Oases Makefile:114: recipe for target 'obj/oases.o' failed
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5.7 years ago

Dear all,

I installed Velvet De novo assembler, compiling with the suggested make command, and it looks like the process was successful because:

$ velveth
velveth - simple hashing program
Version 1.2.10
...

I then tried to install Oases with the reccomended syntax but there were plenty of errors:

$ make 'VELVET_DIR=~/src/velvet'
rm -f obj/*.o obj/dbg/*.o 
cd ~/src/velvet && make -e obj
make[1]: Entering directory '/home/gigiux/src/velvet'
rm obj/*.o obj/dbg/*.o 
rm: cannot remove 'obj/dbg/*.o': No such file or directory
Makefile:51: recipe for target 'cleanobj' failed
make[1]: [cleanobj] Error 1 (ignored)
mkdir -p obj
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=64 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=64 -D CATEGORIES=2 -c src/run.c -o obj/run.o 
In file included from src/run.h:34:0,
                 from src/run.c:31:
src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined
 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined
 extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined
 extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined
 extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
...
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=64 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o 
In file included from src/locallyCorrectedGraph.c:25:0:
src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined
 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined
 extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined
 extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined
 extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=64 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o 
In file included from src/graphReConstruction.c:33:0:
src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined
 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined
 extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined
 extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined
 extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=64 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o 
In file included from src/roadMap.c:26:0:
src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined
 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined
 extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined
 extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined
 extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=64 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o 
In file included from src/run.h:34:0,
                 from src/preGraph.c:35:
src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined
 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined
 extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined
 extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined
 extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=64 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o 
src/preGraphConstruction.c: In function ‘createPreNodes’:
src/preGraphConstruction.c:414:2: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  if (sequenceCount_pg(preGraph) > 0 && !fgets(line, lineLength, file))
  ^~
src/preGraphConstruction.c:416:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
   seqReadInfo->m_pFile = file;
   ^~~~~~~~~~~
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=64 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=64 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o 
In file included from src/readCoherentGraph.c:25:0:
src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined
 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined
 extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined
 extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined
 extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=64 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=64 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o 
src/kmer.c:31:22: warning: ‘charLeftFilter’ defined but not used [-Wunused-const-variable=]
 static const uint8_t charLeftFilter = (uint8_t) 3 << 6;
                      ^~~~~~~~~~~~~~
src/kmer.c:30:23: warning: ‘intLeftFilter’ defined but not used [-Wunused-const-variable=]
 static const uint16_t intLeftFilter = (uint16_t) 3 << 14;
                       ^~~~~~~~~~~~~
src/kmer.c:29:23: warning: ‘longLeftFilter’ defined but not used [-Wunused-const-variable=]
 static const uint32_t longLeftFilter = (uint32_t) 3 << 30;
                       ^~~~~~~~~~~~~~
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=64 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o 
In file included from src/scaffold.c:32:0:
src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined
 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined
 extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined
 extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined
 extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=64 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o 
In file included from src/kmerOccurenceTable.c:27:0:
src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined
 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
                    ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined
 extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
                           ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined
 extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined
 extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=64 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=64 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o 
src/autoOpen.c: In function ‘pcloseNoStderr’:
src/autoOpen.c:49:6: warning: variable ‘rc’ set but not used [-Wunused-but-set-variable]
  int rc, status;
      ^~
src/autoOpen.c: At top level:
src/autoOpen.c:56:19: warning: duplicate ‘const’ declaration specifier [-Wduplicate-decl-specifier]
 static const char const* decompressors[] = {"","pigz", "gunzip", "pbunzip2", "bunzip2", NULL};
                   ^~~~~
src/autoOpen.c: In function ‘popenNoStderr’:
src/autoOpen.c:28:3: warning: ignoring return value of ‘dup’, declared with attribute warn_unused_result [-Wunused-result]
   dup(out[1]);
   ^~~~~~~~~~~
make[1]: Leaving directory '/home/gigiux/src/velvet'
mkdir -p obj
gcc -Wall -O3 -D MAXKMERLENGTH=64 -D CATEGORIES=2 -c src/oases.c -o obj/oases.o -I~/src/velvet/src
src/oases.c:25:10: fatal error: globals.h: No such file or directory
 #include "globals.h"
          ^~~~~~~~~~~
compilation terminated.
Makefile:114: recipe for target 'obj/oases.o' failed
make: *** [obj/oases.o] Error 1

The content of ~/src/velvet is:

