install error related to dendextend package about slingshot HOT 15 CLOSED

Hey @amolinaro91 ,

Thanks for the report! Unfortunately, I don't know what's happening here. slingshot doesn't import from dendextend and neither does clusterExperiment, which was my first guess for where this might be coming from. It's possible that this is related to BiocLite(which is no longer the recommended installation method), so can you try installing slingshot with BiocManager?

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("kstreet13/slingshot")

This worked for me after updating to 3.6, but I'm on a mac, so if it doesn't work for you, could you let me know?
Thanks!
Kelly

from slingshot.

Hi Kelly,

Unfortunately I'm still getting the same exact error. I also tried removing and reinstalling dendextend, but that's didnt help.

Any other ideas?

Thanks!
Alyssa

if (!requireNamespace("BiocManager", quietly=TRUE))

• install.packages("BiocManager")
  

BiocManager::install("kstreet13/slingshot")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing github package(s) 'kstreet13/slingshot'
Downloading GitHub repo kstreet13/slingshot@master
These packages have more recent versions available.
Which would you like to update?

1: All
2: CRAN packages only
3: None
4: BiocParallel (1.17.18 -> 1.17.19) [CRAN]
5: clusterEx... (2.3.0 -> 2.3.3 ) [CRAN]
6: HDF5Array (1.11.1 -> 1.11.12) [CRAN]

Enter one or more numbers separated by spaces, or an empty line to cancel
1: 3
√ checking for file 'C:\Users\Alyssa\AppData\Local\Temp\Rtmp2x7MmN\remotes49a4511d2ee5\kstreet13-slingshot-d6df7c6/DESCRIPTION' ...

• preparing 'slingshot':
  √ checking DESCRIPTION meta-information ...
• checking for LF line-endings in source and make files and shell scripts
• checking for empty or unneeded directories
• looking to see if a 'data/datalist' file should be added
• building 'slingshot_1.1.3.tar.gz'

• installing source package 'slingshot' ...
  ** using staged installation
  ** R
  ** data
  ** inst
  ** byte-compile and prepare package for lazy loading
  Error: object 'as.phylo.dendrogram' is not exported by 'namespace:dendextend'
  Execution halted
  ERROR: lazy loading failed for package 'slingshot'
• removing 'C:/Users/Alyssa/Documents/R/win-library/3.6/slingshot'
  Error in i.p(...) :
  (converted from warning) installation of package ‘C:/Users/Alyssa/AppData/Local/Temp/Rtmp2x7MmN/file49a47a6b614d/slingshot_1.1.3.tar.gz’ had non-zero exit status

from slingshot.

Yep, I also meet the same problem. Possibly dendextend does not support the function anymore. But since it seems that slingshot does not use dendextend (at least directly), could you have a check whether the two packages are related indirectly?

I use R 3.6 and slingshot 3.9 (developmental). I use Rstudio in Windows 10.

from slingshot.

It looks like that function ('as.phylo.dendrogram') is part of the dendextend package, but not exported and it is a combination of functions from the ape package (seen here).

This seems to have been noted and corrected in earlier versions of clusterExperiment, so I don't think the issue is with that dependency. I went through the rest of the slingshot dependencies and couldn't find any that import (or ImportFrom) dendextend, so I still don't know what's causing this, but I'll continue to look into it. If there is some indirect link between slingshot and dendextend, it appears to be at least a couple levels deep.

from slingshot.

As far as I can tell, clusterExperiment is the only connection between slingshot and dendextend. When I updated to R 3.6, I had some difficulty installing it due to issues with the gsl package, but there was no mention of dendextend. Could one of you (@amolinaro91 @jimlin1668478052) please reproduce this error and then show me your sessionInfo() so I can check which versions we have of all these packages?

from slingshot.

Hi, I am also experiencing this error. R 3.6.0, Windows 10.

library(slingshot)

Loading required package: princurve
Registered S3 methods overwritten by 'ggplot2':
method from
[.quosures rlang
c.quosures rlang
print.quosures rlang
Error: package or namespace load failed for ‘slingshot’:
object ‘as.phylo.dendrogram’ is not exported by 'namespace:dendextend'

sessionInfo()

R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server >= 2012 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 LC_MONETARY=English_Canada.1252
[4] LC_NUMERIC=C LC_TIME=English_Canada.1252

