Appveyor and Travis CI to catch Linux (and Windows) installation issues. What OS are you installing this on, by the way? Looks likes Mac? |
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Tried it again on Mac and Linux (redhat?) and got the same error again |
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And do you know which version of Red Hat? |
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It might also be helpful to know if the Mac version of R is the homebrew version or one installed from https://cran.r-project.org/bin/macosx/ -- and do any other packages that use C++ get loaded correctly? |
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The Rcpp FAQ PDF http://dirk.eddelbuettel.com/code/rcpp/Rcpp-FAQ.pdf mentions "symbols not found" errors when registering dynamically loaded symbols and ensuring the RcppExports files are correctly regenerated. I've updated the |
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Just realized that my redhat install is actually getting stuck on RcppParallel, so I'll need to fix that first |
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Hi, I am having the same issue. I am on Mac (v 10.13.1) and R 3.3. My C++ packages appear to be loading correctly. Here is the error message Thanks for your help. == Error in dyn.load(file, DLLpath = DLLpath, ...) : |
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I'm sorry it's still not working for people on Macs. I've added OS X to the Travis CI configuration, but it's building correctly on there. I don't know if the output there is helpful. Are you using the CRAN R or one from Homebrew? Is there any chance that other C++ libraries were built with clang but uwot is being forced to use gcc or something? I don't have access to a Mac so I can't do a lot more than google for similar error messages. |
jlmelville
added
bug
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Thanks for the prompt answer. I am using CRAN R, and as far as I can see clang is used. I tried the suggestions from Rccp FAQ pdf and removed R/RcppExports.R and src/RcppExports.cpp and then rebuild the package. Unfortunately, the error persists. Not sure what to do, since I know nothing of Rccp. I'll update my R version do a clean install and see how that goes. I'll report the results. |
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I noticed that this thread has not had any recent activity. Despite the fact that I have previously been able to install uwot, I have also experienced the problem described above and first noticed it ~2 weeks ago. Trying to install again today, I noted that it is still an issue. Since I was previously able to install the package I gradually stepped backwards in the commit history to find a "version" I can currently install. It turns out that although I can install 347f45d (Link to RcppParallel and RcppAnnoy., Jun 23), I cannot install 45fa4bd (Multi-threaded NN search., Jun 23). It would seem that either a) something in the later commit broke installation on some OSX or b) something has subsequently changed on some OSX since that change which has broken the installation. I am using R version 3.5.1 and will include the full output at installation below. Hopefully this "clue" might help identify the issue so that it can be resolved. Installing uwot
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Thank you for the detective work, @jasonserviss. Is this the error message from the latest build or from 45fa4bd? The only thing that jumps out at me from the diff between the two commits is that I was mixing Previous reported errors are from symbols from functions in Otherwise it might mean that there is a problem with TBB. Seems hard to believe that RcppParallel could be correctly built and installed if TBB wasn't around, so I would expect to see that error if for some reason we aren't including TBB at link time. With Unfortunately, I don't have this information in the travis Mac CI. The contents of |
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It looks as though the error message was potentially from an earlier build (my fault, sorry for the confusion). The installation from both the most recent commit (sorry still not working) and the commit that worked (347f45d) are shown below. Below that I show devtools::install_github('jlmelville/uwot', ref = 'def7898e7738f63f5be5ce9aa811baad4f6909b7')
#> Downloading GitHub repo jlmelville/uwot@def7898e7738f63f5be5ce9aa811baad4f6909b7
#> from URL https://api.github.com/repos/jlmelville/uwot/zipball/def7898e7738f63f5be5ce9aa811baad4f6909b7
#> Installing uwot
#> '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file \
#> --no-environ --no-save --no-restore --quiet CMD INSTALL \
#> '/private/var/folders/6w/_8bn209n7_dbqbk7hdst6hfm0000gp/T/RtmpFkwl6D/devtoolsd9c14db71ce9/jlmelville-uwot-def7898' \
#> --library='/Library/Frameworks/R.framework/Versions/3.5/Resources/library' \
#> --install-tests
#>
#> Installation failed: Command failed (1)
devtools::install_github('jlmelville/uwot', ref = '347f45d4ed1fd0c9f4377bb10b0acf36c9ac2c7a')
#> Downloading GitHub repo jlmelville/uwot@347f45d4ed1fd0c9f4377bb10b0acf36c9ac2c7a
#> from URL https://api.github.com/repos/jlmelville/uwot/zipball/347f45d4ed1fd0c9f4377bb10b0acf36c9ac2c7a
#> Installing uwot
#> '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file \
#> --no-environ --no-save --no-restore --quiet CMD INSTALL \
#> '/private/var/folders/6w/_8bn209n7_dbqbk7hdst6hfm0000gp/T/RtmpFkwl6D/devtoolsd9c172a7b431/jlmelville-uwot-347f45d' \
#> --library='/Library/Frameworks/R.framework/Versions/3.5/Resources/library' \
#> --install-tests
#> standard output and standard error * installing *source* package ‘uwot’ ...
