Installation issue

[vmsatya]

Hi Gad,

@gabraham I am using the following to install the package: install_github("gabraham/plink2R/plink2R",repos = NULL)
It would be great if you can help resolve the issue.
R version: 3.5.1
Rstudio version: 1.1.456

Downloading GitHub repo gabraham/plink2R@master
from URL https://api.github.com/repos/gabraham/plink2R/zipball/master
Installing plink2R
"C:/PROGRA1/R/R-351.1/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL
"C:/Users/manven01/AppData/Local/Temp/RtmpUFFSUM/devtoolsf2c62c34267/gabraham-plink2R-d74be01/plink2R"
--library="C:/Users/manven01/Documents/R/win-library/3.5" --install-tests

• installing source package 'plink2R' ...
  ** libs

*** arch - i386
c:/Rtools/mingw_32/bin/g++ -I"C:/PROGRA1/R/R-351.1/include" -DNDEBUG -I"C:/Users/manven01/Documents/R/win-library/3.5/Rcpp/include" -I"C:/Users/manven01/Documents/R/win-library/3.5/RcppEigen/include" -O2 -Wall -mtune=generic -c data.cpp -o data.o
data.cpp: In constructor 'Data::Data(const char*, const char*, bool)':
data.cpp:9:21: error: 'time' was not declared in this scope
srand48(time(NULL));
^
data.cpp:9:22: error: 'srand48' was not declared in this scope
srand48(time(NULL));
^
data.cpp: In member function 'void Data::read_bed(int)':
data.cpp:243:31: error: 'drand48' was not declared in this scope
double r = drand48();
^
make: *** [data.o] Error 1
ERROR: compilation failed for package 'plink2R'

• removing 'C:/Users/manven01/Documents/R/win-library/3.5/plink2R'
  In R CMD INSTALL
  Installation failed: Command failed (1)

[EngineerCoding]

Cannot reproduce this issue on an unix system. Are you sure you have fortran installed? (A common issue when install R packages)

[xueweic]

ERROR: compilation failed for package 'plink2R'

• removing 'C:/Users/xueweic/Documents/R/win-library/3.5/plink2R'
  In R CMD INSTALL
  Error in i.p(...) :
  (converted from warning) installation of package ‘C:/Users/xueweic/AppData/Local/Temp/Rtmp42YaP7/file4504773d1f/plink2R_1.1.tar.gz’ had non-zero exit status

when I install this package, I also have the installation issue. The error is showed above. I do not know how to deal it?

[jluyapan]

I have a problem with installing this package in Rstudio. I am using the latest version of MacOS Mojave (Version 10.14.3) and Xcode (Version 10.2.1). I get this error when I am trying to build the library. My R version is 3.6.0 and RStudio version is 1.1.463. I really appreciate your help to resolve this issue.

clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o plink2R.so data.o plink2R.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-plink2R/00new/plink2R/libs
** R
** byte-compile and prepare package for lazy loading
** help
Error : (converted from warning) /private/var/folders/_r/ckjtsgqx10bbvv0hy1mpgx2m0000gn/T/RtmpFXdQI3/R.INSTALL2c3285b0f33/plink2R/man/plink2R-package.Rd:33: All text must be in a section
ERROR: installing Rd objects failed for package ‘plink2R’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/plink2R’
Error in i.p(...) : 
  (converted from warning) installation of package ‘/var/folders/_r/ckjtsgqx10bbvv0hy1mpgx2m0000gn/T//RtmpRwdeIb/file1ad2afed51/plink2R_1.1.tar.gz’ had non-zero exit status

[GELINER]

Hi Gad,
@gabraham I am using the following to install the package: install_github("gabraham/plink2R/plink2R",repos = NULL)
It would be great if you can help resolve the issue.
R version: 3.5.1
Rstudio version: 1.1.456
Downloading GitHub repo gabraham/plink2R@master
from URL https://api.github.com/repos/gabraham/plink2R/zipball/master
Installing plink2R
"C:/PROGRA1/R/R-351.1/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL
"C:/Users/manven01/AppData/Local/Temp/RtmpUFFSUM/devtoolsf2c62c34267/gabraham-plink2R-d74be01/plink2R"
--library="C:/Users/manven01/Documents/R/win-library/3.5" --install-tests

installing source package 'plink2R' ...
** libs

*** arch - i386
c:/Rtools/mingw_32/bin/g++ -I"C:/PROGRA1/R/R-351.1/include" -DNDEBUG -I"C:/Users/manven01/Documents/R/win-library/3.5/Rcpp/include" -I"C:/Users/manven01/Documents/R/win-library/3.5/RcppEigen/include" -O2 -Wall -mtune=generic -c data.cpp -o data.o
data.cpp: In constructor 'Data::Data(const char*, const char*, bool)':
data.cpp:9:21: error: 'time' was not declared in this scope
srand48(time(NULL));
^
data.cpp:9:22: error: 'srand48' was not declared in this scope
srand48(time(NULL));
^
data.cpp: In member function 'void Data::read_bed(int)':
data.cpp:243:31: error: 'drand48' was not declared in this scope
double r = drand48();
^
make: *** [data.o] Error 1
ERROR: compilation failed for package 'plink2R'

removing 'C:/Users/manven01/Documents/R/win-library/3.5/plink2R'
In R CMD INSTALL
Installation failed: Command failed (1)

I meet the same problem. Do you know how to fix it?

[irgp2019]

Hi.
Could anyone fix this error?

[Patricklv]

Please try the link here if you are still in trouble of getting it installed.