Date: Sat, 4 Aug 2012 00:20:11 GMT From: "Reed A. Cartwright" <cartwright@asu.edu> To: freebsd-ports-bugs@FreeBSD.org Subject: Re: ports/169920: Update biology/mafft to latest version Message-ID: <201208040020.q740KBA2091133@freefall.freebsd.org>
next in thread | raw e-mail | index | archive | help
The following reply was made to PR ports/169920; it has been noted by GNATS. From: "Reed A. Cartwright" <cartwright@asu.edu> To: Michael Scheidell <scheidell@freebsd.org> Cc: bug-followup@freebsd.org Subject: Re: ports/169920: Update biology/mafft to latest version Date: Fri, 3 Aug 2012 17:18:07 -0700 --e89a8f3ba6b73ae30104c66594eb Content-Type: text/plain; charset=ISO-8859-1 1) I've attached a new patch made between biology/mafft.orig and biology/mafft 2) I've run portlint -abmt, and it returns two warnings, one is a false positive and the other has to do with lack of master sites. 3) I've joined freebsd-ports and have read the porter's handbook. Let me know if you need anything else. On Fri, Aug 3, 2012 at 2:54 AM, Michael Scheidell <scheidell@freebsd.org> wrote: > Greetings: > > Thank you for your submission for biology/mafft. > > Your work is greatly appreciated. > > A couple of issues, first: > you should read the porters handbook on the FreeBSD.org web site, and join > the mailing list 'freebsd-ports'. > > You will find both of these resources invaluable as you work on this and > other FreeBSD ports. > > Also, you need to product the patch using 'diff -ruN' (needs a unified diff, > and -N is just in case) > > run 'portlint -abmt' after you patch the port, and test to make sure it not > only compiles, but packages as well. (and pkg_delete or make deinstall > erases all 'new' files) > > One more thing that you might find helpful. FreeBSD is now using subversion > on its ports src tree. You should be able to find information on the > porters handbook, and or here to help you use svn for your work. > > (then, you can just use 'svn diff' ). > > Once you create a proper patch, you can upload it using a mail client that > can handle attachments, > to: bug-followup@FreeBSD.org > subject: Re: ports/169920: Update biology/mafft to latest version > > Thanks again for your help. > > (note: as far as changing maintainers, that is up to the current maintainer. > Only they can give up maintainership under normal circumstances) > > -- > Michael Scheidell, CTO >> | SECNAP Network Security Corporation > d: +1.561.948.2259 > w: