HDF5Array installation issue

[ytakemon]

Hello, I am trying to install your package. However, I am getting the following error, and I am not sure how to troubleshoot it.

R version/ Machine used: R version 4.0.2 (2020-06-22) Platform: x86_64-centos7-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Thank you in advance! Yuka

> BiocManager::install("HDF5Array")
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: http://cran.rstudio.com/

Bioconductor version 3.11 (BiocManager 1.30.18), R 4.0.2 (2020-06-22)
Installing package(s) 'HDF5Array'
trying URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/HDF5Array_1.16.1.tar.gz'
Content type 'application/octet-stream' length 8063240 bytes (7.7 MB)
==================================================
downloaded 7.7 MB

* installing *source* package ‘HDF5Array’ ...
** using staged installation
** libs
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/gcc -I"/gsc/software/linux-x86_64-centos7/R-4.0.2/lib64/R/include" -DNDEBUG  -I'/home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0/S4Vectors/include' -I'/home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -c H5DSetDescriptor.c -o H5DSetDescriptor.o
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/gcc -I"/gsc/software/linux-x86_64-centos7/R-4.0.2/lib64/R/include" -DNDEBUG  -I'/home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0/S4Vectors/include' -I'/home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -c R_init_HDF5Array.c -o R_init_HDF5Array.o
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/gcc -I"/gsc/software/linux-x86_64-centos7/R-4.0.2/lib64/R/include" -DNDEBUG  -I'/home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0/S4Vectors/include' -I'/home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/gcc -I"/gsc/software/linux-x86_64-centos7/R-4.0.2/lib64/R/include" -DNDEBUG  -I'/home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0/S4Vectors/include' -I'/home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -c array_selection.c -o array_selection.o
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/gcc -I"/gsc/software/linux-x86_64-centos7/R-4.0.2/lib64/R/include" -DNDEBUG  -I'/home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0/S4Vectors/include' -I'/home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -c h5dimscales.c -o h5dimscales.o
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/gcc -I"/gsc/software/linux-x86_64-centos7/R-4.0.2/lib64/R/include" -DNDEBUG  -I'/home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0/S4Vectors/include' -I'/home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0/Rhdf5lib/include' -I/usr/local/include   -fpic  -g -O2  -c h5mread.c -o h5mread.o
/gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/gcc -shared -L/gsc/software/linux-x86_64-centos7/R-4.0.2/lib64/R/lib -L/gsc/software/linux-x86_64-centos7/gcc-7.2.0/lib64 -o HDF5Array.so H5DSetDescriptor.o R_init_HDF5Array.o S4Vectors_stubs.o array_selection.o h5dimscales.o h5mread.o /home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0/Rhdf5lib/lib/libhdf5_hl.a /home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0/Rhdf5lib/lib/libhdf5.a /home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0/Rhdf5lib/lib/libsz.a -lz -L/gsc/software/linux-x86_64-centos7/R-4.0.2/lib64/R/lib -lR
installing to /home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0/00LOCK-HDF5Array/00new/HDF5Array/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error in conformMethod(signature, mnames, fnames, f, fdef, definition) :
  in method for ‘write_block’ with signature ‘sink="HDF5RealizationSink"’: formal arguments (sink = "HDF5RealizationSink", viewport = "HDF5RealizationSink", block = "HDF5RealizationSink") omitted in the method definition cannot be in the signature
Error: unable to load R code in package ‘HDF5Array’
Execution halted
ERROR: lazy loading failed for package ‘HDF5Array’
* removing ‘/home/ytakemon/R/x86_64-centos7-linux-gnu-library/4.0/HDF5Array’

The downloaded source packages are in
    ‘/tmp/RtmpeZKl8C/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /gsc/software/linux-x86_64-centos7/R-4.0.2/lib64/R/library
  packages:
    boot, class, cluster, codetools, foreign, KernSmooth, lattice, MASS,
    Matrix, mgcv, nlme, nnet, rpart, spatial, survival
Old packages: 'ade4', 'BiocManager', 'bslib', 'callr', 'colourpicker', 'dials',
  'evaluate', 'future', 'future.apply', 'g3viz', 'ggfun', 'ggh4x', 'ggplot2',
  'ggrepel', 'igraph', 'lme4', 'lubridate', 'markdown', 'memuse', 'nloptr',
  'pkgload', 'plotly', 'processx', 'ps', 'RcppArmadillo', 'RcppEigen',
  'RcppTOML', 'recipes', 'rgl', 'rmarkdown', 'Rook', 'rstatix', 'R.utils',
  'segmented', 'SeuratObject', 'shiny', 'sp', 'spatstat.random', 'stringdist',
  'styler', 'XML', 'zip'
Update all/some/none? [a/s/n]: n
Warning message:
In install.packages(...) :
  installation of package ‘HDF5Array’ had non-zero exit status

[hpages]

Hi,

You seem to be having a mix of incompatible package versions on your machine. You can check this with BiocManager::valid(), and then fix by following the instructions suggested by BiocManager::valid's diagnostic message.

But more importantly: Bioconductor 3.11 is 2.5 year old and no longer supported! Bioconductor has a release every 6 months. The latest version is BioC 3.16. It was just released last week: https://bioconductor.org/news/bioc_3_16_release/

You are strongly advised to update your installation to use this new version. Note that BioC 3.16 requires R 4.2 so you will also need to update your R installation.

H.

[ytakemon]

Thanks for the quick response! I'll give that a try and contact our IT department to get the latest version. Unfortunately (and annoyingly), I don't have of control of installations so my R version is often out of date.

[hpages]

OK, good luck with your IT people. Closing this now. Don't hesitate to re-open if the issue persists.