I hope this message finds you well. I am writing to report a potential bug in the getGEO() function of the GEOquery package, specifically concerning the handling of encoding parameters and error management.
Upon attempting to utilize the encoding parameter with the getGEO() function, I encountered an error indicating that the parameter is unused. This suggests that the function does not currently support the direct specification of encoding, potentially leading to challenges in processing files with various encodings.
Furthermore, when running the function with the GSEMatrix parameter set to TRUE for downloading the latest GSExxx data, I encountered errors. For instance, executing GSE233761 <- getGEO('GSE233761', GSEMatrix = TRUE, destdir = "D:/GEOtemp") resulted in an error, while setting GSEMatrix to FALSE led to multiple warnings. These issues seem to arise during the parsing of Matrix files.
While the documentation advises using alternative methods such as iconv for handling encoding problems post-file retrieval, the inability to directly specify encoding within getGEO() could be considered a limitation, particularly for users dealing with diverse datasets.
Moreover, the occurrence of errors and warnings during the retrieval process, especially when attempting to download the latest datasets, suggests potential issues with error handling within the function.
Addressing these concerns by enabling users to specify encoding directly within the getGEO() function and ensuring robust error management during data retrieval would significantly enhance the package’s usability and reliability for users across various data sources.
Thank you for considering this feedback. Should you require additional details or assistance in resolving these issues, please feel free to reach out to me.
I hope this message finds you well. I am writing to report a potential bug in the getGEO() function of the GEOquery package, specifically concerning the handling of encoding parameters and error management.
Upon attempting to utilize the encoding parameter with the getGEO() function, I encountered an error indicating that the parameter is unused. This suggests that the function does not currently support the direct specification of encoding, potentially leading to challenges in processing files with various encodings.
Furthermore, when running the function with the GSEMatrix parameter set to TRUE for downloading the latest GSExxx data, I encountered errors. For instance, executing GSE233761 <- getGEO('GSE233761', GSEMatrix = TRUE, destdir = "D:/GEOtemp") resulted in an error, while setting GSEMatrix to FALSE led to multiple warnings. These issues seem to arise during the parsing of Matrix files.
While the documentation advises using alternative methods such as iconv for handling encoding problems post-file retrieval, the inability to directly specify encoding within getGEO() could be considered a limitation, particularly for users dealing with diverse datasets.
Moreover, the occurrence of errors and warnings during the retrieval process, especially when attempting to download the latest datasets, suggests potential issues with error handling within the function.
Addressing these concerns by enabling users to specify encoding directly within the getGEO() function and ensuring robust error management during data retrieval would significantly enhance the package’s usability and reliability for users across various data sources.
Thank you for considering this feedback. Should you require additional details or assistance in resolving these issues, please feel free to reach out to me.
Sincerely, Guossin.
![Uploading pic_2.png…]()