http://people.freebsd.org/~scheidell -- Reed A. Cartwright, PhD Assistant Professor of Genomics, Evolution, and Bioinformatics School of Life Sciences Center for Evolutionary Medicine and Informatics The Biodesign Institute Arizona State University --e89a8f3ba6b73ae30104c66594eb Content-Type: application/octet-stream; name="mafft.patch" Content-Disposition: attachment; filename="mafft.patch" Content-Transfer-Encoding: base64 X-Attachment-Id: f_h5fyhlfx0 ZGlmZiAtcnVOIG1hZmZ0Lm9yaWcvTWFrZWZpbGUgbWFmZnQvTWFrZWZpbGUKLS0tIG1hZmZ0Lm9y aWcvTWFrZWZpbGUJMjAxMi0wNy0xMyAxMzo0NzoyMC43Nzc2OTgzNzQgLTA3MDAKKysrIG1hZmZ0 L01ha2VmaWxlCTIwMTItMDctMTYgMTU6MDM6MjYuMTUyNjQwMDk1IC0wNzAwCkBAIC03LDM0ICs3 LDY4IEBACiAjCiAKIFBPUlROQU1FPQltYWZmdAotUE9SVFZFUlNJT049CTUuNzQzCitQT1JUVkVS U0lPTj0JNi45MDMKIENBVEVHT1JJRVM9CWJpb2xvZ3kKLU1BU1RFUl9TSVRFUz0JaHR0cDovL2Fs aWduLmJtci5reXVzaHUtdS5hYy5qcC9tYWZmdC9zb2Z0d2FyZS8KLURJU1ROQU1FPQkke1BPUlRO QU1FfS0ke1BPUlRWRVJTSU9OfS1zcmMKK01BU1RFUl9TSVRFUz0JaHR0cDovL21hZmZ0LmNicmMu anAvYWxpZ25tZW50L3NvZnR3YXJlLworRElTVE5BTUU9CSR7UE9SVE5BTUV9LSR7UE9SVFZFUlNJ T059LXdpdGhvdXQtZXh0ZW5zaW9ucy1zcmMKIEVYVFJBQ1RfU1VGWD0JLnRnegogCiBNQUlOVEFJ TkVSPQlmZXJuYW5AaWliLnVuc2FtLmVkdS5hcgotQ09NTUVOVD0JTXVsdGlwbGUgc2VxdWVuY2Ug YWxpZ25tZW50cyBiYXNlZCBvbiBmYXN0IEZvdXJpZXIgdHJhbnNmb3JtCitDT01NRU5UPQlNdWx0 aXBsZSBhbGlnbm1lbnQgcHJvZ3JhbSBmb3IgYW1pbm8gYWNpZCBvciBudWNsZW90aWRlIHNlcXVl bmNlcworCitMSUNFTlNFPQlCU0QKIAogUlVOX0RFUEVORFM9CWxhdjJwczoke1BPUlRTRElSfS9i aW9sb2d5L2Zhc3RhMwogCi1XUktTUkM9CQkke1dSS0RJUn0vJHtQT1JUTkFNRX0tJHtQT1JUVkVS U0lPTn0KLUJVSUxEX1dSS1NSQz0JJHtXUktTUkN9L3NyYworV1JLU1JDPQkJJHtXUktESVJ9LyR7 UE9SVE5BTUV9LSR7UE9SVFZFUlNJT059LXdpdGhvdXQtZXh0ZW5zaW9ucworQlVJTERfV1JLU1JD PQkke1dSS1NSQ30vY29yZQorCitVU0VfR01BS0U9CXllcworCitNQU4xPQkJbWFmZnQuMSBtYWZm dC1ob21vbG9ncy4xCisKK0xJQkVYRUNfRklMRVM9CWR2dGRpdHIgZG5kZmFzdDcgZG5kYmxhc3Qg c2V4dGV0NSBtYWZmdC1kaXN0YW5jZSBwYWlybG9jYWxhbGlnbiBcCisJCXBhaXIyaGF0M3MgbXVs dGkyaGF0M3Mgcm5hdGVzdCBwYWlyYXNoIGFkZHNpbmdsZSBzcGxpdHRiZmFzdCBcCisJCWRpc3R0 YmZhc3QgdGJmYXN0IG1hZmZ0LXByb2ZpbGUgZjJjbCBtY2Nhc2tpbGx3cmFwIGNvbnRyYWZvbGR3 cmFwIFwKKwkJY291bnRsZW4gc2VxMnJlZ3RhYmxlIHJlZ3RhYmxlMnNlcSBzY29yZSBnZXRsYWcg ZG5kcHJlIGRuZHByZTIgXAorCQlzZXRjb3JlIHJlcGxhY2V1IHJlc3RvcmV1IHNldGRpcmVjdGlv biBtYWtlZGlyZWN0aW9ubGlzdCB2ZXJzaW9uCitTQ1JJUFRfRklMRVM9CW1hZmZ0IG1hZmZ0LWhv bW9sb2dzLnJiCitMTl9GSUxFUz0JZWluc2kgZmZ0bnMgZmZ0bnNpIGdpbnNpIGxpbnNpIG1hZmZ0 LWVpbnNpIG1hZmZ0LWZmdG5zIFwKKwkJbWFmZnQtZmZ0bnNpIG1hZmZ0LWdpbnNpIG1hZmZ0LWxp