> 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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