Re: PSPP-BUG: Bug Report for PSPP 0.7.8 on Fedora

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Re: PSPP-BUG: Bug Report for PSPP 0.7.8 on Fedora

From:	Eliana
Subject:	Re: PSPP-BUG: Bug Report for PSPP 0.7.8 on Fedora
Date:	Sat, 3 Mar 2012 19:59:42 -0800
Dear Ben,

Sorry, I did not know you needed that, I was just following the
instructions in the output   It was so far above the instructions and
error listing , I did not even see it, but just reran on a smaller
sample so I can provide that to you.

Note that the complaints pspp made about inappropriate data were due
to my not yet having figured out where in the first line of code to
put /FIRSTCASE=2.  I have now got that working but the program I reran
to provide you with output, I left without the firstcase statement as
in the original run.

Before I paste that long output here, let me mention that after
getting John's response to a different query on  pspp-help, I revised
the program in two ways and got it to run successfully, so I think the
issue may just be it had no error message to catch my error?

I am new and believed the manual when it said blank lines could be
used to finish a command.    Once I added a period at the end of the
last line, it ran smoothly.

I will attach the program file I used to recreate the scenario.

I am running this on my friend's Fedora 12 via ssh, he installed the
most recent RPM he could find for Fedora.  I do not know if he got it
from the git repository.

Full output is below my signature.

thanks,
eliana

Mar03-09:36 PM> cat testprogram4bug.txt|pspp
headof-cb-me-20120221sorted-1.csv:1.16-1.25: warning: Data for variable CHROM
is not valid as format F: Field contents are not numeric.

headof-cb-me-20120221sorted-1.csv:1.27-1.40:
warning: Data for variable START is not valid
as format F: Field contents are not numeric.

headof-cb-me-20120221sorted-1.csv:1.42-1.53:
warning: Data for variable STOP is not valid
as format F: Field contents are not numeric.

headof-cb-me-20120221sorted-1.csv:1.55-1.66:
warning: Data for variable SIZE is not valid
as format F: Field contents are not numeric.

headof-cb-me-20120221sorted-1.csv:1.68-1.80:
warning: Data for variable SNPS is not valid
as format F: Field contents are not numeric.

