Problem installing fcgene using cygwin64.

Question

[paulwjeffries]

I am trying to install fcgene so that I can convert vcf dosage files to plink files. It seems that I have successfully configured, but "make" produced two error codes [Makefile:33: fcgene.o] Error 1 [Makefile:23: all] Error 2

It is possible to run the program without installing it, but when I type "fcgene", I get an error message that the program can’t run because the file libgcc_s_dw2-1.dll can’t be found. I copied that file into the same directory as fcgene.exe but then got an error message that libstdc++-6.dll could not be found.

I seem not to have some files in the right place, but I did not think fcgene had any dependencies. Is there some library I should install in the fcgene directory? Or is there a way to compile and run the program without the files.

All help will be appreciated.

C:\Users\jp\fcGene>sh configure
configure: line 1316: AC_INIT_AUTOMAKE: command not found
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking for g++... g++
checking for C++ compiler default output file name... a.exe
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... .exe
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... none
checking how to run the C++ preprocessor... g++ -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking sys/timeb.h usability... yes
checking sys/timeb.h presence... yes
checking for sys/timeb.h... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for the MATH library headers... MATH Library was found
checking for the ZLIB library headers... ZLIB Library was found
------------------------------------------------------------------------
configure:  fcGENE can read and write gezipped files ending with *.gz.
------------------------------------------------------------------------
checking for stdbool.h that conforms to C99... no
checking for _Bool... no
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for error_at_line... no
checking whether sys/types.h defines makedev... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for floor... yes
checking for pow... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/config.h
config.status: src/config.h is unchanged
config.status: executing depfiles commands

C:\Users\jp\fcGene>make
make -C src  all
make[1]: Entering directory '/cygdrive/c/Users/jp/fcGene/src'
g++ -g -c -Wall -O3 -I. -DUNIX   fcgene.cpp
In file included from machdat.h:16:0,
                 from plinksnp.h:19,
                 from fcgene.h:20,
                 from fcgene.cpp:16:
gz_stream.h: In constructor 'IFS::IFS(const char*, const char*)':
gz_stream.h:187:20: error: 'fopen64' was not declared in this scope
          { _file = fopen64(filename, mode); }
                    ^~~~~~~
gz_stream.h:187:20: note: suggested alternative: 'fopen'
          { _file = fopen64(filename, mode); }
                    ^~~~~~~
                    fopen
make[1]: *** [Makefile:33: fcgene.o] Error 1
make[1]: Leaving directory '/cygdrive/c/Users/jp/fcGene/src'
make: *** [Makefile:23: all] Error 2

[WouterDeCoster]

Can you use the Windows 10 Subsystem for Linux?

[paulwjeffries]

Unfortunately, I inherited a machine that is running Windows 7.

[WouterDeCoster]

I have never used it because I use Ubuntu, but have heard a lot of trouble about cygwin. What about installing Linux, in a virtual machine or dual boot?

[jared.andrews07]

That is rough, Windows 10 Subsytem for Linux is really good. It is definitely worth the ~$40 to upgrade if you are going to continually doing bioinformatics on a Windows machine.

A VM running Ubuntu is probably your best bet, to be honest. There are a lot of tutorials on how to set them up, and they usually work pretty well, albeit a lot slower than typical given they only have access to a fraction of your system's resources.