Installation issue

[nad7wf]

install_github('tpook92/HaploBlocker', subdir='pkg')
Downloading GitHub repo tpook92/HaploBlocker@master
✔ checking for file ‘/tmp/Rtmp0X7mO3/remotes183cd52cc0601/tpook92-HaploBlocker-80a8a0c/pkg/DESCRIPTION’ ... OK
─ preparing ‘HaploBlocker’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘HaploBlocker_1.6.06.tar.gz’
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'

Installing package into ‘/home/nad7wf/R/x86_64-conda_cos6-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)

• installing source package ‘HaploBlocker’ ...
  ** using staged installation
  ** libs
  x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -I"/scratch/nad7wf/miniconda/envs/r-env/lib/R/include" -DNDEBUG -I"/storage/hpc/scratch/nad7wf/miniconda/envs/r-env/lib/R/library/RandomFieldsUtils/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /scratch/nad7wf/miniconda/envs/r-env/include -I/scratch/nad7wf/miniconda/envs/r-env/include -Wl,-rpath-link,/scratch/nad7wf/miniconda/envs/r-env/lib -fopenmp -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /scratch/nad7wf/miniconda/envs/r-env/include -fdebug-prefix-map=/tmp/build/80754af9/r-base_1589917437985/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/scratch/nad7wf/miniconda/envs/r-env=/usr/local/src/conda-prefix -c chaploblocker.cc -o chaploblocker.o
  x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -I"/scratch/nad7wf/miniconda/envs/r-env/lib/R/include" -DNDEBUG -I"/storage/hpc/scratch/nad7wf/miniconda/envs/r-env/lib/R/library/RandomFieldsUtils/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /scratch/nad7wf/miniconda/envs/r-env/include -I/scratch/nad7wf/miniconda/envs/r-env/include -Wl,-rpath-link,/scratch/nad7wf/miniconda/envs/r-env/lib -fopenmp -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /scratch/nad7wf/miniconda/envs/r-env/include -fdebug-prefix-map=/tmp/build/80754af9/r-base_1589917437985/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/scratch/nad7wf/miniconda/envs/r-env=/usr/local/src/conda-prefix -c initNerror.cc -o initNerror.o
  x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -I"/scratch/nad7wf/miniconda/envs/r-env/lib/R/include" -DNDEBUG -I"/storage/hpc/scratch/nad7wf/miniconda/envs/r-env/lib/R/library/RandomFieldsUtils/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /scratch/nad7wf/miniconda/envs/r-env/include -I/scratch/nad7wf/miniconda/envs/r-env/include -Wl,-rpath-link,/scratch/nad7wf/miniconda/envs/r-env/lib -fopenmp -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /scratch/nad7wf/miniconda/envs/r-env/include -fdebug-prefix-map=/tmp/build/80754af9/r-base_1589917437985/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/scratch/nad7wf/miniconda/envs/r-env=/usr/local/src/conda-prefix -c kleinkram.cc -o kleinkram.o
  In file included from kleinkram.cc:27:0:
  xport_import.h:35:8: error: 'utilsparam_NULL_type' does not name a type; did you mean 'solve_NULL_type'?
  CALL(utilsparam_NULL);
  ^
  xport_import.h:43:27: note: in definition of macro 'CALL'
  #define CALL(what) extern what##type Ext##what
  ^~~~
  xport_import.h:44:1: note: in expansion of macro 'UTILSCALLS'
  UTILSCALLS;
  ^~~~~~~~~~
  xport_import.h:36:8: error: 'utilsparam_DELETE_type' does not name a type; did you mean 'solve_DELETE_type'?
  CALL(utilsparam_DELETE);
  ^
  xport_import.h:43:27: note: in definition of macro 'CALL'
  #define CALL(what) extern what##type Ext##what
  ^~~~
  xport_import.h:44:1: note: in expansion of macro 'UTILSCALLS'
  UTILSCALLS;
  ^~~~~~~~~~
  kleinkram.cc:43:25: error: 'LAST_R_TYPE_NAME' was not declared in this scope
  const char RTYPE_NAMES[LAST_R_TYPE_NAME + 1] = {
  ^~~~~~~~~~~~~~~~
  In file included from /storage/hpc/scratch/nad7wf/miniconda/envs/r-env/lib/R/library/RandomFieldsUtils/include/zzz_RandomFieldsUtils.h:30:0,
  from xport_import.h:28,
  from kleinkram.cc:27:
  kleinkram.cc: In function 'double Real(SEXP, char, int)':
  kleinkram.cc:762:11: error: 'R_TYPE_NAME' was not declared in this scope
  name, R_TYPE_NAME(TYPEOF(p)));
  ^
  /storage/hpc/scratch/nad7wf/miniconda/envs/r-env/lib/R/library/RandomFieldsUtils/include/errors_messages.h:204:27: note: in definition of macro 'RFERROR2'
  SPRINTF(ERR_STR, M, A,B); RFERROR(ERR_STR);}
  ^
  kleinkram.cc:762:11: note: suggested alternative: 'RAISE_NAMED'
  name, R_TYPE_NAME(TYPEOF(p)));
  ^
  /storage/hpc/scratch/nad7wf/miniconda/envs/r-env/lib/R/library/RandomFieldsUtils/include/errors_messages.h:204:27: note: in definition of macro 'RFERROR2'
  SPRINTF(ERR_STR, M, A,B); RFERROR(ERR_STR);}
  ^
  kleinkram.cc: In function 'int Integer(SEXP, char*, int, bool)':
  kleinkram.cc:808:11: error: 'R_TYPE_NAME' was not declared in this scope
  name, R_TYPE_NAME(TYPEOF(p)));
  ^
  /storage/hpc/scratch/nad7wf/miniconda/envs/r-env/lib/R/library/RandomFieldsUtils/include/errors_messages.h:204:27: note: in definition of macro 'RFERROR2'
  SPRINTF(ERR_STR, M, A,B); RFERROR(ERR_STR);}
  ^
  kleinkram.cc:808:11: note: suggested alternative: 'RAISE_NAMED'
  name, R_TYPE_NAME(TYPEOF(p)));
  ^
  /storage/hpc/scratch/nad7wf/miniconda/envs/r-env/lib/R/library/RandomFieldsUtils/include/errors_messages.h:204:27: note: in definition of macro 'RFERROR2'
  SPRINTF(ERR_STR, M, A,B); RFERROR(ERR_STR);}
  ^
  make: *** [/scratch/nad7wf/miniconda/envs/r-env/lib/R/etc/Makeconf:173: kleinkram.o] Error 1
  ERROR: compilation failed for package ‘HaploBlocker’
• removing ‘/home/nad7wf/R/x86_64-conda_cos6-linux-gnu-library/3.6/HaploBlocker’
  Error in i.p(...) :
  (converted from warning) installation of package ‘/tmp/Rtmp0X7mO3/file183cd3d643554/HaploBlocker_1.6.06.tar.gz’ had non-zero exit status

[tpook92]

Sorry for the late response - not sure how your thread got lost with me...
HaploBlocker 1.6.6 (which is on Github) requires RandomFieldsUtils (0.6.6). I am assuming your error is caused by an older version of RandomFieldsUtils that was automatically installed from CRAN. github_install does not work for RandomFieldsUtils. Instead you probably would have to download it directly from github: https://github.com/tpook92/HaploBlocker