Install failed with "Error: object ‘tbl_dt’ is not exported by 'namespace:dtplyr'"

[BlanQwall]

🐛 Bug

Dear all,

I failed in installing Immunarch always with this error:

Error: object ‘tbl_dt’ is not exported by 'namespace:dtplyr'
Execution halted
ERROR: lazy loading failed for package ‘immunarch’

I tried install automatically:
devtools::install_url("https://github.com/immunomind/immunarch/raw/master/immunarch.tar.gz")
or manually:

install.packages(c("BiocManager", "covr", "dbscan", "doFuture", "DT", "future", "glmnet", "hdf5r", "hexbin", "Hmisc", "plotly", "prodlim", "R.oo", "RcppAnnoy", "RcppArmadillo", "RcppParallel", "RJSONIO", "rvest", "Seurat", "slam"))
devtools::install_local("~/Downloads/immunarch.tar.gz", dependencies=T)

I tried remove.packages(dtplyr) and reinstall it and it didn't help.
Here's the traceback():

8: stop(remote_install_error(remotes[[i]], e))
7: value[[3L]](cond)
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
4: tryCatch(res[[i]] <- install_remote(remotes[[i]], ...), error = function(e) {
       stop(remote_install_error(remotes[[i]], e))
   })
3: install_remotes(remotes, dependencies = dependencies, upgrade = upgrade, 
       force = force, quiet = quiet, build = build, build_opts = build_opts, 
       build_manual = build_manual, build_vignettes = build_vignettes, 
       repos = repos, type = type, ...)
2: pkgbuild::with_build_tools({
       ellipsis::check_dots_used(action = getOption("devtools.ellipsis_action", 
           rlang::warn))
       {
           remotes <- lapply(path, local_remote, subdir = subdir)
           install_remotes(remotes, dependencies = dependencies, 
               upgrade = upgrade, force = force, quiet = quiet, 
               build = build, build_opts = build_opts, build_manual = build_manual, 
               build_vignettes = build_vignettes, repos = repos, 
               type = type, ...)
       }
   }, required = FALSE)
1: devtools::install_local("~/Downloads/immunarch.tar.gz", dependencies = T)

here's 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/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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

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

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3        rstudioapi_0.10   magrittr_1.5      usethis_1.5.1     devtools_2.2.1    pkgload_1.0.2    
 [7] R6_2.4.1          rlang_0.4.1       tools_3.6.1       pkgbuild_1.0.6    sessioninfo_1.1.1 cli_1.1.0        
[13] withr_2.1.2       ellipsis_0.3.0    remotes_2.1.0     assertthat_0.2.1  digest_0.6.22     rprojroot_1.3-2  
[19] crayon_1.3.4      processx_3.4.1    callr_3.3.2       fs_1.3.1          ps_1.3.0          testthat_2.3.0   
[25] memoise_1.1.0     glue_1.3.1        compiler_3.6.1    desc_1.2.0        backports_1.1.5   prettyunits_1.0.2 

I think this should not be a big issue but I cannot make it through. Hope anyone would help me. Thanks a lot to the community!

[amayer21]

Hello,
Sorry I can't help but wanted to say that I have the same problem on a macbook with R version 3.5.2. Exact same error message and traceback. My sessionInfo() is

R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3        rstudioapi_0.10   magrittr_1.5      usethis_1.5.1     devtools_2.2.1    pkgload_1.0.2     R6_2.4.1         
 [8] rlang_0.4.1       tools_3.5.2       pkgbuild_1.0.6    sessioninfo_1.1.1 cli_1.1.0         withr_2.1.2       ellipsis_0.3.0   
[15] remotes_2.1.0     yaml_2.2.0        assertthat_0.2.1  digest_0.6.22     rprojroot_1.3-2   crayon_1.3.4      processx_3.3.0   
[22] callr_3.2.0       fs_1.3.1          ps_1.3.0          testthat_2.3.0    memoise_1.1.0     glue_1.3.1        compiler_3.5.2   
[29] desc_1.2.0        backports_1.1.5   prettyunits_1.0.2

Any help or advice very much appreciated.
Thank you very much.
Best,
Alice

[vadimnazarov]

Dear everyone,

thank you for using immunarch and getting back us with the feedback! We are working on fixing this error. The reason for the error is because the dtplyr package updated to 1.0.0 version and broke some major parts of our code. We will fix it ASAP and message you here. Thank you!

[vadimnazarov]

Dear everyone,

can you try updating to the latest version of immunarch, and also update all your packages?

Update immunarch via executing the following command:

devtools::install_url("https://github.com/immunomind/immunarch/raw/master/immunarch.tar.gz")

To update packages in RStudio go to Tools > Check for Package Updates. If updates are available, select All , and click Install Updates.

[BlanQwall]

Dear everyone,

can you try updating to the latest version of immunarch, and also update all your packages?

Update immunarch via executing the following command:

devtools::install_url("https://github.com/immunomind/immunarch/raw/master/immunarch.tar.gz")

To update packages in RStudio go to Tools > Check for Package Updates. If updates are available, select All , and click Install Updates.

It works now. Thank you very much for the fast response!