BiocManager::install("EnsDb.Hsapiens.v75") install fails with non-zero exit status
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@saadmurtazakhan-6782
Last seen 7 months ago
United States

Hi I am trying to use signac https://satijalab.org/signac/articles/pbmc_vignette.html with R version 4.0.3 (2020-10-10). Whenever I install EnsDb.Hsapiens.v75 (a required package needed to be used with signac) with BiocManager::install("EnsDb.Hsapiens.v75") it fails with the following error. I was wondering how I can successfully install this package with R 4.0.3 or does it even work with it?

Below is the error I see.

BiocManager::install("EnsDb.Hsapiens.v75")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'EnsDb.Hsapiens.v75'
trying URL 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/EnsDb.Hsapiens.v75_2.99.0.tar.gz'
Content type 'application/x-gzip' length 79029669 bytes (75.4 MB)
==================================================
downloaded 75.4 MB

* installing *source* package ‘EnsDb.Hsapiens.v75’ ...
** using staged installation
** R
** inst
Warning in file.append(to[okay], from[okay]) :
  write error during file append
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for 'EnsDb.Hsapiens.v75':
 .onLoad failed in loadNamespace() for 'EnsDb.Hsapiens.v75', details:
  call: EnsDb(system.file("extdata", files[[i]], package = pkgname, lib.loc = libname))
  error: Database does not have any tables!
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/khan.saad/RLibs_cellassignfinal4.0.3/EnsDb.Hsapiens.v75’

The downloaded source packages are in
    '/tmp/104007.tmpdir/Rtmp0YwPtP/downloaded_packages'
Installation path not writeable, unable to update packages: arrow, backports,
  blogdown, broom, DBI, DT, forcats, gert, git2r, gitcreds, hms, knitr, Lahman,
  memoise, patchwork, rappdirs, reprex, RMariaDB, rmarkdown, RPostgres,
  RSQLite, rticles, servr, tinytex, usethis, xaringan, xfun, boot, class,
  codetools, foreign, KernSmooth, Matrix, nlme, nnet, spatial
Old packages: 'ggthemes', 'princurve'
Update all/some/none? [a/s/n]: n
Warning message:
In install.packages(...) :
  installation of package 'EnsDb.Hsapiens.v75' had non-zero exit status
biocmanager Install • 358 views
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@james-w-macdonald-5106
Last seen 15 hours ago
United States

I can't replicate the error, so maybe you just need to restart R and try again?

> install("EnsDb.Hsapiens.v75")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.2 (2020-06-22)
Installing package(s) 'EnsDb.Hsapiens.v75'
trying URL 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/E                                                                                                                                                             nsDb.Hsapiens.v75_2.99.0.tar.gz'
Content type 'application/x-gzip' length 79029669 bytes (75.4 MB)
==================================================
downloaded 75.4 MB

* installing *source* package ‘EnsDb.Hsapiens.v75’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (EnsDb.Hsapiens.v75)

But that version of Ensembl is positively ancient, and you probably don't want that one? There are any number of EnsDbs on the AnnotationHub that are far newer that you might consider.

> library(AnnotationHub)
> hub <- AnnotationHub()
snapshotDate(): 2020-10-27
> query(hub, c("Homo sapiens","ensdb"))
AnnotationHub with 17 records
# snapshotDate(): 2020-10-27
# $dataprovider: Ensembl
# $species: Homo sapiens
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH53211"]]'

            title
  AH53211 | Ensembl 87 EnsDb for Homo Sapiens
  AH53715 | Ensembl 88 EnsDb for Homo Sapiens
  AH56681 | Ensembl 89 EnsDb for Homo Sapiens
  AH57757 | Ensembl 90 EnsDb for Homo Sapiens
  AH60773 | Ensembl 91 EnsDb for Homo Sapiens
  ...       ...
  AH75011 | Ensembl 98 EnsDb for Homo sapiens
  AH78783 | Ensembl 99 EnsDb for Homo sapiens
  AH79689 | Ensembl 100 EnsDb for Homo sapiens
  AH83216 | Ensembl 101 EnsDb for Homo sapiens
  AH89180 | Ensembl 102 EnsDb for Homo sapiens

And as the message says, you can get any one of those by doing e.g.,

> ensdb <- hub[["AH89180"]]

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