Error: package or namespace load failed for ‘GenomeInfoDb’; there is no package called ‘GenomeInfoDbData’

[chancharikmitra]

I am having this issue of my jupyter notebook not being able to find the GenomeInfoDbData package even though it is already installed in my conda environment. Note: I am trying to use this package as part of the SpatialExperiment library.

Conda Version: 4.14.0 Running locally on macOS 11.6 Environment Dependencies: requirements.txt

Error Readout when running library(SpatialExperiment) in a jupyter notebook:

`Loading required package: SingleCellExperiment

Loading required package: SummarizedExperiment

Loading required package: MatrixGenerics

Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges

Loading required package: stats4

Loading required package: BiocGenerics

Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

expand.grid

Loading required package: IRanges

Loading required package: GenomeInfoDb

Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘GenomeInfoDbData’

Error: package ‘GenomeInfoDb’ could not be loaded Traceback:

1. library(SpatialExperiment)
2. .getRequiredPackages2(pkgInfo, quietly = quietly)
3. library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, . quietly = quietly)
4. .getRequiredPackages2(pkgInfo, quietly = quietly)
5. library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, . quietly = quietly)
6. .getRequiredPackages2(pkgInfo, quietly = quietly)
7. library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, . quietly = quietly)
8. .getRequiredPackages2(pkgInfo, quietly = quietly)
9. stop(gettextf("package %s could not be loaded", sQuote(pkg)), . call. = FALSE, domain = NA)`

[hpages]

This looks like a conda environment/configuration problem. How do you know that GenomeInfoDbData is already installed in your conda environment. Can you library(GenomeInfoDbData)?

Note that Bioconductor has no control on how Bioconductor packages get re-distributed and installed via conda. The only installation method that we support is BiocManager::install().

[chancharikmitra]

This looks like a conda environment/configuration problem. How do you know that GenomeInfoDbData is already installed in your conda environment. Can you library(GenomeInfoDbData)?

Note that Bioconductor has no control on how Bioconductor packages get re-distributed and installed via conda. The only installation method that we support is BiocManager::install().

I see. The requirements.txt file includes every package that is installed on the environment. This comes from running conda list. GenomeInfoDBData specifically version 1.2.4 is included. So you're saying this is likely a conda issue then? If that is the case, maybe I'll transfer this issue to bioconda.

[hpages]

The requirements.txt file includes every package that is installed on the environment. This comes from running conda list.

Sounds good but that's not direct evidence that you actually have GenomeInfoDbData installed in your conda environment, and that the package can be loaded. Only way to know for sure is to try library(GenomeInfoDbData). Did you try that?

[chancharikmitra]

@hpages Ah, I see what you are saying. library(GenomeInfoDbData) gives me

Error in library(GenomeInfoDbData): there is no package called ‘GenomeInfoDbData’ Traceback:

1. library(GenomeInfoDbData)

Oddly enough, conda says this package is already installed when I try to reinstall it.

[hpages]

library(GenomeInfoDbData) is telling the truth: you don't have GenomeInfoDbData installed. Or maybe it is installed, but in the "wrong" place, whatever that means in the context of a conda installation.

Anyways, this is a conda installation issue. Can't help you with that, sorry.