R安装程序包失败

Question

我正在尝试安装R版本4.0.0中的包路径视图。我首先没有出现问题地安装了biocmanager，然后按照指示使用了以下命令：

BiocManager::install("pathview")

但是，它无法安装，并出现以下错误：

BiocManager::install("pathview")
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cran.csiro.au

Bioconductor version 3.12 (BiocManager 1.30.16), R 4.0.0 (2020-04-24)
Installing package(s) 'pathview'
also installing the dependencies ‘RSQLite’, ‘AnnotationDbi’, ‘org.Hs.eg.db’

trying URL 'https://cran.csiro.au/src/contrib/RSQLite_2.2.7.tar.gz'
Content type 'application/x-gzip' length 3616162 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/AnnotationDbi_1.52.0.tar.gz'
Content type 'application/x-gzip' length 4338642 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

trying URL 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/org.Hs.eg.db_3.12.0.tar.gz'
Content type 'application/x-gzip' length 83225518 bytes (79.4 MB)
==================================================
downloaded 79.4 MB

trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/pathview_1.30.1.tar.gz'
Content type 'application/x-gzip' length 2192604 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

* installing *source* package ‘RSQLite’ ...
** package ‘RSQLite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
icpc -std=gnu++11 -I"/apps/R/4.0.0/lib64/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/home/590/mr8122/R/x86_64-pc-linux-gnu-library/4.0/plogr/include' -I'/home/590/mr8122/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c DbColumn.cpp -o DbColumn.o
In file included from vendor/boost/container/stable_vector.hpp(68),
                 from RSQLite.h(14),
                 from pch.h(1),
                 from DbColumn.cpp(1):
vendor/boost/container/vector.hpp(2705): warning #2196: routine is both "inline" and "noinline"
     BOOST_CONTAINER_NOINLINE iterator priv_insert_forward_range_no_capacity
     ^

In file included from vendor/boost/container/stable_vector.hpp(68),
                 from RSQLite.h(14),
                 from pch.h(1),
                 from DbColumn.cpp(1):
vendor/boost/container/vector.hpp(2722): warning #2196: routine is both "inline" and "noinline"
     BOOST_CONTAINER_NOINLINE iterator priv_insert_forward_range_no_capacity
     ^

In file included from vendor/boost/preprocessor/control/while.hpp(323),
                 from vendor/boost/preprocessor/arithmetic/add.hpp(60),
                 from vendor/boost/mpl/aux_/preprocessor/def_params_tail.hpp(66),
                 from vendor/boost/mpl/aux_/na_spec.hpp(28),
                 from vendor/boost/mpl/if.hpp(19),
                 from vendor/boost/ptr_container/detail/default_deleter.hpp(15),
                 from vendor/boost/ptr_container/detail/static_move_ptr.hpp(23),
                 from vendor/boost/ptr_container/detail/reversible_ptr_container.hpp(22),
                 from vendor/boost/ptr_container/ptr_sequence_adapter.hpp(20),
                 from vendor/boost/ptr_container/ptr_vector.hpp(20),
                 from RSQLite.h(15),
                 from pch.h(1),
                 from DbColumn.cpp(1):
vendor/boost/preprocessor/list/fold_left.hpp(341): catastrophic error: cannot open source file "boost/preprocessor/list/detail/edg/fold_left.hpp"
  #    include <boost/preprocessor/list/detail/edg/fold_left.hpp>
                                                                 ^

compilation aborted for DbColumn.cpp (code 4)
make: *** [/apps/R/4.0.0/lib64/R/etc/Makeconf:176: DbColumn.o] Error 4
ERROR: compilation failed for package ‘RSQLite’
* removing ‘/home/590/mr8122/R/x86_64-pc-linux-gnu-library/4.0/RSQLite’
ERROR: dependency ‘RSQLite’ is not available for package ‘AnnotationDbi’
* removing ‘/home/590/mr8122/R/x86_64-pc-linux-gnu-library/4.0/AnnotationDbi’
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘org.Hs.eg.db’
* removing ‘/home/590/mr8122/R/x86_64-pc-linux-gnu-library/4.0/org.Hs.eg.db’
ERROR: dependencies ‘AnnotationDbi’, ‘org.Hs.eg.db’ are not available for package ‘pathview’
* removing ‘/home/590/mr8122/R/x86_64-pc-linux-gnu-library/4.0/pathview’

The downloaded source packages are in
    ‘/scratch/ki16/mr8122/tmp/RtmpYxgwWN/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /apps/R/4.0.0/lib64/R/library
  packages:
    boot, class, cluster, codetools, foreign, KernSmooth, lattice, MASS,
    Matrix, mgcv, nlme, nnet, spatial, survival
Warning messages:
1: In .inet_warning(msg) :
  installation of package ‘RSQLite’ had non-zero exit status
2: In .inet_warning(msg) :
  installation of package ‘AnnotationDbi’ had non-zero exit status
3: In .inet_warning(msg) :
  installation of package ‘org.Hs.eg.db’ had non-zero exit status
4: In .inet_warning(msg) :
  installation of package ‘pathview’ had non-zero exit status

有人知道这可能失败的原因吗？

Answer 1

RSQLite找不到Boost。我建议从源代码安装Boost，然后重新尝试R包安装。

我最初在使用BiocManager安装biomaRt时看到了这个错误。在安装Boost之后，我成功地安装了RSQLite。根据您的系统和安装，可能需要进一步操作库路径，以允许R找到新的Boost安装。