Bioconductor/Icens

[macOS] Installation fails with Clang: `Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input`

Closed this issue · 2 comments

barracuda156 commented

While for me locally Icens builds fine with GCC, on CI with Clang it fails, both Bioconductor release version and the latest master:

  --->  Configuring R-Icens
  DEBUG: Preferred compilers: clang macports-clang-16 macports-clang-15 macports-clang-14 macports-clang-13 macports-clang-12 macports-clang-11 macports-clang-10 macports-clang-9.0
  DEBUG: Using compiler 'MacPorts Clang 15'
  DEBUG: Executing proc-pre-org.macports.configure-configure-0
  DEBUG: Active variants check for source-type install considers depends_fetch depends_extract depends_lib depends_build depends_run: R-CRAN-recommended clang-15 R
  DEBUG: Executing proc-pre-org.macports.configure-configure-1
  DEBUG: compilers.enforce_c list: 
  DEBUG: compilers.enforce_fortran list: 
  DEBUG: compilers.enforce_some_fortran list: 
  DEBUG: Executing org.macports.configure (R-Icens)
  DEBUG: Environment: 
  CC='/opt/local/bin/clang-mp-15'
  CC_PRINT_OPTIONS='YES'
  CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-Icens/R-Icens/work/.CC_PRINT_OPTIONS'
  CFLAGS='-pipe -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk'
  CPATH='/opt/local/include'
  CPPFLAGS='-I/opt/local/include -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk'
  CXX='/opt/local/bin/clang++-mp-15'
  CXXFLAGS='-pipe -Os -stdlib=libc++ -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk'
  DEVELOPER_DIR='/Library/Developer/CommandLineTools'
  F90FLAGS='-pipe -Os'
  FCFLAGS='-pipe -Os'
  FFLAGS='-pipe -Os'
  INSTALL='/usr/bin/install -c'
  LDFLAGS='-L/opt/local/lib -Wl,-headerpad_max_install_names -Wl,-rpath,/opt/local/lib/libgcc -Wl,-syslibroot,/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk'
  LIBRARY_PATH='/opt/local/lib'
  MACOSX_DEPLOYMENT_TARGET='13.0'
  OBJC='/opt/local/bin/clang-mp-15'
  OBJCFLAGS='-pipe -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk'
  OBJCXX='/opt/local/bin/clang++-mp-15'
  OBJCXXFLAGS='-pipe -Os -stdlib=libc++ -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk'
  SDKROOT='/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk'
  DEBUG: system:  cd "/opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-Icens/R-Icens/work/Icens" && /opt/local/bin/R CMD build . --no-manual --no-build-vignettes 
  Executing:  cd "/opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-Icens/R-Icens/work/Icens" && /opt/local/bin/R CMD build . --no-manual --no-build-vignettes 
  * checking for file ‘./DESCRIPTION’ ... OK
  * preparing ‘Icens’:
  * checking DESCRIPTION meta-information ... OK
  * checking for LF line-endings in source and make files and shell scripts
  * checking for empty or unneeded directories
  * looking to see if a ‘data/datalist’ file should be added
  * re-saving .R files as .rda
  Warning in file(file, "rt") :
    file("") only supports open = "w+" and open = "w+b": using the former
  Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
    no lines available in input
  Execution halted
  Command failed:  cd "/opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-Icens/R-Icens/work/Icens" && /opt/local/bin/R CMD build . --no-manual --no-build-vignettes 
  Exit code: 1
  Error: Failed to configure R-Icens: configure failure: command execution failed
  DEBUG: Error code: NONE
  DEBUG: Backtrace: configure failure: command execution failed
      while executing
  "$procedure $targetname"
  Error: See /opt/local/var/macports/logs/_Users_runner_work_macports-ports_macports-ports_ports_R_R-Icens/R-Icens/main.log for details.
  Error: Follow https://guide.macports.org/#project.tickets if you believe there is a bug.
  Error: Processing of port R-Icens failed
hpages commented

According to the output produced by your CI, the command that failed is /opt/local/bin/R CMD build . --no-manual --no-build-vignettes. Supposedly the command was run from within the Icens source tree.

But:

  • We don't know where you got the Icens source tree from.
  • We don't know what version of R you are using.
  • You're not using the same R CMD build options as we do: --keep-empty-dirs and --no-resave-data (see).

FWIW here is the output of R CMD build --keep-empty-dirs --no-resave-data on my laptop:

hpages@XPS15:~$ git clone https://github.com/Bioconductor/Icens
Cloning into 'Icens'...
remote: Enumerating objects: 379, done.
remote: Counting objects: 100% (53/53), done.
remote: Compressing objects: 100% (29/29), done.
remote: Total 379 (delta 32), reused 45 (delta 24), pack-reused 326
Receiving objects: 100% (379/379), 73.39 KiB | 1.03 MiB/s, done.
Resolving deltas: 100% (232/232), done.

hpages@XPS15:~$ R CMD build --keep-empty-dirs --no-resave-data Icens
* checking for file ‘Icens/DESCRIPTION’ ... OK
* preparing ‘Icens’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘Icens_1.75.0.tar.gz’

Output of R CMD INSTALL:

hpages@XPS15:~$ R CMD INSTALL Icens_1.75.0.tar.gz
* installing to library ‘/home/hpages/R/R-4.4.r85510/site-library’
* installing *source* package ‘Icens’ ...
** using staged installation
** R
** data
** 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 (Icens)

Using R Under development (unstable) (2023-11-11 r85510) on Ubuntu 23.10:

hpages@XPS15:~$ R --version
R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

Note that Icens contains no native code hence there's nothing to compile so not sure how the specific compiler would matter when running R CMD build on the package.

Plus Icens has no configure script so it's not clear why you get a "configure failure".

What do you get when you run R CMD build --keep-empty-dirs --no-resave-data manually on the package source tree? What's your version of R? Are you on an intel Mac, arm64 Mac, or powerpc Mac?

Thanks,
H.

barracuda156 commented

@hpages Thank you, passing --no-resave-data helped, it installs fine on CI now. (I mentioned clang just for the sake of providing info, since for w/e reason I did not get an error locally, where I used gcc.)
Closing the issue since it is fixed now.

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