nothing is generated when choosing "select words to analyze". #1135
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Version number of KH Coder3.Beta.07b Details about the error or the problemnothing is generated when choosing "select words to analyze". This function worked earlier in the day, but then I had to edit the list of words as some of them were like stopwords. I edited it in Excel, and then saved as .txt. but now nothing works. Contents of the console windowTerminal outputLast login: Tue Sep 12 00:48:55 on ttys000
mycomp@80:38:fb:8c:e1:1e ~ % bash -c ' cd "/Users/mycomp/Desktop/khcoder3/";export LANG_BAK=$LANG;export TMPDIR="/Users/mycomp/Desktop/khcoder3/config";export LANG=ja_JP.UTF-8;export LC_ALL=ja_JP.UTF-8;export XMODIFIERS="@im=uim";export GTK_IM_MODULE=uim;export DYLD_FALLBACK_LIBRARY_PATH="/Users/mycomp/Desktop/khcoder3/deps/mysql-5.6.17/lib"; ./x_mac64'
Encoding of this Console: UTF-8
Encoding of this file system: UTF-8
Perl/Tk: 804.032
This is KH Coder 3.Beta.07b on darwin.
CWD: /Users/mycomp/Desktop/khcoder3
Executing Mac OS X 64-bit Package
Checking MySQL connection...
Starting MySQL...
2023-09-12 00:51:22 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2023-09-12 00:51:22 28301 [Warning] Setting lower_case_table_names=2 because file system for /Users/mycomp/Desktop/khcoder3/deps/mysql-5.6.17/data/ is case insensitive
2023-09-12 00:51:22 28301 [Note] Plugin 'FEDERATED' is disabled.
2023-09-12 00:51:22 28301 [Warning] Using unique option prefix innodb-locks instead of innodb-locks-unsafe-for-binlog is deprecated and will be removed in a future release. Please use the full name instead.
2023-09-12 00:51:22 28301 [Warning] Using unique option prefix innodb-cmp instead of innodb-cmp-per-index-enabled is deprecated and will be removed in a future release. Please use the full name instead.
2023-09-12 00:51:22 28301 [Note] Plugin 'InnoDB' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_TRX' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_LOCK_WAITS' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_CMP_RESET' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_CMPMEM' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_CMPMEM_RESET' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_CMP_PER_INDEX_RESET' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_BUFFER_PAGE' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_BUFFER_PAGE_LRU' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_BUFFER_POOL_STATS' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_METRICS' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_FT_DEFAULT_STOPWORD' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_FT_DELETED' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_FT_BEING_DELETED' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_FT_CONFIG' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_FT_INDEX_CACHE' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_FT_INDEX_TABLE' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_SYS_TABLES' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_SYS_TABLESTATS' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_SYS_INDEXES' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_SYS_COLUMNS' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_SYS_FIELDS' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_SYS_FOREIGN' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_SYS_FOREIGN_COLS' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_SYS_TABLESPACES' is disabled.
2023-09-12 00:51:22 28301 [Note] Plugin 'INNODB_SYS_DATAFILES' is disabled.
2023-09-12 00:51:22 28301 [Warning] Info table is not ready to be used. Table 'mysql.slave_master_info' cannot be opened.
2023-09-12 00:51:22 28301 [Warning] Info table is not ready to be used. Table 'mysql.slave_relay_log_info' cannot be opened.
2023-09-12 00:51:22 28301 [Note] Event Scheduler: Loaded 0 events
2023-09-12 00:51:22 28301 [Note] /Users/mycomp/Desktop/khcoder3/deps/mysql-5.6.17/bin/mysqld: ready for connections.
Version: '5.6.17' socket: '/tmp/mysql.sock.khc3' port: 0 MySQL Community Server (GPL)
sh: /Library/Frameworks/UIM.framework/Versions/Current/bin/uim-xim: No such file or directory
starting R: "/Users/mycomp/Desktop/khcoder3/deps/R-3.1.0/Resources/bin/R" --slave --vanilla
ram_r 16384
R Version: 3.1, x86_64
Using un-threaded functions...
Connected to MySQL 5.6, khc6.
MySQL integrity check: pass, /Users/mycomp/Desktop/khcoder3/deps/mysql-5.6.17
Checking icode (en)... ascii
Trying out a different dialog method for darwin...
Checking icode (en)... ascii
cmdline: java -showversion -mx300m -cp /Users/mycomp/Desktop/khcoder3/deps/stanford-postagger/stanford-postagger.jar edu.stanford.nlp.tagger.maxent.MaxentTaggerServer -outputFormat xml -outputFormatOptions lemmatize -port 32020 -model /Users/mycomp/Desktop/khcoder3/deps/stanford-postagger/models/wsj-0-18-left3words-distsim.tagger
Starting server, pid: 28508, Connecting.openjdk version "1.8.0_212"
OpenJDK Runtime Environment (AdoptOpenJDK)(build 1.8.0_212-b04)
OpenJDK 64-Bit Server VM (AdoptOpenJDK)(build 25.212-b04, mixed mode)
Loading default properties from tagger /Users/mycomp/Desktop/khcoder3/deps/stanford-postagger/models/wsj-0-18-left3words-distsim.tagger
Reading POS tagger model from /Users/mycomp/Desktop/khcoder3/deps/stanford-postagger/models/wsj-0-18-left3words-distsim.tagger ... .done [0.8 sec].
