John
Thanks I though that might be ther problem
here we go - hope this all makes sense
Bob
Robert@DESKTOP-14EL82S ~
$ cygcheck -f /usr/bin/less
less-481-1
Robert@DESKTOP-14EL82S ~
$ cygcheck less
Found: C:\cygwin64\bin\less.exe
C:\cygwin64\bin\less.exe
C:\cygwin64\bin\cygwin1.dll
C:\Windows\system32\KERNEL32.dll
C:\Windows\system32\ntdll.dll
C:\Windows\system32\KERNELBASE.dll
C:\cygwin64\bin\cygncursesw-10.dll
Robert@DESKTOP-14EL82S ~
$ cygcheck -v -h program
Here is where the OS will find your program, and which dlls
will be used for it. Use -v to see DLL version info
cygcheck: could not find 'program'
Robert@DESKTOP-14EL82S ~
$ cygcheck -c -v packages
Cygwin Package Information
Last downloaded files to: C:\Users\Robert\Downloads
Last downloaded files from: ftp://mirror.csclub.uwaterloo.ca/cygwin/
Package Version Status
Robert@DESKTOP-14EL82S ~
Robert@DESKTOP-14EL82S ~
$ cygcheck -s -v -r -h>cygcheck_output.txt
cygcheck: dump_sysinfo: GetVolumeInformation() for drive Q: failed: 5
Robert@DESKTOP-14EL82S ~
$ getconf -a
PATH /bin:/usr/bin
POSIX_V7_ILP32_OFF32_CFLAGS undefined
POSIX_V7_ILP32_OFF32_LDFLAGS undefined
POSIX_V7_ILP32_OFF32_LIBS undefined
POSIX_V7_ILP32_OFFBIG_CFLAGS undefined
POSIX_V7_ILP32_OFFBIG_LDFLAGS undefined
POSIX_V7_ILP32_OFFBIG_LIBS undefined
POSIX_V7_LP64_OFF64_CFLAGS
POSIX_V7_LP64_OFF64_LDFLAGS
POSIX_V7_LP64_OFF64_LIBS
POSIX_V7_LPBIG_OFFBIG_CFLAGS
POSIX_V7_LPBIG_OFFBIG_LDFLAGS
POSIX_V7_LPBIG_OFFBIG_LIBS
POSIX_V7_THREADS_CFLAGS
POSIX_V7_THREADS_LDFLAGS
POSIX_V7_WIDTH_RESTRICTED_ENVS POSIX_V6_LP64_OFF64
POSIX_V6_ILP32_OFF32_CFLAGS undefined
POSIX_V6_ILP32_OFF32_LDFLAGS undefined
POSIX_V6_ILP32_OFF32_LIBS undefined
POSIX_V6_ILP32_OFFBIG_CFLAGS undefined
POSIX_V6_ILP32_OFFBIG_LDFLAGS undefined
POSIX_V6_ILP32_OFFBIG_LIBS undefined
POSIX_V6_LP64_OFF64_CFLAGS
POSIX_V6_LP64_OFF64_LDFLAGS
POSIX_V6_LP64_OFF64_LIBS
POSIX_V6_LPBIG_OFFBIG_CFLAGS
POSIX_V6_LPBIG_OFFBIG_LDFLAGS
POSIX_V6_LPBIG_OFFBIG_LIBS
POSIX_V6_WIDTH_RESTRICTED_ENVS POSIX_V6_LP64_OFF64
XBS5_ILP32_OFF32_CFLAGS undefined
XBS5_ILP32_OFF32_LDFLAGS undefined
XBS5_ILP32_OFF32_LIBS undefined
XBS5_ILP32_OFF32_LINTFLAGS undefined
XBS5_ILP32_OFFBIG_CFLAGS undefined
XBS5_ILP32_OFFBIG_LDFLAGS undefined
XBS5_ILP32_OFFBIG_LIBS undefined
XBS5_ILP32_OFFBIG_LINTFLAGS undefined
XBS5_LP64_OFF64_CFLAGS
