Re error after installing cygwin64 4.3.1.1

Re error after installing cygwin64 4.3.1.1

[Robert May]

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-1.3
$ make
gcc -pthread   -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o libbam.a htslib-1.3/libhts.a -lncursesw -lm -lz -ldl
errmod.o: In function `cal_coef':
/usr/local/bin/samtools-1.3/errmod.c:85: undefined reference to `expl'
/usr/local/bin/samtools-1.3/errmod.c:85:(.text+0xc81): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `expl'
/usr/local/bin/samtools-1.3/errmod.c:86: undefined reference to `logl'
/usr/local/bin/samtools-1.3/errmod.c:86:(.text+0xca5): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `logl'
collect2: error: ld returned 1 exit status
Makefile:140: recipe for target 'samtools' failed
make: *** [samtools] Error 1

this is the culprit I believe 
errmod.o: In function `cal_coef':
regards
Bob

 Bob May
DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Surname and ISOGG YTree 		 	   		  
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Re: Re error after installing cygwin64 4.3.1.1

[Marco Atzeri]

On 27/01/2016 05:24, Robert May wrote:
> 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-1.3
> $ make
> gcc -pthread   -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o libbam.a htslib-1.3/libhts.a -lncursesw -lm -lz -ldl
> errmod.o: In function `cal_coef':
> /usr/local/bin/samtools-1.3/errmod.c:85: undefined reference to `expl'
> /usr/local/bin/samtools-1.3/errmod.c:85:(.text+0xc81): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `expl'
> /usr/local/bin/samtools-1.3/errmod.c:86: undefined reference to `logl'
> /usr/local/bin/samtools-1.3/errmod.c:86:(.text+0xca5): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `logl'
> collect2: error: ld returned 1 exit status
> Makefile:140: recipe for target 'samtools' failed
> make: *** [samtools] Error 1
>
> this is the culprit I believe
> errmod.o: In function `cal_coef':
> regards
> Bob
>
>   Bob May

Hi Bob,
as I mentioned expl and logl are not available yet on cygwin.

One workaround with less accuracy is to replace them with exp and log


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FW: Re Samtools error after installing cygwin64 4.3.1.1

[Robert May]

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 SA Family & Tyler Surname and ISOGG YTree

> From: tpibob@gmail.com
> To: cygwin@cygwin.com
> Subject: Re error after installing cygwin64 4.3.1.1
> Date: Wed, 27 Jan 2016 14:24:21 +1000
> 
> 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-1.3
> $ make
> gcc -pthread   -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o libbam.a htslib-1.3/libhts.a -lncursesw -lm -lz -ldl
> errmod.o: In function `cal_coef':
> /usr/local/bin/samtools-1.3/errmod.c:85: undefined reference to `expl'
> /usr/local/bin/samtools-1.3/errmod.c:85:(.text+0xc81): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `expl'
> /usr/local/bin/samtools-1.3/errmod.c:86: undefined reference to `logl'
> /usr/local/bin/samtools-1.3/errmod.c:86:(.text+0xca5): relocation truncated to fit: R_X86_64_PC32 against undefined symbol `logl'
> collect2: error: ld returned 1 exit status
> Makefile:140: recipe for target 'samtools' failed
> make: *** [samtools] Error 1
> 
> this is the culprit I believe 
> errmod.o: In function `cal_coef':
> regards
> Bob
> 
>  Bob May
> DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Surname and ISOGG YTree 		 	   		  
 		 	   		   		 	   		  
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Re error after installing cygwin64 4.3.1.1

[Robert May]

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 correctly "they say" copy your "package" "program" to the usr/local/bin foler and then in cycgwin use cd drive:/cygwin64/usr/local/bin and the use the followinf commands or script to install the package/program

Bob



htslib configure - make - make install ok
>
> samtools configure ok
>
> Robert@DESKTOP-14EL82S /usr/local/bin/samtools-1.3

Personal preference: in general "/usr/local/bin" is not the place
that I will use as build area.

> $ ./configure

can you please clarify what is your problem ?

I tried to build samtools-1.3 and it has at least two issue
for a porting to cygwin:

- on Makefile there is a -rdynamic that does not work on cygwin
- the package require expl and logl that are not yet available in cygwin



Regards
Marco

 Bob May
DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Surname and ISOGG YTree 		 	   		  
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