compilation failed for package ‘protolite’

[renanmacedosem]

Hi!

I am trying to install geojsonio package and it seems I could not finish this process because I can not install protolite package. There is an issue in some parts. Please, can you help to figure out what should be the issue?

Also, I tried to reinstall the Linux dependencies:sudo apt-get install -y libprotobuf-dev protobuf-compiler and I still have the same issue.

Error message:

In file included from geobuf.cpp:1:
geobuf.pb.h:10:10: fatal error: google/protobuf/port_def.inc: No such file or directory
   10 | #include <google/protobuf/port_def.inc>
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:177: geobuf.o] Error 1
ERROR: compilation failed for package ‘protolite’
* removing ‘/home/renan/R/x86_64-pc-linux-gnu-library/3.6/protolite’
Warning in install.packages :
  installation of package ‘protolite’ had non-zero exit status
ERROR: dependency ‘protolite’ is not available for package ‘geojson’
* removing ‘/home/renan/R/x86_64-pc-linux-gnu-library/3.6/geojson’
Warning in install.packages :
  installation of package ‘geojson’ had non-zero exit status
ERROR: dependency ‘geojson’ is not available for package ‘geojsonio’
* removing ‘/home/renan/R/x86_64-pc-linux-gnu-library/3.6/geojsonio’
Warning in install.packages :
  installation of package ‘geojsonio’ had non-zero exit status

Session info:

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C               LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8     LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8    LC_PAPER=en_CA.UTF-8      
 [8] LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] bigrquery_1.4.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9       rstudioapi_0.14  magrittr_2.0.3   rappdirs_0.3.3   bit_4.0.5        here_1.0.1       lattice_0.20-45  R6_2.5.1         rlang_1.0.6      fansi_1.0.3      httr_1.4.4       tools_3.6.3     
[13] grid_3.6.3       png_0.1-8        utf8_1.2.2       cli_3.4.1        DBI_1.1.3        rprojroot_2.0.3  bit64_4.0.5      assertthat_0.2.1 tibble_3.1.8     gargle_1.2.1     lifecycle_1.0.3  Matrix_1.2-18   
[25] vctrs_0.5.1      fs_1.5.2         glue_1.6.2       compiler_3.6.3   pillar_1.8.1     reticulate_1.26  jsonlite_1.8.3   pkgconfig_2.0.3 

Thanks!

[jeroen]

Can you show the command you used and the full install log pls

[renanmacedosem]

So, I solved the problem. I had an old R version (3.6.3) and did not realize it. After removing this version and installing 4.2.2 this problem was solved.

Sorry for bothering you.

Thanks for your time and quickly answer.

[renanmacedosem]

> install.packages('protolite')
trying URL 'https://cloud.r-project.org/src/contrib/protolite_2.1.3.tar.gz'
Content type 'application/x-gzip' length 25173 bytes (24 KB)
==================================================
downloaded 24 KB

* installing *source* package ‘protolite’ ...
** package ‘protolite’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-pthread
Using PKG_LIBS=-lprotobuf -pthread
Using C++17 compiler: g++ -std=gnu++17
Using libprotoc 3.14.0 from /home/renan/.local/share/r-miniconda/envs/r-reticulate/bin/protoc
Warning: protoc version libprotoc 3.14.0 might not match libproto version 3.6.1.
** libs
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DUSENEWAPI -I'/home/renan/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DUSENEWAPI -I'/home/renan/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'   -fvisibility=hidden -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c geobuf.cpp -o geobuf.o
In file included from geobuf.cpp:1:
geobuf.pb.h:10:10: fatal error: google/protobuf/port_def.inc: No such file or directory
   10 | #include <google/protobuf/port_def.inc>
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:178: geobuf.o] Error 1
ERROR: compilation failed for package ‘protolite’
* removing ‘/home/renan/R/x86_64-pc-linux-gnu-library/4.2/protolite’
Warning in install.packages :
  installation of package ‘protolite’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/RtmpEwnQ4U/downloaded_packages’