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elbamos / largeVis

An implementation of the largeVis algorithm for visualizing large, high-dimensional datasets, for R
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Error in newest R package version #41

Closed rwarnung closed 7 years ago

rwarnung commented 7 years ago

Hi, I get an error, when I load the package:

> library(largeVis)

Loading required package: Matrix Error : object ‘opticsXi’ is not exported by 'namespace:dbscan' Error: package or namespace load failed for ‘largeVis’

my sessionInfo() is below. When I google I find this - so somebody else has had this error too. They point to the CRAN page where this error apears too: https://cran.r-project.org/web/checks/check_results_largeVis.html

Is there an issue with the newest version? Thank you!

R version 3.3.1 (2016-06-21) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] Matrix_1.2-6

loaded via a namespace (and not attached): [1] tools_3.3.1 Rcpp_0.12.7 grid_3.3.1 dbscan_1.0-0 lattice_0.20-33

elbamos commented 7 years ago

One of the packages it depends on changes the name of a function last week. I'll be putting up a fix this week.

On Feb 16, 2017, at 8:22 AM, Richard Warnung notifications@github.com wrote:

Hi, I get an error, when I load the package:

library(largeVis)

Loading required package: Matrix Error : object ‘opticsXi’ is not exported by 'namespace:dbscan' Error: package or namespace load failed for ‘largeVis’

my sessionInfo() is below. When I google I find this - so somebody else has had this error too. They point to the CRAN page where this error apears too: https://cran.r-project.org/web/checks/check_results_largeVis.html

Is there an issue with the newest version? Thank you!

R version 3.3.1 (2016-06-21) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] Matrix_1.2-6

loaded via a namespace (and not attached): [1] tools_3.3.1 Rcpp_0.12.7 grid_3.3.1 dbscan_1.0-0 lattice_0.20-33

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elbamos commented 7 years ago

@rwarnung @pablo14 try the version in my develop branch.

rwarnung commented 7 years ago

@elbamos works fine for me under windows. Thank you!

pablo14 commented 7 years ago

Thanks @elbamos for the following up. It's not working in mac. Now the install.packages("largeVis") works, but when I do the library(largeVis) it throws the same error:

> library(largeVis)
Loading required package: Matrix
Error : object ‘opticsXi’ is not exported by 'namespace:dbscan'
Error: package or namespace load failed for ‘largeVis’

Here my session:

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.1
elbamos commented 7 years ago

If you're seeing that error message are you sure you're using the one from the development branch?

On Feb 23, 2017, at 10:55 AM, Pablo Casas notifications@github.com wrote:

Thanks @elbamos for the following up. It's not working in mac. Now the install.packages("largeVis") works, but when I do the library(largeVis) it throws the same error:

library(largeVis) Loading required package: Matrix Error : object ‘opticsXi’ is not exported by 'namespace:dbscan' Error: package or namespace load failed for ‘largeVis’ Here my session:

sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS Sierra 10.12.1 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

pablo14 commented 7 years ago

That error appears when I try to install from CRAN: install.packages("largeVis") After your last comment, I tried to instal by:

install_github("elbamos/largeVis")

But it failed with other error.

How can I install from the dev branch you mentioned?

elbamos commented 7 years ago

install_github("elbamos/largeVis", ref = "develop")

pablo14 commented 7 years ago

Thanks! Now it works, but I had one more problem:

ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [largeVis.so] Error 1
ERROR: compilation failed for package ‘largeVis’

This solves this problem: http://thecoatlessprofessor.com/programming/rcpp-rcpparmadillo-and-os-x-mavericks-lgfortran-and-lquadmath-error/

After this, I successfully tested some examples from the vignette.

elbamos commented 7 years ago

Looks like you haven't setup your compiler properly.

On Feb 24, 2017, at 12:24 PM, Pablo Casas notifications@github.com wrote:

Thanks! Now it works, but I had one more problem:

ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2' ld: library not found for -lgfortran clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [largeVis.so] Error 1 ERROR: compilation failed for package ‘largeVis’ This solves this problem: http://thecoatlessprofessor.com/programming/rcpp-rcpparmadillo-and-os-x-mavericks-lgfortran-and-lquadmath-error/

After this, I successfully tested some examples from the vignette.

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pablo14 commented 7 years ago

I wrote a post that I'm close to publish and i mention this package, I'd like to avoid the readers regarding the error message when they do install.packages("largeVis"). Do you suggest I offer them to install the package by: install_github("elbamos/largeVis", ref = "develop") instead?

elbamos commented 7 years ago

Actually I'm prepping that as a release. I suggest installing from ref = "release/0.2", but it should be on CRAN in a few days.

Thanks, and I look forward to reading the post!

On Feb 28, 2017, at 11:09 AM, Pablo Casas notifications@github.com wrote:

I wrote a post that I'm close to publish and i mention this package, I'd like to avoid the readers regarding the error message when they do install.packages("largeVis"). Do you suggest I offer them to install the package by: install_github("elbamos/largeVis", ref = "develop") instead?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

pablo14 commented 7 years ago

Thanks for the support. The post: http://blog.datascienceheroes.com/playing-with-dimensions-from-clustering-pca-t-sne-to-carl-sagan/