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我正在尝试将doParallel软件包安装在我没有 root 权限的共享集群(平台:x86_64-redhat-linux-gnu)上。集群正在运行 R 版本 3.5.0(我已经询问是否可以更新)。

我已经粘贴了install.packages("doParallel",dependencies=T)下面的输出。R 声明dplyr需要recipes但无法找到。但是我已经安装dplyr并且可以毫无问题地加载它。另一个需要的包doParallelcaret,它又需要recipes. 由于之前的安装caret失败,安装失败recipes。R 还声称foreach需要doParallel但无法找到,即使我之前安装了它并且可以加载它。

我试过单独安装这些包,但它导致许多其他依赖项和 R 抱怨包不可用。对于类似的问题,我已经尝试了许多关于 SO 的建议,包括:

  • 删除旧的 R 库并重新安装包
  • 手动安装依赖包(将源文件放在 R 应该能够找到它们的地方)
  • 关闭所有 R 进程并重新启动
  • 许多解决方案似乎涉及 Windows 安装和使用 RStudio 的问题。这些无关紧要,因为这是一台 linux 机器,我正在从命令行执行所有操作。

R 在尝试安装时会给出以下警告消息doParallel

警告:包 'dplyr' 是在 R 版本 3.5.3 下构建的

也许这就是问题的根源。不幸的是,我无法控制集群上的 R 更新。

感谢您提供有关解决方案的任何建议。

添加@r2evans 请求的输出(感谢您对此进行调查):

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

loaded via a namespace (and not attached):
[1] compiler_3.5.0
> .libPaths()
[1] "/<path to personal library>" "/usr/lib64/R/library"               
[3] "/usr/share/R/library"  
> install.packages("doParallel",dependencies=T)
Installing package into ‘...’ <path omitted for security reasons>
(as ‘lib’ is unspecified)
also installing the dependencies ‘recipes’, ‘caret’

trying URL 'https://cran.us.r-project.org/src/contrib/recipes_0.1.13.tar.gz'
Content type 'application/octet-stream' length 633375 bytes (618 KB)
==================================================
downloaded 618 KB

trying URL 'https://cran.us.r-project.org/src/contrib/caret_6.0-86.tar.gz'
Content type 'application/octet-stream' length 5264447 bytes (5.0 MB)
==================================================
downloaded 5.0 MB

trying URL 'https://cran.us.r-project.org/src/contrib/doParallel_1.0.15.tar.gz'
Content type 'application/octet-stream' length 173578 bytes (169 KB)
==================================================
downloaded 169 KB

* installing *source* package ‘recipes’ ...
** package ‘recipes’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: package ‘dplyr’ was built under R version 3.5.3
** help
*** installing help indices
  converting help for package ‘recipes’
    finding HTML links ... done
    add_step                                html  
    bake                                    html  
    finding level-2 HTML links ... done

    check_class                             html  
    check_cols                              html  
    check_missing                           html  
    check_name                              html  
    check_new_values                        html  
    check_range                             html  
    check_type                              html  
    detect_step                             html  
    discretize                              html  
    fixed                                   html  
    format_ch_vec                           html  
    formula.recipe                          html  
    fully_trained                           html  
    has_role                                html  
    juice                                   html  
    names0                                  html  
    prep                                    html  
    prepper                                 html  
    print.recipe                            html  
    rand_id                                 html  
    recipe                                  html  
    recipes-internal                        html  
    recipes                                 html  
    recipes_pkg_check                       html  
    reexports                               html  
    roles                                   html  
    selections                              html  
    step                                    html  
    step_BoxCox                             html  
    step_YeoJohnson                         html  
    step_arrange                            html  
    step_bagimpute                          html  
    step_bin2factor                         html  
    step_bs                                 html  
    step_center                             html  
    step_classdist                          html  
    step_corr                               html  
    step_count                              html  
    step_cut                                html  
    step_date                               html  
    step_depth                              html  
    step_discretize                         html  
    step_downsample                         html  
    step_dummy                              html  
    step_factor2string                      html  
    step_filter                             html  
    step_geodist                            html  
    step_holiday                            html  
    step_hyperbolic                         html  
    step_ica                                html  
    step_integer                            html  
    step_interact                           html  
    step_intercept                          html  
    step_inverse                            html  
    step_invlogit                           html  
    step_isomap                             html  
    step_knnimpute                          html  
    step_kpca                               html  
    step_kpca_poly                          html  
    step_kpca_rbf                           html  
    step_lag                                html  
    step_lincomb                            html  
    step_log                                html  
    step_logit                              html  
    step_lowerimpute                        html  
    step_meanimpute                         html  
    step_medianimpute                       html  
    step_modeimpute                         html  
    step_mutate                             html  
    step_mutate_at                          html  
    step_naomit                             html  
    step_nnmf                               html  
    step_normalize                          html  
    step_novel                              html  
    step_ns                                 html  
    step_num2factor                         html  
    step_nzv                                html  
    step_ordinalscore                       html  
    step_other                              html  
    step_pca                                html  
    step_pls                                html  
    step_poly                               html  
    step_profile                            html  
    step_range                              html  
    step_ratio                              html  
    step_regex                              html  
    step_relevel                            html  
    step_relu                               html  
    step_rename                             html  
    step_rename_at                          html  
    step_rm                                 html  
    step_rollimpute                         html  
    step_sample                             html  
    step_scale                              html  
    step_shuffle                            html  
    step_slice                              html  
    step_spatialsign                        html  
    step_sqrt                               html  
    step_string2factor                      html  
    step_unknown                            html  
    step_unorder                            html  
    step_upsample                           html  
    step_window                             html  
    step_zv                                 html  
    summary.recipe                          html  
    terms_select                            html  
    tidy.recipe                             html  
    tunable.step                            html  
    update.step                             html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error : package ‘dplyr’ required by ‘recipes’ could not be found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/rigel/stats/users/gjw10/rpackages2/recipes’
* installing *source* package ‘doParallel’ ...
** package ‘doParallel’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘doParallel’
    finding HTML links ... done
    doParallel-package                      html  
    registerDoParallel                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error : package ‘foreach’ required by ‘doParallel’ could not be found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘&lt;path to personal library>/doParallel’
ERROR: dependency ‘recipes’ is not available for package ‘caret’
* removing ‘&lt;path to personal library>/caret’

The downloaded source packages are in

    ‘/tmp/Rtmpyd0cpT/downloaded_packages’

Warning messages:
1: In install.packages("doParallel", dependencies = T) :
  installation of package ‘recipes’ had non-zero exit status
2: In install.packages("doParallel", dependencies = T) :
  installation of package ‘doParallel’ had non-zero exit status
3: In install.packages("doParallel", dependencies = T) :
  installation of package ‘caret’ had non-zero exit status
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