$ ls -l
total 1008
-rw-r--r--  1 gigiux gigiux  12690 Oct 17  2013 ChangeLog
-rw-r--r--  1 gigiux gigiux  90537 Oct 17  2013 Columbus_manual.pdf
drwxr-xr-x 17 gigiux gigiux   4096 Oct 17  2013 contrib
-rw-r--r--  1 gigiux gigiux   1956 Oct 17  2013 CREDITS.txt
drwxr-xr-x  2 gigiux gigiux   4096 Oct 17  2013 data
drwxr-xr-x  2 gigiux gigiux   4096 Oct 17  2013 debian
drwxr-xr-x  3 gigiux gigiux   4096 Oct 17  2013 doc
-rw-r--r--  1 gigiux gigiux    456 Oct 17  2013 For_MAC_or_SPARC_users.txt
-rw-r--r--  1 gigiux gigiux  17988 Oct 17  2013 LICENSE.txt
-rw-r--r--  1 gigiux gigiux   6742 Oct 17  2013 Makefile
-rw-r--r--  1 gigiux gigiux 431022 Oct 17  2013 Manual.pdf
drwxr-xr-x  2 gigiux gigiux   4096 Apr  4 16:56 obj
-rw-r--r--  1 gigiux gigiux   1117 Oct 17  2013 README.txt
drwxr-xr-x  2 gigiux gigiux   4096 Oct 17  2013 src
drwxr-xr-x  2 gigiux gigiux   4096 Oct 17  2013 tests
drwxr-xr-x  3 gigiux gigiux   4096 Oct 17  2013 third-party
-rwxr-xr-x  1 gigiux gigiux     26 Oct 17  2013 update_velvet.sh
-rwxr-xr-x  1 gigiux gigiux 307016 Apr  4 16:48 velvetg
-rwxr-xr-x  1 gigiux gigiux  99584 Apr  4 16:48 velveth

What did I get wrong?

Thank you
software error installation De novo assembly • 3.3k views
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0
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Have you tried installation using bioconda? https://anaconda.org/bioconda/oases

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0
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no, this bioconda comes out a lot of times in the installation issues but I am not a fan. If a program claims that it can be installed on a command line procedure, why do I need to move to another product? yes, conda can make it easier to install software, but if the installation does not work because something is missing to complete the installation, I prefer to see where the error is rather than having stuff running under the hood...

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but if the installation does not work because something is missing to complete the installation, I prefer to see where the error is rather than having stuff running under the hood

So you rather struggle with dependencies and installation problems, and have other people help you here than using a solution which is designed to solve dependency issues? Okay, have fun.

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but without such fun i wouldn't learn, would I?

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1
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You wouldn't waste your time, no.

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1
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I doubt that going through hundreds of lines of compilation messages you'll get any more insight into that tool. Better focus on downstream analysis that the compilation process.

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0
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I'm sure you also wouldn't waste the time of volunteers on a Q&A forum with questions like this.

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0
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as far as I can see velvet comes as a git submodule : https://github.com/dzerbino/oases/tree/master

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this is not the folder given from the official site, anyhow I tried but I got:

$ make
make -e -C velvet obj
make[1]: Entering directory '/home/gigiux/src/oases/velvet'
make[1]: *** No rule to make target 'obj'. Stop.
make[1]: Leaving directory '/home/gigiux/src/oases/velvet'
Makefile:74: recipe for target 'velvet' failed
make: *** [velvet] Error 2
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0
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5.7 years ago
h.mon 35k

When reporting on compilation issues, do say the operating system and the compiler names and versions.

Try to compile Oases with:

make 'VELVET_DIR=/home/gigiux/src/velvet'
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0
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The OS is Ubuntu 18 with GCC 7.3.0. I tried also the absolute path but there is a still error:

cd doc; make
make[1]: Entering directory '/home/gigiux/src/oases/doc'
cd manual && make
make[2]: Entering directory '/home/gigiux/src/oases/doc/manual'
pdflatex OasesManual
make[2]: pdflatex: Command not found
Makefile:2: recipe for target 'default' failed
make[2]: *** [default] Error 127
make[2]: Leaving directory '/home/gigiux/src/oases/doc/manual'
Makefile:2: recipe for target 'default' failed
make[1]: *** [default] Error 2
make[1]: Leaving directory '/home/gigiux/src/oases/doc'
Makefile:90: recipe for target 'OasesManual.pdf' failed
make: *** [OasesManual.pdf] Error 2
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enter image description here

Really though, do you not have better things to do with your time?

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prefer to see where the error is rather than having stuff running under the hood...

make[2]: pdflatex: Command not found

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I can see that: latex was missing and now it worked: oases - Version 0.2.08 installed, thank you.

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