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Full Discussion: C command not found
Top Forums Shell Programming and Scripting C command not found Post 302916943 by Corona688 on Friday 12th of September 2014 03:17:22 PM
Old 09-12-2014
I don't recognize that error at all. I certainly have no 'C' program on my system or see anything in my makefiles that would provoke such a message.

Code:
$ mfold SEQ='M23263_rna_300-1.txt' RUN_TYPE=text NA=RNA MA
mfold version 3.6
Invalid entry:  MA on command line.

$

Actually -- I just noticed one big difference between what I did and what you did! Out of habit, I ran ./configure and not ./Configure.bash.

To be precise, I ran ./configure --prefix=/home/username/archive/mfold. The prefix is where it installs -- I put it in my home directory. /usr/local/ would be a decent choice if you needed it to be global to the machine. You'd need to add it to your path to use it, PATH="${PATH}:/usr/local/bin" but it'd be separate from your system utilities and easy to remove if needed.

Last edited by Corona688; 09-12-2014 at 04:22 PM..
 

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Unicode::Japanese::JA(3pm)				User Contributed Perl Documentation				Unicode::Japanese::JA(3pm)

NAME
Unicode::Japanese::JA - XXXXXXXXXX XX
use Unicode::Japanese; use Unicode::Japanese qw(unijp); # convert utf8 -> sjis print Unicode::Japanese->new($str)->sjis; print unijp($str)->sjis; # same as above. # convert sjis -> utf8 print Unicode::Japanese->new($str,'sjis')->get; # convert sjis (imode_EMOJI) -> utf8 print Unicode::Japanese->new($str,'sjis-imode')->get; # convert zenkaku (utf8) -> hankaku (utf8) print Unicode::Japanese->new($str)->z2h->get; XX
Unicode::Japanese XXXXXXXXXXXXXXXXXXXXXXXXXXX XX o Unicode::Japanese XXXXXXXXXUTF-8 XXXXXXXXXXX o XS XX/XXXXXXXXXXXXXXXX XS XXXXXXXXXXXXXXXXX No-XS XXXXXXXXXXXXXXXXXXXX (Japanese.pm XXXXXXXXXXXXXX)X o XXXXXXXXXXXXXXXXXXXXXXXXXXXX o XXXX (DoCoMo i-modeXKDDI AU, Softbank Mobile, ASTEL dot-i) XXXXX Unicode XXXXXXXXXXXXXXXXDB XXXXXXXXXXXXXXX o XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX o SJIS XX MS-CP932 XXXXX Unicode XXXXXXXXXXXX o Unicode -> SJISXXXEUC-JP/JISX XXXXXXXXSJIS XXXXXXXXXX &#dddd; XXXXXXXXX XXXUnicodeXXXXXXXXXXXXXXX '?'XXXXX. XX, XXXXXXXXXXXX, XXXXXXXXXXXX'?'XXXXX. o Perl-5.8.0 XXXXXX, utf8 XXXXXXXXXXXXX. utf-8 `XXX'X XXXXX utf8() XXXXX, utf-8 `XX'X XXXXX getu() XXXXXXXXX. get() XXXXXXXXXX utf-8 `XXX'X XXXXX (XXXXXXXXXXXXXXXXX). sjis(), jis(), utf8(), etc.. XXXXXXXXXXXXXXX. new, set, getcode XXXXXXXXX, utf8-flaged/bytes XXXXXX. XXXXXXXX
o perl 5.10.x, 5.8.x, etc. (5.004 XX). o (XXXXOK) C XXXXX. XXXXXXXX XS X Pure Perl XXXXXXXXXX. C XXXXXXXXXXXX, Unicode::Japanese X Pure Perl XXXXXXXXXXXXXXXXXX. o (XXXXOK) XXXXX Test.pm XX Test::More. XXXXXXXXXXXXXXXXXX. XXXX
