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CRG-Barcelona / libbeato

Library combining some HTS stuff, core wiggle stuff, Jim Kent's libary.
GNU General Public License v3.0
3 stars 7 forks source link

Broken compilation #6

Open mimame opened 5 years ago

mimame commented 5 years ago

Hi @andypohl

libbeato can't be compiled with the last changes

The bad commit found using git bisect is: 5be49bece6c04cd40157445a9eedecdf9421ee2d

Thanks a lot in advance

Making all in beato
make[2]: Entering directory '/tmp/libbeato/beato'
gcc -DHAVE_CONFIG_H -I. -I..    -I.. -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -fno-strict-aliasing -g -O2 -MT bbiAugment.o -MD -MP -MF .deps/bbiAugment.Tpo -c -o bbiAugment.o bbiAugment.c
In file included from bbiAugment.c:1:
../beato/bbiAugment.h:9:52: error: unknown type name ‘bits32’
 struct bbiFile* bbiFileOpenWithDir(char* fileName, bits32 sig, char* typeName, char* udcDir);
                                                    ^~~~~~
In file included from bbiAugment.c:2:
../jkweb/bPlusTree.h:57:5: error: unknown type name ‘bits32’
     bits32 blockSize;  /* Size of block. */
     ^~~~~~
../jkweb/bPlusTree.h:58:5: error: unknown type name ‘bits32’
     bits32 keySize;  /* Size of keys. */
     ^~~~~~
../jkweb/bPlusTree.h:59:5: error: unknown type name ‘bits32’
     bits32 valSize;  /* Size of values. */
     ^~~~~~
../jkweb/bPlusTree.h:60:5: error: unknown type name ‘bits64’
     bits64 itemCount;  /* Number of items indexed. */
     ^~~~~~
../jkweb/bPlusTree.h:61:5: error: unknown type name ‘boolean’
     boolean isSwapped;  /* If TRUE need to byte swap everything. */
     ^~~~~~~
../jkweb/bPlusTree.h:62:5: error: unknown type name ‘bits64’
     bits64 rootOffset;  /* Offset of root block. */
     ^~~~~~
../jkweb/bPlusTree.h:77:1: error: unknown type name ‘boolean’
 boolean bptFileFind(struct bptFile *bpt, void *key, int keySize, void *val, int valSize);
 ^~~~~~~
../jkweb/bPlusTree.h:96:39: error: unknown type name ‘bits64’
 void bptKeyAtPos(struct bptFile *bpt, bits64 itemPos, void *result);
                                       ^~~~~~
../jkweb/bPlusTree.h:102:45: error: unknown type name ‘bits64’
 void bptStringKeyAtPos(struct bptFile *bpt, bits64 itemPos, char *result, int maxResultSize);
                                             ^~~~~~
../jkweb/bPlusTree.h:109:2: error: unknown type name ‘bits64’
  bits64 itemCount,  /* Number of elements in array. */
  ^~~~~~
../jkweb/bPlusTree.h:110:2: error: unknown type name ‘bits32’
  bits32 blockSize, /* B+ tree block size - # of children for each node. */
  ^~~~~~
../jkweb/bPlusTree.h:112:2: error: unknown type name ‘bits32’
  bits32 keySize,      /* Size of key */
  ^~~~~~
../jkweb/bPlusTree.h:114:2: error: unknown type name ‘bits32’
  bits32 valSize,      /* Size of value */
  ^~~~~~
../jkweb/bPlusTree.h:118:64: error: unknown type name ‘bits64’
 void bptFileBulkIndexToOpenFile(void *itemArray, int itemSize, bits64 itemCount, bits32 blockSize,
                                                                ^~~~~~
../jkweb/bPlusTree.h:118:82: error: unknown type name ‘bits32’
 void bptFileBulkIndexToOpenFile(void *itemArray, int itemSize, bits64 itemCount, bits32 blockSize,
                                                                                  ^~~~~~
../jkweb/bPlusTree.h:119:50: error: unknown type name ‘bits32’
  void (*fetchKey)(const void *va, char *keyBuf), bits32 keySize,
                                                  ^~~~~~
../jkweb/bPlusTree.h:120:37: error: unknown type name ‘bits32’
  void* (*fetchVal)(const void *va), bits32 valSize, FILE *f);
                                     ^~~~~~
../jkweb/bPlusTree.h:120:53: error: unknown type name ‘FILE’
  void* (*fetchVal)(const void *va), bits32 valSize, FILE *f);
                                                     ^~~~
../jkweb/bPlusTree.h:120:53: note: ‘FILE’ is defined in header ‘<stdio.h>’; did you forget to ‘#include <stdio.h>’?
../jkweb/bPlusTree.h:1:1:
+#include <stdio.h>
 /* bptFile - B+ Trees.  These are a method of indexing data similar to binary trees, but
../jkweb/bPlusTree.h:120:53:
  void* (*fetchVal)(const void *va), bits32 valSize, FILE *f);
                                                     ^~~~
