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bnprks / BPCells

Scaling Single Cell Analysis to Millions of Cells
https://bnprks.github.io/BPCells
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Instlaling BPCells in a conda environment in a linux server #112

Open Dario-Rocha opened 1 month ago

Dario-Rocha commented 1 month ago

Hello BPCells team I am currently trying to install this package in a conda environment created in a linux server for which I have no sudo access. I am not very keen on informatics, so I am trying my best with what I can find online. Right now I have stumbled into this error and I don't want to mess up things so I am asking for some help before fiddling with stuff.

Through the terminal, connected to the server I installed R and remotes

conda create -n env_seurat5 python=3.9
conda activate env_seurat5
conda install -c r r-essentials
conda install -c anaconda hdf5
R
install.packages('remotes')
remotes::install_github("bnprks/BPCells/r")

After a long processing time, these messages are displayed

printed messages Running `R CMD build`... * checking for file ‘/local/scratch/24970639.torque6.curie.fr/RtmpD7TujN/remotes7e41524bc38/bnprks-BPCells-5677cf1/r/DESCRIPTION’ ... OK * preparing ‘BPCells’: * checking DESCRIPTION meta-information ... OK * cleaning src * running ‘cleanup’ * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘BPCells_0.2.0.tar.gz’ * installing *source* package ‘BPCells’ ... ** using staged installation Testing hdf5 by compiling example program... Found working hdf5 HDF5_CFLAGS='' HDF5_LIBS='-lhdf5' Testing C++17 filesystem feature support... Testing availability of highway SIMD library... Building highway SIMD library from source ** libs using C++ compiler: ‘x86_64-conda-linux-gnu-c++ (Anaconda gcc) 11.2.0’ x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bitpacking_io.cpp -o bitpacking_io.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c clustering.cpp -o clustering.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c fragment_io.cpp -o fragment_io.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c fragment_utils.cpp -o fragment_utils.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c matrix_io.cpp -o matrix_io.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c matrix_transforms.cpp -o matrix_transforms.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c matrix_utils.cpp -o matrix_utils.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c R_array_io.cpp -o R_array_io.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c R_highfive_logger.cpp -o R_highfive_logger.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/arrayIO/array_interfaces.cpp -o bpcells-cpp/arrayIO/array_interfaces.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/arrayIO/binaryfile.cpp -o bpcells-cpp/arrayIO/binaryfile.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/arrayIO/bp128.cpp -o bpcells-cpp/arrayIO/bp128.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/arrayIO/hdf5.cpp -o bpcells-cpp/arrayIO/hdf5.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/arrayIO/vector.cpp -o bpcells-cpp/arrayIO/vector.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/fragmentIterators/BedFragments.cpp -o bpcells-cpp/fragmentIterators/BedFragments.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/fragmentIterators/CellSelect.cpp -o bpcells-cpp/fragmentIterators/CellSelect.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/fragmentIterators/ChrSelect.cpp -o bpcells-cpp/fragmentIterators/ChrSelect.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/fragmentIterators/FragmentIterator.cpp -o bpcells-cpp/fragmentIterators/FragmentIterator.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/fragmentIterators/LengthSelect.cpp -o bpcells-cpp/fragmentIterators/LengthSelect.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/fragmentIterators/MergeFragments.cpp -o bpcells-cpp/fragmentIterators/MergeFragments.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/fragmentIterators/RegionSelect.cpp -o bpcells-cpp/fragmentIterators/RegionSelect.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/fragmentIterators/Rename.cpp -o bpcells-cpp/fragmentIterators/Rename.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/fragmentIterators/ShiftCoords.cpp -o bpcells-cpp/fragmentIterators/ShiftCoords.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/fragmentIterators/StoredFragments.cpp -o bpcells-cpp/fragmentIterators/StoredFragments.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/fragmentUtils/BedgraphWriter.cpp -o bpcells-cpp/fragmentUtils/BedgraphWriter.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/fragmentUtils/FootprintMatrix.cpp -o bpcells-cpp/fragmentUtils/FootprintMatrix.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/fragmentUtils/InsertionIterator.cpp -o bpcells-cpp/fragmentUtils/InsertionIterator.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/matrixIterators/ImportMatrixHDF5.cpp -o bpcells-cpp/matrixIterators/ImportMatrixHDF5.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/matrixIterators/PeakMatrix.cpp -o bpcells-cpp/matrixIterators/PeakMatrix.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/matrixIterators/TileMatrix.cpp -o bpcells-cpp/matrixIterators/TileMatrix.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/matrixIterators/MatrixStats.cpp -o bpcells-cpp/matrixIterators/MatrixStats.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/matrixIterators/MatrixMarketImport.cpp -o bpcells-cpp/matrixIterators/MatrixMarketImport.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/matrixIterators/SVD.cpp -o bpcells-cpp/matrixIterators/SVD.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/matrixTransforms/Binarize.cpp -o bpcells-cpp/matrixTransforms/Binarize.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/matrixTransforms/LinearResidual.cpp -o bpcells-cpp/matrixTransforms/LinearResidual.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/matrixTransforms/Log1p.cpp -o bpcells-cpp/matrixTransforms/Log1p.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/matrixTransforms/Min.cpp -o bpcells-cpp/matrixTransforms/Min.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/matrixTransforms/MatrixTransform.cpp -o bpcells-cpp/matrixTransforms/MatrixTransform.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/matrixTransforms/Pow.cpp -o bpcells-cpp/matrixTransforms/Pow.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/matrixTransforms/Round.cpp -o bpcells-cpp/matrixTransforms/Round.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/matrixTransforms/SCTransform.cpp -o bpcells-cpp/matrixTransforms/SCTransform.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/matrixTransforms/Scale.cpp -o bpcells-cpp/matrixTransforms/Scale.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/matrixTransforms/Shift.cpp -o bpcells-cpp/matrixTransforms/Shift.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/matrixUtils/WilcoxonRankSum.cpp -o bpcells-cpp/matrixUtils/WilcoxonRankSum.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/simd/bp128/current_target.cpp -o bpcells-cpp/simd/bp128/current_target.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/simd/bp128/d1_maxbits.cpp -o bpcells-cpp/simd/bp128/d1_maxbits.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/simd/bp128/d1_pack.cpp -o bpcells-cpp/simd/bp128/d1_pack.o x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/include" -DNDEBUG -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/Rcpp/include' -I'/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/RcppEigen/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -I/data/users/drocha/miniconda3/envs/env_seurat5/include -Wl,-rpath-link,/data/users/drocha/miniconda3/envs/env_seurat5/lib -Ibpcells-cpp -I../tools/highway/include -Ivendor -std=c++17 -DRCPP_EIGEN -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS -Wno-ignored-attributes -Wno-unknown-pragmas -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data/users/drocha/miniconda3/envs/env_seurat5/include -fdebug-prefix-map=/workspace/croot/r-base_1695428141831/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/data/users/drocha/miniconda3/envs/env_seurat5=/usr/local/src/conda-prefix -c bpcells-cpp/simd/bp128/d1_unpack.cpp -o bpcells-cpp/simd/bp128/d1_unpack.o