.. ok. Tagging... ok.
done: 00:00:09
Checking icode (en)... ascii
Checking icode (en)... ascii
Trying out a different dialog method for darwin...
Trying out a different dialog method for darwin...
Checking icode (en)... ascii
Checking icode (en)... ascii
cmdline: java -showversion -mx300m -cp /Users/mycomp/Desktop/khcoder3/deps/stanford-postagger/stanford-postagger.jar edu.stanford.nlp.tagger.maxent.MaxentTaggerServer -outputFormat xml -outputFormatOptions lemmatize -port 32020 -model /Users/mycomp/Desktop/khcoder3/deps/stanford-postagger/models/wsj-0-18-left3words-distsim.tagger
Starting server, pid: 28518, Connecting.openjdk version "1.8.0_212"
OpenJDK Runtime Environment (AdoptOpenJDK)(build 1.8.0_212-b04)
OpenJDK 64-Bit Server VM (AdoptOpenJDK)(build 25.212-b04, mixed mode)
Loading default properties from tagger /Users/mycomp/Desktop/khcoder3/deps/stanford-postagger/models/wsj-0-18-left3words-distsim.tagger
Reading POS tagger model from /Users/mycomp/Desktop/khcoder3/deps/stanford-postagger/models/wsj-0-18-left3words-distsim.tagger ... .done [0.7 sec].
.. ok. Tagging... ok.
Morpho1 16 wallclock secs ( 7.72 usr 0.21 sys + 8.31 cusr 0.71 csys = 16.95 CPU)
Single row: 348 bytes
The HEAP table will eat approx. 16MB; We have 1024MB max.
Read 1 wallclock secs ( 0.01 usr 0.03 sys + 0.01 cusr 0.01 csys = 0.06 CPU)
Format 0 wallclock secs ( 0.02 usr + 0.00 sys = 0.02 CPU)
Checking icode (en)... ascii
Checking icode (en)... ascii
Strat1 2 wallclock secs ( 0.20 usr + 0.01 sys = 0.21 CPU)
Strat2 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
RawTXT 0 wallclock secs ( 0.04 usr + 0.00 sys = 0.04 CPU)
df: heap df: heap df: heap df 1 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
fc 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
Check 0 wallclock secs ( 0.01 usr + 0.00 sys = 0.01 CPU)
fix_morpho 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
fix_unknown 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
fix_headings 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
make_cache 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
clear_tmp 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
MySQL: FLUSH
Morpho File: /Users/mycomp/Desktop/khcoder3/config/khc6/khc6_ch.txt
Trying out a different dialog method for darwin...
ok |
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Replies: 8 comments 13 replies
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Can you attach the files? The target text file. |
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what is the target text file?
It is definitely something wrong with the new text file callsed "cluster1_terms_narrow.txt"
I have just tried the old txt file (called cluster1_terms_text.txt) and it has just worked fine.
Here is the terminal output for the old file that has just worked:
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MySQL: FLUSH
Morpho File: /Users/mycomp/Desktop/khcoder3/config/khc6/khc6_ch.txt
Trying out a different dialog method for darwin...
ok ok ok ok Checking icode (en)... ascii
new default extension: .txt
Checking icode (en)... ascii
Trying out a different dialog method for darwin...
Trying out a different dialog method for darwin...
Checking icode (en)... ascii
Checking icode (en)... ascii
cmdline: java -showversion -mx300m -cp /Users/mycomp/Desktop/khcoder3/deps/stanford-postagger/stanford-postagger.jar edu.stanford.nlp.tagger.maxent.MaxentTaggerServer -outputFormat xml -outputFormatOptions lemmatize -port 32020 -model /Users/mycomp/Desktop/khcoder3/deps/stanford-postagger/models/wsj-0-18-left3words-distsim.tagger
Starting server, pid: 2018, Connecting.openjdk version "1.8.0_212"
OpenJDK Runtime Environment (AdoptOpenJDK)(build 1.8.0_212-b04)
OpenJDK 64-Bit Server VM (AdoptOpenJDK)(build 25.212-b04, mixed mode)
Loading default properties from tagger /Users/mycomp/Desktop/khcoder3/deps/stanford-postagger/models/wsj-0-18-left3words-distsim.tagger
Reading POS tagger model from /Users/mycomp/Desktop/khcoder3/deps/stanford-postagger/models/wsj-0-18-left3words-distsim.tagger ... .done [0.8 sec].
.. ok. Tagging... ok.
