Additional linux dependency: v8

[hansthompson]

Hi. I love all your work and this package is great.

I tried installing this package on ubuntu and it is asking me for v8.

> install.packages("geojsonio")
Installing package into ‘/home/ht/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
also installing the dependency ‘V8’

trying URL 'https://cran.rstudio.com/src/contrib/V8_0.8.tar.gz'
Content type 'application/x-gzip' length 111572 bytes (108 KB)
==================================================
downloaded 108 KB

trying URL 'https://cran.rstudio.com/src/contrib/geojsonio_0.1.4.tar.gz'
Content type 'application/x-gzip' length 2898101 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

* installing *source* package ‘V8’ ...
** package ‘V8’ successfully unpacked and MD5 sums checked
Package libv8 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libv8.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libv8' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lv8
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libv8 was not found. Try installing:
 * deb: libv8-3.14-dev | libv8-dev (Debian, Ubuntu)
 * rpm: v8-devel (Fedora, EPEL)
 * brew: v8-315 (OSX) -- NOT regular v8! Tap from homebrew/versions
 * csw: libv8_dev (Solaris)
If libv8 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libv8.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘V8’
* removing ‘/home/ht/R/x86_64-pc-linux-gnu-library/3.2/V8’
Warning in install.packages :
  installation of package ‘V8’ had non-zero exit status
ERROR: dependency ‘V8’ is not available for package ‘geojsonio’
* removing ‘/home/ht/R/x86_64-pc-linux-gnu-library/3.2/geojsonio’
Warning in install.packages :
  installation of package ‘geojsonio’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/RtmporI7r9/downloaded_packages’

I installed libv8-dev and it worked fine. I'm not even sure if this is an issue as it is listed in the error message to install it.

[sckott]

hi @hansthompson thanks for the kind words 😸

Right, libv8 is required, and there's not really a machine actionable way to make that install in R that I know of.

@jeroenooms do you think I should have the line you have in SysReq's https://github.com/jeroenooms/V8/blob/master/DESCRIPTION#L15 in this pkg (and others that import the V8 R client)

[jeroen]

No that makes no sense, libv8 is a dependency of v8. You shouldn't list recursive dependencies in your description, that would be silly :) From what I read above everything did exactly what it needed to do. geojsonio depends on v8, which kindly explained the user that libv8 is required on linux.

[sckott]

thanks for your help

[sckott]

thanks @hansthompson - looks like there's nothing to change in the package, but thanks for dropping in - and let me know of any further issues

[kshll6]

I had some sort of a similar problem. I tried installing 'geojsonio' for R on ubuntu, and it said I needed to install 'ibv8-3.14-dev' or 'libv8-dev'. Howeverm, when I install either of the two, I get the following error message:
"Warning in install.packages : package ‘libv8-dev’ is not available (for R version 3.2.2)"

Does anyone have a solution for this?

[ateucher]

@kshll6 libv8 is a system dependency for the V8 R package, which geojsonio depends on. You'll need to install libv8 on your system by running sudo apt-get install libv8-dev in your terminal.

[paternogbc]

Thanks a lot @ateucher!

[Bio-designer]

I got the following error:

/usr/bin/ld: cannot find -lv8
collect2: error: ld returned 1 exit status
make: *** [V8.so] Error 1
ERROR: compilation failed for package ‘V8’

when I use
R CMD INSTALL V8_1.5.tar.gz
--configure-vars='INCLUDE_DIR=... LIB_DIR=...'

I am stuck now.

[sckott]

@Bio-designer what operating system are you on? and did you install the v8 system library https://github.com/jeroen/V8#installation ?

[florianm]

After upgrading to Ubuntu to 19.10 "Effin' Eoan", geojsonio functions failed with ibv8.so.3.14.5: cannot open shared object file. This was fixed by re-installing R pkg V8. Blood, sweat, tears, and solution in details.

geojsonio can't find libv8.so

areas_sf <- geojsonio::as.json(area_records$features) %>% geojsonsf::geojson_sf()
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/florian/R/x86_64-pc-linux-gnu-library/3.6/V8/libs/V8.so':
  libv8.so.3.14.5: cannot open shared object file: No such file or directory

Attempting re-installing geojsonio

> install.packages("geojsonio")
Installing package into ‘/home/florian/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/geojsonio_0.8.0.tar.gz'
Content type 'application/x-gzip' length 1974552 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

