Using Emacs 23.2.1 on Ubuntu Lucid, any mode based on Comint inserts occasional line breaks for larger outputs (see example Shell and SQL mode output, below). I've tried this in both SQL Mode and Shell Mode, with the same result in either case. Running similar commands in a plain terminal emulator does not cause these problems (for both shell mode and mysql mode commands).
Things I have tried:
Using MySQL in SQL Mode, adding the following flags: -A, -C, -t, -f, -n, and setting max_allowed_packet to 16MB.
Setting comint-buffer-maximum-size to 10240.
None of these have any effect on this behavior.
If I scroll up to the lines in question and delete the line breaks, the output then appears correctly, so a possible solution to this problem could involve a hook that deletes every 4096th character, if such a thing is possible.
Note: In the terminal examples, the output appears to be cut off at points other than every 4096 characters. In SQL-mode, it is exactly every 4096 (a suspicious number indeed).
Here is some sample output:
brent#battlecruiser:/$ for i in {1..4096}; do echo -n 0; done; echo;
0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
In this case, it should print out a single line of 0s, but in fact has inserted a new line character after 904 characters.
Also an Example in SQL Mode using MySQL:
mysql> show variables like '%n%';
+-----------------------------------------+----------------------------------+
| Variable_name | Value |
+-----------------------------------------+----------------------------------+
| auto_increment_increment | 1 |
| auto_increment_offset | 1 |
| binlog_cache_size | 32768 |
| binlog_format | STATEMENT |
| bulk_insert_buffer_size | 8388608 |
| character_set_client | utf8 |
| character_set_connection | utf8 |
| collation_connection | utf8_general_ci |
| collation_database | latin1_swedish_ci |
| collation_server | latin1_swedish_ci |
| completion_type | 0 |
| concurrent_insert | 1 |
| connect_timeout | 10 |
| delayed_insert_limit | 100 |
| delayed_insert_timeout | 300 |
| div_precision_increment | 4 |
| engine_condition_pushdown | ON |
| error_count | 0 |
| event_scheduler | OFF |
| foreign_key_checks | ON |
| ft_boolean_syntax | + -><()~*:""&| |
| ft_max_word_len | 84 |
| ft_min_word_len | 4 |
| ft_query_expansion_limit | 20 |
| general_log | OFF |
| general_log_file | /var/lib/mysql/battlecruiser.log |
| group_concat_max_len | 1024 |
| have_community_features | YES |
| have_dynamic_loading | YES |
| have_innodb | YES |
| have_ndbcluster | NO |
| have_openssl | DISABLED |
| have_partitioning | YES |
| have_symlink | YES |
| hostname | battlecruiser |
| identity | 0 |
| ignore_builtin_innodb | OFF |
| init_connect | |
| init_file | |
| init_slave | |
| innodb_adaptive_hash_index | ON |
| innodb_additional_mem_pool_size | 1048576 |
| innodb_autoextend_increment | 8 |
| innodb_autoinc_lock_mode | 1 |
| innodb_buffer_pool_size | 8388608 |
| innodb_checksums | ON |
| innodb_commit_concurrency | 0 |
| innodb_concurrency_tickets | 500 |
| innodb_data_file_path | ibdata1:10M:autoextend
|
| innodb_data_home_dir | |
| innodb_doublewrite | ON |
| innodb_fast_shutdown | 1 |
| innodb_file_io_threads | 4 |
| innodb_file_per_table | OFF |
| innodb_flush_log_at_trx_commit | 1 |
| innodb_flush_method | |
| innodb_force_recovery | 0 |
| innodb_lock_wait_timeout | 50 |
| innodb_locks_unsafe_for_binlog | OFF |
| innodb_log_buffer_size | 1048576 |
| innodb_log_file_size | 5242880 |
| innodb_log_files_in_group | 2 |
| innodb_log_group_home_dir | ./ |
