guilhermesena1
commented
3 years ago I can reproduce this when cloning and using autoreconf -i, which gives me the log below. However, if I go to src/smithlab_cpp and run autoreconf -i there as well, the recursive configuration works fine.
If that is the source of the problem, I think we just need to make clear that, if the repo is cloned and the user wishes to use autotools, it needs to be run in both those directories.
Log autoreconf -i only in the root directory:
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
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 whether make supports nested variables... (cached) yes
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++... gcc3
checking whether g++ supports C++11 features with -std=c++11... yes
checking for ranlib... ranlib
checking for library containing hts_version... -lhts
checking for library containing zlibVersion... -lz
checking for library containing cblas_dgemm... -lgslcblas
checking for library containing gsl_blas_dgemm... -lgsl
checking that generated files are newer than configure... done
=== configuring in src/smithlab_cpp (/home/sena/methpipe/src/smithlab_cpp)
configure: WARNING: no configuration information is in src/smithlab_cpp
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commandsLog with autoreconf -i in both root and src/smithlab_cpp
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
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 whether make supports nested variables... (cached) yes
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++... gcc3
checking whether g++ supports C++11 features with -std=c++11... yes
checking for ranlib... ranlib
checking for library containing hts_version... -lhts
checking for library containing zlibVersion... -lz
checking for library containing cblas_dgemm... -lgslcblas
checking for library containing gsl_blas_dgemm... -lgsl
checking that generated files are newer than configure... done
=== configuring in src/smithlab_cpp (/home/sena/methpipe/src/smithlab_cpp)
configure: running /bin/bash ./configure '--prefix=/home/sena/methpipe' --disable-option-checking '--enable-hts' '--srcdir=.' --cache-file=
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
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 for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++... gcc3
checking whether g++ supports C++11 features with -std=c++11... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for ar... ar
checking the archiver (ar) interface... ar
checking for ranlib... ranlib
checking for hts_version in -lhts... yes
checking for zlibVersion in -lz... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
terencewtli
autoreconf -idoes not produce these two lines (which are produced by the currentmasterclone) in the currentsam_pre_releaseclone:I thought it was because of this line, but it's identical in both
configure.acversions in current clone and methpipe-4.1.2, and methpipe-4.1.2 recursive config works fine.AX_SUBDIRS_CONFIGURE([src/smithlab_cpp], [--enable-hts])