Error of Installing the V3.2.3 seurat

[Chen-Guanming]

Hi all:
I have some problem in installing the old version seurat.
I tested many different methods to solve the problem but I can't.
Would you help me?
Thanks!

my version information:

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 processx_3.5.0 compiler_3.6.0 R6_2.5.0 assertthat_0.2.1 cli_2.3.1
[7] prettyunits_1.1.1 tools_3.6.0 glue_1.4.2 crayon_1.4.1 remotes_2.2.0 callr_3.5.1
[13] ps_1.6.0 pkgbuild_1.2.0 rlang_0.4.10

when I used the code(remotes::install_version("Seurat", version = "3.2.3")), I will get the below information:

Downloading package from url: https://cran.rstudio.com//src/contrib/Archive/Seurat/Seurat_3.2.2.tar.gz
Skipping 5 packages ahead of CRAN: abind, base64enc, colorspace, xtable, png
Installing package into ‘/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)

• installing source package ‘Seurat’ ...
  ** package ‘Seurat’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I"/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/Rcpp/include" -I"/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/RcppEigen/include" -I"/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/RcppProgress/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c ModularityOptimizer.cpp -o ModularityOptimizer.o
  ModularityOptimizer.cpp: In function ‘std::shared_ptrModularityOptimizer::Network ModularityOptimizer::matrixToNetwork(IVector&, IVector&, DVector&, int, int)’:
  ModularityOptimizer.cpp:761:7: warning: unused variable ‘n1_max’ [-Wunused-variable]
  int n1_max = *std::max_element(node1.cbegin(), node1.cend());
  ^
  ModularityOptimizer.cpp:762:7: warning: unused variable ‘n2_max’ [-Wunused-variable]
  int n2_max = *std::max_element(node2.cbegin(), node2.cend());
  ^
  g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I"/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/Rcpp/include" -I"/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/RcppEigen/include" -I"/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/RcppProgress/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c RModularityOptimizer.cpp -o RModularityOptimizer.o
  g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I"/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/Rcpp/include" -I"/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/RcppEigen/include" -I"/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/RcppProgress/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
  g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I"/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/Rcpp/include" -I"/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/RcppEigen/include" -I"/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/RcppProgress/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c data_manipulation.cpp -o data_manipulation.o
  data_manipulation.cpp: In function ‘Eigen::SparseMatrix<double, 0, int> RowMergeMatricesList(Rcpp::List, Rcpp::List, std::vector<std::basic_string >)’:
  data_manipulation.cpp:151:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j = 0; j < mat_vec.size(); j++) {
  ^
  g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I"/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/Rcpp/include" -I"/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/RcppEigen/include" -I"/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/RcppProgress/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c integration.cpp -o integration.o
  integration.cpp: In function ‘Eigen::SparseMatrix<double, 0, int> FindWeightsC(Eigen::SparseMatrix<double, 0, int>, Rcpp::NumericVector, Eigen::MatrixXd, std::vector<std::basic_string >, std::vector<std::basic_string >, Eigen::MatrixXd, Eigen::VectorXd, double, double, bool)’:
  integration.cpp:30:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i<anchor_cells2.size(); ++i){
  ^
  integration.cpp:48:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int j=0; j<mnn_idx.size(); ++j){
  ^
  g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I"/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/Rcpp/include" -I"/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/RcppEigen/include" -I"/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/RcppProgress/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c snn.cpp -o snn.o
  gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I"/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/Rcpp/include" -I"/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/RcppEigen/include" -I"/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/RcppProgress/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c valid_pointer.c -o valid_pointer.o
  g++ -m64 -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o Seurat.so ModularityOptimizer.o RModularityOptimizer.o RcppExports.o data_manipulation.o integration.o snn.o valid_pointer.o -L/usr/lib64/R/lib -lR
  installing to /home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/00LOCK-Seurat/00new/Seurat/libs
  ** R
  ** data
  *** moving datasets to lazyload DB
  Warning: namespace ‘Seurat’ is not available and has been replaced
  by .GlobalEnv when processing object ‘pbmc_small’
  Warning: namespace ‘Seurat’ is not available and has been replaced
  by .GlobalEnv when processing object ‘pbmc_small’
  ** inst
  ** byte-compile and prepare package for lazy loading
  Error: object ‘markvario’ is not exported by 'namespace:spatstat'
  Execution halted
  ERROR: lazy loading failed for package ‘Seurat’
• removing ‘/home/chengm/R/x86_64-redhat-linux-gnu-library/3.6/Seurat’
  Error: Failed to install 'unknown package' from URL:
  (converted from warning) installation of package ‘/tmp/Rtmp6vTn2y/remotes292c375d71990/Seurat’ had non-zero exit status

[skashin]

Hi,

I am getting the same error. Is there an easy way to fix it?

Thanks,
Seva

[Chen-Guanming]

Hi, I not sure whether you are the same error with me, but you can see the #4226 which may be can help you if you error is&nbsp;Error: object ‘markvario’ is not exported by 'namespace:spatstat'.&nbsp;&nbsp;You can follow the method of user lldelisle, but you must not update packages when you install Seurat, because this error maybe happen due to the package&nbsp;spatstat changed the package structure. &nbsp; best wish, Chen ------------------&nbsp;Original&nbsp;------------------ From: &nbsp;"Seva ***@***.***&gt;; Date: &nbsp;Wed, Mar 31, 2021 06:18 PM To: ***@***.***&gt;; Cc: ***@***.***&gt;; "State ***@***.***&gt;; Subject: &nbsp;Re: [satijalab/seurat] Error of Installing the V3.2.3 seurat (#4283) &nbsp; Hi, I am getting the same error. Is there an easy way to fix it? Thanks, Seva — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub, or unsubscribe.

[skashin]

Hi Chen,

Thanks, I will give it a try!

Best,
Seva