In file included from ../jkweb/bbiFile.h:6,
                 from bbiAugment.c:3:
../jkweb/cirTree.h:20:5: error: unknown type name ‘boolean’
     boolean isSwapped;  /* If TRUE need to byte swap everything. */
     ^~~~~~~
../jkweb/cirTree.h:21:5: error: unknown type name ‘bits64’
     bits64 rootOffset;  /* Offset of root block. */
     ^~~~~~
../jkweb/cirTree.h:22:5: error: unknown type name ‘bits32’
     bits32 blockSize;  /* Size of block. */
     ^~~~~~
../jkweb/cirTree.h:23:5: error: unknown type name ‘bits64’
     bits64 itemCount;  /* Number of items indexed. */
     ^~~~~~
../jkweb/cirTree.h:24:5: error: unknown type name ‘bits32’
     bits32 startChromIx; /* First chromosome in file. */
     ^~~~~~
../jkweb/cirTree.h:25:5: error: unknown type name ‘bits32’
     bits32 startBase;  /* Starting base position. */
     ^~~~~~
../jkweb/cirTree.h:26:5: error: unknown type name ‘bits32’
     bits32 endChromIx;  /* Ending chromosome in file. */
     ^~~~~~
../jkweb/cirTree.h:27:5: error: unknown type name ‘bits32’
     bits32 endBase;  /* Ending base position. */
     ^~~~~~
../jkweb/cirTree.h:28:5: error: unknown type name ‘bits64’
     bits64 fileSize;  /* Total size of index file. */
     ^~~~~~
../jkweb/cirTree.h:29:5: error: unknown type name ‘bits32’
     bits32 itemsPerSlot; /* Max number of items to put in each index slot at lowest level. */
     ^~~~~~
../jkweb/cirTree.h:46:2: error: unknown type name ‘bits32’
  bits32 chromIx, bits32 start, bits32 end);
  ^~~~~~
../jkweb/cirTree.h:46:18: error: unknown type name ‘bits32’
  bits32 chromIx, bits32 start, bits32 end);
                  ^~~~~~
../jkweb/cirTree.h:46:32: error: unknown type name ‘bits32’
  bits32 chromIx, bits32 start, bits32 end);
                                ^~~~~~
../jkweb/cirTree.h:54:5: error: unknown type name ‘bits32’
     bits32 chromIx; /* Chromosome id. */
     ^~~~~~
../jkweb/cirTree.h:55:5: error: unknown type name ‘bits32’
     bits32 start; /* Start position in chromosome. */
     ^~~~~~
../jkweb/cirTree.h:56:5: error: unknown type name ‘bits32’
     bits32 end;  /* One past last base in interval in chromosome. */
     ^~~~~~
../jkweb/cirTree.h:60:33: error: unknown type name ‘bits64’
  void *itemArray, int itemSize, bits64 itemCount,
                                 ^~~~~~
../jkweb/cirTree.h:61:2: error: unknown type name ‘bits32’
  bits32 blockSize, bits32 itemsPerSlot,
  ^~~~~~
../jkweb/cirTree.h:61:20: error: unknown type name ‘bits32’
  bits32 blockSize, bits32 itemsPerSlot,
                    ^~~~~~
../jkweb/cirTree.h:64:2: error: unknown type name ‘bits64’
  bits64 (*fetchOffset)(const void *va, void *context),
  ^~~~~~
../jkweb/cirTree.h:65:2: error: unknown type name ‘bits64’
  bits64 endFileOffset, FILE *f);
  ^~~~~~
../jkweb/cirTree.h:65:24: error: unknown type name ‘FILE’
  bits64 endFileOffset, FILE *f);
                        ^~~~
../jkweb/cirTree.h:65:24: note: ‘FILE’ is defined in header ‘<stdio.h>’; did you forget to ‘#include <stdio.h>’?
../jkweb/cirTree.h:1:1:
+#include <stdio.h>
 /* cirTree chromosome id r tree.  Part of a system to index chromosome ranges - things of
../jkweb/cirTree.h:65:24:
  bits64 endFileOffset, FILE *f);
                        ^~~~
../jkweb/cirTree.h:72:2: error: unknown type name ‘bits64’
  bits64 itemCount,  /* Number of elements in array. */
  ^~~~~~
../jkweb/cirTree.h:73:2: error: unknown type name ‘bits32’
  bits32 blockSize, /* R tree block size - # of children for each node. */
  ^~~~~~
../jkweb/cirTree.h:74:2: error: unknown type name ‘bits32’
  bits32 itemsPerSlot, /* Number of items to put in each index slot at lowest level. */
  ^~~~~~
../jkweb/cirTree.h:77:2: error: unknown type name ‘bits64’
  bits64 (*fetchOffset)(const void *va, void *context), /* Given item, return file offset */
  ^~~~~~
../jkweb/cirTree.h:78:2: error: unknown type name ‘bits64’
  bits64 endFileOffset,     /* Last position in file we index. */
  ^~~~~~
make[2]: *** [Makefile:419: bbiAugment.o] Error 1
make[2]: Leaving directory '/tmp/libbeato/beato'
make[1]: *** [Makefile:634: all-recursive] Error 1
make[1]: Leaving directory '/tmp/libbeato'
make: *** [Makefile:551: all] Error 2
xingjianfeng100 commented 5 years ago

