Comments (11)
I'm not able to test on Ubuntu 18.04 via travis-ci or rhub (both are stuck on the 16.04 LTS distro). Superficially, this looks like an issue with RCppEigen. What versions of RCppEigen and TMB are you running?
from animotum.
sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS
Matrix products: default
BLAS:
/usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 LC_COLLATE=C.UTF-8 [5] LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 LC_PAPER=C.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] TMB_1.7.15 RcppEigen_0.3.3.5.0
loaded via a namespace (and not attached): [1] compiler_3.6.0 Matrix_1.2-17 tools_3.6.0 Rcpp_1.0.1 grid_3.6.0 lattice_0.20-38
The error prints a BUNCH of stuff that looks like:
/home/rstudio/R/x86_64-pc-linux-gnu-library/3.6/TMB/include/atomic_math.hpp:426:1: required from ‘void atomic::matmul(const CppAD::vector&, CppAD::vector&) [with Double = double]’
/home/rstudio/R/x86_64-pc-linux-gnu-library/3.6/TMB/include/atomic_math.hpp:426:1: required from ‘bool atomic::atomicmatmul::forward(size_t, size_t, const CppAD::vector&, CppAD::vector&, const CppAD::vector&, CppAD::vector&) [with Type = double; size_t = long unsigned int]’
foieGras.cpp:21:1: required from here
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:960:8: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type {aka __vector(2) double}’ [-Wignored-attributes]
This works on my mac using install.packages('foieGras')
.
sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] foieGras_0.4.01 RcppEigen_0.3.3.5.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.2 lubridate_1.7.4 lattice_0.20-38 tidyr_1.0.0 listenv_0.7.0 prettyunits_1.0.2
[7] class_7.3-14 ps_1.3.0 utf8_1.1.4 assertthat_0.2.1 zeallot_0.1.0 rprojroot_1.3-2
[13] digest_0.6.22 R6_2.4.0 backports_1.1.5 e1071_1.7-2 ggplot2_3.2.1 pillar_1.4.2
[19] rlang_0.4.1 lazyeval_0.2.2 curl_3.3 rstudioapi_0.9.0 furrr_0.1.0 callr_3.3.2
[25] Matrix_1.2-15 desc_1.2.0 devtools_2.2.1 stringr_1.4.0 TMB_1.7.15 munsell_0.5.0
[31] compiler_3.5.2 argosfilter_0.63 pkgconfig_2.0.3 pkgbuild_1.0.6 globals_0.12.4 tidyselect_0.2.5
[37] tibble_2.1.3 gridExtra_2.3 codetools_0.2-15 fansi_0.4.0 future_1.14.0 crayon_1.3.4
[43] dplyr_0.8.3 withr_2.1.2 sf_0.8-0 grid_3.5.2 gtable_0.3.0 lifecycle_0.1.0
[49] DBI_1.0.0 magrittr_1.5 units_0.6-5 scales_1.0.0 KernSmooth_2.23-15 cli_1.1.0
[55] stringi_1.4.3 fs_1.3.1 remotes_2.1.0 testthat_2.3.0 ellipsis_0.3.0 vctrs_0.2.0
[61] tools_3.5.2 glue_1.3.1 purrr_0.3.3 processx_3.4.1 pkgload_1.0.2 parallel_3.5.2
[67] colorspace_1.4-1 sessioninfo_1.1.1 classInt_0.4-2 memoise_1.1.0 usethis_1.5.1
from animotum.
Ok, nothing unusual with the pkg versions. The RCppEigen msgs are warnings that can't easily be silenced. What does your ~/.R/Makevars file look like?
I'll try to get a local install of ubuntu 18.04 running so I can hopefully reproduce this
from animotum.
I've tested the install on a fresh ubuntu 18.04 instances and can confirm that a lot of compiler warnings are generated but they're just warnings. It takes a while (maybe 2-5 min) but eventually the compiler finishes and the package builds:
foieGras.cpp:21:1: required from here
/homevol/rstudio/R/x86_64-pc-linux-gnu-library/3.6/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:960:8: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
(cd TMB; /usr/lib/R/bin/Rscript --no-save --no-restore compile.R)
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o foieGras.so foieGras.o -L/usr/lib/R/lib -lR
installing to /homevol/rstudio/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-foieGras/00new/foieGras/libs
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (foieGras)
from animotum.
sessionInfo()
?
from animotum.
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] foieGras_0.4.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.3 compiler_3.6.1 pillar_1.4.2 TMB_1.7.15
[5] class_7.3-15 prettyunits_1.0.2 remotes_2.1.0 tools_3.6.1
[9] zeallot_0.1.0 digest_0.6.22 pkgbuild_1.0.5 lifecycle_0.1.0
[13] lubridate_1.7.4 gtable_0.3.0 tibble_2.1.3 lattice_0.20-38
[17] pkgconfig_2.0.3 rlang_0.4.1 Matrix_1.2-17 DBI_1.0.0
[21] cli_1.1.0 curl_4.2 parallel_3.6.1 e1071_1.7-2
[25] gridExtra_2.3 stringr_1.4.0 argosfilter_0.63 furrr_0.1.0
[29] withr_2.1.2 dplyr_0.8.3 vctrs_0.2.0 globals_0.12.4
[33] classInt_0.4-2 rprojroot_1.3-2 grid_3.6.1 tidyselect_0.2.5
[37] glue_1.3.1 sf_0.8-0 listenv_0.7.0 R6_2.4.1
[41] processx_3.4.1 tidyr_1.0.0 callr_3.3.2 purrr_0.3.3
[45] ggplot2_3.2.1 magrittr_1.5 units_0.6-5 scales_1.0.0
[49] backports_1.1.5 ps_1.3.0 codetools_0.2-16 assertthat_0.2.1
[53] colorspace_1.4-1 future_1.15.0 KernSmooth_2.23-16 stringi_1.4.3
[57] lazyeval_0.2.2 munsell_0.5.0 crayon_1.3.4```
from animotum.