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

other attached packages:
[1] Biobase_2.43.1 BiocGenerics_0.29.2 princurve_2.1.3

loaded via a namespace (and not attached):
[1] viridis_0.5.1 viridisLite_0.3.0 foreach_1.4.4 assertthat_0.2.1
[5] stats4_3.6.0 GenomeInfoDbData_1.2.1 robustbase_0.93-4 yaml_2.2.0
[9] pillar_1.3.1 lattice_0.20-38 glue_1.3.1 limma_3.39.19
[13] digest_0.6.18 GenomicRanges_1.35.2 RColorBrewer_1.1-2 XVector_0.23.2
[17] colorspace_1.4-1 Matrix_1.2-17 plyr_1.8.4 pkgconfig_2.0.2
[21] bibtex_0.4.2 zlibbioc_1.29.0 purrr_0.3.2 xtable_1.8-4
[25] mvtnorm_1.0-10 scales_1.0.0 whisker_0.3-2 RSpectra_0.14-0
[29] BiocParallel_1.17.18 tibble_2.1.1 pkgmaker_0.27 IRanges_2.17.6
[33] ggplot2_3.1.1 withr_2.1.2 SummarizedExperiment_1.13.0 nnet_7.3-12
[37] lazyeval_0.2.2 magrittr_1.5 crayon_1.3.4 mclust_5.4.3
[41] doParallel_1.0.14 nlme_3.1-139 MASS_7.3-51.4 NMF_0.21.0
[45] class_7.3-15 tools_3.6.0 registry_0.5-1 matrixStats_0.54.0
[49] gridBase_0.4-7 trimcluster_0.1-2.1 stringr_1.4.0 kernlab_0.9-27
[53] S4Vectors_0.21.24 munsell_0.5.0 cluster_2.0.8 rngtools_1.3.1.1
[57] DelayedArray_0.9.9 fpc_2.1-11.2 compiler_3.6.0 GenomeInfoDb_1.19.3
[61] rlang_0.3.4 grid_3.6.0 RCurl_1.95-4.12 iterators_1.0.10
[65] rstudioapi_0.10 SingleCellExperiment_1.5.2 bitops_1.0-6 gtable_0.3.0
[69] codetools_0.2-16 flexmix_2.3-15 reshape2_1.4.3 R6_2.4.0
[73] gridExtra_2.3 prabclus_2.2-7 dplyr_0.8.0.1 dendextend_1.10.0
[77] ape_5.3 modeltools_0.2-22 stringi_1.4.3 Rcpp_1.0.1
[81] DEoptimR_1.0-8 tidyselect_0.2.5 diptest_0.75-7

from slingshot.

Thanks, @wvictor14 !

It looks like you don't have a couple packages that slingshot imports from, which may be causing this issue? Specifically, clusterExperiment and igraph seem like the most likely candidates for this particular problem (the only other missing package is rgl, which is for 3D plotting, so probably unrelated to dendextend). If you install these two packages, does the error persist?

Thanks,
Kelly

for convenience:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("clusterExperiment")
BiocManager::install("igraph")

from slingshot.

It still seems not to work even after installing the packages you mentioned.

> library(slingshot)
Loading required package: princurve
Error: package or namespace load failed for ‘slingshot’:
 object ‘as.phylo.dendrogram’ is not exported by 'namespace:dendextend'
> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
 [1] princurve_2.1.3             SingleCellExperiment_1.5.2  SummarizedExperiment_1.13.0
 [4] DelayedArray_0.9.9          BiocParallel_1.17.18        matrixStats_0.54.0         
 [7] Biobase_2.43.1              GenomicRanges_1.35.1        GenomeInfoDb_1.19.3        
[10] IRanges_2.17.5              S4Vectors_0.21.24           BiocGenerics_0.29.2        

loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning messages:
1: In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'cluster' is missing or broken
2: In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'igraph' is missing or broken
3: In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'lmtest' is missing or broken

from slingshot.

Hmm...apologies, I'm really not sure what's going on, here.

Some of my collaborators apparently faced similar issues on a Linux cluster and they were able to get around them by installing slingshot and clusterExperiment from source (you can download the source packages either from Bioconductor or GitHub and then use install.packages with the arguments type = "source", repos = NULL). For clusterExperiment, however, they had to manually comment out the code in the src/Makevars file. I'm guessing that on Windows, you would have to do the same for the src/Makevars.win file?

from slingshot.

Hi @kstreet13,

I've installed those packages, yet still unable to load slingshot. I also tried loading those libraries before slingshot, and noticed that when loading clusterExperiment, I get the same dendextend error message:

> library(clusterExperiment)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply,
    parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colnames, colSums, dirname, do.call, duplicated, eval, evalq, Filter, Find, get,
    grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
    rowMeans, rownames, rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges

Attaching package: ‘IRanges’

The following object is masked from ‘package:grDevices’:

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages
    'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from ‘package:base’:

    aperm, apply, rowsum

Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang
Error: package or namespace load failed for ‘clusterExperiment’:
 object ‘as.phylo.dendrogram’ is not exported by 'namespace:dendextend'
> library(igraph)

Attaching package: ‘igraph’

