google/protobuf/inlined_string_field.h no such file or directory #17

pelacables · 2022-03-29T09:18:54Z

Trying to build it on R 4.1.2 with gcc 10.3.0 and getting the error:

  CXX      google/protobuf/compiler/csharp/csharp_wrapper_field.lo
  CXXLD    libprotoc.la
  CXXLD    protoc
./.libs/libprotoc.so: error: undefined reference to 'scc_info_FileDescriptorProto_google_2fprotobuf_2fdescri
ptor_2eproto'
./.libs/libprotoc.so: error: undefined reference to 'descriptor_table_google_2fprotobuf_2fdescriptor_2eproto
'
collect2: error: ld returned 1 exit status
make[1]: *** [protoc] Error 1
make[1]: Leaving directory `/tmp/RtmpOoKxyP/R.INSTALL2c35616a567e5/RProtoBufLib/src/protobuf-3.13.0/src'
make: *** [install-recursive] Error 1
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -shared -fpic -I../inst/include/ -I/tmp/RtmpOoKxyP/R.INSTALL2c35616a567e5/RProtoBufLib/src/
pb_build/include/ -o GatingSet_pb_lib/libGatingSet.pb.so GatingSet_pb_lib/GatingSet.pb.cc
In file included from GatingSet_pb_lib/GatingSet.pb.cc:4:
../inst/include/cytolib/GatingSet.pb.h:17:2: error: #error This file was generated by an older version of pr
otoc which is
   17 | #error This file was generated by an older version of protoc which is
      |  ^~~~~
../inst/include/cytolib/GatingSet.pb.h:18:2: error: #error incompatible with your Protocol Buffer headers. P
lease
   18 | #error incompatible with your Protocol Buffer headers. Please
      |  ^~~~~
../inst/include/cytolib/GatingSet.pb.h:19:2: error: #error regenerate this file with a newer version of prot
oc.
   19 | #error regenerate this file with a newer version of protoc.
      |  ^~~~~
In file included from GatingSet_pb_lib/GatingSet.pb.cc:4:
../inst/include/cytolib/GatingSet.pb.h:28:10: fatal error: google/protobuf/inlined_string_field.h: No such f
ile or directory
   28 | #include <google/protobuf/inlined_string_field.h>
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
ERROR: compilation failed for package ‘RProtoBufLib’
* removing ‘/apps/prod/easybuild/sl7.x86_64.foss-2021a/software/BiocLibrary/3.14-foss-2021a-R-4.1.2/site-lib
rary/RProtoBufLib’

let me know what other info do you need.

The text was updated successfully, but these errors were encountered:

mikejiang · 2022-03-29T16:39:46Z

Can you try the latest master branch from GitHub?or from bioconductor http://bioconductor.org/packages/3.15/bioc/html/RProtoBufLib.html?

pelacables · 2022-03-30T06:15:54Z

g++ -std=gnu++11 -shared -fpic -I../inst/include/ -I/tmp/Rtmp6AhM8F/R.INSTALL40da345dc5cf/RProtoBufLib/src/pb_build/include/ -o GatingSet_pb_lib/libGatingSet.pb.so GatingSet_pb_lib/GatingSet.pb.cc
In file included from GatingSet_pb_lib/GatingSet.pb.cc:4:
../inst/include/cytolib/GatingSet.pb.h:17:2: error: #error This file was generated by an older version of protoc which is
17 | #error This file was generated by an older version of protoc which is
| ^~~~~
../inst/include/cytolib/GatingSet.pb.h:18:2: error: #error incompatible with your Protocol Buffer headers. Please
18 | #error incompatible with your Protocol Buffer headers. Please
| ^~~~~
../inst/include/cytolib/GatingSet.pb.h:19:2: error: #error regenerate this file with a newer version of protoc.
19 | #error regenerate this file with a newer version of protoc.
| ^~~~~
In file included from GatingSet_pb_lib/GatingSet.pb.cc:4:
../inst/include/cytolib/GatingSet.pb.h:28:10: fatal error: google/protobuf/inlined_string_field.h: No such file or directory
28 | #include
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [libGatingSet.pb] Error 1

what version do I need for the headers?

