Installation error

[mazzalab]

Description I'm in a Ubuntu (latest) Docker container. I've just installed R through conda: RUN mamba install -y -c conda-forge r-base=4.3.2

When I run this command: RUN R -e 'BiocManager::install("PureCN", dependencies=TRUE, ask = F)'

I get the error below.

...
ranlib libstreamvbyte.a 
make[2]: ranlib: No such file or directory
make[2]: *** [Makefile:27: libstreamvbyte.a] Error 127
make[2]: Leaving directory '/tmp/RtmpSR9TfQ/R.INSTALL12d7724e3388c/rhdf5filters/src/vbz/third_party/streamvbyte'
make[1]: *** [Makefile:30: streamvbyte] Error 2
make[1]: Leaving directory '/tmp/RtmpSR9TfQ/R.INSTALL12d7724e3388c/rhdf5filters/src/vbz'
make: *** [Makevars:29: libH5Zvbz.so] Error 2
ERROR: compilation failed for package ‘rhdf5filters’
* removing ‘/root/miniforge3/lib/R/library/rhdf5filters’
ERROR: dependency ‘rhdf5filters’ is not available for package ‘rhdf5’
* removing ‘/root/miniforge3/lib/R/library/rhdf5’
ERROR: dependency ‘rhdf5’ is not available for package ‘PureCN’
* removing ‘/root/miniforge3/lib/R/library/PureCN’

The downloaded source packages are in
        ‘/tmp/RtmpDvJHJY/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(...) :
  installation of package ‘rhdf5filters’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘rhdf5’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘PureCN’ had non-zero exit status

What am I doing wrong?

Env Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)

Session Info R version 4.3.2 (2023-10-31) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Ubuntu 22.04.3 LTS

Matrix products: default BLAS/LAPACK: /root/miniforge3/lib/libopenblasp-r0.3.25.so; LAPACK version 3.11.0

locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

time zone: NA tzcode source: system (glibc)

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

other attached packages: [1] BiocManager_1.30.22

loaded via a namespace (and not attached): [1] compiler_4.3.2 tools_4.3.2

[mazzalab]

OK I've the solution:

For some reason, ranlib was not installed on my Docker machine. I've then just installed it: apt-get install binutils

and then I could install Purecn flawlessly.

[lima1]

See also here our Dockerfile: https://github.com/lima1/PureCN/blob/RELEASE_3_18/Dockerfile

[mazzalab]

great thanks!