I tried the CRAN and GitHub install on both Ubuntu 18.04.2 and 18.04.3 with matching versions of Rcpp
(1.0.3) and TMB
(1.7.15) to your install. I'm wondering if this issue might be related to running RStudio server on Ubuntu in an AWS EC2 instance. I'm running an RStudio server install from here.
from animotum.
Not sure what has changed since I had this issue but the install from Github is working now.
devtools::install_github('ianjonsen/foieGras')
> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 LC_COLLATE=C.UTF-8 [5] LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 LC_PAPER=C.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] foieGras_0.4.01 tags2etuff_0.0.0.9000 analyzePSAT_0.1.0 rgdal_1.4-4
[5] gridExtra_2.3 adehabitatLT_0.3.23 CircStats_0.2-6 boot_1.3-20
[9] MASS_7.3-51.1 adehabitatMA_0.3.13 ade4_1.7-13 raster_2.9-5
[13] sp_1.3-2 plyr_1.8.4 drake_7.4.0 tidyr_1.0.2
[17] dplyr_0.8.3 ggplot2_3.2.1 lubridate_1.7.4 fields_10.0
[21] maps_3.3.0 spam_2.5-1 dotCall64_1.0-0 pracma_2.2.5
[25] Matrix_1.2-17 oce_1.1-1 gsw_1.0-5 testthat_2.1.1
loaded via a namespace (and not attached):
[1] fs_1.3.0 sf_0.8-0 usethis_1.5.0 devtools_2.0.2 RColorBrewer_1.1-2
[6] rprojroot_1.3-2 tools_3.6.0 TMB_1.7.16 backports_1.1.5 R6_2.4.1
[11] KernSmooth_2.23-15 DBI_1.1.0 lazyeval_0.2.2 colorspace_1.4-1 withr_2.1.2
[16] tidyselect_0.2.5 prettyunits_1.0.2 processx_3.3.0 curl_3.3 compiler_3.6.0
[21] cli_1.1.0 desc_1.2.0 scales_1.0.0 classInt_0.4-2 callr_3.2.0
[26] argosfilter_0.63 stringr_1.4.0 digest_0.6.23 pkgconfig_2.0.3 sessioninfo_1.1.1
[31] plotrix_3.7-6 rlang_0.4.3 rstudioapi_0.10 magrittr_1.5 Rcpp_1.0.3
[36] munsell_0.5.0 lifecycle_0.1.0 furrr_0.1.0 stringi_1.4.3 storr_1.2.1
[41] pkgbuild_1.0.3 parallel_3.6.0 listenv_0.8.0 crayon_1.3.4 lattice_0.20-38
[46] zeallot_0.1.0 ps_1.3.0 pillar_1.4.3 igraph_1.2.4.1 base64url_1.4
[51] codetools_0.2-16 pkgload_1.0.2 glue_1.3.1 remotes_2.0.4 vctrs_0.2.2
[56] gtable_0.3.0 purrr_0.3.3 future_1.16.0 assertthat_0.2.1 e1071_1.7-3
[61] class_7.3-15 tibble_2.1.3 memoise_1.1.0 units_0.6-5 globals_0.12.5
from animotum.
glad to hear that, though I haven't pushed any updates since late-November so it's a mystery to me as well.
from animotum.
going to close this issue if you haven't had additional install problems since
from animotum.
from animotum.
Related Issues (20)
- min.dt likely not working as intended HOT 13
- map fit_ssm HOT 1
- when none of the input locations from any of the tracks are on land, route_path fails HOT 1
- installation and library(aniMotum) on M2 MBP HOT 4
- Package `foieGras` archived on CRAN and will be removed from the Tracking CTV HOT 1
- error with map function HOT 1
- When running function fit_ssm : Error in MakeADFun. Is someone familiar? HOT 2
- errors when running fit_ssm in animotum HOT 8
- Issue in installing foieGras package in RStudio HOT 3
- Error in if (p.GL > 0.75) { : missing value where TRUE/FALSE needed HOT 5
- not sure if bug or system issue HOT 3
- Error with sim_fit() using different gradient raster HOT 9
- rep$pdHess : $ operator is invalid for atomic vector — Error when fitting ssm HOT 9
- Error in strsplit(names(map), "_") : non-character argument HOT 1
- osar function not finishing the run HOT 2
- Date/time variable not detected in data HOT 6
- Missing packages for Mac M1 binary? HOT 3
- Issue with grad object for sim_fit() HOT 1
- manual download binary version animotum HOT 1
- Error when fitting an example fit_ssm: Error in updateCholesky(L, hessian.random) HOT 3
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from animotum.