installation problem with dextract #19

Mr-Inamn · 2017-09-13T03:10:45Z

Hi,
I am installing DEXTRACT. The dextract_makefile is as follows.
`CFLAGS = -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing
CC = gcc

all: dextract dexta undexta dexqv undexqv

dextract:
${CC} $(CFLAGS) -I$(HDF5_INCLUDE) -L$(HDF5_LIB) -o dextract dextract.c DB.c QV.c -lhdf5

dexta:
${CC} ${CFLAGS} -o dexta gdexta.c DB.c QV.c

undexta:
${CC} ${CFLAGS} -o undexta undexta.c DB.c QV.c

dexqv:
${CC} ${CFLAGS} -o dexqv dexqv.c DB.c QV.c

undexqv:
${CC} ${CFLAGS} -o undexqv undexqv.c DB.c QV.c`

And when I run make -f dextract_makefile, error exists. Could anyone give me a copy of the gdexta.c file? Many thanks.
gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o dexta gdexta.c DB.c QV.c gcc: error: gdexta.c: No such file or directory make: *** [dexta] Error 1

The text was updated successfully, but these errors were encountered:

Mr-Inamn · 2017-09-13T03:19:14Z

Then I rename the gdexta.c to dexta.c. The installation succeeded. Is it correct?

tiramisutes · 2017-09-25T03:07:21Z

I have the same question. And how to continue?

yangziyi1990 · 2017-10-09T02:37:59Z

Yes, I have the same problem~
$make -f dextract_makefile
gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o dexta gdexta.c DB.c QV.c
gcc: gdexta.c: No such file or directory
make: *** [dexta] Error 1

How to solve this problem?

billzt · 2017-10-13T08:22:28Z

Obviously it is a typo

george-githinji · 2017-10-23T11:33:35Z

It would be nice then to add the following to the installation guide in the README.

open the dextract_makefile using a text editor. 
Go to line 10
change  gdexta.c to dexta

xingjianfeng100 · 2017-12-15T07:36:45Z

when I run "make -f dextract_makefile",why it tell me "gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -I/home/xingjianfeng/hdf5/include -L/home/xingjianfeng/hdf5/lib -o dextract dextract.c DB.c QV.c -lhdf5
QV.c: In function ‘Build_Table’:
QV.c:127:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
{ uint64 symbol = (uint64) (node->lft);
^
QV.c: In function ‘Huffman’:
QV.c:174:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
node[value].lft = (HTree *) (uint64) i;
^
/tmp/ccLAXel3.o: In function main': dextract.c:(.text.startup+0x13b): undefined reference to parse_filter'
dextract.c:(.text.startup+0x271): undefined reference to initBaxData' dextract.c:(.text.startup+0x368): undefined reference to getBaxData'
dextract.c:(.text.startup+0x383): undefined reference to nextSubread' dextract.c:(.text.startup+0x39d): undefined reference to nextSubread'
dextract.c:(.text.startup+0x3c4): undefined reference to evaluate_bax_filter' dextract.c:(.text.startup+0xa04): undefined reference to sam_close'
dextract.c:(.text.startup+0xb3f): undefined reference to sam_open' dextract.c:(.text.startup+0xb5f): undefined reference to sam_header_process'
dextract.c:(.text.startup+0xbab): undefined reference to sam_record_extract' dextract.c:(.text.startup+0xbbe): undefined reference to SAM_EOF'
dextract.c:(.text.startup+0xbd3): undefined reference to evaluate_bam_filter' dextract.c:(.text.startup+0x1031): undefined reference to getBaxData'
dextract.c:(.text.startup+0x11fb): undefined reference to sam_open' dextract.c:(.text.startup+0x1362): undefined reference to parse_filter'
dextract.c:(.text.startup+0x15df): undefined reference to `printBaxError'
collect2: error: ld returned 1 exit status
dextract_makefile:7: recipe for target 'dextract' failed"

xiaochuanle · 2017-12-18T13:04:42Z

Dear all, Thanks very much for improving mecat. We have updated the dextract_makefile and fixed this error.

bbalog87 · 2018-04-24T09:04:47Z

Obviously the error is not still fixed? Because I am still getting teh same error while installing dextract:

gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -I/home/jnguinka/mecat/hdf5/include/ -L/home/jnguinka/mecat/hdf5/lib/ -o dextract dextract.c DB.c QV.c -lhdf5
/tmp/ccWFocxk.o: In function `main':
dextract.c:(.text.startup+0x119): undefined reference to `parse_filter'
dextract.c:(.text.startup+0x230): undefined reference to `initBaxData'
dextract.c:(.text.startup+0x317): undefined reference to `getBaxData'
dextract.c:(.text.startup+0x331): undefined reference to `nextSubread'
dextract.c:(.text.startup+0x353): undefined reference to `nextSubread'
dextract.c:(.text.startup+0x374): undefined reference to `evaluate_bax_filter'
dextract.c:(.text.startup+0xaee): undefined reference to `sam_close'
dextract.c:(.text.startup+0xd00): undefined reference to `sam_open'
dextract.c:(.text.startup+0xd16): undefined reference to `sam_header_process'
dextract.c:(.text.startup+0xd4e): undefined reference to `sam_record_extract'
dextract.c:(.text.startup+0xd61): undefined reference to `SAM_EOF'
dextract.c:(.text.startup+0xd74): undefined reference to `evaluate_bam_filter'
dextract.c:(.text.startup+0x115d): undefined reference to `getBaxData'
dextract.c:(.text.startup+0x125a): undefined reference to `sam_open'
dextract.c:(.text.startup+0x13f3): undefined reference to `parse_filter'
dextract.c:(.text.startup+0x17af): undefined reference to `printBaxError'
collect2: error: ld returned 1 exit status
dextract_makefile:7: recipe for target 'dextract' failed
make: *** [dextract] Error 1

lorenzoditucci · 2018-04-30T18:54:23Z

Hi, I am having the same issue as @bbalog87
Is there any news?

Rooksie · 2018-05-03T20:09:17Z

Hi! I looked at the original makefile from DEXTRACTOR and was able to fix the above "undefined reference to" error messages. I had to add 3 more .c files and -lz to the end of one command:

If you edit the dextractor_makefile (line 7) to be:
${CC} $(CFLAGS) -I$(HDF5_INCLUDE) -L$(HDF5_LIB) -o dextract dextract.c sam.c bax.c expr.c DB.c QV.c -lhdf5 -lz

This allowed dextract to install, and I have now successfully extracted fasta sequences from 14 sets of bax.h5 files. (Although that too did not work the way MECAT said, instead of all files being in reads.fasta, they are in files named the same as the bax.h5 files with .fasta endings)

Good luck to all.

ctcncgr · 2018-05-09T22:03:22Z

I was having the same issue with undefined reference errors. I basically just grepped for these methods as they didn't seem to be hdf5 linker related and found them.

@Rooksie answered correctly above. The methods that are missing are contained in these c files and their headers. Including these in the compile fixes this issue. I am sure the install instructions should be changed, or the makefile could make objects out of these and then link them itself.

bbalog87 · 2018-05-30T12:32:37Z

Please could update or edit the dextractor_makefile (line 7) in the github repository to be:
${CC} $(CFLAGS) -I$(HDF5_INCLUDE) -L$(HDF5_LIB) -o dextract dextract.c sam.c bax.c expr.c DB.c QV.c -lhdf5 -lz

This would definitively fix this error.
Thanks

X-WJ · 2018-06-13T12:00:20Z

when i added these c files,another bugs occured

/usr/local/HDF_Group/HDF5/1.8.15/lib/libhdf5.a(H5PL.c.o): In function H5PL__open': H5PL.c:(.text+0xf22): undefined reference to dlopen'
H5PL.c:(.text+0xf34): undefined reference to dlerror' H5PL.c:(.text+0xf56): undefined reference to dlsym'
/usr/local/HDF_Group/HDF5/1.8.15/lib/libhdf5.a(H5PL.c.o): In function H5PL__search_table': H5PL.c:(.text+0x135d): undefined reference to dlsym'
/usr/local/HDF_Group/HDF5/1.8.15/lib/libhdf5.a(H5PL.c.o): In function H5PL__close': H5PL.c:(.text+0x1492): undefined reference to dlclose'
/usr/local/HDF_Group/HDF5/1.8.15/lib/libhdf5.a(H5Tconv.c.o): In function H5T__conv_b_b': H5Tconv.c:(.text+0x4891): undefined reference to ceil'
H5Tconv.c:(.text+0x49ba): undefined reference to ceil' /usr/local/HDF_Group/HDF5/1.8.15/lib/libhdf5.a(H5Tconv.c.o): In function H5T__conv_i_i':
H5Tconv.c:(.text+0xb657): undefined reference to ceil' H5Tconv.c:(.text+0xb77c): undefined reference to ceil'
/usr/local/HDF_Group/HDF5/1.8.15/lib/libhdf5.a(H5Tconv.c.o): In function H5T__conv_f_f': H5Tconv.c:(.text+0xd695): undefined reference to ceil'
/usr/local/HDF_Group/HDF5/1.8.15/lib/libhdf5.a(H5Tconv.c.o):H5Tconv.c:(.text+0xd7bd): more undefined references to ceil' follow /usr/local/HDF_Group/HDF5/1.8.15/lib/libhdf5.a(H5Tconv.c.o): In function H5T__conv_f_i':
H5Tconv.c:(.text+0xd25fe): undefined reference to pow' /usr/local/HDF_Group/HDF5/1.8.15/lib/libhdf5.a(H5Tconv.c.o): In function H5T__conv_i_f':
H5Tconv.c:(.text+0xd4862): undefined reference to ceil' H5Tconv.c:(.text+0xd4987): undefined reference to ceil'
H5Tconv.c:(.text+0xd5475): undefined reference to pow' /usr/local/HDF_Group/HDF5/1.8.15/lib/libhdf5.a(H5Zscaleoffset.c.o): In function H5Z_scaleoffset_rnd':
H5Zscaleoffset.c:(.text+0x3952): undefined reference to ceil' H5Zscaleoffset.c:(.text+0x396f): undefined reference to floor'
/usr/local/HDF_Group/HDF5/1.8.15/lib/libhdf5.a(H5Zscaleoffset.c.o): In function H5Z_scaleoffset_precompress_fd': H5Zscaleoffset.c:(.text+0xa485): undefined reference to pow'
H5Zscaleoffset.c:(.text+0xa535): undefined reference to pow' H5Zscaleoffset.c:(.text+0xa60f): undefined reference to pow'
H5Zscaleoffset.c:(.text+0xa64d): undefined reference to pow' H5Zscaleoffset.c:(.text+0xa6ae): undefined reference to pow'
/usr/local/HDF_Group/HDF5/1.8.15/lib/libhdf5.a(H5Zscaleoffset.c.o):H5Zscaleoffset.c:(.text+0xa6ec): more undefined references to `pow' follow
collect2: error: ld returned 1 exit status
dextract_makefile:7: recipe for target 'dextract' failed
make: *** [dextract] Error 1