Similar problem has been solved in https://github.com/CRG-Barcelona/bwtool/issues/65; you should alter the firt order for "#include <jkweb/common.h>" in bbiAugment.c file.

enidzy commented 5 years ago

Similar problem has been solved in CRG-Barcelona/bwtool#65; you should alter the firt order for "#include <jkweb/common.h>" in bbiAugment.c file. Could you explain it more clearly? I have the same problem and do not know how to do Thank you in advance

xingjianfeng100 commented 5 years ago

open libbeato/beato/bbiAugment.c, write "

include <jkweb/common.h>

include <beato/bbiAugment.h>

include <jkweb/bPlusTree.h>

include <jkweb/bbiFile.h>

include <jkweb/cirTree.h>

include <jkweb/hash.h>

include <jkweb/hmmstats.h>

include <jkweb/linefile.h>

include <jkweb/obscure.h>

include <jkweb/sig.h>

include <jkweb/udc.h>

include <jkweb/zlibFace.h>

" instead of "

include <beato/bbiAugment.h>

include <jkweb/bPlusTree.h>

include <jkweb/bbiFile.h>

include <jkweb/cirTree.h>

include <jkweb/common.h>

include <jkweb/hash.h>

include <jkweb/hmmstats.h>

include <jkweb/linefile.h>

include <jkweb/obscure.h>

include <jkweb/sig.h>

include <jkweb/udc.h>

include <jkweb/zlibFace.h>

"

Similar problem has been solved in CRG-Barcelona/bwtool#65; you should alter the firt order for "#include <jkweb/common.h>" in bbiAugment.c file. Could you explain it more clearly? I have the same problem and do not know how to do Thank you in advance

open libbeato/beato/bbiAugment.c, write "

include <jkweb/common.h>

include <beato/bbiAugment.h>

include <jkweb/bPlusTree.h>

include <jkweb/bbiFile.h>

include <jkweb/cirTree.h>

include <jkweb/hash.h>

include <jkweb/hmmstats.h>

include <jkweb/linefile.h>

include <jkweb/obscure.h>

include <jkweb/sig.h>

include <jkweb/udc.h>

include <jkweb/zlibFace.h>

" instead of "

include <beato/bbiAugment.h>

include <jkweb/bPlusTree.h>

include <jkweb/bbiFile.h>

include <jkweb/cirTree.h>

include <jkweb/common.h>

include <jkweb/hash.h>

include <jkweb/hmmstats.h>

include <jkweb/linefile.h>

include <jkweb/obscure.h>

include <jkweb/sig.h>

include <jkweb/udc.h>

include <jkweb/zlibFace.h>

"

xymia commented 5 years ago

I fixed this error according to your prompts, and then I encountered a new error.

