FW: Re Samtools error after installing cygwin64 4.3.1.1

MarcoYes got samtools configure make install samtools = samtools index appears What I did line 26 added -std=gnu99 line 31 added -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=logline 87 removed -rdynamic am about to try the program out Bob  Bob May DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve

Re: stampy error running Make after installing update 2.4.1.1 to Cygwin64

I still can.t make sense of it below is the contents of makefile the end of running make is still the same $ make makefile:1: *** missing separator.  Stop. maybe someone can make sense of the below Bob m# # - the linux x86-64 platform is supported, with Python 2.7.  Both #   2- and 4-byte

Re: tree puzzle error running Configure after installing update 2.4.1.1 to Cygwin64

cyg Simple OK replaced the two files config.guess and config.sub with a 2016 timestamp and ran make again. like samtools it has a couple of warning for terms like But it does not get the job done. the problem area seems to be in this area of make ppuzzle.c: In function ‘PP_Update_Rates’: ppuzz

bcftools error running Make after installing update 2.4.1.1 to Cygwin64

I have had another look at Makefile and I changed c to gnu in this line 40 -std=gnu99 CFLAGS   = -g -Wall -Wc++-compat -O2  -std=gnu99 I had also removed -rdynamic in  line 185 so it now reads $(CC)  $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS) and ran make agai

Re error after installing cygwin64 4.3.1.1

Marco what I have done is in makefile line 26CFLAGS   = -g -Wall -O2   -std=gnu99 ## added -std=gnu99 above line 66 ALL_LDFLAGS  =  $(HTSLIB_LDFLAGS) $(LDFLAGS) ## remove -rdynamic from ALL_LDFLAGS above and this is the result of the next make run Robert@DESKTOP-14EL82S /usr/local/bin/samtools-1.

Re error after installing cygwin64 4.3.1.1

Marco The choice of using usr/local/bin was the way to go according to the INSTALL instructions with most of the programs. some use ./confire    -    make - make install some use  make make install I think one used just make and one used Build. If I remember the wording correc

tree puzzle error running Configure after installing update 2.4.1.1 to Cygwin64

Robert@DESKTOP-14EL82S /usr/local/bin/tree-puzzle-5.3.rc16-windows $ ./configure checking build system type... ./config.guess: unable to guess system type This script, last modified 2004-08-11, has failed to recognize the operating system you are using. It is advised that you download the most up

stampy error running Make after installing update 2.4.1.1 to Cygwin64

obert@DESKTOP-14EL82S /cygdrive/c/cygwin64/usr/local/bin/stampy-1.0.28 $ make makefile:1: *** missing separator.  Stop.  Bob May DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Surname and ISOGG YTree -- Problem reports: http://cygw

Platypus error running Build after installing update 2.4.1.1 to Cygwin64

Robert@DESKTOP-14EL82S /usr/local/bin/Platypus_0.8.1 $ ./buildPlatypus.sh Building Platypus running build running build_py running build running build_py running build running build_py running build running build_py running build running build_py running build running build_py running build running

bwa error running Make and Make Install after installing update 2.4.1.1 to Cygwin64

Robert@DESKTOP-14EL82S /usr/local/bin/bwa-0.7.12 $ ./configure -bash: ./configure: No such file or directory Robert@DESKTOP-14EL82S /usr/local/bin/bwa-0.7.12 $ make make: Nothing to be done for 'all'. Robert@DESKTOP-14EL82S /usr/local/bin/bwa-0.7.12 $ make install make: *** No rule to make targe

bcftools error running Make after installing update 2.4.1.1 to Cygwin64

error running Make after installing update 2.4.1.1 to Cygwin64 Robert@DESKTOP-14EL82S /usr/local/bin/bcftools-1.3 $ make   many warnings are given in the following text - see end for error message echo '#define BCFTOOLS_VERSION "1.3"'> version.h gcc -g -Wall -Wc++-compat -O2  -std=c99 -I. -Ihtsl

Samtools error running Make after installing update 2.4.1.1 to Cygwin64

htslib configure - make - make install ok samtools configure ok  then when it came ro running Main samtools i get Robert@DESKTOP-14EL82S /usr/local/bin/samtools-1.3 $ make make: *** No rule to make target 'kfunc.c', needed by 'kfunc.o'.  Stop.  Bob May DNA Projects I2b L415, I2c L596 HG, Sprig

Updated Cygwin64 with 2.4.1.1

Instalation error -/unknown package x3270.sh exit code 1 this is an issue completely unrelated to the rest of your mail This he error message that was displasyed at the end of the install of 2.4.1.1 I have not idea of its importance to cygwin or any other programs I am installing So I guess th

Updated Cygwin64 with 2.4.1.1

Instalation error -/unknown package x3270.sh exit code 1 htslib configure - make - make install ok samtools configure ok Robert@DESKTOP-14EL82S /usr/local/bin/samtools-1.3 $ ./configure checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default out