and finally this error:

{standard input}: Assembler messages: {standard input}:151241: Warning: end of file not at end of a line; newline inserted {standard input}: Error: open CFI at the end of file; missing .cfi_endproc directive x86_64-conda-linux-gnu-c++: fatal error: Killed signal terminated program cc1plus compilation terminated. make: *** [/data/users/drocha/miniconda3/envs/env_seurat5/lib/R/etc/Makeconf:200: bpcells-cpp/simd/bp128/d1_unpack.o] Error 1 ERROR: compilation failed for package ‘BPCells’

  • removing ‘/bioinfo/users/drocha/miniconda3/envs/env_seurat5/lib/R/library/BPCells’

What should I try to do? what other specifications would be useful to diagnose this?

bnprks commented 1 month ago

Hi @Dario-Rocha,

How much memory did you have allocated on your server when you were running install_github?

The error x86_64-conda-linux-gnu-c++: fatal error: Killed signal terminated program cc1plus compilation terminated suggests that something killed one of the compilation processes, which I think would most likely be due to out of memory (assuming that it wasn't a person manually killing the process). Or if you run on a cluster that kills jobs that take too much time that could also be a possibility.

If you have any line setting MAKEFLAGS in your ~/.R/Makevars file, that also could be increasing the total memory used by having many compilation jobs running at once.

I'm fairly confident that this specific error would have to do with resource constraints on the server you were using, though that doesn't mean there won't be other issues once you get further through the compilation process. Personally, I've tended to run into weird errors using conda to install R packages but hopefully you will have better luck.

-Ben