The following objects are masked from ‘package:DelayedArray’:

    path, simplify

The following object is masked from ‘package:GenomicRanges’:

    union

The following object is masked from ‘package:IRanges’:

    union

The following object is masked from ‘package:S4Vectors’:

    union

The following objects are masked from ‘package:BiocGenerics’:

    normalize, path, union

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

> library(slingshot)
Loading required package: princurve
Error: package or namespace load failed for ‘slingshot’:
 object ‘as.phylo.dendrogram’ is not exported by 'namespace:dendextend'
> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server >= 2012 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252    LC_MONETARY=English_Canada.1252 LC_NUMERIC=C                    LC_TIME=English_Canada.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] princurve_2.1.3             igraph_1.2.4.1              SingleCellExperiment_1.5.2  SummarizedExperiment_1.13.0 DelayedArray_0.9.9          BiocParallel_1.17.18       
 [7] matrixStats_0.54.0          Biobase_2.43.1              GenomicRanges_1.35.2        GenomeInfoDb_1.19.3         IRanges_2.17.6              S4Vectors_0.21.24          
[13] BiocGenerics_0.29.2        

loaded via a namespace (and not attached):
 [1] viridis_0.5.1          viridisLite_0.3.0      foreach_1.4.4          assertthat_0.2.1       GenomeInfoDbData_1.2.1 yaml_2.2.0             robustbase_0.93-4     
 [8] pillar_1.3.1           lattice_0.20-38        glue_1.3.1             limma_3.39.19          digest_0.6.18          RColorBrewer_1.1-2     XVector_0.23.2        
[15] colorspace_1.4-1       Matrix_1.2-17          plyr_1.8.4             pkgconfig_2.0.2        bibtex_0.4.2           zlibbioc_1.29.0        purrr_0.3.2           
[22] xtable_1.8-4           mvtnorm_1.0-10         scales_1.0.0           whisker_0.3-2          RSpectra_0.14-0        tibble_2.1.1           pkgmaker_0.27         
[29] ggplot2_3.1.1          withr_2.1.2            nnet_7.3-12            lazyeval_0.2.2         magrittr_1.5           crayon_1.3.4           mclust_5.4.3          
[36] doParallel_1.0.14      nlme_3.1-139           MASS_7.3-51.4          NMF_0.21.0             class_7.3-15           tools_3.6.0            registry_0.5-1        
[43] gridBase_0.4-7         trimcluster_0.1-2.1    stringr_1.4.0          kernlab_0.9-27         munsell_0.5.0          cluster_2.0.8          rngtools_1.3.1.1      
[50] fpc_2.1-11.2           compiler_3.6.0         rlang_0.3.4            grid_3.6.0             RCurl_1.95-4.12        iterators_1.0.10       rstudioapi_0.10       
[57] bitops_1.0-6           gtable_0.3.0           codetools_0.2-16       flexmix_2.3-15         reshape2_1.4.3         R6_2.4.0               gridExtra_2.3         
[64] prabclus_2.2-7         dplyr_0.8.0.1          dendextend_1.10.0      ape_5.3                modeltools_0.2-22      stringi_1.4.3          Rcpp_1.0.1            
[71] DEoptimR_1.0-8         tidyselect_0.2.5       diptest_0.75-7    

from slingshot.

I think I found something! In the dendextend NAMESPACE there is an explicit check for whether or not to export the function as.phylo.dendrogram (link: https://github.com/talgalili/dendextend/blob/68e008f7e69b09e1502590d3f4d57991ff27ae0e/NAMESPACE#L4 ). Perhaps if you commented out these lines and added export(as.phylo.dendrogram), then installed dendextend from source?

from slingshot.

Hello,

I've been having the same issue and have been following along. When I change the NAMESPACE file I cannot install the package from source because of the error "file 'NAMESPACE' has the wrong MD5 checksum." Is there a way to work around this error?

I fixed this by just deleting the MD5 file all together which allowed R to install dendextend with the modified NAMESPACE file. However, after installing the modified dendextend, re-installing slingshot, and closing and re-opening R I still am given the same error that 'as.phylo.dendrogram' is not exported by 'namespace:dendextend'"

Got it to load!
When I used BiocManager to install clusterExperiments it was installing version 2.3, not 2.4. Once I source installed version 2.4 of clusterExperiments and made the NAMESPACE change that was recommended, the slingshot library was able to load.

from slingshot.

@kstreet13
Nice catch! This workaround does indeed work. Slingshot has loaded for me. Will test out the package this weekend. Thanks for the help!

from slingshot.

In my case the solution ended up just being the clusterExperiments issue. BiocManager installs version 2.3 of clusterExperiments if you are running Windows, you need to source install version 2.4. That fixes the dendextend error, even if you install the regular version without the edited NAMESPACE file. Slingshot now loads great, if you are on Windows you just have to make sure you install clusterExperiments version 2.4

from slingshot.

Ok, just so we have it all in one place, it sounds like the two things that have worked are:

1. install the latest version of clusterExperiment (>=2.4).
2. download the dendextend source package, modify the NAMESPACE to export as.phylo.dendrogram regardless of which R version is running, and delete the MD5 file.

Thanks for your help and patience, everyone! I'm going to close this issue, but if anybody is still having trouble, feel free to re-open or contact me.

from slingshot.