Something wrong when making bwtool

[Tracy-QY]

When I run the command "make" in the bwtool folder, there is something wrong and I don't know how to fix it. Could you pleas help me to fix this problem?

$ make
/Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive
Making all in tests
make[2]: Nothing to be done for `all'.
gcc -DHAVE_CONFIG_H -I. -I/sw/include -MT aggregate.o -MD -MP -MF .deps/aggregate.Tpo -c -o aggregate.o aggregate.c
aggregate.c:7:26: fatal error: jkweb/common.h: No such file or directory
compilation terminated.
make[2]: *** [aggregate.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

I think the build of libbeator seemed to be normal.

Thank you!

[andypohl]

Sorry for not replying earlier. I need more information about all the commands you've executed, not just the "make" command that is breaking. How did you run the configure script? What were the commands you ran when installing libbeato? If you installed libbeato in the way bwtool is expecting, then I'm guessing you should have common.h located in /sw/include/jkweb? Can you locate common.h?

[ghuls]

I think I had the same problem:

git clone 'https://github.com/CRG-Barcelona/bwtool'
git clone 'https://github.com/CRG-Barcelona/libbeato'

cd libbeato
./configure
make

cd ../bwtool
./configure CFLAGS='-I../libbeato' LDFLAGS='-L../libbeato/jkweb -L../libbeato/beato'
make

It would be nice if this instructions are mentioned somewhere.

[andypohl]

The instructions are on the wiki page. The INSTALL file is made by autotools. Maybe it should mention the wiki at the top. The README is simply a mention of the wiki.

[ghuls]

@andypohl I now remember why I did not look at the wiki.

README.md has just the link to the github page instead of to
https://github.com/andypohl/bwtool/wiki

The README file has the correct link.

[cattapre]

I cannot make in the bwtool folder.
./configure seems to run fine.
Please see my errors
Rinaldos-MacBook-Pro:bwtool rinaldo$ ./configure
checking build system type... x86_64-apple-darwin15.6.0
checking host system type... x86_64-apple-darwin15.6.0
checking target system type... x86_64-apple-darwin15.6.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for ranlib... ranlib
checking whether to enable maintainer-specific portions of Makefiles... no
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking jkweb/common.h usability... no
checking jkweb/common.h presence... no
checking for jkweb/common.h... no
checking beato/bigs.h usability... no
checking beato/bigs.h presence... no
checking for beato/bigs.h... no
checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking sys/file.h usability... yes
checking sys/file.h presence... yes
checking for sys/file.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking sys/statvfs.h usability... yes
checking sys/statvfs.h presence... yes
checking for sys/statvfs.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking syslog.h usability... yes
checking syslog.h presence... yes
checking for syslog.h... yes
checking termios.h usability... yes
checking termios.h presence... yes
checking for termios.h... yes
checking for unistd.h... (cached) yes
checking utime.h usability... yes
checking utime.h presence... yes
checking for utime.h... yes
checking for library containing pthread_create... none required
checking for library containing pow... none required
checking for library containing zlibVersion... -lz
checking for library containing slSort... -ljkweb
checking checking for beato library containing perBaseWigFree... no
checking checking for beato library (compiled with htslib) containing perBaseWigFree... -lbeato -lhts
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for int16_t... yes
checking for int32_t... yes
checking for int64_t... yes
checking for int8_t... yes
checking for off_t... yes
checking for pid_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for uid_t in sys/types.h... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint8_t... yes
checking vfork.h usability... no
checking vfork.h presence... no
checking for vfork.h... no
checking for fork... yes
checking for vfork... yes
checking for working fork... no
checking for working vfork... (cached) yes
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... no
checking whether time.h and sys/time.h may both be included... yes
checking for sys/time.h... (cached) yes
checking for unistd.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for sys/param.h... yes
checking for alarm... yes
checking for working mktime... no
checking for getpagesize... yes
checking for working mmap... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... no
checking for working strtod... no
checking for pow... yes
checking for bzero... yes
checking for dup2... yes
checking for floor... yes
checking for getcwd... yes
checking for gettimeofday... yes
checking for memmove... yes
checking for memset... yes
checking for mkdir... yes
checking for munmap... yes
checking for pow... (cached) yes
checking for putenv... yes
checking for regcomp... yes
checking for rint... yes
checking for select... yes
checking for setenv... yes
checking for socket... yes
checking for sqrt... yes
checking for strcasecmp... yes
checking for strchr... yes
checking for strcspn... yes
checking for strdup... yes
checking for strerror... yes
checking for strrchr... yes
checking for strspn... yes
checking for strstr... yes
checking for strtol... yes
checking for tzset... yes
checking for uname... yes
checking for utime... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating tests/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
Rinaldos-MacBook-Pro:bwtool rinaldo$ make
/Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive
Making all in tests
make[2]: Nothing to be done for `all'.
gcc -DHAVE_CONFIG_H -I. -g -O2 -MT aggregate.o -MD -MP -MF .deps/aggregate.Tpo -c -o aggregate.o aggregate.c
aggregate.c:7:26: fatal error: jkweb/common.h: No such file or directory
#include <jkweb/common.h>
^
compilation terminated.
make[2]: *** [aggregate.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

[andypohl]

Set CFLAGS and LDFLAGS to a path depending on where you installed libbeato.
https://github.com/andypohl/bwtool/wiki

[xiaoyonf]

Hi I have the make issue. My error messages as follows:
xiaoyongs-mbp:libbeato MyBioinformatics$ make
/Applications/Xcode.app/Contents/Developer/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 -O0 -I/Users/MyBioinformatics/include -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* typ...
^
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 *v...
^
../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...
^
../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 fo...
^
../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 it...
^
../jkweb/bPlusTree.h:118:82: error: unknown type name 'bits32'
...*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);
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[2]: *** [bbiAugment.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

PLEASE HELP, THANKS!

