Question: 'make' command repeated message while installing vcftools on Ubuntu 14.04 LTS.
0
gravatar for ravi.uhdnis
2.9 years ago by
ravi.uhdnis150
United States
ravi.uhdnis150 wrote:

Hi,

I downloaded vcftools (vcftools-master.zip), unzipped it to make vcftools-master, then run following commands in it:

./autogen.sh
./configure
make

but, the make output is repeatedly giving following message:

*******************************************
/bin/bash ./config.status --recheck
running CONFIG_SHELL=/bin/bash /bin/bash ./configure --no-create --no-recursion
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
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 for style of include used by make... GNU
checking dependency style of g++... gcc3
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 how to run the C preprocessor... gcc -E
checking for perl... /usr/bin/perl
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for ZLIB... yes
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/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 arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for int16_t... yes
checking for int32_t... yes
checking for int64_t... yes
checking for int8_t... yes
checking for off_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint8_t... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for error_at_line... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for gethostbyaddr... yes
checking for gethostbyname... yes
checking for memset... yes
checking for pow... no
checking for select... yes
checking for socket... yes
checking for sqrt... no
checking for strchr... yes
checking for strdup... yes
checking for strerror... yes
checking for strstr... yes
checking for strtol... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
 /bin/bash ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/cpp/Makefile
config.status: creating src/perl/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
make: Warning: File `Makefile.am' has modification time 2.5e+04 s in the future
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /home/rsindhu/ngSoftwares/vcftools-master/missing aclocal-1.14 
 cd . && /bin/bash /home/rsindhu/ngSoftwares/vcftools-master/missing automake-1.14 --foreign
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /home/rsindhu/ngSoftwares/vcftools-master/missing autoconf
/bin/bash ./config.status --recheck
*********************************************

this message keep on repeating, it would be great if anyone suggest me what's required to properly install vcftools on my Ubuntu machine.

Thanks.

software error • 1.2k views
ADD COMMENTlink modified 2.9 years ago by RamRS20k • written 2.9 years ago by ravi.uhdnis150
1

Why not sudo apt-get install vcftools?

ADD REPLYlink written 2.9 years ago by RamRS20k

because i knew that FTP proxy permission were blocked for my system BUT i tried your suggestion and it worked !! Surely, proxy permission are changed now as earlier it always gave error of internet connectivity. Lesson for today, always try the simplest ist. Thank you Ram.

ADD REPLYlink written 2.9 years ago by ravi.uhdnis150

Ah, I see. Remember, most installations allow for a custom directory, so you can user-install at a local dir even if you don't have permissions to write to usr/local/bin or wherever the default location is.

ADD REPLYlink written 2.9 years ago by RamRS20k

thanks for the information. the only problem was the connectivity to internet while using apt-get command earlier, since it is working now..it's best way to install any software by this way.

ADD REPLYlink written 2.9 years ago by ravi.uhdnis150
0
gravatar for Pierre Lindenbaum
2.9 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:

Reading the manual (0.1.13):

Compiling:
    To compile and install VCFtools, you should type 'make' in the 
    vcftools folder.

why did you

./autogen.sh
./configure
make

?

ADD COMMENTlink written 2.9 years ago by Pierre Lindenbaum118k

I downloaded vcftools (vcftools-master.zip) from Github (https://github.com/vcftools/vcftools), unzipped it to make vcftools-master folder. There were following files in it : drwxrwxr-x 4 rsindhu rsindhu 4096 May 5 2016 src -rw-rw-r-- 1 rsindhu rsindhu 1928 May 5 2016 README.md -rw-rw-r-- 1 rsindhu rsindhu 260 May 5 2016 Makefile.am -rw-rw-r-- 1 rsindhu rsindhu 7652 May 5 2016 LICENSE drwxrwxr-x 2 rsindhu rsindhu 4096 May 5 2016 examples -rw-rw-r-- 1 rsindhu rsindhu 2093 May 5 2016 configure.ac drwxrwxr-x 2 rsindhu rsindhu 4096 May 5 2016 build-aux -rwxr-xr-x 1 rsindhu rsindhu 26 May 5 2016 autogen.sh

And, it was instructed in the README.md file...in order to build vcftools from Github


Build from GitHub

git clone https://github.com/vcftools/vcftools.git
cd vcftools
./autogen.sh
./configure
make
make install

You many need sudo permissions to run make install.


So, this was the way i was following but didn't crossed 'make' point. If one downloads the vcftools_v.tar.gz file, then it forms vcftools_v folder...followed by make command in it to install vcftools.

ADD REPLYlink written 2.9 years ago by ravi.uhdnis150

Oh , I see I was wrong, sorry, I downloaded an old source from sourceforge.

ADD REPLYlink written 2.9 years ago by Pierre Lindenbaum118k

I think one can install vcftools by either of these two ways. The way you told me, i was able to install it but couldn't put in my PATH. Therefore, i tried the other way and apt-get install command made my job done. thanks for comments.

ADD REPLYlink written 2.9 years ago by ravi.uhdnis150

Why would you be unable to put it in your PATH?

ADD REPLYlink written 2.9 years ago by RamRS20k

a little incorrect comment by me (above), i put vcftools in my in .bash_profile file without any issue, sourced it but it didn't worked (vcftools)....like many others e.g. bcftools, samtools in the path. PATH=$PATH:/home/rsindhu/ngSoftwares/vcftools-vcftools-678e892/cpp export PATH even tried /bin instead of /cpp but no use !!.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by ravi.uhdnis150

Did it say command not found? What do you see when you add the directory to your $PATH and then run which vctools

ADD REPLYlink written 2.9 years ago by RamRS20k

I guess so, now since it is successfully installed it is showing as which vcftools => /usr/bin/vcftools. Also, similar other packages (samtools, bcftools) also installed in /usr/bin. It means nothing is placed in my class path, i installed them using apt-get install long before and forget their original source directory. I think it was showing "command not found" before it wasn't installed correctly. Sorry, i hardly use this system so can't figure out things at early. Do i need to write in .bash_profile or .bashrc in order to put a package in my path ?.

ADD REPLYlink written 2.9 years ago by ravi.uhdnis150

Ah...I got it !! I need to write in .bashrc and source it rather than in .bash_profile. I tried with plink as PATH=$PATH:/home/rsindhu/ngSoftwares/PLINK/plink-1.07-x86_64 , export PATH ; source .bashrc and it worked !!.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by ravi.uhdnis150
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