Final Cluster Centers
#=====#==============================#
#     |            Cluster           #
#     +---+---+---+--------+---------#
#     | 1 | 2 | 3 |    4   |    5    #
#     +---+---+---+--------+---------#
#START| 0 | 0 | 0 |27491087|111800463#
#STOP | 0 | 0 | 0 |29785241|114764058#
#SIZE |.00|.00|.00|  2.06  |   2.50  #
#SNPS | 0 | 0 | 0 |   567  |   717   #
#=====#===#===#===#========#=========#
*** glibc detected *** pspp: munmap_chunk(): invalid pointer: 0x08255c30 ***
======= Backtrace: =========
/lib/libc.so.6(-0xffb512af)[0x25ad51]
/usr/lib/libgsl.so.0(gsl_block_long_free+0x2a)[0x7403fba]
/usr/lib/libgsl.so.0(gsl_vector_long_free+0x43)[0x75354e3]
/usr/lib/libpspp-0.7.8.so(cmd_quick_cluster+0x1112)[0x14ce82]
/usr/lib/libpspp-0.7.8.so(cmd_parse_in_state+0x1e3)[0x11c543]
/usr/lib/libpspp-0.7.8.so(cmd_parse+0x5a)[0x11cb6a]
pspp[0x804a0f7]
/lib/libc.so.6(__libc_start_main+0xe6)[0x202bb6]
pspp[0x804a299]
======= Memory map: ========
00101000-001e4000 r-xp 00000000 08:02 5530516
  /usr/lib/libpspp-0.7.8.so
001e4000-001e9000 r--p 000e2000 08:02 5530516
  /usr/lib/libpspp-0.7.8.so
001e9000-001eb000 rw-p 000e7000 08:02 5530516
  /usr/lib/libpspp-0.7.8.so
001eb000-001ec000 rw-p 00000000 00:00 0
001ec000-0035e000 r-xp 00000000 08:02 1345970
  /lib/libc-2.11.2.so
0035e000-0035f000 ---p 00172000 08:02 1345970
  /lib/libc-2.11.2.so
0035f000-00361000 r--p 00172000 08:02 1345970
  /lib/libc-2.11.2.so
00361000-00362000 rw-p 00174000 08:02 1345970
  /lib/libc-2.11.2.so
00362000-00365000 rw-p 00000000 00:00 0
00365000-0037a000 r-xp 00000000 08:02 1346024
  /lib/libresolv-2.11.2.so
0037a000-0037b000 r--p 00014000 08:02 1346024
  /lib/libresolv-2.11.2.so
0037b000-0037c000 rw-p 00015000 08:02 1346024
  /lib/libresolv-2.11.2.so
0037c000-0037e000 rw-p 00000000 00:00 0
0037e000-00386000 r-xp 00000000 08:02 1572870
  /lib/libkrb5support.so.0.1
00386000-00387000 rw-p 00008000 08:02 1572870
  /lib/libkrb5support.so.0.1
00387000-00389000 r-xp 00000000 08:02 3279279
  /lib/libkeyutils-1.2.so
00389000-0038a000 rw-p 00001000 08:02 3279279
  /lib/libkeyutils-1.2.so
0038a000-003a7000 r-xp 00000000 08:02 5532569
  /usr/lib/libxcb.so.1.1.0
003a7000-003a8000 rw-p 0001c000 08:02 5532569
  /usr/lib/libxcb.so.1.1.0
003a8000-003aa000 r-xp 00000000 08:02 5532568
  /usr/lib/libXau.so.6.0.0
003aa000-003ab000 rw-p 00001000 08:02 5532568
  /usr/lib/libXau.so.6.0.0
003ab000-003c8000 r-xp 00000000 08:02 1346028
  /lib/libgcc_s-4.4.4-20100630.so.1
003c8000-003c9000 rw-p 0001d000 08:02 1346028
  /lib/libgcc_s-4.4.4-20100630.so.1
0041e000-0043c000 r-xp 00000000 08:02 1345969
  /lib/ld-2.11.2.so
0043c000-0043d000 r--p 0001d000 08:02 1345969
  /lib/ld-2.11.2.so
0043d000-0043e000 rw-p 0001e000 08:02 1345969
  /lib/ld-2.11.2.so
0055e000-0055f000 r-xp 00000000 00:00 0
  [vdso]
005bb000-005e3000 r-xp 00000000 08:02 1345984
  /lib/libm-2.11.2.so
005e3000-005e4000 r--p 00027000 08:02 1345984
  /lib/libm-2.11.2.so
005e4000-005e5000 rw-p 00028000 08:02 1345984
  /lib/libm-2.11.2.so
005e7000-005ea000 r-xp 00000000 08:02 1345987
  /lib/libdl-2.11.2.so
005ea000-005eb000 r--p 00002000 08:02 1345987
  /lib/libdl-2.11.2.so
005eb000-005ec000 rw-p 00003000 08:02 1345987
  /lib/libdl-2.11.2.so
005ee000-00604000 r-xp 00000000 08:02 1345981
  /lib/libpthread-2.11.2.so
00604000-00605000 r--p 00016000 08:02 1345981
  /lib/libpthread-2.11.2.so
00605000-00606000 rw-p 00017000 08:02 1345981
  /lib/libpthread-2.11.2.so
00606000-00608000 rw-p 00000000 00:00 0
0060a000-00655000 r-xp 00000000 08:02 5532959
  /usr/lib/libldap_r-2.4.so.2.5.2
00655000-00657000 rw-p 0004a000 08:02 5532959
  /usr/lib/libldap_r-2.4.so.2.5.2
