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PaulingLiu / scibet

A portable and fast single cell type identifier
BSD 3-Clause "New" or "Revised" License
61 stars 11 forks source link

Package installation error #8

Open s-yadav21 opened 3 years ago

s-yadav21 commented 3 years ago

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 commented 3 years ago

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

image

ZebinWen commented 3 years ago

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 commented 2 years ago

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 commented 2 years ago

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

amanzju commented 2 years ago

@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 commented 2 years ago

@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 commented 1 year ago

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'

Cloudy-Zhuang commented 1 year ago

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