Installation of FlowSOM failed

[akhst7]

Hi,

Installation of FlowSOM failed with a following message:

Error: Failed to install 'FlowSOM' from GitHub:
  System command error, exit status: 1, stdout + stderr (last 10 lines):
E> installing to /private/var/folders/wr/dljlk_z934d83zpz6r0fx3n1l1pf6f/T/RtmpjYWCJx/Rinstf161704759c1/00LOCK-FlowSOM/00new/FlowSOM/libs
E> ** R
E> ** inst
E> ** byte-compile and prepare package for lazy loading
E> Error: object ‘getIndiceMat’ is not exported by 'namespace:flowWorkspace'
E> Execution halted
E> ERROR: lazy loading failed for package ‘FlowSOM’
E> * removing ‘/private/var/folders/wr/dljlk_z934d83zpz6r0fx3n1l1pf6f/T/RtmpjYWCJx/Rinstf161704759c1/FlowSOM’
E>       -----------------------------------
E> ERROR: package installation failed

A culprit is object ‘getIndiceMat’ is not exported by 'namespace:flowWorkspace'. flowWorkspace is installed as follows;

packageVersion("flowWorkspace")
[1] ‘3.33.9’

Here is sessionInfo;

sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin18.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /usr/local/Cellar/openblas/0.3.7/lib/libopenblasp-r0.3.7.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     

other attached packages:
 [1] flowWorkspace_3.33.9 biomaRt_2.41.8       Rsubread_1.99.3      edgeR_3.27.13        limma_3.41.16       
 [6] fastcluster_1.1.25   TeachingDemos_2.10   ggpubr_0.2.3         magrittr_1.5         ggplot2_3.2.1       
[11] data.table_1.12.2    stringr_1.4.0        BiocManager_1.30.4   devtools_2.2.1       usethis_1.5.1       

loaded via a namespace (and not attached):
 [1] ncdfFlow_2.31.4      matrixStats_0.55.0   fs_1.3.1             bit64_0.9-7          RColorBrewer_1.1-2  
 [6] progress_1.2.2       httr_1.4.1           rprojroot_1.3-2      Rgraphviz_2.29.0     tools_3.6.1         
[11] backports_1.1.4      R6_2.4.0             DT_0.9               KernSmooth_2.23-15   DBI_1.0.0           
[16] lazyeval_0.2.2       BiocGenerics_0.31.6  colorspace_1.4-1     withr_2.1.2          gridExtra_2.3       
[21] tidyselect_0.2.5     prettyunits_1.0.2    processx_3.4.1       bit_1.1-14           curl_4.2            
[26] compiler_3.6.1       graph_1.63.0         cli_1.1.0            Biobase_2.45.1       desc_1.2.0          
[31] scales_1.0.0         hexbin_1.27.3        callr_3.3.2          askpass_1.1          rappdirs_0.3.1      
[36] digest_0.6.21        pkgconfig_2.0.3      htmltools_0.3.6      sessioninfo_1.1.1    dbplyr_1.4.2        
[41] htmlwidgets_1.3      rlang_0.4.0          rstudioapi_0.10      flowCore_1.51.7      RSQLite_2.1.2       
[46] dplyr_0.8.3          Rcpp_1.0.2           munsell_0.5.0        S4Vectors_0.23.23    stringi_1.4.3       
[51] MASS_7.3-51.4        zlibbioc_1.31.0      pkgbuild_1.0.5       BiocFileCache_1.9.1  grid_3.6.1          
[56] blob_1.2.0           parallel_3.6.1       crayon_1.3.4         lattice_0.20-38      hms_0.5.1           
[61] locfit_1.5-9.1       zeallot_0.1.0        ps_1.3.0             pillar_1.4.2         ggsignif_0.6.0      
[66] stats4_3.6.1         pkgload_1.0.2        XML_3.98-1.20        glue_1.3.1           latticeExtra_0.6-28 
[71] remotes_2.1.0        RcppParallel_4.4.3   vctrs_0.2.0          testthat_2.2.1       gtable_0.3.0        
[76] openssl_1.4.1        purrr_0.3.2          assertthat_0.2.1     IDPmisc_1.1.19       tibble_2.1.3        
[81] flowViz_1.49.2       AnnotationDbi_1.47.1 memoise_1.1.0        IRanges_2.19.16      ellipsis_0.3.0

and my OSX version;

sw_vers
ProductName:    Mac OS X
ProductVersion: 10.14.6
BuildVersion:   18G95

Any help will be appreciated.

Thanks.

[SofieVG]

Hi,

If I see correctly, you are on the devel version of flowWorkspace, in which they changed many function names. I now pushed a devel branch to the FlowSOM github as well, if you install from this branch, hopefully it will work!

[akhst7]

Hi,

Yeah, I am using the dev version of flowWorkspace. I had a lot of trouble installing it too. Anyway, It looks like saeyslab/FlowSOM is the same as a dev in your dev branch ? I tried to install it from the dev branch but there appears to be no commit from the dev branch ?

[SofieVG]

The version on saeyslab/FlowSOM should always be the same as the master branch of SofieVG/FlowSOM (I try to always commit to both).

Did you try to install devtools::install_github("SofieVG/FlowSOM", ref = "devel") ?

[akhst7]

Thanks. I got it to install. I made a typo error which was causing a previous installation error message. I will give this a shot and see.