00657000-00658000 rw-p 00000000 00:00 0
0069f000-006d0000 r-xp 00000000 08:02 5535788
  /usr/lib/libgslcblas.so.0.0.0
006d0000-006d1000 rw-p 00030000 08:02 5535788
  /usr/lib/libgslcblas.so.0.0.0
006df000-006e2000 r-xp 00000000 08:02 1572884
  /lib/libgmodule-2.0.so.0.2200.5
006e2000-006e3000 rw-p 00002000 08:02 1572884
  /lib/libgmodule-2.0.so.0.2200.5
006e5000-0070d000 r-xp 00000000 08:02 5532848
  /usr/lib/libpangoft2-1.0.so.0.2600.2
0070d000-0070e000 rw-p 00028000 08:02 5532848
  /usr/lib/libpangoft2-1.0.so.0.2600.2
0072e000-00732000 r-xp 00000000 08:02 1572886
  /lib/libgthread-2.0.so.0.2200.5
00732000-00733000 rw-p 00003000 08:02 1572886
  /lib/libgthread-2.0.so.0.2200.5
00733000-008a6000 r-xp 00000000 08:02 5530595
  /usr/lib/libcrypto.so.1.0.0b
008a6000-008ba000 rw-p 00172000 08:02 5530595
  /usr/lib/libcrypto.so.1.0.0b
008ba000-008bd000 rw-p 00000000 00:00 0
0096c000-00988000 r-xp 00000000 08:02 1346054
  /lib/libselinux.so.1
00988000-00989000 r--p 0001b000 08:02 1346054
  /lib/libselinux.so.1
00989000-0098a000 rw-p 0001c000 08:02 1346054
  /lib/libselinux.so.1
0098c000-00999000 r-xp 00000000 08:02 5532489
  /usr/lib/liblber-2.4.so.2.5.2
00999000-0099a000 rw-p 0000d000 08:02 5532489
  /usr/lib/liblber-2.4.so.2.5.2
0099c000-0099e000 r-xp 00000000 08:02 8290633
  /lib/libcom_err.so.2.1
0099e000-0099f000 rw-p 00002000 08:02 8290633
  /lib/libcom_err.so.2.1
009a1000-009a8000 r-xp 00000000 08:02 1572885
  /lib/librt-2.11.2.so
009a8000-009a9000 r--p 00006000 08:02 1572885
  /lib/librt-2.11.2.so
009a9000-009aa000 rw-p 00007000 08:02 1572885
  /lib/librt-2.11.2.so
009c8000-00a5c000 r-xp 00000000 08:02 5532565
  /usr/lib/libfreetype.so.6.3.22
00a5c000-00a60000 rw-p 00094000 08:02 5532565
  /usr/lib/libfreetype.so.6.3.22
00a62000-00a88000 r-xp 00000000 08:02 1345985
  /lib/libexpat.so.1.5.2
00a88000-00a8a000 rw-p 00025000 08:02 1345985
  /lib/libexpat.so.1.5.2
00ab6000-00ae9000 r-xp 00000000 08:02 5532566
  /usr/lib/libfontconfig.so.1.4.4
00ae9000-00aeb000 rw-p 00032000 08:02 5532566
  /usr/lib/libfontconfig.so.1.4.4
00afd000-00b05000 r-xp 00000000 08:02 5532617
  /usr/lib/libXrender.so.1.3.0
00b05000-00b06000 rw-p 00008000 08:02 5532617
  /usr/lib/libXrender.so.1.3.0
00b32000-00b75000 r-xp 00000000 08:02 1572887
  /lib/libgobject-2.0.so.0.2200.5
00b75000-00b76000 rw-p 00043000 08:02 1572887
  /lib/libgobject-2.0.so.0.2200.5
00b78000-00b9d000 r-xp 00000000 08:02 5536477
  /usr/lib/libpq.so.5.2
00b9d000-00b9f000 rw-p 00024000 08:02 5536477
  /usr/lib/libpq.so.5.2
00bc3000-00bd8000 r-xp 00000000 08:02 1346055
  /lib/libz.so.1.2.5
00bd8000-00bd9000 rw-p 00014000 08:02 1346055
  /lib/libz.so.1.2.5
00bdb000-00c02000 r-xp 00000000 08:02 5535690
  /usr/lib/libpng12.so.0.44.0
00c02000-00c03000 rw-p 00026000 08:02 5535690
  /usr/lib/libpng12.so.0.44.0
00c05000-00c10000 r-xp 00000000 08:02 5536354
  /usr/lib/libpangocairo-1.0.so.0.2600.2
00c10000-00c11000 rw-p 0000a000 08:02 5536354
  /usr/lib/libpangocairo-1.0.so.0.2600.2
00c20000-00c80000 r-xp 00000000 08:02 5531136
  /usr/lib/libpixman-1.so.0.16.6
00c80000-00c82000 rw-p 00060000 08:02 5531136
  /usr/lib/libpixman-1.so.0.16.6
00caf000-00d02000 r-xp 00000000 08:02 5536393
  /usr/lib/libssl.so.1.0.0b
00d02000-00d06000 rw-p 00053000 08:02 5536393
  /usr/lib/libssl.so.1.0.0b
00d3f000-00dbd000 r-xp 00000000 08:02 5536353
  /usr/lib/libcairo.so.2.10800.8
00dbd000-00dbf000 rw-p 0007e000 08:02 5536353
  /usr/lib/libcairo.so.2.10800.8
00dbf000-00ef3000 r-xp 00000000 08:02 5532602
  /usr/lib/libX11.so.6.3.0
00ef3000-00ef7000 rw-p 00133000 08:02 5532602
  /usr/lib/libX11.so.6.3.0
02832000-0285f000 r-xp 00000000 08:02 8290637
  /lib/libgssapi_krb5.so.2.2
