Installation fails on Ubuntu about animotum

[ianjonsen]

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?

[camrinbraun]

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

[ianjonsen]

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

[ianjonsen]

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)

[camrinbraun]

sessionInfo()?

[ianjonsen]

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```

[camrinbraun]

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.

[camrinbraun]

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

[ianjonsen]

glad to hear that, though I haven't pushed any updates since late-November so it's a mystery to me as well.

[ianjonsen]

going to close this issue if you haven't had additional install problems since

[camrinbraun]

All good.

…

On Mar 3, 2020, at 4:31 AM, Ian Jonsen ***@***.***> wrote: going to close this issue if you haven't had additional install problems since — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#10>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AC3IYIHR72K4TZOTNDCQV4LRFT2BFANCNFSM4JLA5WAA>.