XBS5_LP64_OFF64_LDFLAGS
XBS5_LP64_OFF64_LIBS
XBS5_LP64_OFF64_LINTFLAGS
XBS5_LPBIG_OFFBIG_CFLAGS
XBS5_LPBIG_OFFBIG_LDFLAGS
XBS5_LPBIG_OFFBIG_LIBS
XBS5_LPBIG_OFFBIG_LINTFLAGS
XBS5_WIDTH_RESTRICTED_ENVS POSIX_V6_LP64_OFF64
V7_ENV POSIXLY_CORRECT=1
V6_ENV POSIXLY_CORRECT=1
_POSIX_AIO_LISTIO_MAX 2
_POSIX_AIO_MAX 1
_POSIX_ARG_MAX 4096
_POSIX_CHILD_MAX 25
_POSIX_CLOCKRES_MIN 20000000
_POSIX_DELAYTIMER_MAX 32
_POSIX_HOST_NAME_MAX 255
_POSIX_LINK_MAX 8
_POSIX_LOGIN_NAME_MAX 9
_POSIX_MAX_CANON 255
_POSIX_MAX_INPUT 255
_POSIX_MQ_OPEN_MAX 8
_POSIX_MQ_PRIO_MAX 32
_POSIX_NAME_MAX 14
_POSIX_NGROUPS_MAX 8
_POSIX_OPEN_MAX 20
_POSIX_PATH_MAX 256
_POSIX_PIPE_BUF 512
_POSIX_RE_DUP_MAX 255
_POSIX_RTSIG_MAX 8
_POSIX_SEM_NSEMS_MAX 256
_POSIX_SEM_VALUE_MAX 32767
_POSIX_SIGQUEUE_MAX 32
_POSIX_SSIZE_MAX 32767
_POSIX_SS_REPL_MAX 4
_POSIX_STREAM_MAX 8
_POSIX_SYMLINK_MAX 255
_POSIX_SYMLOOP_MAX 8
_POSIX_THREAD_DESTRUCTOR_ITERATIONS 4
_POSIX_THREAD_KEYS_MAX 128
_POSIX_THREAD_THREADS_MAX 64
_POSIX_TIMER_MAX 32
_POSIX_TRACE_EVENT_NAME_MAX 30
_POSIX_TRACE_NAME_MAX 8
_POSIX_TRACE_SYS_MAX 8
_POSIX_TRACE_USER_EVENT_MAX 32
_POSIX_TTY_NAME_MAX 9
_POSIX_TZNAME_MAX 6
_POSIX2_BC_BASE_MAX 99
_POSIX2_BC_DIM_MAX 2048
_POSIX2_BC_SCALE_MAX 99
_POSIX2_BC_STRING_MAX 1000
_POSIX2_COLL_WEIGHTS_MAX 2
_POSIX2_EXPR_NEXT_MAX 32
_POSIX2_LINE_MAX 2048
_POSIX2_RE_DUP_MAX 255
_XOPEN_IOV_MAX 16
_XOPEN_NAME_MAX 255
_XOPEN_PATH_MAX 1024
CHAR_BIT 8
CHAR_MAX 127
CHAR_MIN -128
INT_MAX 2147483647
INT_MIN -2147483648
LLONG_MIN -9223372036854775808
LLONG_MAX 9223372036854775807
LONG_BIT 64
LONG_MAX 9223372036854775807
LONG_MIN -9223372036854775808
MB_LEN_MAX 8
SCHAR_MAX 127
SCHAR_MIN -128
SHRT_MAX 32767
SHRT_MIN -32768
SSIZE_MAX 9223372036854775807
UCHAR_MAX 255
UINT_MAX 4294967295
ULLONG_MAX -1
ULONG_MAX -1
USHRT_MAX 65535
WORD_BIT 32
NL_ARGMAX 9
ML_LANGMAX 14
NL_MSGMAX 32767
NL_SETMAX 255
NL_TEXTMAX 2048
NZERO 20
POSIX2_BC_BASE_MAX 99
POSIX2_BC_DIM_MAX 2048
POSIX2_BC_SCALE_MAX 99
POSIX2_BC_STRING_MAX 1000
POSIX2_COLL_WEIGHTS_MAX 2
POSIX2_EXPR_NEXT_MAX 32
POSIX2_LINE_MAX 2048
POSIX2_RE_DUP_MAX 255
ARG_MAX 32000
ATEXIT_MAX 32
BC_BASE_MAX 99
BC_DIM_MAX 2048
BC_SCALE_MAX 99
BC_STRING_MAX 1000
CHILD_MAX 256
CLK_TCK 1000
EXPR_NEST_MAX 32
GETGR_R_SIZE_MAX 16384
GETPW_R_SIZE_MAX 16384
HOST_NAME_MAX 255
IOV_MAX 1024
LINE_MAX 2048
LOGIN_NAME_MAX 256