$s = Unicode::Japanese->new($str [, $icode [, $encode]]) XXX Unicode::Japanese XXXXXXXXXXXXX XXXXXXXXXXXX"set" XXXXXXXXXXX $s = unijp($str [, $icode [, $encode]]) Unicode::Janaese->new(...) XXX. $s->set($str [, $icode [, $encode]]) $str: XXX $icode: XXXXXXXXXXXXXXXX 'utf8' $encode: XXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXX XXXXXXXXXXXXX UTF-8 XXXXXXXX XXXXXXXXXX: auto utf8 ucs2 ucs4 utf16-be utf16-le utf16 utf32-be utf32-le utf32 sjis cp932 euc euc-jp jis sjis-imode sjis-imode1 sjis-imode2 utf8-imode utf8-imode1 utf8-imode2 sjis-doti sjis-doti1 sjis-jsky sjis-jsky1 sjis-jsky2 jis-jsky jis-jsky1 jis-jsky2 utf8-jsky utf8-jsky1 utf8-jsky2 sjis-au sjis-au1 sjis-au2 jis-au jis-au1 jis-au2 sjis-icon-au sjis-icon-au1 sjis-icon-au2 euc-icon-au euc-icon-au1 euc-icon-au2 jis-icon-au jis-icon-au1 jis-icon-au2 utf8-icon-au utf8-icon-au1 utf8-icon-au2 ascii binary ( XXX.) XXXXXXXXXXXXXXXX'auto' XXXXXXXXXXXXXX 'auto' XXXXXXXXXXXXXgetcode() XXXXXXX XXXXXX XXXXXXXXXXXX'base64' XXXXXXXXX base64 XXXXXXXXXbase64 XXXXXXXXX Unicode::Japanese XXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 'binary' XXXXXXX sjis-imodeXsjis-dotiXXXXXXXXXX &#dddd; X XXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXX sjis, utf8 XXXXXXXXXXXXXXXXXsjisX sjis-auXsjis-doti XXXXXXXXXXXXXXXXXsjis-auX XXXXXX $str = $s->get $str: XXX(UTF-8) XXXX UTF-8 XXXXXXXXXXX XXX `XXX' X XXXXXX, XXXXXXXXXXXXXXXXX. XXXXXXXXX utf8() XXXXX, XXXXXXXX getu() XXXXXXXXXXXXXXXXX. $str = $s->getu $str: XXX(UTF-8) XXXX UTF-8 XXXXXXXXXXX Perl-5.8.0 XXXXXXX, utf-8 XXXXXXX utf-8 XXXXXX XXXX. $code = $s->getcode($str) $str: XXX $code: XXXXXXXXXXX XXXXXXX($str)XXXXXXXXXXXXXXX XXXXXX, XXXX, XXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX (PurePerlX) 1. UTF-32 X BOM XXXXXutf32 XXXXXXX 2. UTF-16 X BOM XXXXXutf16 XXXXXXX 3. UTF-32BE XXXXXXXXXXXutf32-be XXXXXXX 4. UTF-32LE XXXXXXXXXXXutf32-le XXXXXXX 5. ESC XX XXX 8 XXXXXXXXXXXXXXXXXXXXXXXascii XXXXX XXESC XXXX ASCII XXXX (0x00-0x1F XX 0x7F) X ascii XXXXXXXXX XX 6. JISXXXXXXXXXXXXXXXXXXXjis XXXXXXX 7. J-PHONE XXXXXXXXXXXXXsjis-jsky XXXXXXX 8. EUC-JP XXXXXXXXXXXXXXeuc XXXXXXX 9. SJIS XXXXXXXXXXXXXXsjis XXXXXXX 10. SJIS XXXX au XXXXXXXXXXXXXXXsjis-au XXXXXXX 11. SJIS X i-mode XXXXXXXXXXXXXXXsjis-imode XXXXXXX 12. SJIS X dot-i XXXXXXXXXXXXXXXsjis-doti XXXXXXX 13. UTF-8 XXXXXXXXXXXutf8 XXXXXXX 14. XXXXXXXXXXXXXXXunknown XXXXXXX (XSX) 1. UTF-32 X BOM XXXXXutf32 XXXXXXX 2. UTF-16 X BOM XXXXXutf16 XXXXXXX 3. XXXXXXXXXX, XXXXXXXXXXXXXXXXXXXXXXXXXX. ascii / euc / sjis / jis / utf8 / utf32-be / utf32-le / sjis-jsky / sjis-imode / sjis-au / sjis-doti 4. XXXXXXXXXXXXXXX, XXXXXXXXXXXXXX, XXXXXXXX. utf32-be / utf32-le / ascii / jis / euc / sjis / sjis-jsky / sjis-imode / sjis-au / sjis-doti / utf8 