inla.qsample failing (it might be R4.0, it might be macOS High Sierra?)

[Daniel Simpson]

Hi everyone,

I've hit an annoying problem with the current version of INLA (testing version downloaded this morning).

> Q = INLA:::inla.rw1(100) + Diagonal(100)

> x = inla.qsample(n=1, Q=Q)

dyld: lazy symbol binding failed: Symbol not found: _dtrsm_

  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/INLA/bin/mac/64bit/inla (which was built for Mac OS X 10.14)

  Expected in: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/INLA/bin/mac/64bit/../../pardiso/libnopardiso/mac/libpardiso600-MACOS-X86-64-RINLA.dylib

dyld: Symbol not found: _dtrsm_

  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/INLA/bin/mac/64bit/inla (which was built for Mac OS X 10.14)

  Expected in: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/INLA/bin/mac/64bit/../../pardiso/libnopardiso/mac/libpardiso600-MACOS-X86-64-RINLA.dylib

Error in file(rng.file, "rb") : cannot open the connection

In addition: Warning message:

In file(rng.file, "rb") :

  cannot open file '/var/folders/0d/jv983_5x6lq1b9qxd7zx3jjc0000gn/T//RtmpYzyPje/file10c2139cb3d48/file10c216499ae0e': No such file or directory

My strong suspicion is it's a mismatch between the binary and my system. Should I upgrade my OS or downgrade my R? (Relevant sessionInfo() below)

Thanks!

Dan

> sessionInfo()

R version 4.0.0 (2020-04-24)

Platform: x86_64-apple-darwin17.0 (64-bit)

Running under: macOS High Sierra 10.13.6

[Helpdesk]

its an error on Mac due to an upgrade in a compiler. That version have
been recompiled with a fix, so just remove the package, and install it
again

H

On Tue, 2020-05-05 at 10:25 -0700, Daniel Simpson wrote:
> Hi everyone,
>
> I've hit an annoying problem with the current version of INLA
> (testing version downloaded this morning).
>
> > Q = INLA:::inla.rw1(100) + Diagonal(100)
> > x = inla.qsample(n=1, Q=Q)
> dyld: lazy symbol binding failed: Symbol not found: _dtrsm_
> Referenced from:
> /Library/Frameworks/R.framework/Versions/4.0/Resources/library/INLA/b
> in/mac/64bit/inla (which was built for Mac OS X 10.14)
> Expected in:
> /Library/Frameworks/R.framework/Versions/4.0/Resources/library/INLA/b
> in/mac/64bit/../../pardiso/libnopardiso/mac/libpardiso600-MACOS-X86-
> 64-RINLA.dylib
>
> dyld: Symbol not found: _dtrsm_
> Referenced from:
> /Library/Frameworks/R.framework/Versions/4.0/Resources/library/INLA/b
> in/mac/64bit/inla (which was built for Mac OS X 10.14)
> Expected in:
> /Library/Frameworks/R.framework/Versions/4.0/Resources/library/INLA/b
> in/mac/64bit/../../pardiso/libnopardiso/mac/libpardiso600-MACOS-X86-
> 64-RINLA.dylib
>

> Error in file(rng.file, "rb") : cannot open the connection
> In addition: Warning message:
> In file(rng.file, "rb") :
> cannot open file
> '/var/folders/0d/jv983_5x6lq1b9qxd7zx3jjc0000gn/T//RtmpYzyPje/file10c
> 2139cb3d48/file10c216499ae0e': No such file or directory
>
> My strong suspicion is it's a mismatch between the binary and my
> system. Should I upgrade my OS or downgrade my R? (Relevant
> sessionInfo() below)
>
> Thanks!
>
> Dan
>
> > sessionInfo()
> R version 4.0.0 (2020-04-24)
> Platform: x86_64-apple-darwin17.0 (64-bit)
> Running under: macOS High Sierra 10.13.6
>

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--
Håvard Rue
Helpdesk
he...@r-inla.org

[Daniel Simpson]

Hi Håvard,

It works just using the standard download script for the stable branch, but not for the testing branch.

With the testing branch I get

> r <- inla(y~1, data = list(y = rnorm(10)))

dyld: lazy symbol binding failed: Symbol not found: _dtrsm_

  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/INLA/bin/mac/64bit/inla (which was built for Mac OS X 10.14)

  Expected in: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/INLA/bin/mac/64bit/../../pardiso/libnopardiso/mac/libpardiso600-MACOS-X86-64-RINLA.dylib

dyld: Symbol not found: _dtrsm_

  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/INLA/bin/mac/64bit/inla (which was built for Mac OS X 10.14)

  Expected in: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/INLA/bin/mac/64bit/../../pardiso/libnopardiso/mac/libpardiso600-MACOS-X86-64-RINLA.dylib

sh: line 1: 70107 Abort trap: 6           '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/INLA/bin/mac/64bit/inla.run' -b -s -v -t 4 '/private/var/folders/0d/jv983_5x6lq1b9qxd7zx3jjc0000gn/T/RtmpWJFCNF/file110f14ced742/Model.ini' > '/private/var/folders/0d/jv983_5x6lq1b9qxd7zx3jjc0000gn/T/RtmpWJFCNF/file110f14ced742/Logfile.txt'

Error in inla.inlaprogram.has.crashed() : 

  The inla-program exited with an error. Unless you interupted it yourself, please rerun with verbose=TRUE and check the output carefully.