** libs
/usr/local/clang4/bin/clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppProgress/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppAnnoy/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
/usr/local/clang4/bin/clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppProgress/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppAnnoy/include" -I/usr/local/include -fPIC -Wall -g -O2 -c gradient.cpp -o gradient.o
/usr/local/clang4/bin/clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppProgress/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppAnnoy/include" -I/usr/local/include -fPIC -Wall -g -O2 -c nn_parallel.cpp -o nn_parallel.o
/usr/local/clang4/bin/clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppProgress/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppAnnoy/include" -I/usr/local/include -fPIC -Wall -g -O2 -c optimize.cpp -o optimize.o
/usr/local/clang4/bin/clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppProgress/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppAnnoy/include" -I/usr/local/include -fPIC -Wall -g -O2 -c perplexity.cpp -o perplexity.o
/usr/local/clang4/bin/clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppProgress/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppAnnoy/include" -I/usr/local/include -fPIC -Wall -g -O2 -c smooth_knn.cpp -o smooth_knn.o
/usr/local/clang4/bin/clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppProgress/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppAnnoy/include" -I/usr/local/include -fPIC -Wall -g -O2 -c supervised.cpp -o supervised.o
/usr/local/clang4/bin/clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppProgress/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppAnnoy/include" -I/usr/local/include -fPIC -Wall -g -O2 -c transform.cpp -o transform.o
/usr/local/clang4/bin/clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/clang4/lib -o uwot.so RcppExports.o gradient.o nn_parallel.o optimize.o perplexity.o smooth_knn.o supervised.o transform.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
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.
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/uwot/libs
** R
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error: package or namespace load failed for ‘uwot’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/uwot/libs/uwot.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/uwot/libs/uwot.so, 6): Symbol not found: __ZN13umap_gradient8clip_maxE
Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/uwot/libs/uwot.so
Expected in: flat namespace
in /Library/Frameworks/R.framework/Versions/3.5/Resources/library/uwot/libs/uwot.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/uwot’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/uwot’
* installing *source* package ‘uwot’ ...
** libs
/usr/local/clang4/bin/clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppProgress/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppAnnoy/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
/usr/local/clang4/bin/clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppProgress/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppAnnoy/include" -I/usr/local/include -fPIC -Wall -g -O2 -c gradient.cpp -o gradient.o
/usr/local/clang4/bin/clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppProgress/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppAnnoy/include" -I/usr/local/include -fPIC -Wall -g -O2 -c optimize.cpp -o optimize.o
/usr/local/clang4/bin/clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppProgress/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppAnnoy/include" -I/usr/local/include -fPIC -Wall -g -O2 -c perplexity.cpp -o perplexity.o
/usr/local/clang4/bin/clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppProgress/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppAnnoy/include" -I/usr/local/include -fPIC -Wall -g -O2 -c smooth_knn.cpp -o smooth_knn.o
/usr/local/clang4/bin/clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/clang4/lib -o uwot.so RcppExports.o gradient.o optimize.o perplexity.o smooth_knn.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
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.