| innodb_max_dirty_pages_pct | 90 |
| innodb_max_purge_lag | 0 |
| innodb_mirrored_log_groups | 1 |
| innodb_open_files | 300 |
| innodb_rollback_on_timeout | OFF |
| innodb_stats_on_metadata | ON |
| innodb_support_xa | ON |
| innodb_sync_spin_loops | 20 |
| innodb_table_locks | ON |
| innodb_thread_concurrency | 8 |
| innodb_thread_sleep_delay | 10000 |
| innodb_use_legacy_cardinality_algorithm | ON |
| insert_id | 0 |
| interactive_timeout | 28800 |
| join_buffer_size | 131072 |
| keep_files_on_create | OFF |
| key_cache_division_limit | 100 |
| language | /usr/share/mysql/english/ |
| last_insert_id | 0 |
| lc_time_names | en_US |
| license | GPL |
| local_infile | ON |
| locked_in_memory | OFF |
| log_bin | OFF |
| log_bin_trust_function_creators | OFF |
| log_bin_trust_routine_creators | OFF |
| log_queries_not_using_indexes | OFF |
| log_warnings | 1 |
| long_query_time | 10.000000 |
| lower_case_table_names | 0 |
| max_binlog_cache_size | 4294963200 |
| max_binlog_size | 104857600 |
| max_connect_errors | 10 |
| max_connections | 151 |
| max_error_count | 64 |
| max_insert_delayed_threads | 20 |
| max_join_size | 18446744073709551615 |
| max_length_for_sort_data | 1024
|
| max_prepared_stmt_count | 16382 |
| max_sort_length | 1024 |
| max_sp_recursion_depth | 0 |
| max_user_connections | 0 |
| max_write_lock_count | 4294967295 |
| min_examined_row_limit | 0 |
| multi_range_count | 256 |
| myisam_data_pointer_size | 6 |
| myisam_recover_options | BACKUP |
| net_buffer_length | 16384 |
| net_read_timeout | 30 |
| net_retry_count | 10 |
| net_write_timeout | 60 |
| new | OFF |
| open_files_limit | 1024 |
| optimizer_prune_level | 1 |
| plugin_dir | /usr/lib/mysql/plugin |
| profiling | OFF |
| profiling_history_size | 15 |
| protocol_version | 10 |
| query_cache_min_res_unit | 4096 |
| query_cache_wlock_invalidate | OFF |
| rand_seed1 | |
| rand_seed2 | |
| range_alloc_block_size | 4096 |
| read_only | OFF |
| read_rnd_buffer_size | 262144 |
| relay_log_index | |
| relay_log_info_file | relay-log.info |
| rpl_recovery_rank | 0 |
| skip_external_locking | ON |
| skip_networking | OFF |
| slave_net_timeout | 3600 |
| slave_transaction_retries | 10 |
| slow_launch_time | 2 |
| sql_auto_is_null | ON |
| sql_log_bin | ON |
| sql_max_join_size | 18446744073709551615 |
| sql_notes | ON |
| sql_slave_skip_counter | |
| sql_warnings | OFF |
| storage_engine | MyISAM |
| sync_binlog | 0 |
| sync_frm | ON |
| system_time_zone | EDT |
| table_definition_cache | 256 |
| table_open_cache | 64 |
| thread_handling | one-thread-per-connection |
| time_zone | SYSTEM |
| transaction_alloc_block_size | 8192 |
| transaction_prealloc_size | 4096 |
| tx_isolation
| REPEATABLE-READ |
| unique_checks | ON |
| version | 5.1.41-3ubuntu12.10 |
| version_comment | (Ubuntu) |
| version_compile_machine | i486 |
| version_compile_os | debian-linux-gnu |
| warning_count | 0 |
+-----------------------------------------+----------------------------------+
159 rows in set (0.00 sec)
Here the output is always interrupted by a newline at exact intervals of 4096 characters.
In addition to possible solutions, any new ways to find more information about what is happening would be appreciated.
I had similar problems, though my breaks seemed to be at 1024 characters (ah-ha! in version 21_1 this was the case). This wasn't that big a deal for me, but I did write something that properly concatenated the results so I could post-process them. That didn't affect the output though, so it won't be much help.