mikejiang · 2022-03-30T17:16:35Z

try remotes::install_github("rglab/RProtoBufLib")
and make sure you don't have another protocol buffer library installed at your system

mikejiang · 2022-03-30T17:19:48Z

Here is my installation output

> remotes::install_github("rglab/RProtoBufLib")
Downloading GitHub repo rglab/RProtoBufLib@HEAD
✓  checking for file ‘/tmp/Rtmpg4aBx8/remotes122b6b46af/RGLab-RProtoBufLib-c362a52/DESCRIPTION’ ...
─  preparing ‘RProtoBufLib’:
✓  checking DESCRIPTION meta-information ...
─  cleaning src
─  running ‘cleanup’
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘RProtoBufLib_2.7.4.tar.gz’
   
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘RProtoBufLib’ ...
** using staged installation
checking for gcc... gcc
...
untarring protobuf ...
building protobuf...
...
make[2]: Leaving directory '/tmp/Rtmpj8QF8G/R.INSTALL1c879451bfc/RProtoBufLib/src/protobuf-3.8.0/src'
make[1]: Leaving directory '/tmp/Rtmpj8QF8G/R.INSTALL1c879451bfc/RProtoBufLib/src/protobuf-3.8.0/src'
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -shared -fpic -I../inst/include/ -I/tmp/Rtmpj8QF8G/R.INSTALL1c879451bfc/RProtoBufLib/src/pb_build/include/ -o GatingSet_pb_lib/libGatingSet.pb.so GatingSet_pb_lib/GatingSet.pb.cc
mkdir -p "/usr/local/lib/R/site-library/00LOCK-RProtoBufLib/00new/RProtoBufLib/include"
cp -r /tmp/Rtmpj8QF8G/R.INSTALL1c879451bfc/RProtoBufLib/src/pb_build/include/google /usr/local/lib/R/site-library/00LOCK-RProtoBufLib/00new/RProtoBufLib/include
mkdir -p "/usr/local/lib/R/site-library/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/"
cp /tmp/Rtmpj8QF8G/R.INSTALL1c879451bfc/RProtoBufLib/src/pb_build/lib/libprotobuf* /usr/local/lib/R/site-library/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/
cp GatingSet_pb_lib/libGatingSet.pb.so /usr/local/lib/R/site-library/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib//libGatingSet.pb.so
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I../inst/include/ -I/tmp/Rtmpj8QF8G/R.INSTALL1c879451bfc/RProtoBufLib/src/pb_build/include/  -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dummy.cpp -o dummy.o
g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o RProtoBufLib.so dummy.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-RProtoBufLib/00new/RProtoBufLib/libs
** R
** inst
** 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 (RProtoBufLib)

pescobar · 2022-03-31T08:54:22Z

I am getting a similar error

/bin/sh ../libtool  --tag=CXX   --mode=link g++ -std=gnu++14 -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare  -O2 -ftree-vectorize -march=x86-64 -mtune=generic -fno-math-errno -pthread  -o protoc google/protobuf/compiler/main.o  libprotobuf.la libprotoc.la -lz
libtool: link: g++ -std=gnu++14 -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -O2 -ftree-vectorize -march=x86-64 -mtune=generic -fno-math-errno -pthread -o .libs/protoc google/protobuf/compiler/main.o  ./.libs/libprotobuf.so ./.libs/libprotoc.so -lz -pthread -Wl,-rpath -Wl,/scratch/RtmpnjUEbS/R.INSTALL5dcf3f3c6dd1/RProtoBufLib/src/pb_build/lib
./.libs/libprotoc.so: error: undefined reference to 'scc_info_FileDescriptorProto_google_2fprotobuf_2fdescriptor_2eproto'
./.libs/libprotoc.so: error: undefined reference to 'descriptor_table_google_2fprotobuf_2fdescriptor_2eproto'
collect2: error: ld returned 1 exit status
make[1]: *** [protoc] Error 1
make[1]: Leaving directory `/scratch/RtmpnjUEbS/R.INSTALL5dcf3f3c6dd1/RProtoBufLib/src/protobuf-3.8.0/src'
make: *** [install-recursive] Error 1
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -shared -fpic -I../inst/include/ -I/scratch/RtmpnjUEbS/R.INSTALL5dcf3f3c6dd1/RProtoBufLib/src/pb_build/include/ -o GatingSet_pb_lib/libGatingSet.pb.so GatingSet_pb_lib/GatingSet.pb.cc
In file included from GatingSet_pb_lib/GatingSet.pb.cc:4:0:
../inst/include/cytolib/GatingSet.pb.h:10:10: fatal error: google/protobuf/port_def.inc: No such file or directory
 #include <google/protobuf/port_def.inc>
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [libGatingSet.pb] Error 1
ERROR: compilation failed for package ‘RProtoBufLib’

pescobar · 2022-03-31T11:54:49Z

after some debugging I realized the problem happens when building the protobuf tarball provided in this repo