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/uwot/libs
** R
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (uwot)Created on 2018-10-12 by the reprex package (v0.2.0). Session infodevtools::session_info()
#> Session info -------------------------------------------------------------
#> setting value
#> version R version 3.5.1 (2018-07-02)
#> system x86_64, darwin15.6.0
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> tz Europe/Stockholm
#> date 2018-10-12
#> Packages -----------------------------------------------------------------
#> package * version date source
#> backports 1.1.2 2017-12-13 CRAN (R 3.5.0)
#> base * 3.5.1 2018-07-05 local
#> compiler 3.5.1 2018-07-05 local
#> curl 3.2 2018-03-28 CRAN (R 3.5.0)
#> datasets * 3.5.1 2018-07-05 local
#> devtools 1.13.6 2018-06-27 CRAN (R 3.5.0)
#> digest 0.6.17 2018-09-12 CRAN (R 3.5.1)
#> evaluate 0.11 2018-07-17 CRAN (R 3.5.0)
#> git2r 0.23.0 2018-07-17 CRAN (R 3.5.0)
#> graphics * 3.5.1 2018-07-05 local
#> grDevices * 3.5.1 2018-07-05 local
#> htmltools 0.3.6 2017-04-28 CRAN (R 3.5.0)
#> httr 1.3.1 2017-08-20 CRAN (R 3.5.0)
#> knitr 1.20 2018-02-20 CRAN (R 3.5.0)
#> magrittr 1.5 2014-11-22 CRAN (R 3.5.0)
#> memoise 1.1.0 2017-04-21 CRAN (R 3.5.0)
#> methods * 3.5.1 2018-07-05 local
#> R6 2.2.2 2017-06-17 CRAN (R 3.5.0)
#> Rcpp 0.12.19 2018-10-01 CRAN (R 3.5.0)
#> rmarkdown 1.10 2018-06-11 cran (@1.10)
#> rprojroot 1.3-2 2018-01-03 CRAN (R 3.5.0)
#> stats * 3.5.1 2018-07-05 local
#> stringi 1.2.4 2018-07-20 CRAN (R 3.5.0)
#> stringr 1.3.1 2018-05-10 CRAN (R 3.5.0)
#> tools 3.5.1 2018-07-05 local
#> utils * 3.5.1 2018-07-05 local
#> withr 2.1.2 2018-03-15 CRAN (R 3.5.0)
#> yaml 2.2.0 2018-07-25 CRAN (R 3.5.0)setwd('~/Desktop/uwot-master/')
readLines('DESCRIPTION')
#> [1] "Package: uwot"
#> [2] "Title: The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction"
#> [3] "Version: 0.0.0.9004"
#> [4] "Authors@R: person(\"James\", \"Melville\", email = \"james.melville@gmail.com\", role = c(\"aut\", \"cre\"))"
#> [5] "Author: James Melville <james.melville@gmail.com>"
#> [6] "Maintainer: James Melville <james.melville@gmail.com>"
#> [7] "Description: The dimensionality reduction method UMAP "
#> [8] " (McInnes and Healy, 2018, <arxiv:1802.03426>). It is similar "
#> [9] " to, but faster than, the t-Distributed Stochastic Neighbor Embedding (t-SNE) "
#> [10] " method."
#> [11] "License: GPL-3"
#> [12] "URL: https://github.com/jlmelville/uwot"
#> [13] "BugReports: https://github.com/jlmelville/uwot/issues"
#> [14] "Encoding: UTF-8"
#> [15] "LazyData: true"
#> [16] "Suggests: testthat,"
#> [17] " covr"
#> [18] "RoxygenNote: 6.1.0"
#> [19] "Depends: Matrix"
#> [20] "LinkingTo: Rcpp, RcppArmadillo, RcppProgress, RcppParallel, RcppAnnoy"
#> [21] "Imports: Rcpp,"
#> [22] " methods,"
#> [23] " FNN,"
#> [24] " RSpectra,"
#> [25] " RcppAnnoy,"
#> [26] " RcppParallel,"
#> [27] " irlba"
#> [28] "SystemRequirements: GNU make"
devtools::load_all('.')
