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talgalili / dendextend

Extending R's Dendrogram Functionality
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Issue with installing Dendextend #78

Closed Mshoukat1992 closed 1 week ago

Mshoukat1992 commented 6 years ago

Hi,

I recently encountered an issue with dendextend which I have historically been using with no issues. When I call the library (library(dendextend)) in bash I get an error following which I uninstalled and reinstalled dendextend which now no longer installs.

I get the following error on installation using install.packages("dendextend")

Error:

Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/local/lib/R/3.5/site-library/mclust/libs/mclust.so': dlopen(/usr/local/lib/R/3.5/site-library/mclust/libs/mclust.so, 6): Library not loaded: /usr/local/opt/gcc/lib/gcc/7/libgfortran.4.dylib Referenced from: /usr/local/lib/R/3.5/site-library/mclust/libs/mclust.so Reason: image not found ERROR: lazy loading failed for package ‘dendextend’

removing ‘/usr/local/lib/R/3.5/site-library/dendextend’ The downloaded source packages are in ‘/private/var/folders/tw/fgxg7p2x1v14h9n_29dv64th0000gn/T/RtmpLoHIjI/downloaded_packages’ Warning message: In install.packages("dendextend") : installation of package ‘dendextend’ had non-zero exit status

I am using the most up to date version of R 1.1.4

Any thoughts on what might be going on here

talgalili commented 6 years ago

Very odd.

Could you please try restarting R, install dendextend, and paste the output. Plus also the output of sessionInfo() ?

On Fri, Jun 8, 2018, 20:45 Mshoukat1992 notifications@github.com wrote:

Hi,

I recently encountered an issue with dendextend which I have historically been using with no issues. When I call the library (library(dendextend)) in bash I get an error following which I uninstalled and reinstalled dendextend which now no longer installs.

I get the following error on installation using install.packages("dendextend")

Error:

Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/local/lib/R/3.5/site-library/mclust/libs/mclust.so': dlopen(/usr/local/lib/R/3.5/site-library/mclust/libs/mclust.so, 6): Library not loaded: /usr/local/opt/gcc/lib/gcc/7/libgfortran.4.dylib Referenced from: /usr/local/lib/R/3.5/site-library/mclust/libs/mclust.so Reason: image not found ERROR: lazy loading failed for package ‘dendextend’

removing ‘/usr/local/lib/R/3.5/site-library/dendextend’ The downloaded source packages are in

‘/private/var/folders/tw/fgxg7p2x1v14h9n_29dv64th0000gn/T/RtmpLoHIjI/downloaded_packages’ Warning message: In install.packages("dendextend") : installation of package ‘dendextend’ had non-zero exit status

I am using the most up to date version of R 1.1.4

Any thoughts on what might be going on here

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Mshoukat1992 commented 6 years ago

I re-ran it and got the same error

install.packages('dendextend') Installing package into ‘/usr/local/lib/R/3.5/site-library’ (as ‘lib’ is unspecified) trying URL 'https://cran.rstudio.com/src/contrib/dendextend_1.8.0.tar.gz' Content type 'application/x-gzip' length 1758392 bytes (1.7 MB)

downloaded 1.7 MB

The downloaded source packages are in ‘/private/var/folders/tw/fgxg7p2x1v14h9n_29dv64th0000gn/T/Rtmp2snGck/downloaded_packages’

sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-apple-darwin17.5.0 (64-bit) Running under: macOS High Sierra 10.13.4

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib

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

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

loaded via a namespace (and not attached): [1] compiler_3.5.0 tools_3.5.0

talgalili commented 6 years ago

Mmm Do you by chance have an older version of R? If so, could you try to repeat the process and see if it works there or not?

