I would like to install the AllPaths with ubuntu in a dell-Pe2950. When I compile it, it keep on warning. At last, only three binary, fileBitvectorOp checkLock and MakeDepend were compiled successfully. Who can tell me how i should do?
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When I configure the program, it tell me that the system miss some C functions. Whether did it lead me failed?
checking for gawk... gawk
checking for a sed that does not truncate output... /bin/sed
checking for bison... bison -y
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for gcc... gcc
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 for flex... flex
checking lex output file root... lex.yy
checking lex library... -lfl
checking whether yytext is a pointer... yes
checking whether ln -s works... yes
checking whether make sets $(MAKE)... yes
checking to see if we need to include the Boost libraries... no
checking to see if we need to include the Xerces libraries... no
checking to see if we need to include the GMP libraries... no
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... 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 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 locale.h usability... yes
checking locale.h presence... yes
checking for locale.h... yes
checking for memory.h... (cached) yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.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/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking wchar.h usability... yes
checking wchar.h presence... yes
checking for wchar.h... yes
configure: VENDOR wasn't set, setting to a default
checking for getline in -lm... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for mode_t... yes
checking for off_t... yes
checking for pid_t... yes
checking for C/C++ restrict keyword... __restrict
checking for size_t... yes
checking for ssize_t... yes
checking whether time.h and sys/time.h may both be included... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for uint8_t... yes
checking for working volatile... yes
checking for ptrdiff_t... yes
checking for ulong... yes
checking whether closedir returns void... no
checking for error_at_line... 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... yes
checking for working vfork... (cached) yes
checking whether gcc needs -traditional... no
checking whether lstat dereferences a symlink specified with a trailing slash... yes
checking whether lstat accepts an empty string... no
checking whether lstat dereferences a symlink specified with a trailing slash... (cached) yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for getpagesize... yes
checking for working mmap... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking types of arguments for select... int,fd_set *,struct timeval *
checking return type of signal handlers... void
checking whether stat accepts an empty string... no
checking for strftime... yes
checking for alarm... yes
checking for atexit... yes
checking for bzero... yes
checking for dup2... yes
checking for floor... no
checking for ftruncate... yes
checking for getcwd... yes
checking for gethostname... yes
checking for getpagesize... (cached) yes
checking for gettimeofday... yes
checking for memchr... yes
checking for memmove... yes
checking for memset... yes
checking for mkdir... yes
checking for mkfifo... yes
checking for munmap... yes
checking for pow... no
checking for putenv... yes
checking for realpath... yes
checking for regcomp... yes
checking for rint... no
checking for rmdir... yes
checking for select... yes
checking for setenv... yes
checking for setlocale... yes
checking for sqrt... no
checking for strcasecmp... yes
checking for strchr... yes
checking for strdup... yes
checking for strerror... yes
checking for strncasecmp... yes
checking for strrchr... yes
checking for strstr... yes
checking for strtol... yes
checking for strtoul... yes
checking for uname... yes
checking to see that gcc is at least version 4.3.2... Yes, gcc version 4.3.2 is fine
checking whether byte ordering is bigendian... no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: config.h is unchanged
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by GATTACATLove this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
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Channel: Articles
07-01-2026, 11:43 AM -
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by SEQadmin2
I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...-
Channel: Articles
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