Package installation on Windows fails

[lucassalas]

Hi Pavlo,

I have some non-blood samples in which I am using RefFreEWAS, I wanted to compare the results using your package. However I cannot install it, I have tried the zip and tarballs and both releases without success. I am working using a Windows 10 Pro machine. Below the error message and session info.

Best,

Lucas

install_github("lutsik/MeDeCom")
Downloading GitHub repo lutsik/MeDeCom@master
from URL https://api.github.com/repos/lutsik/MeDeCom/zipball/master
Installing MeDeCom
"C:/Users/LUCASS1/DOCUME1/R/R-34~1.1/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL "C:/Users/Lucas
Salas/AppData/Local/Temp/RtmpaCqxak/devtools148904fb619b1/lutsik-MeDeCom-1c31de6" --library="C:/Users/Lucas Salas/Documents/R/R-3.4.1/library" --install-tests

• installing source package 'MeDeCom' ...
  ** libs
  C:/RBuildTools/3.4/mingw_64/bin/g++ -I"C:/Users/LUCASS1/DOCUME1/R/R-341.1/include" -DNDEBUG -I"C:/Users/Lucas Salas/Documents/R/R-3.4.1/library/Rcpp/include" -I"C:/Users/Lucas Salas/Documents/R/R-3.4.1/library/RcppEigen/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -IC:/Users/LUCASS1/DOCUME1/R/R-341.1/library/Rcpp/include -I. -fopenmp -O2 -Wall -mtune=core2 -c HCLasso.cpp -o HCLasso.o
  HCLasso.cpp: In function 'void SetInput(double*, double*, double, double*, double*, ptrdiff_t)':
  HCLasso.cpp:85:37: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'void dcopy_(CONST_BLINT, CONST_BLDOU, CONST_BLINT, BLDOU, CONST_BLINT)'
  dcopy(&ks, G, &ione, Hess, &ione);
  ^
  HCLasso.cpp:86:43: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'void daxpy_(CONST_BLINT, CONST_BLDOU, CONST_BLDOU, CONST_BLINT, BLDOU, CONST_BLINT)'
  daxpy(&ks, &one, G, &ione, Hess, &ione);
  ^
  HCLasso.cpp: In function 'void GetGrad(double*, double*, double*, double*, ptrdiff_t)':
  HCLasso.cpp:112:68: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '2' to 'void dgemv_(BLCHAR, CONST_BLINT, CONST_BLINT, CONST_BLDOU, CONST_BLDOU, CONST_BLINT, CONST_BLDOU, CONST_BLINT, CONST_BLDOU, BLDOU, CONST_BLINT)'
  dgemv(chn, &k, &k, &one, Hess, &k, x, &ione, &zero, grad, &ione);
  ^
  HCLasso.cpp:115:46: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'void daxpy_(CONST_BLINT, CONST_BLDOU, CONST_BLDOU, CONST_BLINT, BLDOU, CONST_BLINT)'
  daxpy(&k, &mone, beta, &ione, grad, &ione);
  ^
  HCLasso.cpp: In function 'double ObjValue(double*, double*, double*, double*, ptrdiff_t)':
  HCLasso.cpp:134:64: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '2' to 'void dgemv_(BLCHAR, CONST_BLINT, CONST_BLINT, CONST_BLDOU, CONST_BLDOU, CONST_BLINT, CONST_BLDOU, CONST_BLINT, CONST_BLDOU, BLDOU, CONST_BLINT)'
  dgemv(chn, &k, &k, &one, G, &k, x, &ione, &zero, tmp, &ione);
  ^
  HCLasso.cpp:137:45: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'void daxpy_(CONST_BLINT, CONST_BLDOU, CONST_BLDOU, CONST_BLINT, BLDOU, CONST_BLINT)'
  daxpy(&k, &mone, beta, &ione, tmp, &ione);
  ^
  HCLasso.cpp:140:53: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'double ddot_(CONST_BLINT, CONST_BLDOU, CONST_BLINT, CONST_BLDOU, CONST_BLINT)'
  double f = (double)ddot(&k, x, &ione, tmp, &ione);
  ^
  HCLasso.cpp: In function 'double GetAlpha(double*, double*, double*, double*, double*, double*, ptrdiff_t)':