make all-recursive make[1]: Entering directory/media/dell/C14D581BDA18EBFA/dcNet/libbeato' Making all in jkweb make[2]: Entering directory /media/dell/C14D581BDA18EBFA/dcNet/libbeato/jkweb' make[2]: Nothing to be done forall'. make[2]: Leaving directory /media/dell/C14D581BDA18EBFA/dcNet/libbeato/jkweb' Making all in beato make[2]: Entering directory/media/dell/C14D581BDA18EBFA/dcNet/libbeato/beato' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -fno-strict-aliasing -g -O0 -I/home/dell/include -MT fastq_stuff.o -MD -MP -MF .deps/fastq_stuff.Tpo -c -o fastq_stuff.o fastq_stuff.c In file included from fastq_stuff.c:5:0: ../beato/fastq_stuff.h:22:1: error: unknown type name ‘boolean’ boolean read_fastq_auto(struct fastq_auto fq, struct lineFile lf, boolean just_seq_qual); ^ ../beato/fastq_stuff.h:22:69: error: unknown type name ‘boolean’ boolean read_fastq_auto(struct fastq_auto fq, struct lineFile lf, boolean just_seq_qual); ^ ../beato/fastq_stuff.h:27:31: error: unknown type name ‘FILE’ void fprint_fastq_auto_normal(FILE* f, struct fastq_auto fq, int wrap_len); ^ fastq_stuff.c: In function ‘read_fastq_auto’: fastq_stuff.c:28:17: warning: variable ‘numWords’ set but not used [-Wunused-but-set-variable] int numWords; ^ make[2]: [fastq_stuff.o] Error 1 make[2]: Leaving directory `/media/dell/C14D581BDA18EBFA/dcNet/libbeato/beato' make[1]: [all-recursive] Error 1 make[1]: Leaving directory /media/dell/C14D581BDA18EBFA/dcNet/libbeato' make: *** [all] Error 2 I think this is also a problem with the header file, but I don't know how to modify it.

mimame commented 5 years ago

@xymia , It's easier rollback to an old commit with git checkout 0c30432af9c7e1e09ba065ad3b2bc042baa54dc2 And then compile

xymia commented 5 years ago

@xymia , It's easier rollback to an old commit with git checkout 0c30432 And then compile

Sorry, can you explain in more detail. I still don't know what to do. Thank you.

mimame commented 5 years ago

git clone https://github.com/CRG-Barcelona/libbeato.git cd libbeato git checkout 0c30432 ./configure make sudo make install

xymia commented 5 years ago

git clone https://github.com/CRG-Barcelona/libbeato.git cd libbeato git checkout 0c30432 ./configure make sudo make install

Thank you very much. I successfully installed it.

stewalsh04 commented 5 years ago

I had the same problem, your solution worked great! Thank you! Also bwtool is great little program! :-)

bobia9991 commented 3 years ago

I have followed your instruction and then i had a new error

metaBigBam.c:489:42: error: read-only variable is not assignable h->cigar_tab[(int)BAM_CIGAR_STR[i]] = i;


metaBigBam.c:502:35: warning: 'cigar_tab' is deprecated: Use bam_cigar_table[]
      instead [-Wdeprecated-declarations]
        op = (uint8_t)*q >= 128? -1 : h->cigar_tab[(int)*q];
                                         ^
/usr/local/include/htslib/sam.h:76:29: note: 'cigar_tab' has been explicitly
      marked deprecated here
    const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
                            ^
/usr/local/include/htslib/hts_defs.h:75:49: note: expanded from macro
      'HTS_DEPRECATED'
#define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message)))

error: error opening '.deps/metaBigBam.Tpo': Permission denied
4 warnings and 2 errors generated.
make[2]: *** [metaBigBam.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Please, help me!