MQ_OPEN_MAX 256
MQ_PRIO_MAX 2147483647
NGROUPS_MAX 1024
OPEN_MAX 256
PAGE_SIZE 65536
PAGESIZE 65536
PTHREAD_DESTRUCTOR_ITERATIONS 1
PTHREAD_KEYS_MAX 1024
PTHREAD_STACK_MIN 65536
PTHREAD_THREADS_MAX undefined
RE_DUP_MAX 255
RTSIG_MAX 33
SEM_NSEMS_MAX undefined
SEM_VALUE_MAX 1147483648
SIGQUEUE_MAX 32
STREAM_MAX 20
SYMLOOP_MAX 10
TIMER_MAX 32
TTY_NAME_MAX 32
_POSIX_ADVISORY_INFO 200112
_POSIX_ASYNCHRONOUS_IO undefined
_POSIX_BARRIERS undefined
_POSIX_CLOCK_SELECTION 200112
_POSIX_CPUTIME 200112
_POSIX_FSYNC 200112
_POSIX_IPV6 200112
_POSIX_JOB_CONTROL 1
_POSIX_MAPPED_FILES 200112
_POSIX_MEMLOCK undefined
_POSIX_MEMLOCK_RANGE 200112
_POSIX_MEMORY_PROTECTION 200112
_POSIX_MESSAGE_PASSING 200112
_POSIX_MONOTONIC_CLOCK 200112
_POSIX_PRIORITIZED_IO undefined
_POSIX_PRIORITY_SCHEDULING 200112
_POSIX_RAW_SOCKETS 200112
_POSIX_READER_WRITER_LOCKS 200112
_POSIX_REALTIME_SIGNALS 200112
_POSIX_REGEXP 1
_POSIX_SAVED_IDS 1
_POSIX_SEMAPHORES 200112
_POSIX_SHARED_MEMORY_OBJECTS 200112
_POSIX_SHELL 1
_POSIX_SPAWN undefined
_POSIX_SPIN_LOCKS 200112
_POSIX_SPORADIC_SERVER undefined
_POSIX_SYNCHRONIZED_IO 200112
_POSIX_THREAD_ATTR_STACKADDR 200112
_POSIX_THREAD_ATTR_STACKSIZE 200112
_POSIX_THREAD_CPUTIME 200112
_POSIX_THREAD_PRIO_INHERIT undefined
_POSIX_THREAD_PRIO_PROTECT undefined
_POSIX_THREAD_PRIORITY_SCHEDULING 200112
_POSIX_THREAD_PROCESS_SHARED 200112
_POSIX_THREAD_ROBUST_PRIO_INHERIT undefined
_POSIX_THREAD_ROBUST_PRIO_PROTECT undefined
_POSIX_THREAD_SAFE_FUNCTIONS 200112
_POSIX_THREAD_SPORADIC_SERVER undefined
_POSIX_THREADS 200112
_POSIX_TIMEOUTS undefined
_POSIX_TIMERS 1
_POSIX_TRACE undefined
_POSIX_TRACE_EVENT_FILTER undefined
_POSIX_TRACE_INHERIT undefined
_POSIX_TRACE_LOG undefined
_POSIX_TYPED_MEMORY_OBJECTS undefined
_POSIX_VERSION 200112
_POSIX_V7_ILP32_OFF32 undefined
_POSIX_V7_ILP32_OFFBIG undefined
_POSIX_V7_LP64_OFF64 1
_POSIX_V7_LPBIG_OFFBIG 1
_POSIX_V6_ILP32_OFF32 undefined
_POSIX_V6_ILP32_OFFBIG undefined
_POSIX_V6_LP64_OFF64 1
_POSIX_V6_LPBIG_OFFBIG 1
_POSIX2_C_BIND 200112
_POSIX2_C_DEV 200112
_POSIX2_CHAR_TERM 200112
_POSIX2_FORT_DEV undefined
_POSIX2_FORT_RUN undefined
_POSIX2_LOCALEDEF undefined
_POSIX2_PBS undefined
_POSIX2_PBS_ACCOUNTING undefined
_POSIX2_PBS_CHECKPOINT undefined
_POSIX2_PBS_LOCATE undefined
_POSIX2_PBS_MESSAGE undefined
_POSIX2_PBS_TRACK undefined