mattsmithau · 2018-06-14T21:17:11Z

Thanks Rooksie....your fixed worked for me, however I had to leave off the -lz or it gave me this error:
gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -I/tools/hdf5-1.8.15/include -L/tools/hdf5-1.8.15/lib -o dextract dextract.c sam.c bax.c expr.c DB.c QV.c -lhdf5 -lz
/tmp/ccQnHm8g.o: In function sam_open': sam.c:(.text+0x3e0): undefined reference to gzbuffer'
collect2: error: ld returned 1 exit status
make: *** [dextract] Error 1

my dextract_makefile on centos:
dextract:
${CC} $(CFLAGS) -I$(HDF5_INCLUDE) -L$(HDF5_LIB) -o dextract dextract.c sam.c bax.c expr.c DB.c QV.c -lhdf5

X-WJ · 2018-06-15T02:02:43Z

emmc，thank you @bbalog87 @mattsmithau I have installed correctly on ubuntu(WSL),but when I go on centos6 ,i met some configure error while i was cmake hdf5 .Anyone knows how it was ? Thanks very much [ 40%] Built target H5make_libsettings
[ 40%] Built target H5detect
[ 40%] Built target hdf5
[ 40%] Built target hdf5_tools
[ 40%] Built target hdf5_test
[ 40%] Linking C executable ../bin/links_env
../bin/libhdf5.a(H5Zdeflate.c.o): In function H5Z_filter_deflate': H5Zdeflate.c:(.text+0x1cb): undefined reference to inflateInit_'
H5Zdeflate.c:(.text+0x24f): undefined reference to inflate' H5Zdeflate.c:(.text+0x27b): undefined reference to inflateEnd'
H5Zdeflate.c:(.text+0x338): undefined reference to inflateEnd' H5Zdeflate.c:(.text+0x44c): undefined reference to inflateEnd'
H5Zdeflate.c:(.text+0x5cc): undefined reference to `compress2'
collect2: ld returned 1 exit status
make[2]: *** [bin/links_env] Error 1
make[1]: *** [test/CMakeFiles/links_env.dir/all] Error 2
make: *** [all] Error 2

Fu-Yilei · 2018-07-10T06:25:39Z

I occurred the same issue with @mattsmithau , I am wondering whether there are any solution to this "gzbuffer" problem. Thanks.

Fu-Yilei · 2018-07-10T07:02:25Z

I found why this issue happens, it is because I did not install zlib in my server.

bioteksampath · 2018-07-27T21:52:48Z

me too

dextract.c:(.text+0x144): undefined reference to parse_filter' dextract.c:(.text+0x25e): undefined reference to initBaxData'
dextract.c:(.text+0x31f): undefined reference to getBaxData' dextract.c:(.text+0x345): undefined reference to nextSubread'
dextract.c:(.text+0x35b): undefined reference to nextSubread' dextract.c:(.text+0x37c): undefined reference to evaluate_bax_filter'
dextract.c:(.text+0x81f): undefined reference to sam_close' dextract.c:(.text+0x8f2): undefined reference to sam_open'
dextract.c:(.text+0x908): undefined reference to sam_header_process' dextract.c:(.text+0x937): undefined reference to sam_record_extract'
dextract.c:(.text+0x94a): undefined reference to SAM_EOF' dextract.c:(.text+0x95d): undefined reference to evaluate_bam_filter'
dextract.c:(.text+0xee7): undefined reference to sam_open' dextract.c:(.text+0x10e3): undefined reference to parse_filter'
dextract.c:(.text+0x1127): undefined reference to `printBaxError'
collect2: ld returned 1 exit status
make: *** [dextract] Error 1

