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Christopher
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@christopher-24156
Last seen 4.1 years 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
Please add the sessionInfo.
The session information is uploaded!
Do you have Rtools installed? Rtools
No, do I need Rtols installed?
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.
And with Rtools:
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.
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.