HELP! Troubleshooting Installing EBImage Package
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@Christopher-24156
Last seen 17 days ago

I am trying to install EBImage based on the installation guidelines. I am unable to do it and have tried updating my version of Rstudio as well as installation through BiocManager. Can someone help, please? I attached my output below Code should be placed in three backticks as shown below

#Input:
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("EBImage")
library(EBImage)

#Output:
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'EBImage'
Package which is only available in source form, and may need compilation of
C/C++/Fortran: ‘EBImage’
These will not be installed
Installation path not writeable, unable to update packages: codetools, KernSmooth, nlme
Old packages: 'colorspace', 'lubridate'
sessionInfo( )

#Session Info()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

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] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] dplyr_1.0.2         crayon_1.3.4        grid_4.0.3          R6_2.5.0           
 [5] lifecycle_0.2.0     gtable_0.3.0        magrittr_1.5        scales_1.1.1       
 [9] ggplot2_3.3.2       pillar_1.4.6        rlang_0.4.8         rstudioapi_0.13    
[13] generics_0.1.0      vctrs_0.3.4         ellipsis_0.3.1      tools_4.0.3        
[17] glue_1.4.2          purrr_0.3.4         munsell_0.5.0       tinytex_0.27       
[21] xfun_0.19           compiler_4.0.3      pkgconfig_2.0.3     colorspace_1.4-1   
[25] BiocManager_1.30.10 tidyselect_1.1.0    tibble_3.0.4
Install CAMERA insta PackageType • 185 views
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Please add the sessionInfo.

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The session information is uploaded!

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Do you have Rtools installed? Rtools

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No, do I need Rtols installed?

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EBImage is currently not building properly on the Bioconductor windows machines which means the binary version is currently unavailable for windows. The maintainers are aware and are waiting on a downstream fix. Until that happens you can try to install the EBImage source version as suggested by the installer, in order to install source versions of packages on windows you would need Rtools.

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And with Rtools:

> install("EBImage")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
Installing package(s) 'EBImage'

Package which is only available in source form, and may need
  compilation of C/C++/Fortran: 'EBImage'
Do you want to attempt to install these from sources? (Yes/no/cancel) yes

installing the source package 'EBImage'

trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/EBImage_4.32.0.tar.gz'
Content type 'application/x-gzip' length 5445556 bytes (5.2 MB)
downloaded 5.2 MB

* installing *source* package 'EBImage' ...
** using staged installation
** libs

*** arch - i386
"C:/rtools40/mingw32/bin/"gcc  -I"c:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG          -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c EBImage.c -o EBImage.o
"C:/rtools40/mingw32/bin/"gcc  -I"c:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG          -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c clahe.c -o clahe.o

< stuff happens>

** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'abind' in package 'EBImage'
** help
*** installing help indices
  converting help for package 'EBImage'
    finding HTML links ... done
    EBImage-defunct                         html  
    EBImage                                 html  
    Image                                   html  
    abind                                   html  
    bwlabel                                 html  
    channel                                 html  
    clahe                                   html  
    colorLabels                             html  
    colormap                                html  
    combine                                 html  
    computeFeatures                         html  
    display-shiny                           html  
    display                                 html  
    finding level-2 HTML links ... done

    distmap                                 html  
    drawCircle                              html  
    equalize                                html  
    fillHull                                html  
    filter2                                 html  
    floodFill                               html  
    gblur                                   html  
    io                                      html  
    localCurvature                          html  
    medianFilter                            html  
    morphology                              html  
    normalize                               html  
    ocontour                                html  
    otsu                                    html  
    paintObjects                            html  
    propagate                               html  
    rmObjects                               html  
    spatial                                 html  
    stackObjects                            html  
    thresh                                  html  
    tile                                    html  
    transpose                               html  
    watershed                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (EBImage)
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If someone asks if you have something installed and provides a link to where you can get the installer, you should feel free to assume that they are saying you need to install it.

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As a warning, I'll note, as others, that EBImage is not building on Windows (click on the 'error' badge at http://bioconductor.org/packages/EBImage). I'd interpret that as a strong warning -- something is wrong with this package to the extent that the Bioconductor release builders cannot build it. Maybe I should not try to build it myself, or at least maybe I should proceed carefully with the interpretation of results?

In this case the package seems not to build because of numerical discrepancies in tests, apparently associated with the tiff library that comes with R for Windows. Installing the package directly gets a version of the package because installation does not require that the tests pass. But the package will manifest the same problems that the maintainer of the package thought important enough to test against. If your use of EBImage relies on the tiff library, then I'd exercise caution.

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Andrzej Oleś • 750
@Andrzej-Oleś-5540
Last seen 17 days ago
Heidelberg, Germany

An updated version of the tiff package which should resolve the build issues has just been published on CRAN.

Thanks for mentioning the numerical discrepancies reported by tests. They are actually not specific to the use of a particular tiff library version. These check sums are very sensitive to any numeric differences down to rounding errors. As a consequence, it's virtually impossible to get the exact same values between different platforms. Their original purpose was mostly for development in order to be able to catch any differences while working on a given platform. Probably something we could improve on and get rid of these spurious messages.

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