On Fri, Jun 8, 2018, 21:27 Mshoukat1992 notifications@github.com wrote:

I re-ran it and got the same error

install.packages('dendextend') Installing package into ‘/usr/local/lib/R/3.5/site-library’ (as ‘lib’ is unspecified) trying URL 'https://cran.rstudio.com/src/contrib/dendextend_1.8.0.tar.gz' Content type 'application/x-gzip' length 1758392 bytes (1.7 MB)

downloaded 1.7 MB

  • installing source package ‘dendextend’ ... package ‘dendextend’ successfully unpacked and MD5 sums checked R ** data * moving datasets to lazyload DB demo inst byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/local/lib/R/3.5/site-library/mclust/libs/mclust.so': dlopen(/usr/local/lib/R/3.5/site-library/mclust/libs/mclust.so, 6): Library not loaded: /usr/local/opt/gcc/lib/gcc/7/libgfortran.4.dylib Referenced from: /usr/local/lib/R/3.5/site-library/mclust/libs/mclust.so Reason: image not found ERROR: lazy loading failed for package ‘dendextend’
  • removing ‘/usr/local/lib/R/3.5/site-library/dendextend’ Warning in install.packages : installation of package ‘dendextend’ had non-zero exit status

The downloaded source packages are in

‘/private/var/folders/tw/fgxg7p2x1v14h9n_29dv64th0000gn/T/Rtmp2snGck/downloaded_packages’

sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-apple-darwin17.5.0 (64-bit) Running under: macOS High Sierra 10.13.4

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib

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

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

loaded via a namespace (and not attached): [1] compiler_3.5.0 tools_3.5.0

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Mshoukat1992 commented 6 years ago

I tried with R 3.3 and experienced the exact same error. what do you propose?

Should I try downloading it seperately as a package and adding it to the library?

talgalili commented 6 years ago

Could you please try running: install.packages("mclust") install.packages("dendextend")

If that doesn't work, please try:

install.packages.2 <- function (pkg) if (!require(pkg)) install.packages(pkg); install.packages.2('devtools')

install.packages.2('Rcpp')

make sure you have Rtools installed first! if not, then run:

install.packages('installr'); install.Rtools()

devtools::install_github('talgalili/dendextend')

Does any of the two work?

Pirshtuk commented 3 years ago

Shiny application failed because of error in package installation.

To Reproduce A) press Run App

install.packages("denextend")

library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'denextend'

B) Or run several times from console

install.packages("denextend") one of them fails same way.

Expected behavior I expecte no loading of the packages, as it is installed.

Additional context

sessionInfo() R version 4.0.5 (2021-03-31) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale: [1] LC_COLLATE=Russian_Russia.1251 LC_CTYPE=Russian_Russia.1251 LC_MONETARY=Russian_Russia.1251 [4] LC_NUMERIC=C LC_TIME=Russian_Russia.1251

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

loaded via a namespace (and not attached): [1] rstudioapi_0.13 magrittr_2.0.1 usethis_2.0.1 devtools_2.4.1
[5] pkgload_1.2.1 R6_2.5.0 rlang_0.4.11 fastmap_1.1.0
[9] tools_4.0.5 pkgbuild_1.2.0 DT_0.18.1 sessioninfo_1.1.1
[13] cli_2.5.0 withr_2.4.2 htmltools_0.5.1.1 ellipsis_0.3.2
[17] remotes_2.3.0 digest_0.6.27 rprojroot_2.0.2 lifecycle_1.0.0
[21] crayon_1.4.1 processx_3.5.2 purrr_0.3.4 callr_3.7.0
[25] htmlwidgets_1.5.3.9000 fs_1.5.0 ps_1.6.0 curl_4.3.1
[29] testthat_3.0.2 glue_1.4.2 memoise_2.0.0 cachem_1.0.5
[33] compiler_4.0.5 desc_1.3.0 prettyunits_1.1.1

Pirshtuk commented 3 years ago

When I publish Shiny App to my shinyapp.io account, I get error and process stops.

Preparing to deploy application...DONE Uploading bundle for application: Unable to retrieve package records for the following packages:

talgalili commented 3 years ago

It says denextend Instead of dendextend

On Tue, 1 Jun 2021, 18:07 Pirshtuk, @.***> wrote:

When I publish Shiny App to my shinyapp.io account, I get error and process stops.

Preparing to deploy application...DONE Uploading bundle for application: Unable to retrieve package records for the following packages:

  • "denextend"... Package 'denextend' not available in repository or locally

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