未找到用于 Bioconductor 包 RBGL 的 R 包 BH

Question

升级后我在安装 RBGL（Bioconductor Boost 库）时遇到了困难。当R CMD build 尝试构建（源）包时遇到错误。从包根目录运行./configure 工作正常；不幸的是，R CMD build 在再次运行configure 之前清理了包。

确切的错误是：

checking R package BH ... no
configure: error: R package BH not found.
ERROR: configuration failed for package ‘RBGL’

手动运行./configure 我得到：

checking R package BH ... yes
configure: creating ./config.status
config.status: creating src/Makevars

特别是，错误来自这一行：AX_R_PACKAGE([BH],,[${R}])。值得注意的是，如果我从配置脚本中删除这一行，包的构建和安装就很好了。

fwiw：

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8       
 [4] LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BH_1.69.0-1

loaded via a namespace (and not attached):
[1] BiocManager_1.30.4 compiler_3.6.1     tools_3.6.1        parallel_3.6.1    

Answer 1

几件快速的事情：

• 您需要向我们展示错误

• 我是 BH 的作者和维护者之一，我在 Ubuntu 上开发；当我说它有效时，请相信我。

• 当我现在尝试时（像你一样使用 R 3.6.1）我收到一个错误来自 BioCManager，如下所示。

• 您可以按照this page 尝试为 RBGL 开发 BioConductor

错误信息

R> BiocManager::install("RBGL")
Error: Bioconductor version '3.8' requires R version '3.5'; \
                                    see https://bioconductor.org/install
R> 

编辑： 进一步研究，只需要从软件包页面手动下载两个 wget 并进行安装：

edd@rob:~$ cd /tmp
edd@rob:/tmp$ wget -q https://bioconductor.org/packages/release/bioc/src/contrib/RBGL_1.60.0.tar.gz
edd@rob:/tmp$ wget -q https://bioconductor.org/packages/release/bioc/src/contrib/graph_1.62.0.tar.gz
edd@rob:/tmp$ install.r graph_1.62.0.tar.gz RBGL_1.60.0.tar.gz  # helper from littler 
* installing *source* package ‘graph’ ...
** using staged installation

** libs
ccache gcc -I"/usr/share/R/include" -DNDEBUG     -fpic  -g -O3 -Wall -pipe -pedantic  -std=gnu99 -c graph.c -o graph.o
ccache gcc -Wl,-S -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o graph.so graph.o -L/usr/lib/R/lib -lR
mv graph.so BioC_graph.so
installing to /usr/local/lib/R/site-library/00LOCK-graph/00new/graph/libs
** R
[... few lines removd ***]
** testing if installed package keeps a record of temporary installation path
* DONE (graph)
* installing *source* package ‘RBGL’ ...
** using staged installation
checking R package BH ... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
ccache g++ -I"/usr/share/R/include" -DNDEBUG -I/usr/local/lib/R/site-library/BH/include  -I"/usr/local/lib/R/site-library/BH/include"   -fpic  -g -O3 -Wall -pipe -pedantic  -c bbc.cpp -o bbc.o
[... lots of output omitted ...]
** testing if installed package keeps a record of temporary installation path
* DONE (RBGL)
edd@rob:/tmp$ 

编辑 2： 正如您提到 configure 的问题，我在解压 tarball 后手动重新运行了这个。而且，不出所料，该构建对我有用，它找到了它。

edd@rob:/tmp/RBGL$ ./configure
checking R package BH ... yes
configure: creating ./config.status
config.status: creating src/Makevars
edd@rob:/tmp/RBGL$

你的 BH 包安装在哪里，为什么你的会话可以找到它而 configire 却没有？您是否以 root 身份运行了一个，而以您的身份运行了一个？