在Ubuntu 20.04上，R 3.6的“ minfi”软件包安装不成功

分类：编程问答

如何解决在Ubuntu 20.04上，R 3.6的“ minfi”软件包安装不成功

我正在Linux上使用R 3.6（这是Linux的最新R版本），我需要对Infinium HumanMethylation450k数据进行甲基化分析，为此，我需要使用“ minfi” R软件包。

为此，我使用了以下代码：

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

我也尝试过：

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

然后：

library(minfi)

这就是我得到的：

库（minfi）中出现错误：没有名为“ minfi”的软件包

安装该软件包后，我还会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,etc)
 * rpm: libcurl-devel (Fedora,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,etc)
 * rpm: libxml2-devel (Fedora,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’,‘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’,‘rtracklayer’,‘biomaRt’ are not available for package ‘GenomicFeatures’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/GenomicFeatures’
ERROR: dependencies ‘GenomeInfoDb’,‘GenomicFeatures’ are not available for package ‘bumphunter’
* removing ‘/home/melshark/R/x86_64-pc-linux-gnu-library/3.6/bumphunter’
ERROR: dependencies ‘GenomicRanges’,‘bumphunter’,‘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)
==================================================

我还尝试了此操作，以检查当前的R版本是否可以使用“ minfi”：

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

这就是我得到的：

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

我还按照@Alexlok的建议安装了libcurl4-openssl-dev和libxml2-dev，显然需要它们，但是现在我得到了不同的错误：

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’,‘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

我该如何解决这个问题？

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