文章/答案/技术大牛

发布

问WGCNA在R中的安装问题
EN

Stack Overflow用户

提问于 2022-11-22 06:17:18

回答 1查看 15关注 0票数 1

当我尝试

install.packages('WGCNA')

我得到以下特别的“警告在install.packages :安装软件包‘WGCNA’有非零退出状态”。

Installing package into ‘/gpfs/HOME/iputilin/R/x86_64-redhat-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/WGCNA_1.71.tar.gz'
Content type 'application/x-gzip' length 1170723 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

* installing *source* package ‘WGCNA’ ...
** package ‘WGCNA’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DWITH_THREADS -I"/gpfs/HOME/iputilin/R/x86_64-redhat-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c corFunctions-utils.c -o corFunctions-utils.o
corFunctions-utils.c: In function ‘threadSlowCalcCor’:
corFunctions-utils.c:891:14: warning: unused variable ‘vy’ [-Wunused-variable]
  891 |   double vx, vy;
      |              ^~
corFunctions-utils.c:891:10: warning: unused variable ‘vx’ [-Wunused-variable]
  891 |   double vx, vy;
      |          ^~
corFunctions-utils.c:890:16: warning: unused variable ‘yy’ [-Wunused-variable]
  890 |   double *xx, *yy;
      |                ^~
corFunctions-utils.c:890:11: warning: unused variable ‘xx’ [-Wunused-variable]
  890 |   double *xx, *yy;
      |           ^~
corFunctions-utils.c: In function ‘threadSlowCalcCor2’:
corFunctions-utils.c:1197:18: warning: unused variable ‘yy’ [-Wunused-variable]
 1197 |   double * xx, * yy;
      |                  ^~
corFunctions-utils.c:1197:12: warning: unused variable ‘xx’ [-Wunused-variable]
 1197 |   double * xx, * yy;
      |            ^~
corFunctions-utils.c: In function ‘threadSlowCalcCor2_weighted’:
corFunctions-utils.c:1376:18: warning: unused variable ‘vy’ [-Wunused-variable]
 1376 |   double vx = 0, vy = 0;
      |                  ^~
corFunctions-utils.c:1376:10: warning: unused variable ‘vx’ [-Wunused-variable]
 1376 |   double vx = 0, vy = 0;
      |          ^~
corFunctions-utils.c:1375:18: warning: unused variable ‘yy’ [-Wunused-variable]
 1375 |   double * xx, * yy;
      |                  ^~
corFunctions-utils.c:1375:12: warning: unused variable ‘xx’ [-Wunused-variable]
 1375 |   double * xx, * yy;
      |            ^~
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DWITH_THREADS -I"/gpfs/HOME/iputilin/R/x86_64-redhat-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c corFunctions.c -o corFunctions.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DWITH_THREADS -I"/gpfs/HOME/iputilin/R/x86_64-redhat-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c myMatrixMultiplication.c -o myMatrixMultiplication.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DWITH_THREADS -I"/gpfs/HOME/iputilin/R/x86_64-redhat-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c networkFunctions.c -o networkFunctions.o
networkFunctions.c: In function ‘tomSimilarityFromAdj’:
networkFunctions.c:260:31: error: expected ‘)’ before ‘FCONE’
  260 |            & beta, tom, nGenes FCONE FCONE);
      |                               ^~~~~~
      |                               )
networkFunctions.c: In function ‘tomSimilarityFromAdj_call’:
networkFunctions.c:604:23: warning: unused variable ‘maxPOutliers’ [-Wunused-variable]
  604 |   double *adj, *tom, *maxPOutliers;
      |                       ^~~~~~~~~~~~
make: *** [networkFunctions.o] Error 1
ERROR: compilation failed for package ‘WGCNA’
* removing ‘/gpfs/HOME/iputilin/R/x86_64-redhat-linux-gnu-library/3.6/WGCNA’

The downloaded source packages are in
        ‘/gpfs/tmp/tmp_genom/RtmpoqXx8J/downloaded_packages’
Warning message:
In install.packages("WGCNA") :
  installation of package ‘WGCNA’ had non-zero exit status

你知不知道为什么会这样，以及如何解决？我并不真正理解这个问题，因为我是WCGNCA的新手，它在R中的应用

installation

package

回答 1

Stack Overflow用户

发布于 2022-11-22 07:44:26

首先，您需要BiocManager：

if (!require("BiocManager", quietly = TRUE))
       install.packages("BiocManager")
BiocManager::install(version = "3.16")

然后，您需要安装没有在CRAN上的软件包：

BiocManager::install(c("GO.db", "preprocessCore", "impute") )

并确保您拥有包描述文件中的所有CRAN托管依赖项(其中包括可能丢失的pkg:Rcpp或需要更新版本)：

Depends: R (>= 3.0), dynamicTreeCut (>= 1.62), fastcluster
Imports: stats, grDevices, utils, matrixStats (>= 0.8.1), Hmisc, splines, 
     foreach, doParallel, survival, parallel, AnnotationDbi, Rcpp (>= 0.11.0)

现在您可能已经准备好安装WGCNA了。

(我在这个缩短版本上取得了成功，但BiocManager将希望更新它所知道的所有包，而且对我来说，这是一个很长的400+包，我正准备上床睡觉，所以我现在让这个漫长的过程运行，以便在我的库中有一个“新鲜”版本的Bioc包。)

票数 2

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/74528234

复制

相似问题

问WGCNA在R中的安装问题
EN

回答 1

Stack Overflow用户

社区

活动

圈层

关于

腾讯云开发者

热门产品

热门推荐

更多推荐

问WGCNA在R中的安装问题EN

回答 1

Stack Overflow用户

社区

活动

圈层

关于

腾讯云开发者

热门产品

热门推荐

更多推荐

问WGCNA在R中的安装问题
EN