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