首页
学习
活动
专区
圈层
工具
发布
首页
学习
活动
专区
圈层
工具
MCP广场
社区首页 >问答首页 >R包biomaRt和此依赖项RSQLite出错

R包biomaRt和此依赖项RSQLite出错
EN

Stack Overflow用户
提问于 2021-04-27 16:26:00
回答 3查看 1.7K关注 0票数 6

我在安装带有bioconductor的biomaRt时遇到问题。我已经在RStudio3.6中没有错误地安装了这个包,但是在conda特定的环境容器中安装了R4.0,我在RSQLite中有一个错误。

下面是这条消息:

代码语言:javascript
运行
复制
x86_64-conda-linux-gnu-c++ -std=gnu++11 -I"/home/legrand-lab/anaconda3/envs/r4-base/lib/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/legrand-lab/anaconda3/envs/r4-base/lib/R/library/plogr/include' -I'/home/legrand-lab/anaconda3/envs/r4-base/lib/R/library/Rcpp/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/legrand-lab/anaconda3/envs/r4-base/include -I/home/legrand-lab/anaconda3/envs/r4-base/include -Wl,-rpath-link,/home/legrand-lab/anaconda3/envs/r4-base/lib  -fvisibility=hidden -fpic  -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/legrand-lab/anaconda3/envs/r4-base/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1616773775410/work=/usr/local/src/conda/r-base-4.0.3 -fdebug-prefix-map=/home/legrand-lab/anaconda3/envs/r4-base=/usr/local/src/conda-prefix  -c SqliteColumnDataSource.cpp -o SqliteColumnDataSource.o
In file included from vendor/boost/math/special_functions/sign.hpp:16,
                 from vendor/boost/lexical_cast/detail/inf_nan.hpp:34,
                 from vendor/boost/lexical_cast/detail/converter_lexical_streams.hpp:63,
                 from vendor/boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from vendor/boost/lexical_cast/try_lexical_convert.hpp:44,
                 from vendor/boost/lexical_cast.hpp:32,
                 from vendor/boost/date_time/format_date_parser.hpp:14,
                 from vendor/boost/date_time/date_generator_parser.hpp:20,
                 from vendor/boost/date_time/date_facet.hpp:25,
                 from vendor/boost/date_time/gregorian/gregorian_io.hpp:16,
                 from vendor/boost/date_time/gregorian/gregorian.hpp:31,
                 from SqliteColumnDataSource.cpp:6:
vendor/boost/math/tools/config.hpp:408:13: fatal error: boost/detail/fenv.hpp: No such file or directory
  408 |    #include <boost/detail/fenv.hpp>
      |             ^~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [/home/legrand-lab/anaconda3/envs/r4-base/lib/R/etc/Makeconf:181 : SqliteColumnDataSource.o] Erreur 1
ERROR: compilation failed for package ‘RSQLite’
* removing ‘/home/legrand-lab/anaconda3/envs/r4-base/lib/R/library/RSQLite’
ERROR: dependency ‘RSQLite’ is not available for package ‘AnnotationDbi’
* removing ‘/home/legrand-lab/anaconda3/envs/r4-base/lib/R/library/AnnotationDbi’
ERROR: dependency ‘RSQLite’ is not available for package ‘BiocFileCache’
* removing ‘/home/legrand-lab/anaconda3/envs/r4-base/lib/R/library/BiocFileCache’
ERROR: dependencies ‘AnnotationDbi’, ‘BiocFileCache’ are not available for package ‘biomaRt’
* removing ‘/home/legrand-lab/anaconda3/envs/r4-base/lib/R/library/biomaRt’

The downloaded source packages are in
    ‘/tmp/RtmpJRLzOp/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(...) :
  installation of package ‘RSQLite’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘AnnotationDbi’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘BiocFileCache’ had non-zero exit status
4: In install.packages(...) :
  installation of package ‘biomaRt’ had non-zero exit status

如果有人有一个想法或解决方案..。

EN

回答 3

Stack Overflow用户

发布于 2021-05-25 15:32:45

日志指示错误来自: fatal error: boost/detail/fenv.hpp:没有这样的文件或目录408 | #include

代码语言:javascript
运行
复制
conda install -c conda-forge boost-cpp

我尝试了一下,然后在R中安装了RSQLite,它可以工作。

代码语言:javascript
运行
复制
install.packages("RSQLite")

票数 8
EN

Stack Overflow用户

发布于 2021-04-28 20:29:32

这个问题也会影响conda包。临时修复似乎是回滚,即remotes::install_version("RSQLite", version = "2.2.5")

请参阅此处的示例:https://github.com/kstawiski/OmicSelector/blob/master/.github/workflows/r.yml#L26

票数 4
EN

Stack Overflow用户

发布于 2021-05-21 21:42:09

代码语言:javascript
运行
复制
conda install -c conda-forge boost-cpp

为我解决了这个问题。

票数 4
EN
页面原文内容由Stack Overflow提供。腾讯云小微IT领域专用引擎提供翻译支持
原文链接:

https://stackoverflow.com/questions/67279457

复制
相关文章

相似问题

领券
问题归档专栏文章快讯文章归档关键词归档开发者手册归档开发者手册 Section 归档