Package installation error

[s-yadav21]

Hi,
Thank you for creating this package. However, when I am trying to install the package on my windows pc, I am getting compilation error:

collect2.exe: error: ld returned 1 exit status no DLL was created ERROR: compilation failed for package 'scibet' Warning message: In i.p(...) : installation of package ‘C:/Users/AppData/Local/Temp/RtmpCmm7o9/file59c23cf6104/scibet_1.0.tar.gz’ had non-zero exit status

[retiii]

Upvote from me, same problem. That message is preceded by many messages like the following, mentioning undefined OpenMP references.

[ZebinWen]

May I see your code? I have encountered the same problem before, but I solved it by installing another version of SciBet, which is SciBetR. This is the code:
if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
devtools::install_github("zwj-tina/scibetR")
You can find more instructions on "http://scibet.cancer-pku.cn/installation.html".

[amanzju]

Hello,
Thank you for developing your new package. I followed "http://scibet.cancer-pku.cn/installation.html" link to use scbetR package in windows system and successfully installed.
However, when I am running scMAGIC function under the scMAGIC package, it's showing the following error "Error in library(scibet) : there is no package called ‘scibet’". That means, inside of scMAGIC function still calling the scibet package that's why it's not working. Thanks in advance to deal with this problem.

[kguion1]

@amanzju I am having the same issue, were you able to fix this?

[amanzju]

@amanzju I am having the same issue, were you able to fix this?

I am still unable to fix this problem on Windows, however, I am working on Linux and it works here.

[kguion1]

@amanzju I don't know if you are still looking to run scMAGIC on windows, but I submitted an issue on the scMAGIC page and he fixed the package to also work with the scibetR version. Originally it was only calling the scibet (Linux version), it should hopefully work now for Windows.

scMAGIC issue #13

[Drjingluo]

Hello, I also meet the same problem of installation on Windows. If anyone could help me?
C:/RBuildTools/4.0/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0ELi1EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b[__ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0ELi1EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b]+0x4c5): undefined reference to `GOMP_parallel'
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'scibet'

• removing 'F:/R-4.1.2/library/scibet'
  Warning message:
  In i.p(...) : installation of package ‘C:/Users/Windows/AppData/Local/Temp/Rtmp44eXIQ/file570132426b8/scibet_1.0.tar.gz’ had non-zero exit status

[Cloudy-Zhuang]

Hello, I also meet the same problem of installation on Windows. If anyone could help me?
C:/RBuildTools/4.0/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0ELi1EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b[__ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0ELi1EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b]+0x4c5): undefined reference to `GOMP_parallel'
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'scibet'

removing 'F:/R-4.1.2/library/scibet'
Warning message:
In i.p(...) : installation of package ‘C:/Users/Windows/AppData/Local/Temp/Rtmp44eXIQ/file570132426b8/scibet_1.0.tar.gz’ had non-zero exit status