* installing *source* package ‘geojsonio’ ...
** package ‘geojsonio’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/florian/R/x86_64-pc-linux-gnu-library/3.6/V8/libs/V8.so':
  libv8.so.3.14.5: cannot open shared object file: No such file or directory
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted

(buzzer sound)

Attempting re-installing system package libv8-dev

$ sudo apt install libv8-dev
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Note, selecting 'libnode-dev' instead of 'libv8-dev'
libnode-dev is already the newest version (10.15.2~dfsg-2ubuntu1).
0 to upgrade, 0 to newly install, 0 to remove and 1 not to upgrade.

So libnode-dev is the new libv8-dev. Not sure whether R pkg V8 knows that.

geojsonio installation still broken

> install.packages("geojsonio")
Installing package into ‘/home/florian/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/geojsonio_0.8.0.tar.gz'
Content type 'application/x-gzip' length 1974552 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

* installing *source* package ‘geojsonio’ ...
** package ‘geojsonio’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/florian/R/x86_64-pc-linux-gnu-library/3.6/V8/libs/V8.so':
  libv8.so.3.14.5: cannot open shared object file: No such file or directory
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted

Solution: re-install R pkg V8

install.packages("V8")

Now, without re-installing geojsonio, geojsonio works again. Phew!

System info

lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 19.10
Release:        19.10
Codename:      effin eoan

Sessioninfo

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 19.10

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C               LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8     LC_MONETARY=en_AU.UTF-8   
 [6] LC_MESSAGES=en_AU.UTF-8    LC_PAPER=en_AU.UTF-8       LC_NAME=C                  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] ggplot2_3.2.1      DT_0.10            listviewer_3.0.0   lubridate_1.7.4    leaflet_2.0.2      skimr_1.0.7        magrittr_1.5      
 [8] tidyr_1.0.0        dplyr_0.8.3        wastdr_0.1.22      usethis_1.5.1.9000

loaded via a namespace (and not attached):
 [1] httr_1.4.1           jsonlite_1.6         shiny_1.4.0          assertthat_0.2.1     sp_1.3-2             pillar_1.4.2         backports_1.1.5     
 [8] lattice_0.20-38      glue_1.3.1           digest_0.6.22        promises_1.1.0       snakecase_0.11.0     colorspace_1.4-1     htmltools_0.4.0     
[15] httpuv_1.5.2         pkgconfig_2.0.3      purrr_0.3.3          xtable_1.8-4         scales_1.0.0         later_1.0.0          tibble_2.1.3        
[22] geojsonio_0.8.0      withr_2.1.2          janitor_1.2.0        lazyeval_0.2.2       crayon_1.3.4         mime_0.7             maptools_0.9-8      
[29] fs_1.3.1             foreign_0.8-72       class_7.3-15         geojsonsf_1.3.0      tools_3.6.1          geojson_0.3.2.9100   lifecycle_0.1.0.9000
[36] stringr_1.4.0        V8_2.3               munsell_0.5.0        packrat_0.5.0        e1071_1.7-2          compiler_3.6.1       jqr_1.1.0           
[43] rlang_0.4.1          units_0.6-5          classInt_0.4-2       grid_3.6.1           rstudioapi_0.10      htmlwidgets_1.5.1    crosstalk_1.0.0     
[50] gtable_0.3.0         DBI_1.0.0            curl_4.2             R6_2.4.1             rgdal_1.4-7          knitr_1.26           fastmap_1.0.1       
[57] rgeos_0.5-2          zeallot_0.1.0        KernSmooth_2.23-16   stringi_1.4.3        Rcpp_1.0.3           sf_0.8-0             vctrs_0.2.0.9007    
[64] tidyselect_0.2.5     xfun_0.11  

[sckott]

thanks @florianm ! for the details, i''m sure this will come in handy for many folks

[jannes-m]

After adding the v8 ppa repository, I additionally needed to purge the libv8-3.14.5 package to make V8 work again

sudo add-apt-repository ppa:cran/v8
apt update
apt install libnode-dev
apt purge libv8-3.14.5
# reinstall V8
R -e 'install.packages("V8")'

[sckott]

thanks @jannes-m for sharing your solution

[github-actions]

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