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install.packages('Seurat')

install.packages('Seurat')

作者: Seurat_Satija | 来源:发表于2021-08-24 14:53 被阅读0次
    > rm(list = ls()) 
    > options()$repos 
                             CRAN 
    "https://cloud.r-project.org" 
    > options()$BioC_mirror
    NULL
    > #options(BioC_mirror="https://mirrors.ustc.edu.cn/bioc/")
    > options(BioC_mirror="http://mirrors.tuna.tsinghua.edu.cn/bioconductor/")
    > options("repos" = c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))
    > options()$repos 
                                            CRAN 
    "https://mirrors.tuna.tsinghua.edu.cn/CRAN/" 
    > options()$BioC_mirror
    [1] "http://mirrors.tuna.tsinghua.edu.cn/bioconductor/"
    > install.packages('Seurat')
    Installing package into '/home/rstudio/R/x86_64-pc-linux-gnu-library/4.1'
    (as 'lib' is unspecified)
    also installing the dependencies 'curl', 'openssl', 'httr', 'plotly'
    
    trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/curl_4.3.2.tar.gz'
    Content type 'application/octet-stream' length 793345 bytes (774 KB)
    ==================================================
    downloaded 774 KB
    
    trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/openssl_1.4.4.tar.gz'
    Content type 'application/octet-stream' length 1311285 bytes (1.3 MB)
    ==================================================
    downloaded 1.3 MB
    
    trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/httr_1.4.2.tar.gz'
    Content type 'application/octet-stream' length 159950 bytes (156 KB)
    ==================================================
    downloaded 156 KB
    
    trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/plotly_4.9.4.1.tar.gz'
    Content type 'application/octet-stream' length 3742653 bytes (3.6 MB)
    ==================================================
    downloaded 3.6 MB
    
    trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/Seurat_4.0.4.tar.gz'
    Content type 'application/octet-stream' length 1460356 bytes (1.4 MB)
    ==================================================
    downloaded 1.4 MB
    
    * installing *source* package 'curl' ...
    ** package 'curl' successfully unpacked and MD5 sums checked
    ** using staged installation
    Package libcurl was not found in the pkg-config search path.
    Perhaps you should add the directory containing `libcurl.pc'
    to the PKG_CONFIG_PATH environment variable
    No package 'libcurl' found
    Package libcurl was not found in the pkg-config search path.
    Perhaps you should add the directory containing `libcurl.pc'
    to the PKG_CONFIG_PATH environment variable
    No package 'libcurl' found
    Using PKG_CFLAGS=
    Using PKG_LIBS=-lcurl
    ------------------------- ANTICONF ERROR ---------------------------
    Configuration failed because libcurl was not found. Try installing:
     * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
     * rpm: libcurl-devel (Fedora, CentOS, RHEL)
     * csw: libcurl_dev (Solaris)
    If libcurl is already installed, check that 'pkg-config' is in your
    PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
    is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
    R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
    --------------------------------------------------------------------
    ERROR: configuration failed for package 'curl'
    * removing '/home/rstudio/R/x86_64-pc-linux-gnu-library/4.1/curl'
    Warning in install.packages :
      installation of package 'curl' had non-zero exit status
    * installing *source* package 'openssl' ...
    ** package 'openssl' successfully unpacked and MD5 sums checked
    ** using staged installation
    Using PKG_CFLAGS=
    --------------------------- [ANTICONF] --------------------------------
    Configuration failed because openssl was not found. Try installing:
     * deb: libssl-dev (Debian, Ubuntu, etc)
     * rpm: openssl-devel (Fedora, CentOS, RHEL)
     * csw: libssl_dev (Solaris)
     * brew: openssl@1.1 (Mac OSX)
    If openssl is already installed, check that 'pkg-config' is in your
    PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config
    is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
    R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
    -------------------------- [ERROR MESSAGE] ---------------------------
    tools/version.c:1:10: fatal error: openssl/opensslv.h: No such file or directory
        1 | #include <openssl/opensslv.h>
          |          ^~~~~~~~~~~~~~~~~~~~
    compilation terminated.
    --------------------------------------------------------------------
    ERROR: configuration failed for package 'openssl'
    * removing '/home/rstudio/R/x86_64-pc-linux-gnu-library/4.1/openssl'
    Warning in install.packages :
      installation of package 'openssl' had non-zero exit status
    ERROR: dependencies 'curl', 'openssl' are not available for package 'httr'
    * removing '/home/rstudio/R/x86_64-pc-linux-gnu-library/4.1/httr'
    Warning in install.packages :
      installation of package 'httr' had non-zero exit status
    ERROR: dependency 'httr' is not available for package 'plotly'
    * removing '/home/rstudio/R/x86_64-pc-linux-gnu-library/4.1/plotly'
    Warning in install.packages :
      installation of package 'plotly' had non-zero exit status
    ERROR: dependencies 'httr', 'plotly' are not available for package 'Seurat'
    * removing '/home/rstudio/R/x86_64-pc-linux-gnu-library/4.1/Seurat'
    Warning in install.packages :
      installation of package 'Seurat' had non-zero exit status
    
    The downloaded source packages are in
        '/tmp/Rtmp1LVDH1/downloaded_packages'
    > library(Seurat)
    

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