Error while runing "snakemake -j4"

[anjackq]

Hi,

I got the following errors while I run the snakemake -j4 command. I guess it is something wrong with the Abseil?

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 4
Rules claiming more threads will be scaled down.
Job stats:
job      count    min threads    max threads
-----  -------  -------------  -------------
all          1              1              1
build        2              4              4
total        3              1              4

Select jobs to execute...

[Thu Nov 17 15:26:17 2022]
rule build:
    input: lib/veins/src/libveins_dbg.so, lib/veins-vlc/src/libveins-vlc_dbg.so, src/Makefile
    output: src/experiment_dbg
    jobid: 1
    reason: Missing output files: src/experiment_dbg
    wildcards: dbg=_dbg
    threads: 4
    resources: tmpdir=/tmp

make: Entering directory '/home/anjie/Desktop/serpentine-env/src'
protobuf/veinsgym.pb.cc
serpentine/GymConnection.cc
serpentine/GymSplitter.cc
In file included from serpentine/GymConnection.cc:23:
In file included from ./serpentine/GymConnection.h:25:
../lib/zmq/src/zmq/zmq.hpp:1205:16: warning: 'send' is deprecated: from 4.3.1, use send taking message_t and send_flags [-Wdeprecated-declarations]
        return send(msg, flags_);
               ^
../lib/zmq/src/zmq/zmq.hpp:1189:5: note: 'send' has been explicitly marked deprecated here
    ZMQ_DEPRECATED("from 4.3.1, use send taking message_t and send_flags")
    ^
../lib/zmq/src/zmq/zmq.hpp:41:31: note: expanded from macro 'ZMQ_DEPRECATED'
#define ZMQ_DEPRECATED(msg) [[deprecated(msg)]]
                              ^
In file included from protobuf/veinsgym.pb.cc:4:
protobuf/veinsgym.pb.h:244:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
protobuf/veinsgym.pb.h:245:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [23]'
    return "veinsgym.proto.Request";
           ^~~~~~~~~~~~~~~~~~~~~~~~
protobuf/veinsgym.pb.h:472:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
protobuf/veinsgym.pb.h:473:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [21]'
    return "veinsgym.proto.Reply";
           ^~~~~~~~~~~~~~~~~~~~~~
protobuf/veinsgym.pb.h:693:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
protobuf/veinsgym.pb.h:694:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [20]'
    return "veinsgym.proto.Init";
           ^~~~~~~~~~~~~~~~~~~~~
protobuf/veinsgym.pb.h:862:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
protobuf/veinsgym.pb.h:863:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [24]'
    return "veinsgym.proto.Shutdown";
           ^~~~~~~~~~~~~~~~~~~~~~~~~
protobuf/veinsgym.pb.h:994:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
protobuf/veinsgym.pb.h:995:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [20]'
    return "veinsgym.proto.Step";
           ^~~~~~~~~~~~~~~~~~~~~
protobuf/veinsgym.pb.h:1180:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
protobuf/veinsgym.pb.h:1181:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [21]'
    return "veinsgym.proto.Space";
           ^~~~~~~~~~~~~~~~~~~~~~
protobuf/veinsgym.pb.h:1453:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
protobuf/veinsgym.pb.h:1454:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [19]'
    return "veinsgym.proto.Box";
           ^~~~~~~~~~~~~~~~~~~~
protobuf/veinsgym.pb.h:1613:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
protobuf/veinsgym.pb.h:1614:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [25]'
    return "veinsgym.proto.Dict.Item";
           ^~~~~~~~~~~~~~~~~~~~~~~~~~
protobuf/veinsgym.pb.h:1785:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
protobuf/veinsgym.pb.h:1786:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [20]'
    return "veinsgym.proto.Dict";
           ^~~~~~~~~~~~~~~~~~~~~
protobuf/veinsgym.pb.h:1943:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [Makefile:107: out/clang-debug//protobuf/veinsgym.pb.o] Error 1
make: *** Waiting for unfinished jobs....
In file included from serpentine/GymSplitter.cc:19:
In file included from serpentine/GymSplitter.h:22:
In file included from ./serpentine/GymConnection.h:25:
../lib/zmq/src/zmq/zmq.hpp:1205:16: warning: 'send' is deprecated: from 4.3.1, use send taking message_t and send_flags [-Wdeprecated-declarations]
        return send(msg, flags_);
               ^
../lib/zmq/src/zmq/zmq.hpp:1189:5: note: 'send' has been explicitly marked deprecated here
    ZMQ_DEPRECATED("from 4.3.1, use send taking message_t and send_flags")
    ^
../lib/zmq/src/zmq/zmq.hpp:41:31: note: expanded from macro 'ZMQ_DEPRECATED'
#define ZMQ_DEPRECATED(msg) [[deprecated(msg)]]
                              ^
In file included from serpentine/GymConnection.cc:23:
In file included from ./serpentine/GymConnection.h:27:
./protobuf/veinsgym.pb.h:244:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
./protobuf/veinsgym.pb.h:245:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [23]'
    return "veinsgym.proto.Request";
           ^~~~~~~~~~~~~~~~~~~~~~~~
./protobuf/veinsgym.pb.h:472:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