Morpho1183 wallclock secs (173.04 usr1.23 sys +9.31 cusr1.45 csys = 185.03 CPU)
Single row: 604 bytes
The HEAP table will eat approx. 24MB; We have 1024MB max.
Read 1 wallclock secs ( 0.00 usr +0.03 sys =0.03 CPU)
Format 1 wallclock secs ( 0.03 usr +0.00 sys =0.03 CPU)
Checking icode (en)... ascii
Checking icode (en)... ascii
Strat1 1 wallclock secs ( 0.28 usr +0.04 sys =0.32 CPU)
Strat2 1 wallclock secs ( 0.00 usr +0.00 sys =0.00 CPU)
RawTXT 0 wallclock secs ( 0.03 usr +0.00 sys =0.03 CPU)
df: heapdf: heapdf: heap df 0 wallclock secs ( 0.01 usr +0.00 sys =0.01 CPU)
fc 1 wallclock secs ( 0.00 usr +0.00 sys =0.00 CPU)
Check 0 wallclock secs ( 0.00 usr +0.00 sys =0.00 CPU)
fix_morpho 0 wallclock secs ( 0.00 usr +0.00 sys =0.00 CPU)
fix_unknown 0 wallclock secs ( 0.00 usr +0.00 sys =0.00 CPU)
fix_headings 0 wallclock secs ( 0.00 usr +0.00 sys =0.00 CPU)
make_cache 0 wallclock secs ( 0.00 usr +0.00 sys =0.00 CPU)
clear_tmp 0 wallclock secs ( 0.01 usr +0.00 sys =0.01 CPU)
MySQL: FLUSH
Morpho File: /Users/mycomp/Desktop/khcoder3/config/khc6/khc6_ch.txt
Trying out a different dialog method for darwin...
ok Checking icode (en)... ascii
~~~~~~~~~~~~~~~~~
Prof. Tatiana Lukoianove, Ph.D.
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Also, when the software works, it takes it about 3 min after I click "Run pre-processing"
When the output is not generated (for example word frequencies), then it takes about 19 seconds after I click "Pre-processing".
Thank you!
Tatiana
Prof. Tatiana Lukoianove, Ph.D.
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It is the file you specified here (when you create a new project):
Can you attach the files here? Let's check the differences of these files. Please note that you have to open this web page to attach files. You can't attach files by sending e-mails. |
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I am not sure if this is helpful, however, I decided to copy the list of new phrases and then "paste and match style" into the old txt file, which works. As a results frequencies are calculated for a few phrases from the list however when I click on the word, I receive the following error message:
[image.png]
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This is the terminal's output for the correctly working file with phrases: Loading default properties from tagger /Users/mycomp/Desktop/khcoder3/deps/stanford-postagger/models/wsj-0-18-left3words-distsim.tagger Loading default properties from tagger /Users/mycomp/Desktop/khcoder3/deps/stanford-postagger/models/wsj-0-18-left3words-distsim.tagger |
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This is file with a smaller number of phrases and it is somehow does not work |
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As you can see the above 2 files with the phrases are very similar and the difference is in the number of the phrases: the new file has few phrases compared to the old one. |
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here is the output for the old file with phrases |
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here is the Terminal's output for the file with phrases, which did not work MySQL: FLUSH Loading default properties from tagger /Users/mycomp/Desktop/khcoder3/deps/stanford-postagger/models/wsj-0-18-left3words-distsim.tagger |
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When you see this, just restart KH Coder. |
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OK, finally we can look into the actual data files. As you can see in the screenshot below, "cluster1_terms_text_narrow.txt" contains unnecessary spaces.
So I deleted the spaces. Can you try this file? |
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Well, right now I am trying with "cluster1_terms_text.txt", but the list in the file is so huge that it is taking a long time to run pre-processing... |
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Here is the results on my environment: cluster1_terms_text.txt: (looks same as yours) cluster1_terms_text_narrow_ed.txt: The edited file cluster1_terms_text_narrow_ed.txt seems to be working on my env. Hint: in the "select words to analyze screen", you can check "Read from a file" and specify a file like "cluster1_terms_text_narrow_ed.txt". This way, you may avoid the above error. |
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Thank you! You made my day! Your file now works for me too. I think my yesterday's file had potentially some special characters, because I transformed it in Excel and then saved in .txt. I wonder if you may suggest a way to work with .txt files to prepare them for the software to ensure that the software can read it. Is it possible to use a .csv file for the "selected words to analyze" option? |
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There were unwanted white space characters (red circles).
In general, we recommend using a text editor that can display & manage white spaces and other special characters. I know some good text editors made in Japan but I am not sure if they have English interface... I have no knowledge about English text editors for macOS... Sorry.
I afraid no. |
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Thank you. I will try to find a software with such functionalities in English. |
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OK, finally we can look into the actual data files.
As you can see in the screenshot below, "cluster1_terms_text_narrow.txt" contains unnecessary spaces.
So I deleted the spaces. Can you try this file?
cluster1_terms_text_narrow_ed.txt