Problem installing DelayedArray
0
0
Entering edit mode
Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 9 weeks ago
United States

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Bioconductor version '3.11' is out-of-date; the current release version '3.12'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?

DelayedArray • 96 views
ADD COMMENT
1
Entering edit mode

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 does BiocManager::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.

ADD REPLY

Login before adding your answer.

Traffic: 402 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6