0285f000-02860000 rw-p 0002d000 08:02 8290637
  /lib/libgssapi_krb5.so.2.2
03257000-0339b000 r-xp 00000000 08:02 5536619
  /usr/lib/libxml2.so.2.7.6
0339b000-033a0000 rw-p 00143000 08:02 5536619
  /usr/lib/libxml2.so.2.7.6
033a0000-033a1000 rw-p 00000000 00:00 0
033a3000-03456000 r-xp 00000000 08:02 5536174
  /usr/lib/libpspp-core-0.7.8.so
03456000-03457000 r--p 000b3000 08:02 5536174
  /usr/lib/libpspp-core-0.7.8.so
03457000-0345c000 rw-p 000b4000 08:02 5536174
  /usr/lib/libpspp-core-0.7.8.so
0345c000-0345f000 rw-p 00000000 00:00 0
03944000-03979000 r-xp 00000000 08:02 3279304
  /lib/libreadline.so.6.0
03979000-0397d000 rw-p 00035000 08:02 3279304
  /lib/libreadline.so.6.0
0397d000-0397e000 rw-p 00000000 00:00 0
03aa1000-03ab7000 r-xp 00000000 08:02 1346034
  /lib/libtinfo.so.5.7
03ab7000-03aba000 rw-p 00015000 08:02 1346034
  /lib/libtinfo.so.5.7
03abc000-03ade000 r-xp 00000000 08:02 3279301
  /lib/libncurses.so.5.7
03ade000-03adf000 rw-p 00021000 08:02 3279301
  /lib/libncurses.so.5.7
03d74000-03d9e000 r-xp 00000000 08:02 1572880
  /lib/libk5crypto.so.3.1
03d9e000-03d9f000 rw-p 0002a000 08:02 1572880
  /lib/libk5crypto.so.3.1
03ed6000-03f1b000 r-xp 00000000 08:02 3276926
  /lib/libfreebl3.so
03f1b000-03f1c000 rw-p 00045000 08:02 3276926
  /lib/libfreebl3.so
03f1c000-03f20000 rw-p 00000000 00:00 0
04282000-04335000 r-xp 00000000 08:02 8290636
  /lib/libkrb5.so.3.3
04335000-0433b000 rw-p 000b3000 08:02 8290636
  /lib/libkrb5.so.3.3
05393000-0539a000 r-xp 00000000 08:02 3276970
  /lib/libcrypt-2.11.2.so
0539a000-0539b000 r--p 00007000 08:02 3276970
  /lib/libcrypt-2.11.2.so
0539b000-0539c000 rw-p 00008000 08:02 3276970
  /lib/libcrypt-2.11.2.so
0539c000-053c3000 rw-p 00000000 00:00 0
05a14000-05afc000 r-xp 00000000 08:02 1572883
  /lib/libglib-2.0.so.0.2200.5
05afc000-05afd000 rw-p 000e8000 08:02 1572883
  /lib/libglib-2.0.so.0.2200.5
05c4d000-05c94000 r-xp 00000000 08:02 5532845
  /usr/lib/libpango-1.0.so.0.2600.2
05c94000-05c96000 rw-p 00047000 08:02 5532845
  /usr/lib/libpango-1.0.so.0.2600.2
07353000-0736c000 r-xp 00000000 08:02 16393
  /usr/lib/libsasl2.so.2.0.23
0736c000-0736d000 rw-p 00018000 08:02 16393
  /usr/lib/libsasl2.so.2.0.23
073c8000-075a9000 r-xp 00000000 08:02 5532867
  /usr/lib/libgsl.so.0.14.0
075a9000-075b3000 rw-p 001e0000 08:02 5532867
  /usr/lib/libgsl.so.0.14.0
08048000-0804d000 r-xp 00000000 08:02 9765274
  /usr/bin/pspp
0804d000-0804e000 r--p 00004000 08:02 9765274
  /usr/bin/pspp
0804e000-08052000 rw-p 00005000 08:02 9765274
  /usr/bin/pspp
08240000-08261000 rw-p 00000000 00:00 0
  [heap]
b7539000-b7739000 r--p 00000000 08:02 24579
  /usr/lib/locale/locale-archive
b7739000-b7745000 rw-p 00000000 00:00 0
b775b000-b775c000 rw-p 00000000 00:00 0
b775c000-b7763000 r--s 00000000 08:02 5570563
  /usr/lib/gconv/gconv-modules.cache
b7763000-b7764000 rw-p 00000000 00:00 0
bf8c2000-bf8d7000 rw-p 00000000 00:00 0
  [stack]
******************************************************
You have discovered a bug in PSPP.  Please report this
to address@hidden  Please include this entire
message, *plus* several lines of output just above it.
For the best chance at having the bug fixed, also
include the syntax file that triggered it and a sample
of any data file used for input.
proximate cause:     Assertion Failure/Abort
version:             GNU pspp 0.7.8 (Sun Dec 18 12:43:01 UTC 2011).
host_system:         i386-redhat-linux-gnu
build_system:        i386-redhat-linux-gnu
locale_dir:          /usr/share/locale
compiler version:    4.6.2 20111027 (Red Hat 4.6.2-1)
******************************************************
Aborted (core dumped)
Mar03-09:36 PM>