5. XXXXXXXXXXXXXXXunknown XXXXXXX XXXXXXXXXXXXXXXXXXXXXXXXXXX o UTF-8 XXXXXXSJISXXXXXXXXXXXXXXXXXX o UCS2 XXXXXXXXXXXX o UTF-16 X BOM XXXXXXXXXXXXXXX o XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX &#dddd; XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX XSXPurePerlXX, XXXXXXXXXXXXXXXXX, XXXXXXXXXXXXXXXX. XX, XXXXXXXXXXXXXsjisXXX, PurePerlXXsjisXXXXXXX XSXXXXXXXX. XXXsjis- jskyXXXXXXXXXXXXX. XX, XX XXXXXXXXXXXXX, euc-jpXXXXX, XXXXXXXXXXXXXXXXX XXXXXX. $code = $s->getcodelist($str) $str: XXX $code: XXXXXXXXXXX XXXXXXX($str)XXXXXXXXXXXXXXX getcode XXXX, XXXXXXXXXXXXXXX XXXXXXX. $str = $s->conv($ocode, $encode) $ocode: XXXXX (XXXXXX) utf8 ucs2 ucs4 utf16 sjis cp932 euc euc-jp jis sjis-imode sjis-imode1 sjis-imode2 utf8-imode utf8-imode1 utf8-imode2 sjis-doti sjis-doti1 sjis-jsky sjis-jsky1 sjis-jsky2 jis-jsky jis-jsky1 jis-jsky2 utf8-jsky utf8-jsky1 utf8-jsky2 sjis-au sjis-au1 sjis-au2 jis-au jis-au1 jis-au2 sjis-icon-au sjis-icon-au1 sjis-icon-au2 euc-icon-au euc-icon-au1 euc-icon-au2 jis-icon-au jis-icon-au1 jis-icon-au2 utf8-icon-au utf8-icon-au1 utf8-icon-au2 binary ( XXX.) XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX $encode: XXXXXXXXXXXXXX $str: XXX XXXXXXXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXX'base64' XXXXXXXXX base64 XXXXXXXXXbase64 XXXXXXXX XXXXXXXXXX perl-5.8.0 XXXXXX, XXX utf-8 XXXXXXXXXXXXXXXXX. $s->tag2bin XXXXXXXXX &#dddd; XXXXXXXXXXXXXXXXXXXXXXXXX $s->z2h XXXXXXXXXXXX $s->h2z XXXXXXXXXXXX $s->hira2kata XXXXXXXXXXXXXXXX $s->kata2hira XXXXXXXXXXXXXXXX $str = $s->jis $str: JIS XXXXXXXXXXXXXXX XXXX JISXISO-2022-JPX XXXXXXXXXXX $str = $s->euc $str: euc-jp XXXXXXXXXXXXXXX XXXX EUC-JP XXXXXXXXXXX $str = $s->utf8 $str: utf-8 XXXXXXXXXXXXXXX XXXX UTF-8 XXXXXXXXXXX perl-5.8.0 XXXXXXX, XXXXXXXXX. $str = $s->ucs2 $str: ucs2 XXXXXXXXXXXXXXX XXXX UCS2 XXXXXXXXXXX $str = $s->ucs4 $str: ucs4 XXXXXXXXXXXXXXX XXXX UCS4 XXXXXXXXXXX $str = $s->utf16 $str: ucs-16 XXXXXXXXXXXXXXX XXXX UTF-16 XXXXXXXXXXX BOMXXXXXXX XXXXXXXXXXXXXXXXXX $str = $s->sjis $str: sjis XXXXXXXXXXXXXXX XXXX SJISXMS-CP932X XXXXXXXXXXX $str = $s->sjis_imode $str: sjis/imodeXXX XXXXXXXXXXXXXXX XXXX i-mode XXXXX SJIS XXXXXXXXXXX XXXimodeXXXXXXXX. $str = $s->sjis_imode1 $str: sjis/imode XXX XXXXXXXXXXXXXXX XXXX i-mode XXXXX SJIS XXXXXXXXXXX XXXXXXXXXXXXX. $str = $s->sjis_imode2 $str: sjis/imode XXX XXXXXXXXXXXXXXX XXXX i-mode XXXXX SJIS XXXXXXXXXXX XXXXX, XXXXXXXXXX. $str = $s->sjis_doti $str: sjis/dot-i XXX XXXXXXXXXXXXXXX XXXX dot-i XXXXX SJIS XXXXXXXXXXX $str = $s->sjis_jsky $str: sjis/j-sky XXX XXXXXXXXXXXXXXX XXXX j-sky XXXXX SJIS XXXXXXXXXXX XXXj-skyXXX(VERSION 0.15 XX, jsky2)XXXXX. $str = $s->sjis_jsky1 $str: sjis/j-sky XXX XXXXXXXXXXXXXXX XXXX j-sky XXXXX SJIS XXXXXXXXXXX Page 1X3 XXXXXXXXXXX. $str = $s->sjis_jsky $str: sjis/j-sky XXX XXXXXXXXXXXXXXX XXXX j-sky XXXXX SJIS XXXXXXXXXXX Page 1X6 XXXXXXXXX. $str = $s->sjis_icon_au $str: sjis/AU iconXX XXXXXXXXXXXXXXX XXXX AU XXXXX SJIS XXXXXXXXXXX $str_arrayref = $s->strcut($len) $len: XXXXXXX(XXXX) $str_arrayref: XXX $lenXXXXXXXXX(XX)XXXXXXXXXXXXXXXX XXXXXXX, utf-8 XXXXXXXutf-8XXXXX. $len = $s->strlen $len: XXXXXXX UTF-8 XXXXXX length() XXXXXXXXXXXXXXXXX 3 XXXXXXXXXXX XXXXXXXXXXXXXXXX SJIS XXXXXXXXXXXXXXXXXX 2 XXXXXX $s->join_csv(@values); @values: XXXXX XXX CSV XXXXXXXXXXXXXXXXXXXXX XXXXXXXXXX(" ")XXXXXXXX @values = $s->split_csv; @values: XXXXX XXXXXXXXXXXXXXXXXX CSV XXXXXXXXXXXXXX XXXXXXXXXXX(" ")XXXXXXXXXXXXXXXX XXX binary XXXXX utf-8 XXXXXXXX. binary XXXXXXXXXXXXXXX. XXXXXXXXXXXXXXXXX
+---------------+----+-----+-------+ |encoding | in | out | guess | +---------------+----+-----+-------+ |auto : OK : -- | ----- | +---------------+----+-----+-------+ |utf8 : OK : OK | OK | |ucs2 : OK : OK | ----- | |ucs4 : OK : OK | ----- | |utf16-be : OK : -- | ----- | |utf16-le : OK : -- | ----- | |utf16 : OK : OK | OK(#) | |utf32-be : OK : -- | OK | |utf32-le : OK : -- | OK | |utf32 : OK : -- | OK(#) | +---------------+----+-----+-------+ |sjis : OK : OK | OK | |cp932 : OK : OK | ----- | |euc : OK : OK | OK | |euc-jp : OK : OK | ----- | |jis : OK : OK | OK | +---------------+----+-----+-------+ |sjis-imode : OK : OK | OK | |sjis-imode1 : OK : OK | ----- | |sjis-imode2 : OK : OK | ----- | |utf8-imode : OK : OK | ----- | |utf8-imode1 : OK : OK | ----- | |utf8-imode2 : OK : OK | ----- | +---------------+----+-----+-------+ |sjis-doti : OK : OK | OK | |sjis-doti1 : OK : OK | ----- | +---------------+----+-----+-------+ |sjis-jsky : OK : OK | OK | |sjis-jsky1 : OK : OK | ----- | |sjis-jsky2 : OK : OK | ----- | |jis-jsky : OK : OK | ----- | |jis-jsky1 : OK : OK | ----- | |jis-jsky2 : OK : OK | ----- | |utf8-jsky : OK : OK | ----- | |utf8-jsky1 : OK : OK | ----- | |utf8-jsky2 : OK : OK | ----- | +---------------+----+-----+-------+ |sjis-au : OK : OK | OK | |sjis-au1 : OK : OK | ----- | |sjis-au2 : OK : OK | ----- | |jis-au : OK : OK | ----- | |jis-au1 : OK : OK | ----- | |jis-au2 : OK : OK | ----- | |sjis-icon-au : OK : OK | ----- | |sjis-icon-au1 : OK : OK | ----- | |sjis-icon-au2 : OK : OK | ----- | |euc-icon-au : OK : OK | ----- | |euc-icon-au1 : OK : OK | ----- | |euc-icon-au2 : OK : OK | ----- | |jis-icon-au : OK : OK | ----- | |jis-icon-au1 : OK : OK | ----- | |jis-icon-au2 : OK : OK | ----- | |utf8-icon-au : OK : OK | ----- | |utf8-icon-au1 : OK : OK | ----- | |utf8-icon-au2 : OK : OK | ----- | +---------------+----+-----+-------+ |ascii : OK : -- | OK | |binary : OK : OK | ----- | +---------------+----+-----+-------+ (#): guessed when it has bom. XXXXXXXX 1. utf32 (#) 2. utf16 (#) 3. utf32-be 4. utf32-le 5. ascii 6. jis 7. sjis-jsky (pp) 8. euc 9. sjis 10. sjis-jsky (xs) 11. sjis-au 12. sjis-imode 13. sjis-doti 14. utf8 15. unknown DESCRIPTION OF UNICODE MAPPING
