'R claims packages that doParallel depends on are not available even though they are installed and can be loaded
I am trying to install the doParallel package on a shared cluster (Platform: x86_64-redhat-linux-gnu) where I do not have root privileges. The cluster is running R version 3.5.0 (I have asked if this can be updated).
I've pasted the output from install.packages("doParallel",dependencies=T) below. R claims that dplyr is required by recipes but could not be found. But I've installed dplyr and can load it without any issues. Another package that doParallel requires is caret, which in turn requires recipes. The installation of caret fails because of the previous failure to install recipes. R also claims that foreach required by doParallel but could not be found, even though I previously installed it and can load it.
I've tried installing these packages separately, but it leads down a rabbit hole of many other dependencies and R complaining that packages are not available. I've tried many of the suggestions on SO for similar problems, including:
- deleting old R libraries and reinstalling packages
- manually installing dependent packages (placing the source files where R should be able to find them)
- shutting down all R processes and restarting
- many of the solution seems to involve issues with Windows installations and working with RStudio. These are not relevant since this is a linux machine and I am doing everything from the command line.
R gives the following warning message when trying to install doParallel:
Warning: package ‘dplyr’ was built under R version 3.5.3
Perhaps that is the source of the problem. Unfortunately, I do not have control over R updates on the cluster.
Thanks for any suggestions about solutions.
UPDATE: the suggestion by @r2evans to install dplyr from source and then install doParallel worked. I was able to install doParallel and its dependencies successfully and execute the R code.
Adding output requested by @r2evans (thanks for looking into this):
> 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 ‘<path to personal library>/doParallel’
ERROR: dependency ‘recipes’ is not available for package ‘caret’
* removing ‘<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
Sources
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Source: Stack Overflow
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