#> Loading uwot
#> Loading required package: Matrix
#> Error in dyn.load(dllfile): unable to load shared object '/Users/jasonserviss/Desktop/uwot-master/src/uwot.so':
#> dlopen(/Users/jasonserviss/Desktop/uwot-master/src/uwot.so, 6): Symbol not found: __ZN13umap_gradient8clip_maxE
#> Referenced from: /Users/jasonserviss/Desktop/uwot-master/src/uwot.so
#> Expected in: flat namespace
#> in /Users/jasonserviss/Desktop/uwot-master/src/uwot.soCreated on 2018-10-12 by the reprex package (v0.2.0). |
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Thanks for the detailed output. The good news is that at least we are back to having a consistent error message. The symbol that can't be found is At this point, I doubt if this will fix the problem, but it might change the error message to something more useful. Some other things to check on: are you using a custom One other thing you could try is installing the package and tell it not to delete devtools::install_github("jlmelville/uwot", args="--no-clean-on-error")Then try running |
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Yes, I have a custom Makevars. It contains: LDFLAGS= -L/usr/local/clang4/lib I ended up with this custom Makevars by enabling OpenMP use in R via: OpenMP in R on OS X. If I temporarily remove the custom Makevars, I can install version 0.0.0.9004 (e34ae33) without any issues. So I guess that might isolate the "problem". I am not so familiar with different compilers to really be able to understand the details of what is going on (you indicate in your comment "some g++ vs clang issue"). Maybe it is possible to setup your Travis build to use clang to help you further diagnose the problem...? Or, alternatively, if I can do anything else on my end let me know. Output below: |
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The problem might not be clang in general, but the version of clang that you're using. I currently know nothing about the various details of what compiler toolchain is used to build the R package binaries on Mac, what versions of which compilers are compatible with each other, what linker flags are needed and so on. I'm sure a definitive answer lies in various FAQs and the combined wisdom of googling for the "symbol not found" error with respect to other Rcpp-using projects, but not being a Mac user, I may not be the right person for this particular job. For now I am suggesting not using a custom |
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I have the same issue on my mac! |
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I did a clean install of R 3.5.1. and the package now installs and I can run the examples. Hope this helps. My OS is 10.13.1 |
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@robsalasco, are you using a custom @good-marketing, glad you got it fixed, were you also using a custom |
Hi @jlmelville! I tried compiling with and without custom Makevars. |
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The good news is that at least I was able to reproduce this error by attempting to build on r-hub with the "macOS 10.9 Mavericks, R-oldrel" configuration. The bad news is I don't know what's causing the problem. |
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I would guess that it's because |
Correctly refer to static data member, fixes #1.
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I don't know why The r-hub "macOS 10.9 Mavericks, R-oldrel" configuration that was failing is now passing again. This gives me hope that we are back to the situation where only custom For anyone else with problems, here's an example of the successful r-hub compilation output. Perhaps someone can compare with the flags and paths they are using and spot any potential differences (this is for R 3.3.3): |
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Possibly something esoteric to do with Edit: see the end of https://en.cppreference.com/w/cpp/language/static, which suggests that we needed a definition in constexpr int umap_gradient::clip_max;
constexpr int apumap_gradient::clip_max;
constexpr int tumap_gradient::clip_max;
constexpr int largevis_gradient::clip_max; |
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@jlmelville 🎉 it works! the current master compiles without problem :) |
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Thanks for the feedback @robsalasco. Hopefully we are back to normal. |
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@jlmelville thanks for the fix! hope the package can be submitted to CRAN soon. |
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uwot is now on CRAN. Hopefully the Mac binaries can be used without problems. I will eventually close this issue if there is no re-occurrence. |
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CRAN version works for me (although I haven't been using a custom Makevars for sometime). |
Correctly refer to static data member, fixes jlmelville#1.
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Hi! I have just installed the CRAN version and most recent Github version and both return the same error when trying to use the Here is my |
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hi @laresbernardo is your install of RcppAnnoy ok? Does |
Hi @jlmelville Thanks for reaching back! Any idea as of why is this happening and/our how to fix it? |
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@laresbernardo this seems to be a problem with installing RcppAnnoy, not a uwot problem so I can only give typical advice about package problems: try removing RcppAnnoy and then reinstalling it. If you are able to, see if upgrading to R 4.0.2 helps. See if CRAN vs installing from the RcppAnnoy github repo makes a difference. Sorry I can't be more help. |
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It seems appropriate to close this after a long period of inactivity (thus guaranteeing it will start causing problems again, but I'll take the risk). |
Thanks for this implementation, really looking forward to having a native R/Rcpp implementation to use on my big datasets!
The package seems to install fine but then there is a problem loading the shared object. I am running this on R3.5. Do you know what this could be?
Error: package or namespace load failed for ‘uwot’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/uwot/libs/uwot.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/uwot/libs/uwot.so, 6): Symbol not found: __ZN13umap_gradient8clip_maxE
Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/uwot/libs/uwot.so
Expected in: flat namespace
in /Library/Frameworks/R.framework/Versions/3.5/Resources/library/uwot/libs/uwot.so
Error: loading failed
Execution halted
ERROR: loading failed
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