_POSIX2_SW_DEV 200112
_POSIX2_UPE 200112
_POSIX2_VERSION 200112
_XBS5_ILP32_OFF32 undefined
_XBS5_ILP32_OFFBIG undefined
_XBS5_LP64_OFF64 1
_XBS5_LPBIG_OFFBIG 1
_XOPEN_CRYPT 1
_XOPEN_ENH_I18N 1
_XOPEN_LEGACY undefined
_XOPEN_REALTIME undefined
_XOPEN_REALTIME_THREADS undefined
_XOPEN_SHM 1
_XOPEN_STREAMS undefined
_XOPEN_UNIX undefined
_XOPEN_UUCP undefined
_XOPEN_VERSION 600
POSIX2_C_BIND 200112
POSIX2_C_DEV 200112
POSIX2_CHAR_TERM 200112
POSIX2_FORT_DEV undefined
POSIX2_FORT_RUN undefined
POSIX2_LOCALEDEF undefined
POSIX2_PBS undefined
POSIX2_PBS_ACCOUNTING undefined
POSIX2_PBS_CHECKPOINT undefined
POSIX2_PBS_LOCATE undefined
POSIX2_PBS_MESSAGE undefined
POSIX2_PBS_TRACK undefined
POSIX2_SW_DEV 200112
POSIX2_UPE 200112
POSIX2_VERSION 200112
LEVEL1_ICACHE_SIZE 32768
LEVEL1_ICACHE_ASSOC 8
LEVEL1_ICACHE_LINESIZE 64
LEVEL1_DCACHE_SIZE 32768
LEVEL1_DCACHE_ASSOC 8
LEVEL1_DCACHE_LINESIZE 64
LEVEL2_CACHE_SIZE 262144
LEVEL2_CACHE_ASSOC 8
LEVEL2_CACHE_LINESIZE 64
LEVEL3_CACHE_SIZE 4194304
LEVEL3_CACHE_ASSOC 16
LEVEL3_CACHE_LINESIZE 64
LEVEL4_CACHE_SIZE 0
LEVEL4_CACHE_ASSOC 0
LEVEL4_CACHE_LINESIZE 0
_NPROCESSORS_CONF 4
_NPROCESSORS_ONLN 4
_AVPHYS_PAGES 32068
_PHYS_PAGES 129240
Robert@DESKTOP-14EL82S ~
$
Bob May
DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Surname
and ISOGG YTree
> Subject: Re: [Samtools-help] Windows10 cygwin64 and samtools problem
> installing
> From: j...@sanger.ac.uk
> Date: Fri, 1 Jan 2016 11:16:02 +1300
> CC: samtools-help@lists.sourceforge.net
> To: tpi...@gmail.com
>
> On 31 Dec 2015, at 10:15, Robert May <tpi...@gmail.com> wrote:
> >
> > I have just installed cygwin64 on a Windows10 machine and have run into
> > problems with installing as below. Any assiance appreciated.
> [...]
> > checking whether the C compiler works... no
> > configure: error: in `/usr/local/bin/htslib-1.3':
> > configure: error: C compiler cannot create executables
> [...]
> >
> > gcc: error: spawn: No such file or directory
>
> It would appear that you do not have a C compiler, working or otherwise.
> When you install Cygwin, development tools such as GCC are not installed by
> default. See https://cygwin.com/faq.html#faq.setup.what-packages .
>
> John
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
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