<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div apple-content-edited="true"><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div></div></div></div></div></div></div><br><div><div>On May 25, 2016, at 23:52, Haruo Suzuki <<a href="mailto:haruo@sfc.keio.ac.jp">haruo@sfc.keio.ac.jp</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Dear Simon,<br><br>FYI<br><br># library(help=seqinr)<br><br>I got the following error messages again although I restarted and reinstalled R:<br>----------<br><blockquote type="cite">library(help=seqinr)<br></blockquote>Error in formatDL(nm, txt, indent = max(nchar(nm, "w")) + 3) : <br> incorrect values of 'indent' and 'width'<br><br><blockquote type="cite">library(seqinr)<br></blockquote>Loading required package: ade4<br><br><blockquote type="cite">sessionInfo()<br></blockquote>R version 3.3.0 (2016-05-03)<br>Platform: x86_64-apple-darwin13.4.0 (64-bit)<br>Running under: OS X 10.9.5 (Mavericks)<br><br>locale:<br>[1] C<br><br>attached base packages:<br>[1] stats graphics grDevices utils datasets methods base <br><br>other attached packages:<br>[1] seqinr_3.1-3 ade4_1.7-4 <br>----------<br><br><br># read.fasta<br><br>In page 196 of the book 'Bioinformatics Data Skills' (<a href="http://shop.oreilly.com/product/0636920030157.do">http://shop.oreilly.com/product/0636920030157.do</a>), it is stated that 'R’s data-reading functions can also read gzipped files directly—there’s no need to uncompress gzipped files first.’<br>The `read.fasta` function of seqinr package can load gzipped files using:<br>----------<br>system('curl -O <a href="ftp://ftp.ncbi.nlm.nih.gov/refseq/release/plasmid/plasmid.1.rna.fna.gz'">ftp://ftp.ncbi.nlm.nih.gov/refseq/release/plasmid/plasmid.1.rna.fna.gz'</a>)<br>lna <- read.fasta(file = "~/plasmid.1.rna.fna.gz", seqtype = c("DNA”))<br>----------<br><br>In page 174 of the book ‘Building Bioinformatics Solutions' (<a href="https://bixsolutions.net">https://bixsolutions.net</a>), it is stated that 'It is even possible to load files directly from remote servers on a network, or on the Internet, simply by specifying a full URL instead of just a file name’.<br>The `read.fasta` function of seqinr package can not load the FASTA file directly from the ftp site, simply by specifying a full URL:<br>----------<br><blockquote type="cite"> lna <- read.fasta(file = "<a href="ftp://ftp.ncbi.nlm.nih.gov/refseq/release/plasmid/plasmid.1.rna.fna.gz">ftp://ftp.ncbi.nlm.nih.gov/refseq/release/plasmid/plasmid.1.rna.fna.gz</a>", seqtype = c("DNA"))<br></blockquote>Error in read.fasta(file = "<a href="ftp://ftp.ncbi.nlm.nih.gov/refseq/release/plasmid/plasmid.1.rna.fna.gz">ftp://ftp.ncbi.nlm.nih.gov/refseq/release/plasmid/plasmid.1.rna.fna.gz</a>", : <br> no line starting with a > character found<br>In addition: There were 16 warnings (use warnings() to see them)<br><blockquote type="cite">warnings()<br></blockquote>Warning messages:<br>1: In readLines(file) : line 1 appears to contain an embedded nul<br><br>*snip*<br><br>15: In readLines(file) : line 39 appears to contain an embedded nul<br>16: In readLines(file) :<br> incomplete final line found on '<a href="ftp://ftp.ncbi.nlm.nih.gov/refseq/release/plasmid/plasmid.1.rna.fna.gz'">ftp://ftp.ncbi.nlm.nih.gov/refseq/release/plasmid/plasmid.1.rna.fna.gz'</a><br>----------<br><br>Best,<br>Haruo<br></blockquote></div><br></body></html>