onLoad failed in loadNamespace() for 'utils', details

Question

I'm currently working on building a distroless R image (though I'm not versed in R)

I'm currently pulling deb packages from https://cloud.r-project.org/bin/linux/debian/buster-cran35/ for amd64 architecture.

I'm able to run R interactively from the image created, however, some of the core libraries are not loaded correctly, and the information on the failure cause in the terminal are scarce.

Below is the output of running the following command: R --verbose

'verbose' and 'quietly' are both true; being verbose then ..
now dyn.load("/usr/lib/R/library/methods/libs/methods.so") ...

R version 3.6.2 (2019-12-12) -- "Dark and Stormy Night"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

'verbose' and 'quietly' are both true; being verbose then ..
'verbose' and 'quietly' are both true; being verbose then ..
now dyn.load("/usr/lib/R/library/utils/libs/utils.so") ...
Garbage collection 1 = 0+0+1 (level 2) ...
12.0 Mbytes of cons cells used (35%)
3.1 Mbytes of vectors used (5%)
Error: package or namespace load failed for 'utils':
 .onLoad failed in loadNamespace() for 'utils', details:
  call: system(paste(which, shQuote(names[i])), intern = TRUE, ignore.stderr = TRUE)
  error: error in running command
'verbose' and 'quietly' are both true; being verbose then ..
now dyn.load("/usr/lib/R/library/grDevices/libs/grDevices.so") ...
'verbose' and 'quietly' are both true; being verbose then ..
now dyn.load("/usr/lib/R/library/graphics/libs/graphics.so") ...
'verbose' and 'quietly' are both true; being verbose then ..
shared object ''utils.so'' already loaded
Error: package or namespace load failed for 'stats':
 .onLoad failed in loadNamespace() for 'utils', details:
  call: system(paste(which, shQuote(names[i])), intern = TRUE, ignore.stderr = TRUE)
  error: error in running command

All dependent libraries for utils.so are found by the ldd command.

Output for the command for ldd utils.so linkage:

/ # ldd /usr/lib/R/library/utils/libs/utils.so
    linux-vdso.so.1 (0x00007ffe772f9000)
    libR.so => /usr/lib/libR.so (0x00007f127acdf000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f127ab1e000)
    libblas.so.3 => /usr/lib/x86_64-linux-gnu/libblas.so.3 (0x00007f127aac3000)
    libgfortran.so.5 => /usr/lib/x86_64-linux-gnu/libgfortran.so.5 (0x00007f127a855000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f127a6d2000)
    libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007f127a690000)
    libreadline.so.7 => /lib/x86_64-linux-gnu/libreadline.so.7 (0x00007f127a441000)
    libpcre2-8.so.0 => /usr/lib/x86_64-linux-gnu/libpcre2-8.so.0 (0x00007f127a3bc000)
    libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 (0x00007f127a348000)
    liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00007f127a320000)
    libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0 (0x00007f127a30d000)
    libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f127a0ef000)
    librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f127a0e3000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f127a0de000)
    libicuuc.so.63 => /usr/lib/x86_64-linux-gnu/libicuuc.so.63 (0x00007f1279f0f000)
    libicui18n.so.63 => /usr/lib/x86_64-linux-gnu/libicui18n.so.63 (0x00007f1279c34000)
    libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007f1279c03000)
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f1279be2000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f127b17f000)
    libopenblas.so.0 => /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (0x00007f12779fc000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f12779e2000)
    libtinfo.so.6 => /lib/x86_64-linux-gnu/libtinfo.so.6 (0x00007f12779b4000)
    libicudata.so.63 => /usr/lib/x86_64-linux-gnu/libicudata.so.63 (0x00007f1275fc4000)
    libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f1275e40000)

What may I be missing here?

And what does "utils.so" already loaded may indicate?

Answer 1

You're missing "which" I think.

In this code chunk system(paste(which, shQuote(names[i])), intern = TRUE, ignore.stderr = TRUE) , which is an object from Sys.which and its value is the string "/usr/bin/which".

You should try installing which .