Unicode XXXXXXXXXXXXXXXXXXXX Shift_JIS MS-CP932 XXX Unicode XXXXXXXXXXXX XXXXXXXXXXXXXURLXXXXXXXXXXXX <ftp://ftp.unicode.org/Public/MAPPINGS/VENDORS/MICSFT/WINDOWS/CP932.TXT> Unicode XX SJIS XXXXXXXXXXXXXXXXXXXXXXXXX XXXXX &#dddd; XXXXXXXXX XXXXXXXXXXX?XXXXXXXXX XXXXXXXX SJIS XXXXXXXXXXXXXXXXXXXXXX?XXXXXXXXX EUC-JP/ISO-2022-JP XXSJISXXXXXXXXXXXUnicode XXXXXXXXXX XXXXXSJIS XXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXX DoCoMo i-mode F800 - F9FF XXXXXXXXXXXXXXXXXXU+0FF800 - U+0FF9FF XXXXXXXXXXXXX ASTEL dot-i F000 - F4FF XXXXXXXXXXXXXXXXXXU+0FF000 - U+0FF4FF XXXXXXXXXXXXX J-PHONE J-SKY J-SKY XXXXXXXXXXXXXXXX "e$" XXXXXXX1XXXXX 1XXXXXXX2XXXXX"x0f"XXXXXXX 1XXXXXXXXXXXXXXXXX2XXXXXXXXXXXXXXXX XXXXXXXXXXXX XX1XXXXX2XXXXXXXX1XXXXXXXX4500 - 47FF XXXXX U+0FFB00 - U+0FFDFF XXXXXXXXXXXXX Unicode::Japanese XXXUnicode XX J-SKY XXXXXXXXXXXXXX 1XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX AU XXXXXXXXXXXXU+0FF500 - U+0FF6FF XXXXXXXXXXXXX PurePerl mode use Unicode::Japanese qw(PurePerl); use XXXXX 'PurePerl' XXXXXXX, XSXXXXXXXXXXXXXXXXXX. XX
XXXXXX "bug-unicode-japanese at rt.cpan.org" XX XXXXXXXX. XXXX http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Unicode-Japanese <http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Unicode-Japanese>. XXX web XXXXXXXXXXXXXXXXXX. XXXXXXXXXX, XXXXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXX. o EUC-JPXJIS XXXXXSJIS XXXXXXXX UTF-8 XXXXXXXXX SJIS XXXXXXXXXXXXXXXXXXXXXXXXXXX o XSXXXXXXXXXXEUC-JPXSJIS(XXXXX)XXXXXXXXX e XXXXXXXEUC-JPXSJIS XXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXX o Japanese.pm XXXXXXXXXXXXXXXXXXFTP X ASCII XXXX XXXXXXXXXXXXXXX XXXX
XXXXXXXXXXXXXXX perldoc XXXXXXXXXXXXXX. perldoc Unicode::Japanese XX, XXXXXXXXXXXXXXXX: o AnnoCPAN: Annotated CPAN documentation http://annocpan.org/dist/Unicode-Japanese <http://annocpan.org/dist/Unicode-Japanese> o CPAN Ratings http://cpanratings.perl.org/d/Unicode-Japanese <http://cpanratings.perl.org/d/Unicode-Japanese> o RT: CPAN's request tracker http://rt.cpan.org/NoAuth/Bugs.html?Dist=Unicode-Japanese <http://rt.cpan.org/NoAuth/Bugs.html?Dist=Unicode-Japanese> o Search CPAN http://search.cpan.org/dist/Unicode-Japanese <http://search.cpan.org/dist/Unicode-Japanese> CREDITS
Thanks very much to: NAKAYAMA Nao SUGIURA Tatsuki & Debian JP Project XXXXXXXXXX
Copyright 2001-2008 SANO Taku (SAWATARI Mikage) and YAMASHINA Hio, all rights reserved. XXXXXXXXXXXXXXXXXXXXXXXX Perl XXX XXXXXX XXXXXXXXXXXXXXXXXXX. perl v5.14.2 2008-08-05 Unicode::Japanese::JA(3pm)
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