On 3/3/12, Ben Pfaff <address@hidden> wrote:
> Eliana <address@hidden> writes:
>
>> this is a bug report, running pspp 0.7.8 on Fedora 12.  Tried running
>> QUICK CLUSTER
>>
>> input program and sample data file are attached.
>>
>> ran from command line with
>>
>> cat testprogram.txt | pspp
>
> When I run this as provided, with the latest PSPP from the Git
> repository, I get the following, without such a report.
>
> What full output do you get?
>
> ----------------------------------------------------------------------
>
> cb-me-20120221sorted-1.csv:1.16-1.25: warning: Data for variable CHROM is
> not
> valid as format F: Field contents are not numeric.
>
> cb-me-20120221sorted-1.csv:1.27-1.40: warning: Data for variable START is
> not
> valid as format F: Field contents are not numeric.
>
> cb-me-20120221sorted-1.csv:1.42-1.53: warning: Data for variable STOP is not
> valid as format F: Field contents are not numeric.
>
> cb-me-20120221sorted-1.csv:1.55-1.66: warning: Data for variable SIZE is not
> valid as format F: Field contents are not numeric.
>
> cb-me-20120221sorted-1.csv:1.68-1.80: warning: Data for variable SNPS is not
> valid as format F: Field contents are not numeric.
>
> Valid cases = 10; cases with missing value(s) = 1.
> +--------#-+--------+--------+--------+--------+--------+----+--------+----+
> |Variable#N|  Mean  |  S.E.  | Std Dev|Variance|Kurtosis|S.E.|Skewness|S.E.|
> |        # |        |  Mean  |        |        |        |Kurt|        |Skew|
> #========#=#========#========#========#========#========#====#========#====#
> |CHROM   #9|    1.00|     .00|     .00|     .00|       .|   .|       .|   .|
> |        # |        |        |        |        |        |    |        |    |
> |START   #9|83697338|21697219|65091658|4.2E+015|    -.38|1.40|    1.01| .72|
> |STOP    #9|86437786|21788956|65366868|4.3E+015|    -.36|1.40|    1.01| .72|
> |SIZE    #9|    2.35|     .44|    1.31|    1.73|    7.25|1.40|    2.60| .72|
> |SNPS    #9|  666.67|   83.33|  250.00|62500.00|    6.62|1.40|    2.46| .72|
> +--------#-+--------+--------+--------+--------+--------+----+--------+----+
>
> +--------#--------+--------+--------+--------+
> |Variable#  Range | Minimum| Maximum|   Sum  |
> |        #        |        |        |        |
> #========#========#========#========#========#
> |CHROM   #     .00|    1.00|    1.00|    9.00|
> |        #        |        |        |        |
> |START   #1.7E+008|20275685|1.9E+008|7.5E+008|
> |STOP    #1.7E+008|21826023|2.0E+008|7.8E+008|
> |SIZE    #    4.31|    1.42|    5.73|   21.18|
> |SNPS    #  800.00|  500.00| 1300.00| 6000.00|
> +--------#--------+--------+--------+--------+
>
> Final Cluster Centers
> #=====#==================#
> #     |      Cluster     #
> #     +--------+---------#
> #     |    1   |    2    #
> #     +--------+---------#
> #START|27491087|111800463#
> #STOP |29785241|114764058#
> #SIZE |  2.06  |   2.50  #
> #SNPS |   567  |   717   #
> #=====#========#=========#
>
> Number of Cases in each Cluster
> #=======#=#=#
> #Cluster|1|3#
> #       |2|6#
> #       | | #
>
> #       | | #
> #Valid  | |9#
> #=======#=#=#
>
> testprogram.txt:18.30: error: FREQUENCIES: Syntax error at `-': expecting
> end
> of command.
>
> testprogram.txt:23.30: error: EXAMINE: Syntax error at `-': expecting end of
> command.
>
> --
> Ben Pfaff
> http://benpfaff.org
>
testprogram4bug.txt
Description: Text document
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PSPP-BUG: Bug Report for PSPP 0.7.8 on Fedora, Eliana, 2012/03/01
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