The root of your problem lies in read_process_output in process.c, which hard codes the 4096:
/* Read pending output from the process channel,
starting with our buffered-ahead character if we have one.
Yield number of decoded characters read.
This function reads at most 4096 characters.
If you want to read all available subprocess output,
you must call it repeatedly until it returns zero.
The characters read are decoded according to PROC's coding-system
for decoding. */
static int
read_process_output (proc, channel)
Lisp_Object proc;
register int channel;
{
// ... snip
int readmax = 4096;
Like you mentioned in your question, a very possible solution to this would be to write a function (call it, clean-up-comint-output-at-4096-chars), and add it to the comint-output-filter-functions. Something like this. Note: untested code.
(add-hook 'comint-output-filter-functions 'clean-up-comint-output-at-4096-chars)
(defun clean-up-comint-output-at-4096-chars (&optional str)
"look for string of 4096 length and remove newline in the buffer"
(let ((magic-block-size 4096))
(save-match-data
(when (= magic-block-size (length str))
;; at the magic block size, look for a newline
(goto-char (point-max))
(when (and (search-backward str nil t)
(progn
(forward-char magic-block-size)
(looking-at "\n")))
(delete-char 1))))))
I have found the solution to this problem. I had put in my configuration file the following code sourced from http://www.emacswiki.org/emacs/SqlMode
(defun sql-add-newline-first (output)
"Add newline to beginning of OUTPUT for `comint-preoutput-filter-functions'"
(concat "\n" output))
(defun sqli-add-hooks ()
"Add hooks to `sql-interactive-mode-hook'."
(add-hook 'comint-preoutput-filter-functions
'sql-add-newline-first))
(add-hook 'sql-interactive-mode-hook 'sqli-add-hooks)
After removing the code (which because it sets the comint-preoutput-filter-functions, affects shell-mode as well), I no longer experience these issues.
My proposed replacement for this code to get the behavior I want (works for me so far):
(defun sql-add-newline-first (output)
"Add newline to beginning of OUTPUT for `comint-preoutput-filter-functions'"
(remove-hook 'comint-preoutput-filter-functions
'sql-add-newline-first)
(concat "\n" output))
(defun sql-send-region-better (start end)
"Send a region to the SQL process."
(interactive "r")
(if (buffer-live-p sql-buffer)
(save-excursion
(add-hook 'comint-preoutput-filter-functions
'sql-add-newline-first)
(comint-send-region sql-buffer start end)
(if (string-match "\n$" (buffer-substring start end))
()
(comint-send-string sql-buffer "\n"))
(message "Sent string to buffer %s." (buffer-name sql-buffer))
(if sql-pop-to-buffer-after-send-region
(pop-to-buffer sql-buffer)
(display-buffer sql-buffer)))
(message "No SQL process started.")))
(defvar sql-mode-map
(let ((map (make-sparse-keymap)))
(define-key map (kbd "C-c C-c") 'sql-send-paragraph)
(define-key map (kbd "C-c C-r") 'sql-send-region-better)
(define-key map (kbd "C-c C-s") 'sql-send-string)
(define-key map (kbd "C-c C-b") 'sql-send-buffer)
map)
"Mode map used for `sql-mode'.")
Essentially, I am adding the hook right before my sql-send-region-better code starts sending output, then inside the hook I am removing the hook again, guaranteeing that it only inserts the one new line that I want.
Here is my implementation of only prepending "\n" once per input:
(defvar sql-last-prompt-pos 1
"position of last prompt when added recording started")
(make-variable-buffer-local 'sql-last-prompt-pos)
(put 'sql-last-prompt-pos 'permanent-local t)
(defun sql-add-newline-first (output)
"Add newline to beginning of OUTPUT for
`comint-preoutput-filter-functions'
This fixes up the display of queries sent to the inferior
buffer programatically. But also adds extra new-line for
interactive commands.
"
(let ((begin-of-prompt
(or (and comint-last-prompt-overlay
;; sometimes this overlay is not on prompt
(save-excursion
(goto-char (overlay-start comint-last-prompt-overlay))
(looking-at-p comint-prompt-regexp)
(point)))
1)))
(if (> begin-of-prompt sql-last-prompt-pos)
(progn
(setq sql-last-prompt-pos begin-of-prompt)
(concat "\n" output))
output)))
(defun le-sqli-setup ()
"Add hooks to `sql-interactive-mode-hook'."