> git clone https://github.com/CRG-Barcelona/libbeato.git
> cd libbeato
> git checkout [0c30432](https://github.com/CRG-Barcelona/libbeato/commit/0c30432af9c7e1e09ba065ad3b2bc042baa54dc2)
> ./configure
> make
> sudo make install
mimame commented 3 years ago

@bobia9991 Please repeat all instructions from zero again because the error you showed error: error opening '.deps/metaBigBam.Tpo': Permission denied it's not related to this

bobia9991 commented 3 years ago

@bobia9991 Please repeat all instructions from zero again because the error you showed error: error opening '.deps/metaBigBam.Tpo': Permission denied it's not related to this

sorry, i have run again without sudo. With sudo, i had a error:

sudo make Password: /Library/Developer/CommandLineTools/usr/bin/make all-recursive Making all in jkweb make[2]: Nothing to be done for `all'. Making all in beato gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -fno-strict-aliasing -g -O2 -MT bbiAugment.o -MD -MP -MF .deps/bbiAugment.Tpo -c -o bbiAugment.o bbiAugment.c mv -f .deps/bbiAugment.Tpo .deps/bbiAugment.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -fno-strict-aliasing -g -O2 -MT metaBigBam.o -MD -MP -MF .deps/metaBigBam.Tpo -c -o metaBigBam.o metaBigBam.c metaBigBam.c:485:12: warning: 'cigar_tab' is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations] if (h->cigar_tab == 0) ^ /usr/local/include/htslib/sam.h:76:29: note: 'cigar_tab' has been explicitly marked deprecated here const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead"); ^ /usr/local/include/htslib/hts_defs.h:75:49: note: expanded from macro 'HTS_DEPRECATED'

define HTS_DEPRECATED(message) attribute ((deprecated (message)))

                                            ^

metaBigBam.c:487:5: warning: 'cigar_tab' is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations] h->cigar_tab = (int8_t)calloc(128, sizeof(int8_t)); ^ /usr/local/include/htslib/sam.h:76:29: note: 'cigar_tab' has been explicitly marked deprecated here const int8_t cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead"); ^ /usr/local/include/htslib/hts_defs.h:75:49: note: expanded from macro 'HTS_DEPRECATED'

define HTS_DEPRECATED(message) attribute ((deprecated (message)))

                                            ^

metaBigBam.c:489:9: warning: 'cigar_tab' is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations] h->cigar_tab[(int)BAM_CIGAR_STR[i]] = i; ^ /usr/local/include/htslib/sam.h:76:29: note: 'cigar_tab' has been explicitly marked deprecated here const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead"); ^ /usr/local/include/htslib/hts_defs.h:75:49: note: expanded from macro 'HTS_DEPRECATED'

define HTS_DEPRECATED(message) attribute ((deprecated (message)))

                                            ^

metaBigBam.c:489:42: error: read-only variable is not assignable h->cigar_tab[(int)BAM_CIGAR_STR[i]] = i;


metaBigBam.c:502:35: warning: 'cigar_tab' is deprecated: Use bam_cigar_table[]
      instead [-Wdeprecated-declarations]
        op = (uint8_t)*q >= 128? -1 : h->cigar_tab[(int)*q];
                                         ^
/usr/local/include/htslib/sam.h:76:29: note: 'cigar_tab' has been explicitly
      marked deprecated here
    const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
                            ^
/usr/local/include/htslib/hts_defs.h:75:49: note: expanded from macro
      'HTS_DEPRECATED'
#define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message)))
                                                ^
4 warnings and 1 error generated.
make[2]: *** [metaBigBam.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
mimame commented 3 years ago

@bobia9991 Please only use sudo for the make install step as it's shown by the instructions

bobia9991 commented 3 years ago

@bobia9991 Please only use sudo for the make install step as it's shown by the instructions

Thanks for your reply. i run make, without sudo. i had a Error:

metaBigBam.c:489:42: error: read-only variable is not assignable h->cigar_tab[(int)BAM_CIGAR_STR[i]] = i;


metaBigBam.c:502:35: warning: 'cigar_tab' is deprecated: Use bam_cigar_table[] instead
      [-Wdeprecated-declarations]
        op = (uint8_t)*q >= 128? -1 : h->cigar_tab[(int)*q];
                                         ^
/usr/local/include/htslib/sam.h:76:29: note: 'cigar_tab' has been explicitly marked
      deprecated here
    const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
                            ^
/usr/local/include/htslib/hts_defs.h:75:49: note: expanded from macro 'HTS_DEPRECATED'
#define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message)))
                                                ^
4 warnings and 1 error generated.
make[2]: *** [metaBigBam.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

This error like #7