The protobuf build problem and workaround is reported here

I could install the package patching the RProtoBufLib like this:

$> mkdir /tmp/rprotobuflib-fix
$> cd /tmp/rprotobuflib-fix
$> wget https://bioconductor.org/packages/release/bioc/src/contrib/RProtoBufLib_2.6.0.tar.gz
$> tar xf RProtoBufLib_2.6.0.tar.gz
$> cd RProtoBufLib/src/
$> tar xf protobuf-3.13.0.tar.gz
$> cd protobuf-3.13.0/
$> wget https://gist.githubusercontent.com/pescobar/f05d3d6b427dae625d5636e2ee441cf7/raw/9a78838cbd53a7479ef099dee261359fc3279624/protobuf-3.8.0.patch
$> patch -p1 < protobuf-3.8.0.patch
$> cd ..
$> rm -fr protobuf-3.13.0.tar.gz
$> tar -czf protobuf-3.13.0.tar.gz protobuf-3.13.0/
$> cd /tmp/rprotobuflib-fix
$> rm RProtoBufLib_2.6.0.tar.gz
$> tar -czf RProtoBufLib_2.6.0.tar.gz RProtoBufLib/

inside R shell:
R> install.packages('/tmp/rprotobuflib-fix/RProtoBufLib_2.6.0.tar.gz', repos = NULL, type="source")

pelacables · 2022-03-31T14:26:33Z

Thanks Pablo :-)

pescobar · 2022-03-31T14:46:38Z

Thanks Pablo :-)

De nada...a ver si pasan menos años hasta el próximo congreso ;) Hasta luego Lucas!

pelacables · 2022-04-01T07:22:38Z

Pues sí, la verdad, ganas de desconectar un poco ya!

mbstadler · 2022-04-22T08:18:45Z

I have experienced the same issue using GCC 10.2.0 on centos 7. Installing the devel version (2.7.4) as suggested by @mikejiang above did not help, but the solution to patch protobuf-3.13.0.tar.gz suggested by @pescobar worked fine. Thanks a lot for posting your recipie!

PedroMilanezAlmeida · 2023-06-08T13:15:08Z

Just fyi, I am having the same issue in R 4.2.1. @mikejiang 's suggestion to install using remotes::install_github("rglab/RProtoBufLib") did not help. Did not try @pescobar 's solution yet.

pelacables · 2023-06-08T13:21:56Z

I was installing this package yesterday and I can confirm that Pablo's solution is still valid.

PedroMilanezAlmeida · 2023-06-08T13:46:50Z

Just reporting back that I cannot install using @pescobar 's strategy (proxy error, setup that I cannot change).

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google/protobuf/inlined_string_field.h no such file or directory #17

google/protobuf/inlined_string_field.h no such file or directory #17

pelacables commented Mar 29, 2022

mikejiang commented Mar 29, 2022

pelacables commented Mar 30, 2022

mikejiang commented Mar 30, 2022

mikejiang commented Mar 30, 2022

pescobar commented Mar 31, 2022

pescobar commented Mar 31, 2022

pelacables commented Mar 31, 2022

pescobar commented Mar 31, 2022

pelacables commented Apr 1, 2022

mbstadler commented Apr 22, 2022

PedroMilanezAlmeida commented Jun 8, 2023

pelacables commented Jun 8, 2023

PedroMilanezAlmeida commented Jun 8, 2023

google/protobuf/inlined_string_field.h no such file or directory #17

google/protobuf/inlined_string_field.h no such file or directory #17

Comments

pelacables commented Mar 29, 2022

mikejiang commented Mar 29, 2022

pelacables commented Mar 30, 2022

mikejiang commented Mar 30, 2022

mikejiang commented Mar 30, 2022

pescobar commented Mar 31, 2022

pescobar commented Mar 31, 2022

pelacables commented Mar 31, 2022

pescobar commented Mar 31, 2022

pelacables commented Apr 1, 2022

mbstadler commented Apr 22, 2022

PedroMilanezAlmeida commented Jun 8, 2023

pelacables commented Jun 8, 2023

PedroMilanezAlmeida commented Jun 8, 2023