Oases intallation problem

Question

[prp291]

Hi all,

I am trying to install the velvet_1.2.10 and oases_0.2.8 on UBUNTU 14.0 server and got this error

-D CATEGORIES=5 -c src/tightString.c -o obj/tightString.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/run.c -o obj/run.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/splay.c -o obj/splay.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/splayTable.c -o obj/splayTable.o 
src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive':
src/splayTable.c:1060:14: warning: variable 'refElem' set but not used [-Wunused-but-set-variable]
      RefInfo refElem;
              ^
src/splayTable.c: In function 'scanReferenceSequences':
src/splayTable.c:877:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, MAXLINE, file);
        ^
src/splayTable.c: In function 'scanBinaryReferenceSequences':
src/splayTable.c:933:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, MAXLINE, file);
        ^
src/splayTable.c:949:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
    fgets(line, MAXLINE, file);
         ^
src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive':
src/splayTable.c:1207:11: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
      fgets(line, MAXLINE, seqFile);
           ^
src/splayTable.c:1213:11: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
      fgets(line, MAXLINE, seqFile);
           ^
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/graph.c -o obj/graph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/run2.c -o obj/run2.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/fibHeap.c -o obj/fibHeap.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/fib.c -o obj/fib.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/passageMarker.c -o obj/passageMarker.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/graphStats.c -o obj/graphStats.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/correctedGraph.c -o obj/correctedGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/dfib.c -o obj/dfib.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/dfibHeap.c -o obj/dfibHeap.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/recycleBin.c -o obj/recycleBin.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/readSet.c -o obj/readSet.o 
src/readSet.c: In function 'readFastXFile':
src/readSet.c:641:21: warning: assignment from incompatible pointer type [enabled by default]
         file.gzFile = file.autoFile = NULL;
                     ^
src/readSet.c: In function 'readFastXPair':
src/readSet.c:680:22: warning: assignment from incompatible pointer type [enabled by default]
         file1.gzFile = file1.autoFile = NULL;
                      ^
src/readSet.c:681:22: warning: assignment from incompatible pointer type [enabled by default]
         file2.gzFile = file2.autoFile = NULL;
                      ^
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/binarySequences.c -o obj/binarySequences.o 
src/binarySequences.c: In function 'importCnyReadSet':
src/binarySequences.c:314:12: warning: variable 'refElem' set but not used [-Wunused-but-set-variable]
    RefInfo refElem;
            ^
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/shortReadPairs.c -o obj/shortReadPairs.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/graphReConstruction.c -o obj/graphReConstruction.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/roadMap.c -o obj/roadMap.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/preGraph.c -o obj/preGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/utility.c -o obj/utility.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/kmer.c -o obj/kmer.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/scaffold.c -o obj/scaffold.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/allocArray.c -o obj/allocArray.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -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: In function 'popenNoStderr':
src/autoOpen.c:28:6: warning: ignoring return value of 'dup', declared with attribute warn_unused_result [-Wunused-result]
   dup(out[1]);
      ^
make[1]: Leaving directory `/home/sanjay/Desktop/velvet_1.2.10'
gcc -Wall -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/oases.c -o obj/oases.o -I~/Desktop/velvet_1.2.10/src
src/oases.c:25:21: fatal error: globals.h: No such file or directory
 #include "globals.h"
                     ^
compilation terminated.

make: *** [obj/oases.o] Error 1

Any suggestions?

Answer 1

[JC]

You need both package directories uncompressed in the same parental directory, for example:

$ git clone git://github.com/dzerbino/velvet.git
$ git clone git://github.com/dzerbino/oases.git
$ cd velvet
$ make
$ cd ../oases
$ make

[prp291]

Thank you very much for your respose. It works for me but I got error like this

ake[1]: Entering directory `/home/sanjay/Desktop/oases/doc'
cd manual && make
make[2]: Entering directory `/home/sanjay/Desktop/oases/doc/manual'
pdflatex OasesManual
make[2]: pdflatex: Command not found
make[2]: *** [default] Error 127
make[2]: Leaving directory `/home/sanjay/Desktop/oases/doc/manual'
make[1]: *** [default] Error 2
make[1]: Leaving directory `/home/sanjay/Desktop/oases/doc'
make: *** [OasesManual.pdf] Error 2

Hope this shouls not be a problem. One more question when I run the 'make' for velvet like this make 'MAXKMERLENGTH=57' 'OPENMP=1' 'BUNDLEDZLIB=1'

a. When I am trying to run oases installation with this command make colordebug 'VELVET_DIR=/path/to/velvet' 'MAXKMERLENGTH=57''BUNDLEDZLIB=1' instead of only 'make' then I got same error. Is it OK to run make only instead of other paramerters?

[JC]

The error is because you need to install pdf2latex, use sudo apt-get install pdf2latex (if the package is called that in Ubuntu, I don't know if it's the name).

The parameters indicate how exactly you want to compile velvet/oases, running make without parameters will use the defaults.