[JiguangPeng]

Hi I have the make issue. My error messages as follows:
xiaoyongs-mbp:libbeato MyBioinformatics$ make
/Applications/Xcode.app/Contents/Developer/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 -O0 -I/Users/MyBioinformatics/include -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* typ...
^
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 *v...
^
../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... ^ ../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 fo... ^ ../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 it...
^
../jkweb/bPlusTree.h:118:82: error: unknown type name 'bits32'
...*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);
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[2]: *** [bbiAugment.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

PLEASE HELP, THANKS!

@xiaoyonf hi, have you solved your problem?

[rmontagn]

Hi, I have the same problem.

In went to /usr/ and followed the instructions:

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

(I had to do it line by line and add a few sudos)

Then I get this error message when I try to run make in the libbeato folder:

sudo make
make  all-recursive
make[1]: Entering directory '/usr/libbeato'
Making all in jkweb
make[2]: Entering directory '/usr/libbeato/jkweb'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/usr/libbeato/jkweb'
Making all in beato
make[2]: Entering directory '/usr/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:1:0:
../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:2:0:
../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);
                                                     ^~~~
In file included from ../jkweb/bbiFile.h:6:0,
                 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: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. */
  ^~~~~~
Makefile:419: recipe for target 'bbiAugment.o' failed
make[2]: *** [bbiAugment.o] Error 1
make[2]: Leaving directory '/usr/libbeato/beato'
Makefile:634: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/usr/libbeato'
Makefile:551: recipe for target 'all' failed
make: *** [all] Error 2

Thoug, I have include/ in /usr/. Does anyone know what the problem is and how to fix it ?

Thanks

[mensenyat]

I am having exactly the same problems. Any solution explained to someone who just started in Linux?

[liukk18]

maybe you can try this : https://travis-ci.org/CRG-Barcelona/libbeato/jobs/279639096

[zhuzn]

cd libbeato/
./configure --prefix=../biosoft/bwtools
make
......
......
make[2]: *** [bbiAugment.o] Error 1
make[2]: Leaving directory ../bwtools/libbeato/beato' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory ../bwtools/libbeato'

How can i fix it？ Thanks

[zhuzn]

Hi, I have the same problem.

In went to /usr/ and followed the instructions:

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

(I had to do it line by line and add a few sudos)

Then I get this error message when I try to run make in the libbeato folder:

sudo make
make  all-recursive
make[1]: Entering directory '/usr/libbeato'
Making all in jkweb
make[2]: Entering directory '/usr/libbeato/jkweb'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/usr/libbeato/jkweb'
Making all in beato
make[2]: Entering directory '/usr/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:1:0:
../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:2:0:
../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);
                                                     ^~~~
In file included from ../jkweb/bbiFile.h:6:0,
                 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: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. */
  ^~~~~~
Makefile:419: recipe for target 'bbiAugment.o' failed
make[2]: *** [bbiAugment.o] Error 1
make[2]: Leaving directory '/usr/libbeato/beato'
Makefile:634: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/usr/libbeato'
Makefile:551: recipe for target 'all' failed
make: *** [all] Error 2

Thoug, I have include/ in /usr/. Does anyone know what the problem is and how to fix it ?

Thanks

hi ，do you solve it? can you tell me the way?

[tamerbio]

hi everyone,
did anyone solve this problem???
best
TA

[Arthur1021]

Try this
https://github.com/andypohl/bwtool-ue

[PoisonAlien]

So after struggling for half a day, going through several github issues, finally was able to compile bwtool. Complete commands in case if anyone is struggling..

git clone 'https://github.com/CRG-Barcelona/bwtool'
git clone 'https://github.com/CRG-Barcelona/libbeato'
git clone https://github.com/madler/zlib

cd libbeato/
git checkout 0c30432af9c7e1e09ba065ad3b2bc042baa54dc2
./configure
make
cd ..

cd zlib
./configure
make
cd ..

cd bwtool/
./configure CFLAGS='-I../libbeato -I../zlib' LDFLAGS='-L../libbeato/jkweb -L../libbeato/beato -L../zlib'
make

[hoondy]

Thanks, @PoisonAlien. I made a small modification to install locally and it worked. I am sharing mine in case.

git clone 'https://github.com/CRG-Barcelona/bwtool'
git clone 'https://github.com/CRG-Barcelona/libbeato'
git clone https://github.com/madler/zlib

cd zlib
./configue --prefix=$HOME
make
cd ..

cd libbeato
git checkout 0c30432af9c7e1e09ba065ad3b2bc042baa54dc2
./configure --prefix=$HOME
make
cd ..

cd bwtool
./configure --prefix=$HOME CFLAGS='-I../libbeato -I../zlib' LDFLAGS='-L../libbeato/jkweb -L../libbeato/beato -L../zlib'
make
make install