![]() For example, run the following command to extract the compress. If you look at the code for utils::untar() you’ll see: # The function definition of utils::untarįunction (tarfile, files = NULL, list = FALSE, exdir = ". 1 In this article you will learn how to extract tar archives into a specific directory, as well as selecting and untarring only specific files and directories. You can use the option -z with the tar command to extract or uncompress the Gzip archive file. show progress and file names while extracting files.-t: List files stored in the archive.-f backup. Uncompressing the tar.gz file is done by utils::untar(). The options used so far as follows: -z: Uncompress the resulting archive with gunzip command or gunzip command.-x: Extract to disk from the archive.-v: Produce verbose output i.e. We were told to try installing R at a location with no spaces, so by this point, R was installed at C:\R\R-3.6.0\, hence the lib specification you see above, though it’s irrelevant for these errors. The default is freadNA, which checks for availability of the R package data.table and the system command unzip. You can even download the file and try to run untar() manually and it will fail. If you search on Google the error message you’ll find links like this one which hint towards an incomplete download. ADD COMMENT link 6.1 years ago by h.mon 34k Login before adding your answer. ‘C:\Users\Leo Collado\AppData\Local\Temp\RtmpqiBJ53\downloaded_packages’ You have to untar GSE57821RAW.tar and then uncompress the counts files, read one by one with read.table () and finally create the ExpressionSet or DGElist objects yourself. Installing package(s) 'BiocVersion', 'DO.db'Ĭontent type 'application/x-gzip' length 1769978 bytes (1.7 MB)Įrror in untar2(tarfile, files, list, exdir, restore_times) : 1 Why would you not want people to have to install your package And, no, I don't think it is possible to do what you want - you need to have the files installed somewhere for library () to work and that is, AFAIK, the only way to really use a package in R. Why? > BiocManager::install('DO.db', lib = 'C:/R/R-3.6.0/library')īioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 () The appropriate command for this is tar xzvf filename, where filename is the name of the. Uncompressing a file in this scenario fails. tar.gz using option -xvzf : This command extracts files from tar archived files. Internally, BiocManager::install() ends up using utils::install.packages(). gzip compression on the tar Archive, using option -z : This command creates a tar file called which is the Archive of. ![]()
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