Entering edit mode
Hello,
I know the latest version of Bioconductor (3.12) is meant to work with R-4.0.3, but I have to use R-4.0.2 for reasons I won't get into here.
I am having trouble installing DelayedArray:
installing to /home/username/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-DelayedArray/00new/DelayedArray/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘rowsum’ in package ‘DelayedArray’
Creating a new generic function for ‘aperm’ in package ‘DelayedArray’
Error in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses, :
no definition was found for superclass “DataTable” in the specification of class “DelayedMatrix”
Error: unable to load R code in package ‘DelayedArray’
Execution halted
ERROR: lazy loading failed for package ‘DelayedArray’
* removing ‘/home/username/R/x86_64-pc-linux-gnu-library/4.0/DelayedArray’
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS/LAPACK: /app/software/OpenBLAS/0.3.7-GCC-8.3.0/lib/libopenblas_haswellp-r0.3.7.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] DelayedDataFrame_1.4.0 DelayedArray_0.14.0 IRanges_2.22.2
[4] matrixStats_0.58.0 S4Vectors_0.26.1 BiocGenerics_0.34.0
[7] BiocManager_1.30.10
loaded via a namespace (and not attached):
[1] compiler_4.0.2 Matrix_1.2-18 tools_4.0.2 grid_4.0.2
[5] lattice_0.20-41
Also, I was a bit confused by the message I saw when loading BiocManager:
> library(BiocManager)
Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help
Bioconductor version '3.11' is out-of-date; the current release version '3.12'
is available with R version '4.0'; see https://bioconductor.org/install
The page referenced there says that Bioc 3.12 is meant for use with R-4.0.3, so I assume that 3.11 is still the correct version for R-4.0.2?
Hi Dan.
sessionInfo()reports that you already have DelayedArray 0.14.0 installed. Are you trying to update it to 0.14.1, which is the latest version available for BioC 3.11? What doesBiocManager::valid()report?Note that even if you are stuck with R 4.0.2, it would be a good idea to switch to Bioconductor 3.12 since BioC 3.11 is no longer supported.
R 4.0.2 has been superseded by R 4.0.3 and both BioC 3.11 and BioC 3.12 are meant to be used with the latter. They likely also work with R 4.0.2, but, as soon as R 4.0.3 became available, the latter became the new target and we started to use it on the build machines. So even though there shouldn't be any significant difference between 4.0.2 and 4.0.3, and I would expect that BioC 3.11 and BioC 3.12 work with both versions of R, we cannot really guarantee that.
Hope this helps,
H.