  HCLasso.cpp:157:35: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'void dcopy_(CONST_BLINT, CONST_BLDOU, CONST_BLINT, BLDOU, CONST_BLINT)'
  dcopy(&k, x, &ione, tmp, &ione);
  ^
  HCLasso.cpp:159:46: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'void daxpy_(CONST_BLINT, CONST_BLDOU, CONST_BLDOU, CONST_BLINT, BLDOU, CONST_BLINT)'
  daxpy(&k, &mone, x_old, &ione, tmp, &ione);
  ^
  HCLasso.cpp:163:36: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'void dcopy_(CONST_BLINT, CONST_BLDOU, CONST_BLINT, BLDOU, CONST_BLINT)'
  dcopy(&k, g, &ione, tmp1, &ione);
  ^
  HCLasso.cpp:165:47: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'void daxpy_(CONST_BLINT, CONST_BLDOU, CONST_BLDOU, CONST_BLINT, BLDOU, CONST_BLINT)'
  daxpy(&k, &mone, g_old, &ione, tmp1, &ione);
  ^
  HCLasso.cpp:168:63: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'double ddot_(CONST_BLINT, CONST_BLDOU, CONST_BLINT, CONST_BLDOU, CONST_BLINT)'
  double numerator = (double)ddot(&k, tmp, &ione, tmp, &ione);
  ^
  HCLasso.cpp:171:66: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'double ddot_(CONST_BLINT, CONST_BLDOU, CONST_BLINT, CONST_BLDOU, CONST_BLINT)'
  double denominator = (double)ddot(&k, tmp, &ione, tmp1, &ione);
  ^
  HCLasso.cpp: In function 'void GetProjStep(double*, double*, double*, double, ptrdiff_t)':
  HCLasso.cpp:198:33: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'void dcopy_(CONST_BLINT, CONST_BLDOU, CONST_BLINT, BLDOU, CONST_BLINT)'
  dcopy(&k, x, &ione, d, &ione);
  ^
  HCLasso.cpp:202:42: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'void daxpy_(CONST_BLINT, CONST_BLDOU, CONST_BLDOU, CONST_BLINT, BLDOU, CONST_BLINT)'
  daxpy(&k, &malpha, g, &ione, d, &ione);
  ^
  HCLasso.cpp:208:40: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'void daxpy_(CONST_BLINT, CONST_BLDOU, CONST_BLDOU, CONST_BLINT, BLDOU, CONST_BLINT)'
  daxpy(&k, &mone, x, &ione, d, &ione);
  ^
  HCLasso.cpp: In function 'double GetDirectDerivative(double*, double*, ptrdiff_t)':
  HCLasso.cpp:219:53: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'double ddot_(CONST_BLINT, CONST_BLDOU, CONST_BLINT, CONST_BLDOU, CONST_BLINT)'
  double sum = (double)ddot(&k, g, &ione, d, &ione);
  ^
  HCLasso.cpp: In function 'double NormOne(double*, ptrdiff_t)':
  HCLasso.cpp:226:36: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'double dasum_(CONST_BLINT, BLDOU, CONST_BLINT)'
  double sum = dasum(&k, x, &ione);
  ^
  HCLasso.cpp: In function 'void HCLasso(double*, double*, double*, double, ptrdiff_t, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*)':
  HCLasso.cpp:290:34: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'void dcopy_(CONST_BLINT, CONST_BLDOU, CONST_BLINT, BLDOU, CONST_BLINT)'
  dcopy(&k, a0, &ione, x, &ione);
  ^
  HCLasso.cpp:296:36: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'void dcopy_(CONST_BLINT, CONST_BLDOU, CONST_BLINT, BLDOU, CONST_BLINT)'
  dcopy(&k, x, &ione, ahat, &ione);
  ^
  HCLasso.cpp:368:71: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '2' to 'void dgemv_(BLCHAR, CONST_BLINT, CONST_BLINT, CONST_BLDOU, CONST_BLDOU, CONST_BLINT, CONST_BLDOU, CONST_BLINT, CONST_BLDOU, BLDOU, CONST_BLINT)'
  dgemv(chn, &k, &k, &one, Hess, &k, d, &ione, &zero, tmp, &ione);
  ^
