mtrussart/CytofRUV

Trouble installing CytofRUV

northern-soul-marie91 opened this issue · 5 comments

northern-soul-marie91 commented

Hi Marie,

I am trying to install CytofRUV and getting the following error:

remotes::install_github("mtrussart/CytofRUV")
Downloading GitHub repo mtrussart/CytofRUV@HEAD
Skipping 10 packages not available: ComplexHeatmap, limma, S4Vectors, SingleCellExperiment, ConsensusClusterPlus, SummarizedExperiment, FlowSOM, flowCore, CATALYST, Biobase
✓ checking for file ‘/private/var/folders/m6/k46f7jvn425_jhm6jwc28dq80000gn/T/RtmpIQisKb/remotes5564306237e2/mtrussart-CytofRUV-e0cc651/DESCRIPTION’ ...
─ preparing ‘CytofRUV’:
✓ checking DESCRIPTION meta-information
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
Removed empty directory ‘CytofRUV/tests’
─ building ‘CytofRUV_0.1.tar.gz’

  • installing source package ‘CytofRUV’ ...
    ** using staged installation
    ** R
    ** data
    *** moving datasets to lazyload DB
    ** inst
    ** byte-compile and prepare package for lazy loading
    Error: .onLoad failed in loadNamespace() for 'Cairo', details:
    call: dyn.load(file, DLLpath = DLLpath, ...)
    error: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Cairo/libs/Cairo.so':
    dlopen(/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Cairo/libs/Cairo.so, 6): Library not loaded: /opt/X11/lib/libXrender.1.dylib
    Referenced from: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Cairo/libs/Cairo.so
    Reason: image not found
    Execution halted
    ERROR: lazy loading failed for package ‘CytofRUV’
  • removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/CytofRUV’
    Warning message:
    In i.p(...) :
    installation of package ‘/var/folders/m6/k46f7jvn425_jhm6jwc28dq80000gn/T//RtmpIQisKb/file556442ef3f/CytofRUV_0.1.tar.gz’ had non-zero exit status

Session info:
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.2.1

Please could you help.

Best wishes,
(another) Marie

mtrussart commented

Hi Marie,

I am not sure what could be the problem, it says "Skipping 10 packages not available: ComplexHeatmap, limma, S4Vectors, SingleCellExperiment, ConsensusClusterPlus, SummarizedExperiment, FlowSOM, flowCore, CATALYST, Biobase". Did you manage to install all libraries dependencies?

It seems it could be related to the ComplexHeatmap package, have a look here: jokergoo/ComplexHeatmap#685

Best wishes,
Marie

northern-soul-marie91 commented

Hi Marie,

Thanks for replying so quickly. It was an issue with ComplexHeatmap as I did not have XQuartz installed. I have now managed to install CytofRUV successfully.

Best wishes,
Marie

mick42-star commented

Hi Marie,
I had same issue when installing CytoRUV however my ComplexHeatmap works fine, What else could be the reasons？

library(devtools)
Loading required package: usethis
install_github('mtrussart/CytofRUV')
Downloading GitHub repo mtrussart/CytofRUV@HEAD
Skipping 10 packages not available: ComplexHeatmap, limma, S4Vectors, SingleCellExperiment, ConsensusClusterPlus, SummarizedExperiment, FlowSOM, flowCore, CATALYST, Biobase
✔ checking for file 'C:\Users\AppData\Local\Temp\RtmpWm3AFB\remotes59b478c76f5f\mtrussart-CytofRUV-7088af8/DESCRIPTION' ...
─ preparing 'CytofRUV':
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
Removed empty directory 'CytofRUV/tests'
─ building 'CytofRUV_0.1.tar.gz'

Installing package into ‘C:/Users/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
ERROR: dependencies 'CATALYST', 'flowCore', 'FlowSOM', 'ConsensusClusterPlus', 'SingleCellExperiment' are not available for package 'CytofRUV'

  • removing 'C:/Users/AppData/Local/R/win-library/4.2/CytofRUV'
    Warning message:
    In i.p(...) :
    installation of package ‘C:/Users/AppData/Local/Temp/RtmpWm3AFB/file59b416cc5061/CytofRUV_0.1.tar.gz’ had non-zero exit status

library(ComplexHeatmap)
Loading required package: grid
========================================
ComplexHeatmap version 2.12.1
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:

  • Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional
    genomic data. Bioinformatics 2016.
  • Gu, Z. Complex Heatmap Visualization. iMeta 2022.

The new InteractiveComplexHeatmap package can directly export static
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
suppressPackageStartupMessages(library(ComplexHeatmap))

SamGG commented

Hi,
This is not the same error although the same warning message is issued. The error is specifically that the dependencies are not installed. So you should have opened a new issue instead of commenting a closed issue. Nevertheless, what you should do is to install the missing dependencies using bioconductor.
Best.

mick42-star commented

Thanks. The problem has been solved.