(add-hook 'comint-preoutput-filter-functions
'sql-add-newline-first t t))
(add-hook 'sql-interactive-mode-hook 'le-sqli-setup)
My solution -- add a newline (but then remove the hook to prevent multiple ones breaking up the text). And then re-add the hook at every input prompt.
(defun sql-add-newline-first (output)
"Add newline to beginning of sql OUTPUT, but remove the hook so
that it doesn't output a newline everytime the output cache is
filled."
(remove-hook 'comint-preoutput-filter-functions 'sql-add-newline-first)
(concat "\n" output))
(defun sql-readd-newline-first (ignore)
"Readd the newline putting hook"
(add-hook 'comint-preoutput-filter-functions 'sql-add-newline-first))
(defun sqli-add-hooks ()
"Add the 'suicidal' newline printing hook, and another hook to
respawn it at every input prompt."
(add-hook 'comint-preoutput-filter-functions 'sql-add-newline-first)
(add-hook 'comint-input-filter-functions 'sql-readd-newline-first))
(add-hook 'sql-interactive-mode-hook 'sqli-add-hooks)
Also, in my case I was using postgresql. Which has the nasty habit of putting extra prompts after a multiline query (like database-# database-# database-# | col | col | ) which pushes the column names away. To solve, I eventually did this:
(defun sql-remove-continuing-prompts (output)
(concat "\n" (replace-regexp-in-string "warren_hero[^=()]# " "" output)))
(defun sqli-add-hooks ()
(add-hook 'comint-preoutput-filter-functions 'sql-remove-continuing-prompts))
(add-hook 'sql-interactive-mode-hook 'sqli-add-hooks)
Related
I have just started using org-mode and org-babel as a lab notebook. I am trying to use a code block to fill in two columns of a table. The code block seems to work for the first column because those are the right numbers. However, when trying to concatenate a string to the file name in column three so the code blocks works on a different set of files it seems to just run the code block on the original files instead, which produces the same output as column one.
#+name: tRNAs
#+begin_src sh :var filename="" :results silent
cd Data/tRNA
grep -c ">" $filename
#+end_src
#+tblname: sequences
| # of Sequences before QC | # after QC | Original File name|
|--------------------------+------------+------------------|
| 681865 | 681865 | read1 |
| 324223 | 324223 | read2 |
| 1014578 | 1014578 | read3 |
| 971965 | 971965 | read4 |
| 931777 | 931777 | read5 |
| 810798 | 810798 | read6 |
| 965134 | 965134 | read7 |
| 718474 | 718474 | read8 |
|--------------------------+------------+------------------|
#+TBLFM: $1='(org-sbe tRNAs (filename (concat "\"" $3 "\"")))
#+TBLFM: $2='(org-sbe tRNAs (filename (concat "\"final_" $3 "\"")))
GNU Emacs 24.4.1 org-mode
Here is an org-mode table
#+TBLNAME: revenue
| / | < | | < | | < | | | | | | | | | | | |
| Product | Year_SUM | Month_SUM | Platform | Platform_SUM | adwo | AdMob | adChina | adSage | appfigures | appdriver | coco | Domob | Dianru | Limei | guohead | youmi |
| | | | | | | | | | | | | | | | | |
|---------+----------+-----------+----------+------------------+------+-------+---------+--------+------------+-----------+------+-------+--------+-------+---------+-------|
| Jan | | | iOS | #ERROR | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| | | | Android | =vsum($6..$>);NE | | 1 | | 1 | | 1 | | 1 | | 1 | | 1 |
|---------+----------+-----------+----------+------------------+------+-------+---------+--------+------------+-----------+------+-------+--------+-------+---------+-------|
| | | | | | | | | | | | | | | | | |
#+TBLFM: $5=vsum($6..$>);NE
As you see ,the formula $5=vsum($6..$>);NE can't be calculated! Here is debug info:
Substitution history of formula
Orig: vsum($6..$>)
$xyz-> vsum($6..$>)
#r$c-> vsum($6..$>)
$1-> vsum((0)..$>)
--------^
Error: Expected `)'
But if I replace the formula with $5=vsum($6..$17) and then it works ,I can't figure out where is the problem?
