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grimbough / rhdf5

Package providing an interface between HDF5 and R
http://bioconductor.org/packages/rhdf5
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Installation failed #142

Open timz0605 opened 4 months ago

timz0605 commented 4 months ago

Hello!

I was trying to install the package using BiocManager::install("rhdf5"), but have been encountering this issue. I am trying to install the package through R 4.2.1 on HPC. Even though I specified the version using the command BiocManager::install("rhdf5", version = "3.16"), I still could not install the package successfully. Would appreciate any help!

ERROR: compilation failed for package ‘Rhdf5lib’
* removing ‘/home/mjzhang/R_libs/4.2.1/Rhdf5lib’
ERROR: dependency ‘Rhdf5lib’ is not available for package ‘rhdf5filters’
* removing ‘/home/mjzhang/R_libs/4.2.1/rhdf5filters’
ERROR: dependencies ‘Rhdf5lib’, ‘rhdf5filters’ are not available for package ‘rhdf5’
* removing ‘/home/mjzhang/R_libs/4.2.1/rhdf5’

The downloaded source packages are in
        ‘/tmp/RtmpzeUlHS/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /share1/R/4.2.1/lib64/R/library
  packages:
    boot, brew, callr, class, cluster, codetools, commonmark, config, curl,
    data.table, DBI, digest, foreign, geometries, geometry, glue, httpuv,
    KernSmooth, lattice, lifecycle, lpSolve, MASS, Matrix, mgcv, nlme, nnet,
    pkgload, pkgmaker, ps, Rcpp, RcppTOML, reticulate, rJava, rlang, rlecuyer,
    Rmpi, roxygen2, rpart, rprojroot, rstudioapi, s2, sf, sfheaders, snowfall,
    spatial, stringi, stringr, survival, tensorflow, tfruns, usethis, V8,
    withr, xfun, yaml, zip
Warning messages:
1: In install.packages(...) :
  installation of package ‘Rhdf5lib’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘rhdf5filters’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘rhdf5’ had non-zero exit status
grimbough commented 4 months ago

Hi,

It looks like the package affected is actually Rhdf5lib, and because that can't be installed you then can't use rhdf5.

To figure out what's going wrong with Rhdf5lib I'll need to see quite a bit more of the installation output. Can you try running this command below, and then share all the output that appears on the screen. There will be quite a lot, but hopefully it'll contain the underlying problem:

BiocManager::install('Rhdf5lib')