Trying to run test command with SCE:

SingleCellExperiment(assays = list(counts=counts_matrix))

Results in following error:

Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object 'normalizenamesreplacement_value' not found

Any suggestions?

sessionInfo()

sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS

Matrix products: default BLAS/LAPACK: /app/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib/libopenblas_prescottp-r0.2.18.so

locale: [1] LCCTYPE=enUS.UTF-8 LCNUMERIC=C LCTIME=enUS.UTF-8
[4] LCCOLLATE=enUS.UTF-8 LCMONETARY=enUS.UTF-8 LCMESSAGES=enUS.UTF-8
[7] LCPAPER=enUS.UTF-8 LCNAME=C LCADDRESS=C
[10] LCTELEPHONE=C LCMEASUREMENT=enUS.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] SingleCellExperiment1.8.0 SummarizedExperiment1.12.0 DelayedArray0.8.0
[4] BiocParallel1.16.6 matrixStats0.54.0 Biobase2.42.0
[7] GenomicRanges1.34.0 GenomeInfoDb1.18.2 Biostrings2.54.0
[10] XVector0.26.0 IRanges2.16.0 S4Vectors0.24.1
[13] BiocGenerics_0.32.0

loaded via a namespace (and not attached): [1] lattice0.20-38 bitops1.0-6 grid3.6.0 zlibbioc1.28.0
[5] Matrix1.2-17 tools3.6.0 RCurl1.95-4.12 yaml2.2.0
[9] compiler3.6.0 BiocManager1.30.10 GenomeInfoDbData_1.2.0

Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object 'normalizenamesreplacement_value' not found

I don't know where that comes from. In fact, I can't even find where this normalizenamesreplacement_value comes from in the Bioconductor code base.

If I had to guess, I would say that the error is caused by the fact that your packages are out of date. For example, the latest version of GenomicRanges is 1.38.0 now, SummarizedExperiment is 1.16.0, and so on. You can test this yourself by running BiocManager::valid(); fix all reported problems and see if the error persists.

Bioconductor packages are designed to work together in unison, so installing packages from different releases of Bioconductor is rarely advisable. In fact, this should not even be possible if you use BiocManager::install(), as described in the instructions; those who deviate from these instructions are assumed to know how what they're doing.