  If this does not help, please contact the developers at <he...@r-inla.org>.

> 

D

[Daniel Simpson]

The "(which was built for Mac OS X 10.14)" messages in the error make me strongly suggest I need to update my OS.

D

[Helpdesk]

On Tue, 2020-05-05 at 14:31 -0400, Daniel Simpson wrote:
> Hi Håvard,
> It works just using the standard download script for the stable
> branch, but not for the testing branch.
>

hmm, it was fixed, but now its not. let me check again...

[Helpdesk]

Should be fine now. just remove the install INLA package and install
the testing version again.

[Cici Chen]

I am having exactly the same problem! And it looks like I am among the rare ones having this problem and cannot really find a solution, despite a long search. 

I decided to run some time-consuming analysis on an older iMac with macOS High Sierra. Because of the specs there was no way for me to upgrade the OS so I am stuck with it. Now INLA won't run and I believe it is a problem with incompatible libraries. I have tried to install/uninstall Rstudio, R, and INLA (stable and testing versions both). Also tried to install INLA directly in R and not R studio (which was suggested in another discussion thread). Nothing worked. 

Is there a solution to this? My session info and INLA error messages are attached below. Many thanks!

> sessionInfo()

R version 4.0.4 (2021-02-15)

Platform: x86_64-apple-darwin17.0 (64-bit)

Running under: macOS High Sierra 10.13.6

Matrix products: default

BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib

LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:

[1] INLA_21.03.17 sp_1.4-5      foreach_1.5.1 Matrix_1.3-2 

loaded via a namespace (and not attached):

[1] compiler_4.0.4     tools_4.0.4        MatrixModels_0.5-0 splines_4.0.4      codetools_0.2-18  

[6] grid_4.0.4         iterators_1.0.13   lattice_0.20-41   

> result = inla(formula, family = "gaussian", data = data)

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin

  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/INLA/bin/mac/64bit/first/libjemalloc.2.dylib (which was built for Mac OS X 10.15)

  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin

  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/INLA/bin/mac/64bit/first/libjemalloc.2.dylib (which was built for Mac OS X 10.15)

  Expected in: /usr/lib/libSystem.B.dylib

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin

  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/INLA/bin/mac/64bit/first/libjemalloc.2.dylib (which was built for Mac OS X 10.15)

  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin

  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/INLA/bin/mac/64bit/first/libjemalloc.2.dylib (which was built for Mac OS X 10.15)

  Expected in: /usr/lib/libSystem.B.dylib

sh: line 1: 76791 Abort trap: 6           '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/INLA/bin/mac/64bit/inla.run' -b -s -v -t4:1 -B0 '/private/var/folders/fx/pfw7fc7d1tnc9z1k9bntmhzr0000gn/T/RtmpSL4Ce0/file1298a172eec75/Model.ini' > '/private/var/folders/fx/pfw7fc7d1tnc9z1k9bntmhzr0000gn/T/RtmpSL4Ce0/file1298a172eec75/Logfile.txt'

Error in inla.inlaprogram.has.crashed() : 

  The inla-program exited with an error. Unless you interupted it yourself, please rerun with verbose=TRUE and check the output carefully.

  If this does not help, please contact the developers at <he...@r-inla.org>.

[Helpdesk]

yes, its an OS issue. I have two availble macs, running 10.14.6 ,
10.15.5. I usually compile on 10.15.5, which is second most recent OS
(which is 11.xx)

as long as I do not have access to a Mac running 10.13 I cannot compile
on it.

it seems that the issue it complains about, is the jemalloc library,
which can be removed. let me check and come back to you

Best
H

he...@r-inla.org

[Cici Chen]

In case this might help with other uses. 

If you have issues of running INLA on macOS High Sierra, can install INLA but have the following error message when running INLA:

"dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin

  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/INLA/bin/mac/64bit/first/libjemalloc.2.dylib (which was built for Mac OS X 10.15)

  Expected in: /usr/lib/libSystem.B.dylib"

Please install the most recent version of INLA (Version_21.03.20) and try the following in R (by setting mkl=FALSE). It should be working just fine.

library(INLA)

inla.setOption(mkl=FALSE)

[milind sharma]

Thanks for the suggestion above. I am currently trying to run an INLA code on MacOS High Sierra and got the same error even after `inla.setOption(mkl=FALSE)`

```

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin

  Referenced from: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/INLA/bin/mac/64bit/first/libjemalloc.2.dylib (which was built for Mac OS X 10.15)

  Expected in: /usr/lib/libSystem.B.dylib

