gabraham/plink2r

Read PLINK BED/BIM/FAM files into R

plink2r's Issues

computational time

Hi Gad,

Thanks for sharing this nice package online! Is there an approximate relationship between computational time and # of SNPs as well as # of individuals for plink2R?

Best,
Rosie

installing the package.

Hi!
Will this package be installable with
devtools::install_github("gabraham/plink2R")

Read_Plink crashes for data set with 637000 SNPs

Hi,

I am using Read_Plink to read a data set of 637000 SNPs and 6000 individuals. The packages installed fine, however when I am trying to run Read_Plink R crashes. I have tried to the code on a machine with RAM of 32 GB and same thing happens. Really appreciate if you can help me with the issue.

Thanks,
Javad Rahimikollu

What is the status of this project?

@gabraham @EngineerCoding

There is a PR from 2016, no entry in CRAN, the link in the readme (https://www.partners.org/~purcell/plink) is dead, but some use in TWAS/FUSION. What is the current state of this project?

ERROR: compilation failed for package 'plink2R'

Hi, there:

Please see the screenshot below, I could NOT install this package into my Windows R 3.6.2.

Can someone please help me to resolve this bug?

Thank you very much & best regards,
Jie

Installation

Hello,

For reference, I am using R Studio 1.1.453, R-3.4.4, Rtools3.4, and Windows 10.

I am having issues installing plink2R through R Studio. I have tried downloading the .zip and installing it as an archive file with no luck. It doesn't show up in the packages tab, and errors out as

`> suppressMessages(library('plink2R'))`
Error in library("plink2R") : ‘plink2R’ is not a valid installed package

I then tried to install using devtools, and came up with this error:

> devtools::install_github("gabraham/plink2R/plink2R")
Downloading GitHub repo gabraham/plink2R@master
from URL https://api.github.com/repos/gabraham/plink2R/zipball/master
Installing plink2R
"C:/PROGRA~1/R/R-34~1.4/bin/x64/R" --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  "C:/Users/vmonl/AppData/Local/Temp/Rtmpc3KOGk/devtools19a471816237/gabraham-plink2R-d74be01/plink2R"  \
  --library="C:/Users/vmonl/Documents/R/win-library/3.4"  \
  --install-tests 

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

*** arch - i386
c:/Rtools/mingw_32/bin/g++  -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG  -I"C:/Users/vmonl/Documents/R/win-library/3.4/Rcpp/include" -I"C:/Users/vmonl/Documents/R/win-library/3.4/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
Warning: running command 'make -f "Makevars.win" -f "C:/PROGRA~1/R/R-34~1.4/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-34~1.4/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="plink2R.dll" OBJECTS="data.o plink2R.o"' had status 2
ERROR: compilation failed for package 'plink2R'
* removing 'C:/Users/vmonl/Documents/R/win-library/3.4/plink2R'
In R CMD INSTALL
Installation failed: Command failed (1)

When that didn't work, I tried:

> devtools::install_github("gabraham/plink2R/plink2R", repos=NULL)
Downloading GitHub repo gabraham/plink2R@master
from URL https://api.github.com/repos/gabraham/plink2R/zipball/master
Installing plink2R
"C:/PROGRA~1/R/R-34~1.4/bin/x64/R" --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  "C:/Users/vmonl/AppData/Local/Temp/Rtmpc3KOGk/devtools19a455557077/gabraham-plink2R-d74be01/plink2R"  \
  --library="C:/Users/vmonl/Documents/R/win-library/3.4"  \
  --install-tests 

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

*** arch - i386
c:/Rtools/mingw_32/bin/g++  -I"C:/PROGRA~1/R/R-34~1.4/include" -DNDEBUG  -I"C:/Users/vmonl/Documents/R/win-library/3.4/Rcpp/include" -I"C:/Users/vmonl/Documents/R/win-library/3.4/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
Warning: running command 'make -f "Makevars.win" -f "C:/PROGRA~1/R/R-34~1.4/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-34~1.4/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="plink2R.dll" OBJECTS="data.o plink2R.o"' had status 2
ERROR: compilation failed for package 'plink2R'
* removing 'C:/Users/vmonl/Documents/R/win-library/3.4/plink2R'
* restoring previous 'C:/Users/vmonl/Documents/R/win-library/3.4/plink2R'
In R CMD INSTALL
Installation failed: Command failed (1)

Any help would be greatly appreciated!

Best,

Vera

devtools::install_github("gabraham/plink2R/plink2R") does not work.Very difficult to install.Can you develop a new installation method?l

Installation issue

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)