X-WJ · 2018-07-29T11:30:08Z

i have solved it with adding zlib in the dextract.c

…

------------------ Original ------------------ From: "Sam"<notifications@github.com>; Date: Sat, Jul 28, 2018 05:52 AM To: "xiaochuanle/MECAT"<MECAT@noreply.github.com>; Cc: "X-WJ"<775868797@qq.com>; "Comment"<comment@noreply.github.com>; Subject: Re: [xiaochuanle/MECAT] installation problem with dextract (#19) me too dextract.c:(.text+0x144): undefined reference to parse_filter' dextract.c:(.text+0x25e): undefined reference toinitBaxData' dextract.c:(.text+0x31f): undefined reference to getBaxData' dextract.c:(.text+0x345): undefined reference tonextSubread' dextract.c:(.text+0x35b): undefined reference to nextSubread' dextract.c:(.text+0x37c): undefined reference toevaluate_bax_filter' dextract.c:(.text+0x81f): undefined reference to sam_close' dextract.c:(.text+0x8f2): undefined reference tosam_open' dextract.c:(.text+0x908): undefined reference to sam_header_process' dextract.c:(.text+0x937): undefined reference tosam_record_extract' dextract.c:(.text+0x94a): undefined reference to SAM_EOF' dextract.c:(.text+0x95d): undefined reference toevaluate_bam_filter' dextract.c:(.text+0xee7): undefined reference to sam_open' dextract.c:(.text+0x10e3): undefined reference toparse_filter' dextract.c:(.text+0x1127): undefined reference to `printBaxError' collect2: ld returned 1 exit status make: *** [dextract] Error 1 — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

gabyrech · 2018-10-05T13:44:59Z

Thanks @Rooksie ! your fixed worked for me!

Jianbing-Hu · 2019-01-04T08:31:53Z

Thanks @Rooksie ! my problem has been solved.

Rooksie mentioned this issue May 11, 2018

undefined reference to multiple functions when trying to make Dextract #48

Open

githubwangqiqi mentioned this issue Jan 4, 2019

dextrac errors #65

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installation problem with dextract #19

installation problem with dextract #19

Mr-Inamn commented Sep 13, 2017

Mr-Inamn commented Sep 13, 2017

tiramisutes commented Sep 25, 2017

yangziyi1990 commented Oct 9, 2017

billzt commented Oct 13, 2017

george-githinji commented Oct 23, 2017

xingjianfeng100 commented Dec 15, 2017

xiaochuanle commented Dec 18, 2017

bbalog87 commented Apr 24, 2018

lorenzoditucci commented Apr 30, 2018

Rooksie commented May 3, 2018 •

edited

ctcncgr commented May 9, 2018

bbalog87 commented May 30, 2018 •

edited

X-WJ commented Jun 13, 2018

mattsmithau commented Jun 14, 2018

X-WJ commented Jun 15, 2018

Fu-Yilei commented Jul 10, 2018

Fu-Yilei commented Jul 10, 2018

bioteksampath commented Jul 27, 2018

X-WJ commented Jul 29, 2018 via email

gabyrech commented Oct 5, 2018

Jianbing-Hu commented Jan 4, 2019

installation problem with dextract #19

installation problem with dextract #19

Comments

Mr-Inamn commented Sep 13, 2017

Mr-Inamn commented Sep 13, 2017

tiramisutes commented Sep 25, 2017

yangziyi1990 commented Oct 9, 2017

billzt commented Oct 13, 2017

george-githinji commented Oct 23, 2017

xingjianfeng100 commented Dec 15, 2017

xiaochuanle commented Dec 18, 2017

bbalog87 commented Apr 24, 2018

lorenzoditucci commented Apr 30, 2018

Rooksie commented May 3, 2018 • edited

ctcncgr commented May 9, 2018

bbalog87 commented May 30, 2018 • edited

X-WJ commented Jun 13, 2018

mattsmithau commented Jun 14, 2018

X-WJ commented Jun 15, 2018

Fu-Yilei commented Jul 10, 2018

Fu-Yilei commented Jul 10, 2018

bioteksampath commented Jul 27, 2018

X-WJ commented Jul 29, 2018 via email

gabyrech commented Oct 5, 2018

Jianbing-Hu commented Jan 4, 2019

Rooksie commented May 3, 2018 •

edited

bbalog87 commented May 30, 2018 •

edited