```

Here is the sessionInfo() output:

```

sessionInfo()

R version 4.1.1 (2021-08-10)

Platform: x86_64-apple-darwin17.0 (64-bit)

Running under: macOS High Sierra 10.13.6

Matrix products: default

BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib

LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] grid      parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:

 [1] lubridate_1.8.0   forcats_0.5.1     stringr_1.4.0     dplyr_1.0.7       purrr_0.3.4       readr_2.0.2       tidyr_1.1.4       tibble_3.1.5      ggplot2_3.3.5    

[10] tidyverse_1.3.1   lattice_0.20-44   abind_1.4-5       fields_13.3       viridis_0.6.2     viridisLite_0.4.0 spam_2.7-0        dotCall64_1.0-1   INLA_21.02.23    

[19] sp_1.4-5          foreach_1.5.1     Matrix_1.3-4     

loaded via a namespace (and not attached):

 [1] httr_1.4.2         maps_3.4.0         bit64_4.0.5        vroom_1.5.5        jsonlite_1.7.2     splines_4.1.1      modelr_0.1.8       assertthat_0.2.1   cellranger_1.1.0  

[10] yaml_2.2.1         pillar_1.6.4       backports_1.3.0    glue_1.4.2         digest_0.6.28      rvest_1.0.2        colorspace_2.0-2   htmltools_0.5.2    pkgconfig_2.0.3   

[19] broom_0.7.9        haven_2.4.3        scales_1.1.1       tzdb_0.2.0         MatrixModels_0.5-0 generics_0.1.1     ellipsis_0.3.2     withr_2.4.2        cli_3.1.0         

[28] magrittr_2.0.1     crayon_1.4.2       readxl_1.3.1       evaluate_0.14      fs_1.5.0           fansi_0.5.0        xml2_1.3.2         tools_4.1.1        hms_1.1.1         

[37] lifecycle_1.0.1    munsell_0.5.0      reprex_2.0.1       compiler_4.1.1     rlang_0.4.12       iterators_1.0.13   rstudioapi_0.13    rmarkdown_2.11     gtable_0.3.0      

[46] codetools_0.2-18   DBI_1.1.1          R6_2.5.1           splancs_2.01-42    gridExtra_2.3      knitr_1.36         rgdal_1.5-27       fastmap_1.1.0      bit_4.0.4         

[55] utf8_1.2.2         stringi_1.7.5      Rcpp_1.0.7         vctrs_0.3.8        dbplyr_2.1.1       tidyselect_1.1.1   xfun_0.27

```

[Helpdesk]

you are running on an (very) old version of MacOS. We are currently
compiling for

kw-16659:~ rueh$ sw_vers
ProductName: Mac OS X
ProductVersion: 10.15.7
BuildVersion: 19H1519


and you have 10.13.

If you upgrade you'll be fine.

> > /Library/Frameworks/R.framework/Versions/4.0/Resources/library/INLA/bi
> > n/mac/64bit/first/libjemalloc.2.dylib (which was built for Mac OS X
> > 10.15)
> >   Expected in: /usr/lib/libSystem.B.dylib"
> >

[Helpdesk]

this version is still 'old' compared to version 11 & the recent 12

On Sat, 2021-10-30 at 23:25 +0300, Helpdesk wrote:
>
> you are running on an (very) old version of MacOS. We are currently
> compiling for
>
> kw-16659:~ rueh$ sw_vers
> ProductName:    Mac OS X
> ProductVersion: 10.15.7
> BuildVersion:   19H1519
>
>
> and you have 10.13.
>
> If you upgrade you'll be fine.
>
>
>
>
> On Sat, 2021-10-30 at 13:23 -0700, milind sharma wrote:
> >
> > Thanks for the suggestion above. I am currently trying to run an
> > INLA
> > code on MacOS High Sierra and got the same error even after
> > `inla.setOption(mkl=FALSE)`
> >
> > ```
> > dyld: lazy symbol binding failed: Symbol not found:
> > ____chkstk_darwin
> >   Referenced from:
> > /Library/Frameworks/R.framework/Versions/4.1/Resources/library/INLA/

> > bin/

> > mac/64bit/first/libjemalloc.2.dylib (which was built for Mac OS X
> > 10.15)
> >   Expected in: /usr/lib/libSystem.B.dylib
> > ```
> >
> > Here is the sessionInfo() output:
> >
> > ```
> > sessionInfo()
> > R version 4.1.1 (2021-08-10)
> > Platform: x86_64-apple-darwin17.0 (64-bit)
> > Running under: macOS High Sierra 10.13.6
> >
> > Matrix products: default
> > BLAS: 
> >  /System/Library/Frameworks/Accelerate.framework/Versions/A/Framewor
> > ks/v
> > ecLib.framework/Versions/A/libBLAS.dylib
> > LAPACK:
> > /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapac

> > k.dy
> > lib
> >
> > locale:
> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >

> > > /Library/Frameworks/R.framework/Versions/4.0/Resources/library/INL
> > > A/bi

[milind sharma]

Nevermind, I realized I had INLA version 21.02.23 and just upgraded using inla.upgrade(testing=TRUE). It works now :)

Thanks!

[Helpdesk]

good to hear!