ncbi
configure assumes /usr/bin/make is gmake, and thus make fails on a system where it isn't
Freebsd 14.2, which configure says is supported. After it runs, it assumes all sorts of incorrect things. To make (ahem) life easier on myself I temporarily made /usr/bin/make into gmake, and undid it after. Detect where gmake is, and use that for running make, not just whatever pops up in the path first.
Font packages, png/tiff/etc packages...to download a file?
Our code does not introduce any of those dependencies.
Font packages, png/tiff/etc packages...to download a file?
Our code does not introduce any of those dependencies.
code requires bison and Doxygen, and Doxygen does. Again, just trying to download a file, not dive down a long list of inter-dependencies
just trying to download a file, not dive down a long list of inter-dependencies
Welcome to computers. They've been like this since ... ever. I understand your frustration. It is a common difficulty that all users (even us developers) have.
The SRA Toolkit has many users. Some of them have different needs than you do.
As to your original complaint, we welcome any changes to the code that you may provide to make non-gmake make work correctly. GNU-isms creep in easily when you don't have access to the non-GNU versions. We try to squash them when we can.
Also, FYI:
You don't have to use make. Our build system uses CMake which itself can use various build systems like make or ninja or even IDE build systems like Visual Studio and Xcode.
To be more helpful, my make (gmake, or cmake) fails as:
-- Build files have been written to: /home/ec2-user/ncbi-outdir/sra-tools/FreeBSD/clang/amd64/rel/obj
make -C /home/ec2-user/ncbi-outdir/sra-tools/FreeBSD/clang/amd64/rel/obj/ --no-print-directory
usage: make [-BeikNnqrSstWwX]
[-C directory] [-D variable] [-d flags] [-f makefile]
[-I directory] [-J private] [-j max_jobs] [-m directory] [-T file]
[-V variable] [-v variable] [variable=value] [target ...]
gmake: *** [/projects/src/sra-tools/build/Makefile.env:134: cmake_ext_tools] Error 2
I'm old and retired and this used to be a thing that happened a lot, and so I think I just instinctively went over and did "mv /usr/bin/make /usr/bin/make.org" and then made a symlink to cmake. The make runs fine until build without changing my real make, and runs fine to complete if I do change it.
just trying to download a file, not dive down a long list of inter-dependencies
Welcome to computers. They've been like this since ... ever. I understand your frustration. It is a common difficulty that all users (even us developers) have.
Oh for sure, and I don't know much about sra-tools so maybe Doxygen was the only way to do certain things, but I also know sometimes people just grab a library from somewhere to do a 1-liner when a 2-liner without it would work fine ;) But if sra-tools has meaningful needs of Doxygen, I guess it does. I'd rather have a rest API I could be told I need to use to download a FASTA file larger than 5gigabases though, and then just toss together some code to do it.
Also, FYI: You don't have to use
make. Our build system usesCMakewhich itself can use various build systems likemakeorninjaor even IDE build systems like Visual Studio and Xcode.
It's a freebsd AWS system tossed together for a simple task (ie, getting my wife to not do her bioinformatics work on her laptop and lose her life's work over a spilled cup of coffee), I don't use IDEs I'm an old unix guy. I do realize that's my own cross not yours :) But running cmake or gmake shouldn't give a failure for it trying to run /usr/bin/make.
As to your original complaint, we welcome any changes to the code that you may provide to make non-
gmakemakework correctly. GNU-isms creep in easily when you don't have access to the non-GNU versions. We try to squash them when we can.
I'll drink a second cup of coffee after I get everything I'm actually trying to do working, and then try to remember how to fix this in configure and put something up. You'll note my GitHub account was silent for 14 years before today, I opened a meadery and stopped trying to save the world from interdependencies when systemd won ;)