&引用；“明菲”；Ubuntu 20.04上R3.6的软件包安装不成功

我在Linux上使用R3.6（这是Linux的最新R版本），我需要对Infinium HumanMethylization450K数据执行甲基化分析，为此我需要“minfi”R包

为此，我使用了以下代码：

install.packages("BiocManager")
BiocManager::install('minfi')
install.packages("minfi")

我也试过：

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("minfi")

然后：

这就是我得到的：

库（minfi）中出错：没有名为“minfi”的包

安装软件包后，我还收到许多警告和错误：

ERROR: compilation failed for package ‘Rhtslib’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib’
* 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: configuration failed for package ‘XML’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/XML’
* 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/melshark/R/x86_64-pc-linux-gnu-library/3.6/curl’
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
** using staged installation
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/RCurl’
* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
** using staged installation
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lxml2
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libxml-2.0 was not found. Try installing:
 * deb: libxml2-dev (Debian, Ubuntu, etc)
 * rpm: libxml2-devel (Fedora, CentOS, RHEL)
 * csw: libxml2_dev (Solaris)
If libxml-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libxml-2.0.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 ‘xml2’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/xml2’
ERROR: dependency ‘openssl’ is not available for package ‘base64’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/base64’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘annotate’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/annotate’
ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘httr’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/httr’
ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/GenomeInfoDb’
ERROR: dependencies ‘curl’, ‘httr’ are not available for package ‘BiocFileCache’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/BiocFileCache’
ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/GenomicRanges’
ERROR: dependency ‘base64’ is not available for package ‘illuminaio’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/illuminaio’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/genefilter’
ERROR: dependencies ‘httr’, ‘xml2’ are not available for package ‘GEOquery’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/GEOquery’
ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’, ‘Rhtslib’ are not available for package ‘Rsamtools’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/Rsamtools’
ERROR: dependencies ‘XML’, ‘httr’, ‘openssl’, ‘BiocFileCache’ are not available for package ‘biomaRt’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/biomaRt’
ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/SummarizedExperiment’
ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘Rsamtools’ are not available for package ‘GenomicAlignments’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/GenomicAlignments’
ERROR: dependencies ‘GenomicRanges’, ‘XML’, ‘GenomeInfoDb’, ‘RCurl’, ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘rtracklayer’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/rtracklayer’
ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’, ‘RCurl’, ‘rtracklayer’, ‘biomaRt’ are not available for package ‘GenomicFeatures’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/GenomicFeatures’
ERROR: dependencies ‘GenomeInfoDb’, ‘GenomicRanges’, ‘GenomicFeatures’ are not available for package ‘bumphunter’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/bumphunter’
ERROR: dependencies ‘GenomicRanges’, ‘SummarizedExperiment’, ‘bumphunter’, ‘GenomeInfoDb’, ‘illuminaio’, ‘genefilter’, ‘GEOquery’ are not available for package ‘minfi’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/minfi’

The downloaded source packages are in
    ‘/tmp/RtmpDInss9/downloaded_packages’
Installation path not writeable, unable to update packages: boot, class, KernSmooth,
  lattice, MASS, mgcv, nlme, nnet, spatial, survival
There were 23 warnings (use warnings() to see them)
> install.packages("minfi")
Installing package into ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘minfi’ is not available (for R version 3.6.3)
> install.packages("BiocManager")
Error in install.packages : Updating loaded packages
> install.packages("BiocManager")
Installing package into ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cran.uni-muenster.de/src/contrib/BiocManager_1.30.10.tar.gz'
Content type 'application/x-gzip' length 40205 bytes (39 KB)
==================================================

我还尝试了这一点，以检查“minfi”是否适用于我当前的R版本：

remove.packages("BiocVersion")
avail <- BiocManager::available()
length(avail)                               # all CRAN & Bioconductor packages
BiocManager::available("minfi")

---

如何解决此问题？

在

库（minfi）

之后出现的错误不如从任何

安装*

函数调用中得到的警告和错误有用。@r2evans我收到许多警告和错误，如：错误：依赖项“基因组范围”、“摘要实验”、“bumphunter”，“GenomeInfo数据库”、“illuminaio”、“genefilter”、“GEOquery”不适用于程序包“minfi”*删除“/home/melshar/R/x86_64-pc-linux-gnu-library/3.6/minfi”是的，这些都很有用。请逐字逐句回答您的问题。@Edo我以前试过这个，但在他们推荐的新安装中出现了问题。它创建了另一个使新安装崩溃的存储库（可能是我做错了什么，对Linux不是很有经验）。Linux也没有4.0官方版本

remove.packages("BiocVersion")
avail <- BiocManager::available()
length(avail)                               # all CRAN & Bioconductor packages
BiocManager::available("minfi")

> avail <- BiocManager::available()
> length(avail)                               # all CRAN & Bioconductor packages
[1] 19463
> BiocManager::available("minfi")
[1] "minfi"         "minfiData"     "minfiDataEPIC"

installing to /home/melshark/R/x86_64-pc-linux-gnu-library/3.6/00LOCK- 
   rtracklayer/00new/rtracklayer/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘offset’ from package ‘stats’ in package ‘rtracklayer’
Creating a generic function from function ‘uri’ in package ‘rtracklayer’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rtracklayer)
ERROR: dependency ‘biomaRt’ is not available for package ‘GenomicFeatures’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/GenomicFeatures’
ERROR: dependency ‘GenomicFeatures’ is not available for package ‘bumphunter’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/bumphunter’
ERROR: dependencies ‘bumphunter’, ‘illuminaio’, ‘GEOquery’ are not available for package ‘minfi’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/minfi’

The downloaded source packages are in
    ‘/tmp/RtmpWmvmxL/downloaded_packages’
Installation path not writeable, unable to update packages: spatial, survival
Warning messages:
1: In install.packages(...) :
  installation of package ‘openssl’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘base64’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘httr’ had non-zero exit status
4: In install.packages(...) :
  installation of package ‘BiocFileCache’ had non-zero exit status
5: In install.packages(...) :
  installation of package ‘illuminaio’ had non-zero exit status
6: In install.packages(...) :
  installation of package ‘GEOquery’ had non-zero exit status
7: In install.packages(...) :
  installation of package ‘biomaRt’ had non-zero exit status
8: In install.packages(...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status
9: In install.packages(...) :
  installation of package ‘bumphunter’ had non-zero exit status
10: In install.packages(...) :
  installation of package ‘minfi’ had non-zero exit status