./protobuf/veinsgym.pb.h:473:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [21]'
    return "veinsgym.proto.Reply";
           ^~~~~~~~~~~~~~~~~~~~~~
./protobuf/veinsgym.pb.h:693:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
./protobuf/veinsgym.pb.h:694:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [20]'
    return "veinsgym.proto.Init";
           ^~~~~~~~~~~~~~~~~~~~~
./protobuf/veinsgym.pb.h:862:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
./protobuf/veinsgym.pb.h:863:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [24]'
    return "veinsgym.proto.Shutdown";
           ^~~~~~~~~~~~~~~~~~~~~~~~~
./protobuf/veinsgym.pb.h:994:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
./protobuf/veinsgym.pb.h:995:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [20]'
    return "veinsgym.proto.Step";
           ^~~~~~~~~~~~~~~~~~~~~
./protobuf/veinsgym.pb.h:1180:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
./protobuf/veinsgym.pb.h:1181:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [21]'
    return "veinsgym.proto.Space";
           ^~~~~~~~~~~~~~~~~~~~~~
./protobuf/veinsgym.pb.h:1453:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
./protobuf/veinsgym.pb.h:1454:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [19]'
    return "veinsgym.proto.Box";
           ^~~~~~~~~~~~~~~~~~~~
./protobuf/veinsgym.pb.h:1613:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
./protobuf/veinsgym.pb.h:1614:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [25]'
    return "veinsgym.proto.Dict.Item";
           ^~~~~~~~~~~~~~~~~~~~~~~~~~
./protobuf/veinsgym.pb.h:1785:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
./protobuf/veinsgym.pb.h:1786:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [20]'
    return "veinsgym.proto.Dict";
           ^~~~~~~~~~~~~~~~~~~~~
./protobuf/veinsgym.pb.h:1943:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
1 warning and 20 errors generated.
make: *** [Makefile:107: out/clang-debug//serpentine/GymConnection.o] Error 1
In file included from serpentine/GymSplitter.cc:19:
In file included from serpentine/GymSplitter.h:22:
In file included from ./serpentine/GymConnection.h:27:
./protobuf/veinsgym.pb.h:244:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
./protobuf/veinsgym.pb.h:245:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [23]'
    return "veinsgym.proto.Request";
           ^~~~~~~~~~~~~~~~~~~~~~~~
./protobuf/veinsgym.pb.h:472:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
./protobuf/veinsgym.pb.h:473:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [21]'
    return "veinsgym.proto.Reply";
           ^~~~~~~~~~~~~~~~~~~~~~
./protobuf/veinsgym.pb.h:693:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
./protobuf/veinsgym.pb.h:694:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [20]'
    return "veinsgym.proto.Init";
           ^~~~~~~~~~~~~~~~~~~~~
./protobuf/veinsgym.pb.h:862:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
./protobuf/veinsgym.pb.h:863:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [24]'
    return "veinsgym.proto.Shutdown";
           ^~~~~~~~~~~~~~~~~~~~~~~~~
./protobuf/veinsgym.pb.h:994:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
./protobuf/veinsgym.pb.h:995:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [20]'
    return "veinsgym.proto.Step";
           ^~~~~~~~~~~~~~~~~~~~~
./protobuf/veinsgym.pb.h:1180:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
./protobuf/veinsgym.pb.h:1181:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [21]'
    return "veinsgym.proto.Space";
           ^~~~~~~~~~~~~~~~~~~~~~
./protobuf/veinsgym.pb.h:1453:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
./protobuf/veinsgym.pb.h:1454:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [19]'
    return "veinsgym.proto.Box";
           ^~~~~~~~~~~~~~~~~~~~
./protobuf/veinsgym.pb.h:1613:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
./protobuf/veinsgym.pb.h:1614:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [25]'
    return "veinsgym.proto.Dict.Item";
           ^~~~~~~~~~~~~~~~~~~~~~~~~~
./protobuf/veinsgym.pb.h:1785:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
./protobuf/veinsgym.pb.h:1786:12: error: cannot initialize return object of type 'int' with an lvalue of type 'const char [20]'
    return "veinsgym.proto.Dict";
           ^~~~~~~~~~~~~~~~~~~~~
./protobuf/veinsgym.pb.h:1943:12: error: no member named 'absl' in the global namespace
  static ::absl::string_view FullMessageName() {
         ~~^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
1 warning and 20 errors generated.
make: *** [Makefile:107: out/clang-debug//serpentine/GymSplitter.o] Error 1
make: Leaving directory '/home/anjie/Desktop/serpentine-env/src'
[Thu Nov 17 15:26:19 2022]
Error in rule build:
    jobid: 1
    input: lib/veins/src/libveins_dbg.so, lib/veins-vlc/src/libveins-vlc_dbg.so, src/Makefile
    output: src/experiment_dbg
    shell:
        make -j4 -C src MODE=debug
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2022-11-17T152617.777940.snakemake.log