I need some help ,appreciate it!
I'd like to do something like this:
How to achieve a row index column in Emacs Org Mode using a Calc column rule
but I'd like the rows to be numbered in reverse order. I suspect this should be very easy, and should have something to do with #>, but e.g. $1=#>-## doesn't work.
You can try this example
| row | data |
|-----+------|
| 8 | |
| 7 | |
|-----+------|
| 6 | |
| 5 | |
| 4 | |
| 3 | 5123 |
| 2 | |
| 1 | 4234 |
#+TBLFM: $1='(- (length org-table-dlines) ##)
Usually I edit source code in emacs with two (emacs-)windows side-by-side -- The second
windows opened via 'C-x 3. Like this:
+------------+-------------+
| | |
| src1 | src2 |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
+------------+-------------+
| mini-buffer |
+------------+-------------+
When I now start compile, eg with F9, the new *compilation* buffer replaces one of my src-buffers.
Instead I would like the *compilation* buffer to open on-top of the mini-buffer, if it is not visible already (if it is, use it, of course).
+------------+-------------+
| | |
| src1 | src2 |
| | |
| | |
| | |
| | |
+------------+-------------+
| |
| *compilation* |
| |
+------------+-------------+
| mini-buffer |
+------------+-------------+
The *compilation*-buffer should have a height of about 30% of the while window or 6-10 lines.
How to accomplish that?
One way to achieve this would be to use popwin.el. I've never used it but it seems pretty customizable and the default config includes *compilation* already.
I convert org-mode table to table.el table. For that I select the table:
| Option | Type | Value | Descr |
| -[no]h | bool | yes | Print |
| -[no]versio | bool | no | Print |
| -nice | int | 0 | Set t |
| -[no]v | bool | no | Be lo |
| -time | real | -1 | Take |
| -[no]rmvsbd | bool | yes | Removvirtual |
| sites | | | |
| -maxwarn | int | 0 | Numbe |
| procenerate | | | |
| unsta | | | |
| -[no]zero | bool | no | Set pthout |
| defau error | | | |
| -[no]renum | bool | yes | Renum |
| atomty | | | |
and press C-c ~. org-mode then asks me
Convert table to table.el table? (y or n)
How do I answer y programmically? I read the docs of that defun -- there's not way to do it with prefix arg.
Similar functionality in bash:
echo y | script-which-asks-y-or-n
C-c ~ calls the command org-table-create-with-table.el, which provides a bunch of wrappers around calling org-table-convert. If you want to use this function when you know you are already in an org-mode table, you don't need the wrappers, you just need the two (and probably only one) commands: org-table-align and org-table-convert.
So if you're doing this interactively, you can just call M-x org-table-convert and you're done. This assumes the table is already aligned. You can do this by hand by tabbing from one cell to the next, which triggers table alignment. Or you can do it with a small function:
(defun my-convert-tables ()
"No questions asked, just convert the table"
(interactive)
(org-table-align)
(org-table-convert))
You can do this programmatically as follows. You would replace the function name test1 with org-table-create-with-table.el in your defadvice functions that would be otherwise the same as those below.
Using defadvice to run some code before and after the function, we can save the function bound to the symbol y-or-n-p to a global variable and rebind it to a function that simply returns true. After the function we then restore the original functionality.
(setq save-y-or-n-p nil)
(defadvice test1 (around always-yes)
(fset 'save-y-or-n-p (symbol-function 'y-or-n-p))
(fset 'y-or-n-p (lambda (s) t))
ad-do-it
(fset 'y-or-n-p (symbol-function 'save-y-or-n-p)))
(defun test1 ()
(interactive)
(if (y-or-n-p "Happy? ")
(insert "Happy day")
(insert "Unhappy day")))