Error in read *.lcd files

[filipevictoria]

I'm trying to use ChromatrographR but every data then I tryed to call the same error occurs, as follow:

Warning in read_chroms(paths = "my path", :
Error in sub("^\037\004|^o\004", "", raw_xml) : input string 1 is invalid
The following chromatograms could not be interpreted: 1, 2, 3, 4, 5
list()
Warning messages:
1: In readLines(path_prop, skipNul = TRUE) :
incomplete final line found on '/var/folders/pl/j44pqpqx7xq6zg1wfr25y_ch0000gn/T/RtmptXE7MM/data_File_Property13828456058bb'
2: In sub("^\037\004|^o\004", "", raw_xml) :
unable to translate '�3.00Admin��1v,�Admin<89>Hg4������1.25-1�Unknownextrato_01Admin<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>...' to a wide string
3: In readLines(path_prop, skipNul = TRUE) :
incomplete final line found on '/var/folders/pl/j44pqpqx7xq6zg1wfr25y_ch0000gn/T/RtmptXE7MM/data_00_File_Property1382838618092'
4: In sub("^\037\004|^o\004", "", raw_xml) :
unable to translate '�3.00Admin{$..�AdminX�<9a>.������1.25-1�Unknownextrato_001Admin<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?...' to a wide string
5: In readLines(path_prop, skipNul = TRUE) :
incomplete final line found on '/var/folders/pl/j44pqpqx7xq6zg1wfr25y_ch0000gn/T/RtmptXE7MM/extrato_1_File_Property138289400e29'
6: In sub("^\037\004|^o\004", "", raw_xml) :
unable to translate '�3.00Admin!n,�Adminclzu,������1.25-1�Unknownextrato_11Admin<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>...' to a wide string
7: In readLines(path_prop, skipNul = TRUE) :
incomplete final line found on '/var/folders/pl/j44pqpqx7xq6zg1wfr25y_ch0000gn/T/RtmptXE7MM/extrato_2_File_Property138284c61aa7d'
8: In sub("^\037\004|^o\004", "", raw_xml) :
unable to translate '�3.00Admin>EI`,�AdminDk*f,������1.25-1�Unknownextrato_21Admin<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?A...' to a wide string
9: In readLines(path_prop, skipNul = TRUE) :
incomplete final line found on '/var/folders/pl/j44pqpqx7xq6zg1wfr25y_ch0000gn/T/RtmptXE7MM/extrato_3_File_Property1382820001bb8'
10: In sub("^\037\004|^o\004", "", raw_xml) :
unable to translate '�3.00Admin{�^R,�Admin<8e>�X,������1.25-1�Unknownextrato_31Admin<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>?<80>...' to a wide string

How can I fix this?

Thanks in advance

[ethanbass]

Hi,
Thanks for posting this issue. It looks to me like there are some special characters in the metadata that are causing the error. You could try setting read_metadata = FALSE in the call to read_chroms and see if this makes the error go away. If not, or if you want to access the metadata, I can try to track down the problem and come up with a patch if you are able to share one of your files with me.
Best,
Ethan

[filipevictoria]

Hi Ethan,
Thanks for you advice, I tried to set for read_metadata = FALSE and the same error occurs. Anyway, I used the shimazdu_ascii option and managed to open my data, but now I can't give the matplot command, but I get this "Error: unexpected '=' in:
"matplot(x = tpoints, y = data[[i]][,lambda],
+ type ="

, I send you both samples of my data in both *.lcd and *.txt format, I'm suspicious that it's really in my files, so if you find any inconsistencies and can help me I appreciate it.
Teste.zip

Thanks in advance

[ethanbass]

Hi,
I only see the ascii file in Teste.zip. Did you mean to include the .lcd file as well? I'd like to take a look at it.
To plot your chromatograms from the ascii files, try:

x <- read_chroms("/Users/ethanbass/Downloads/Teste/data_01.txt", format_in="shimadzu_ascii")
tpoints <- as.numeric(rownames(x[[1]][[1]]))
matplot(tpoints, x[[1]][[1]], type='l')

[filipevictoria]

Dear Ethan Thanks again for help me in my issues. Follow the lcd file by mail. Filipe Em qui., 14 de nov. de 2024 às 12:58, Ethan Bass ***@***.***> escreveu:

…

Hi, I only see the ascii file in Teste.zip. Did you mean to include the .lcd file as well? I'd like to take a look at it. To plot your chromatograms from the ascii files, try: x <- read_chroms("/Users/ethanbass/Downloads/Teste/data_01.txt", format_in="shimadzu_ascii") tpoints <- as.numeric(rownames(x[[1]][[1]])) matplot(tpoints, x[[1]][[1]], type='l') — Reply to this email directly, view it on GitHub <#34 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHYFW2VSQ3JQJQLMTLV43YL2ATCA7AVCNFSM6AAAAABRWH637SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINZWG44DIMBVGU> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[ethanbass]

Still didn't get the LCD. did you send it to ethanbass@gmail.com ?

[ethanbass]

Hi,
Thanks for sharing the example file. Your file doesn't contain either of the streams that I have been using to extract information about the retention times in other LCD files. Once I figure out where the times are stored, I should be able to make a patch for the LCD parser.

[ethanbass]

This should be fixed by ethanbass/chromConverter@d7faa83. I had to infer the retention times based solely only on the interval between points (which is encoded in the chromatogram streams), assuming that the times start at 0.

The metadata for your files is also in a completely different format than other LCD files I've seen. I did my best to decode it, but there are still some fields missing.