BFAST: the Blat-like Fast Accurate Search Tool
Home Page: http://bfast.sf.net
License: GNU General Public License v2.0
I improve human lives
by creating software
for biologists and clinicians
to accelerate breakthroughs in genomics science
configure.ac says:
CFLAGS="${default_CFLAGS} ${extended_CFLAGS}";
This overwrites any CFLAGS the user may have specified. Please don't! You can of course add your own CFLAGS before and/or after what the user specifies, but please don't completely ignore what the user specifies.
Hello,
I am trying to include BFast into a library for automatic compilation of bioinformatics software (SMBL --https://github.com/karel-brinda/smbl). The main supported systems are Linux and MacOS but I try to make it work in CygWin as well because many developers and users have Windows-based laptops and for testing purposes, CygWin works well.
Nevertheless, for BFast I am getting the error below when I try to compile in CygWin. Is there any way how to compile it in CygWin?
Thanks.
$ ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
/home/Karel/git_repos/bfast/config/missing: Unknown `--is-lightweight' option
Try `/home/Karel/git_repos/bfast/config/missing --help' for more information
configure: WARNING: 'missing' script is too old or missing
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking build system type... config/config.guess: unable to guess system type
This script, last modified 2005-07-08, has failed to recognize
the operating system you are using. It is advised that you
download the most up to date version of the config scripts from
http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.guess
and
http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.sub
If the version you run (config/config.guess) is already up to date, please
send the following data and any information you think might be
pertinent to <[email protected]> in order to provide the needed
information to handle your system.
config.guess timestamp = 2005-07-08
uname -m = x86_64
uname -r = 1.7.35(0.287/5/3)
uname -s = CYGWIN_NT-6.1
uname -v = 2015-03-04 12:09
/usr/bin/uname -p = unknown
/bin/uname -X =
hostinfo =
/bin/universe =
/usr/bin/arch -k =
/bin/arch = x86_64
/usr/bin/oslevel =
/usr/convex/getsysinfo =
UNAME_MACHINE = x86_64
UNAME_RELEASE = 1.7.35(0.287/5/3)
UNAME_SYSTEM = CYGWIN_NT-6.1
UNAME_VERSION = 2015-03-04 12:09
configure: error: cannot guess build type; you must specify one
The latest tag in this git repo is 0.6.5a but 0.7.0a was released on SourceForge 6 months after that. Please make the 0.7.0a tag available here.
with bfast 0.7.0a:
BfastPostProcess.c:270:23: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if(args->pairing < 0 && 3 < args->pairing) {
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
1 warning generated.
BFAST appears to presume older semantics of "inline":
AlignedReadConvert.o: In function `AlignedReadConvertPrintAlignedEntryToCIGAR':
./bfast/AlignedReadConvert.c:794: undefined reference to `ToUpper'
./bfast/AlignedReadConvert.c:742: undefined reference to `ToUpper'
./bfast/AlignedReadConvert.c:742: undefined reference to `ToUpper'
./bfast/AlignedReadConvert.c:783: undefined reference to `ToUpper'
RGBinary.o: In function `RGBinaryRead':
./bfast/RGBinary.c:167: undefined reference to `ToUpper'
RGMatch.o:/tmp/BFAST/bfast/RGMatch.c:794: more undefined references to `ToUpper' follow
Align.o: In function `AlignExact':
./bfast/Align.c:517: undefined reference to `ScoringMatrixGetNTScore'
./bfast/Align.c:510: undefined reference to `ScoringMatrixGetColorScore'
AlignNTSpace.o: In function `AlignNTSpaceUngapped':
./bfast/AlignNTSpace.c:49: undefined reference to `ScoringMatrixGetNTScore'
AlignNTSpace.o: In function `AlignNTSpaceFillInCell':
./bfast/AlignNTSpace.c:539: undefined reference to `ScoringMatrixGetNTScore'
./bfast/AlignNTSpace.c:539: undefined reference to `ScoringMatrixGetNTScore'
AlignNTSpace.o: In function `AlignNTSpaceGappedConstrained':
./bfast/AlignNTSpace.c:186: undefined reference to `ScoringMatrixGetNTScore'
AlignNTSpace.o: In function `AlignNTSpaceFillInCell':
./bfast/AlignNTSpace.c:539: undefined reference to `ScoringMatrixGetNTScore'
AlignColorSpace.o: In function `AlignColorSpaceUngappedGetBest':
./bfast/AlignColorSpace.c:185: undefined reference to `ScoringMatrixGetColorScore'
./bfast/AlignColorSpace.c:189: undefined reference to `ScoringMatrixGetNTScore'
AlignColorSpace.o: In function `AlignColorSpaceFillInCell':
./bfast/AlignColorSpace.c:914: undefined reference to `ScoringMatrixGetNTScore'
./bfast/AlignColorSpace.c:915: undefined reference to `ScoringMatrixGetColorScore'
./bfast/AlignColorSpace.c:1024: undefined reference to `ScoringMatrixGetColorScore'
AlignColorSpace.o: In function `AlignColorSpaceGappedConstrained':
./bfast/AlignColorSpace.c:401: undefined reference to `ScoringMatrixGetNTScore'
./bfast/AlignColorSpace.c:402: undefined reference to `ScoringMatrixGetColorScore'
./bfast/AlignColorSpace.c:351: undefined reference to `ScoringMatrixGetColorScore'
./bfast/AlignColorSpace.c:352: undefined reference to `ScoringMatrixGetNTScore'
The workaround when using gcc 5.4.0 is to explicitly compile with CPPFLAGS = -std=gnu89 (see gcc docs) in:
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