Question: Oases intallation problem
0
gravatar for prp291
4.4 years ago by
prp29150
United States
prp29150 wrote:

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 suggestion?

rna-seq velvet oases assembly • 1.8k views
ADD COMMENTlink modified 4.4 years ago by JC7.4k • written 4.4 years ago by prp29150
1
gravatar for JC
4.4 years ago by
JC7.4k
Mexico
JC7.4k wrote:

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
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by JC7.4k

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?
ADD REPLYlink written 4.4 years ago by prp29150

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.

 


 

ADD REPLYlink written 4.4 years ago by JC7.4k
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