[英]R packages failing to install
I am trying to install the package pathview in R version 4.0.0.我正在尝试在 R 版本 4.0.0 中安装包 pathview。 I first installed biocmanager without issue then used this command as directed:
我首先安装 biocmanager 没有问题,然后按照指示使用此命令:
BiocManager::install("pathview")
However it failed to install with the following error:但是安装失败,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
Does anyone know why this might be failing?有谁知道为什么这可能会失败?
RSQLite is failing to find Boost . RSQLite 未能找到Boost 。 I recommend installing Boost from source and then re-attempting the R package install.
我建议从源代码安装 Boost,然后重新尝试安装 R 包。
I was originally seeing this error when installing biomaRt with BiocManager.我最初是在使用 BiocManager 安装 biomaRt 时看到此错误的。 After installing Boost, I was successfully able to install RSQLite.
安装Boost后,我成功安装了RSQLite。 Depending on your system and installation, it may require further manipulation of your library paths to allow R to find your new Boost install.
根据您的系统和安装,可能需要进一步操作您的库路径以允许 R 找到您的新 Boost 安装。
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