  HCLasso.cpp:369:53: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'double ddot_(CONST_BLINT, CONST_BLDOU, CONST_BLINT, CONST_BLDOU, CONST_BLINT)'
  Quad = (double)ddot(&k, d, &ione, tmp, &ione);
  ^
  HCLasso.cpp:420:41: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'void dcopy_(CONST_BLINT, CONST_BLDOU, CONST_BLINT, BLDOU, CONST_BLINT)'
  dcopy(&k, x, &ione, x_old, &ione);
  ^
  HCLasso.cpp:421:41: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'void daxpy_(CONST_BLINT, CONST_BLDOU, CONST_BLDOU, CONST_BLINT, BLDOU, CONST_BLINT)'
  daxpy(&k, &t, d, &ione, x, &ione);
  ^
  HCLasso.cpp:431:41: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'void dcopy_(CONST_BLINT, CONST_BLDOU, CONST_BLINT, BLDOU, CONST_BLINT)'
  dcopy(&k, g, &ione, g_old, &ione);
  ^
  HCLasso.cpp:442:44: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'void dcopy_(CONST_BLINT, CONST_BLDOU, CONST_BLINT, BLDOU, CONST_BLINT)'
  dcopy(&k, x, &ione, ahat, &ione);
  ^
  HCLasso.cpp:448:39: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'void dcopy_(CONST_BLINT, CONST_BLDOU, CONST_BLINT, BLDOU, CONST_BLINT)'
  dcopy(&k, x, &ione, tmp, &ione);
  ^
  HCLasso.cpp:449:46: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'void daxpy_(CONST_BLINT, CONST_BLDOU, CONST_BLDOU, CONST_BLINT, BLDOU, CONST_BLINT)'
  daxpy(&k, &mone, g, &ione, tmp, &ione);
  ^
  HCLasso.cpp:451:46: error: cannot convert 'ptrdiff_t* {aka long long int*}' to 'CONST_BLINT {aka const long int*}' for argument '1' to 'void daxpy_(CONST_BLINT, CONST_BLDOU, CONST_BLDOU, CONST_BLINT, BLDOU, CONST_BLINT)'
  daxpy(&k, &mone, x, &ione, tmp, &ione);
  ^
  make: *** [HCLasso.o] Error 1
  Warning: running command 'make -f "Makevars.win" -f "C:/Users/LUCASS1/DOCUME1/R/R-341.1/etc/x64/Makeconf" -f "C:/Users/LUCASS1/DOCUME1/R/R-341.1/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="MeDeCom.dll" WIN=64 TCLBIN=64 OBJECTS="HCLasso.o QuadHC.o RProjSplxBox.o RQuadSimplex.o RQuadSimplexBox.o RcppExports.o cppTAfact.o"' had status 2
  ERROR: compilation failed for package 'MeDeCom'
• removing 'C:/Users/Lucas Salas/Documents/R/R-3.4.1/library/MeDeCom'
• restoring previous 'C:/Users/Lucas Salas/Documents/R/R-3.4.1/library/MeDeCom'
  Installation failed: Command failed (1)

sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] devtools_1.13.3

loaded via a namespace (and not attached):
[1] httr_1.3.1 compiler_3.4.1 R6_2.2.2 tools_3.4.1 withr_2.0.0 curl_2.8.1 memoise_1.1.0 knitr_1.17 git2r_0.19.0 digest_0.6.12

[lutsik]

Dear Lucas,

As stated in our vignette, at the moment MeDeCom runs on *nix-like platforms only. Windows support is on our list of priorities.

Best regards,

Pavlo

[lutsik]

I fixed this and a few other "easy" problems (see branch "remove_mpi"). The compilation (on x64) now proceeds to cppTAfact.cpp and segfaults at the same place somewhere in Eigen:
`
....Eigen/src/core/products/GeneralMatrixVector.h:322:1 : Internal compiler error: Segmentation fault
'
@dQuz could you perhaps have a closer look?

On i386 compilation terminates earlier due to reaching memory limits (I am pretty sure cppTAfact is not going to work on 32-bit, @nikitaved can you comment?).

[lutsik]

The package now compiles on Windows (branch remove_mpi), but the execution times increased, due to inability to use multicore functionality.