bnNpIG1hZmZ0LW53bnMgbWFmZnQtbnduc2kgXAorCQltYWZmdC1xaW5zaSBtYWZmdC14aW5zaSBu d25zIG53bnNpCiAKLU1BS0VfRU5WKz0JQ0ZMQUc9IiR7Q0ZMQUdTfSIKKy5pbmNsdWRlIDxic2Qu cG9ydC5wcmUubWs+CiAKIHBvc3QtcGF0Y2g6Ci0JQCR7UkVJTlBMQUNFX0NNRH0gLUUgJ3MsXihD Q3xQUkVGSVgpID0sXDEgPz0sJyBcCi0JCSR7V1JLU1JDfS9zcmMvTWFrZWZpbGUKKwlAJHtSRUlO UExBQ0VfQ01EfSAtZSAnc3wtbHB0aHJlYWR8JHtQVEhSRUFEX0xJQlN9fCcgXAorCSAgICAgICAg ICAgICAgICAgIC1lICdzfF5NQU5ESVIgPSAuKiQkfE1BTkRJUiA9ICQkKE1BTlBSRUZJWCkvbWFu L21hbjF8JyBcCisJICAgICAgICAgICAgICAgICAgLWUgJ3N8XlBSRUZJWCA9IC4qJCR8fCcgXAor CSAgICAgICAgICAgICAgICAgIC1lICdzfF5DQyA9IC4qJCR8fCcgXAorCSAgICAgICAgICAgICAg ICAgIC1lICdzfF5DRkxBR1MgPSAuKiQkfHwnIFwKKwkJJHtCVUlMRF9XUktTUkN9L01ha2VmaWxl CiAKIGRvLWluc3RhbGw6Ci0JJHtJTlNUQUxMX1NDUklQVH0gJHtXUktTUkN9L3NjcmlwdHMvbWFm ZnQgJHtQUkVGSVh9L2JpbgotCSR7SU5TVEFMTF9QUk9HUkFNfSAke1dSS1NSQ30vYmluYXJpZXMv KiAke1BSRUZJWH0vYmluCi0JQCAke01LRElSfSAke0VYQU1QTEVTRElSfQorCUAke01LRElSfSAk e1BSRUZJWH0vbGliZXhlYy8ke1BPUlROQU1FfQorLmZvciBleGVjIGluICR7TElCRVhFQ19GSUxF U30KKwkke0lOU1RBTExfUFJPR1JBTX0gJHtXUktTUkN9L2JpbmFyaWVzLyR7ZXhlY30gJHtQUkVG SVh9L2xpYmV4ZWMvJHtQT1JUTkFNRX0KKy5lbmRmb3IKKy5mb3IgZXhlYyBpbiAke1NDUklQVF9G SUxFU30KKwkke0lOU1RBTExfU0NSSVBUfSAke1dSS1NSQ30vc2NyaXB0cy8ke2V4ZWN9ICR7UFJF RklYfS9iaW4KKy5lbmRmb3IKKy5mb3IgZXhlYyBpbiAke0xOX0ZJTEVTfQorCSR7TE59IC1mcyAk e1BSRUZJWH0vYmluL21hZmZ0ICR7UFJFRklYfS9iaW4vJHtleGVjfQorLmVuZGZvcgorCSR7TE59 IC1mcyAke1BSRUZJWH0vbGliZXhlYy8ke1BPUlROQU1FfS9tYWZmdC1kaXN0YW5jZSAke1BSRUZJ WH0vYmluL21hZmZ0LWRpc3RhbmNlCisJJHtMTn0gLWZzICR7UFJFRklYfS9saWJleGVjLyR7UE9S VE5BTUV9L21hZmZ0LXByb2ZpbGUgJHtQUkVGSVh9L2Jpbi9tYWZmdC1wcm9maWxlCisuZm9yIG1h biBpbiAke01BTjF9CisJJHtJTlNUQUxMX01BTn0gJHtXUktTUkN9L2JpbmFyaWVzLyR7bWFufSAk e01BTjFQUkVGSVh9L21hbi9tYW4xCisuZW5kZm9yCisJQCR7TUtESVJ9ICR7RVhBTVBMRVNESVJ9 CiAJJHtJTlNUQUxMX0RBVEF9ICR7V1JLU1JDfS90ZXN0LyogJHtFWEFNUExFU0RJUn0KIC5pZiAh ZGVmaW5lZChOT1BPUlRET0NTKQotCUAgJHtNS0RJUn0gJHtET0NTRElSfQorCUAke01LRElSfSAk e0RPQ1NESVJ9CiAJJHtJTlNUQUxMX0RBVEF9ICR7V1JLU1JDfS9yZWFkbWUgJHtET0NTRElSfQor CSR7SU5TVEFMTF9EQVRBfSAke1dSS1NSQ30vbGljZW5zZSAke0RPQ1NESVJ9CiAuZW5kaWYKIAot LmluY2x1ZGUgPGJzZC5wb3J0Lm1rPgorLmluY2x1ZGUgPGJzZC5wb3J0LnBvc3QubWs+CmRpZmYg LXJ1TiBtYWZmdC5vcmlnL2Rpc3RpbmZvIG1hZmZ0L2Rpc3RpbmZvCi0tLSBtYWZmdC5vcmlnL2Rp c3RpbmZvCTIwMTItMDctMTMgMTM6NDc6MjAuNzc3Njk4Mzc0IC0wNzAwCisrKyBtYWZmdC9kaXN0 aW5mbwkyMDEyLTA3LTEzIDE0OjE3OjQ2LjI2OTcyODM1NyAtMDcwMApAQCAtMSwyICsxLDIgQEAK LVNIQTI1NiAobWFmZnQtNS43NDMtc3JjLnRneikgPSA3YmYwZDQ1MGZlYTFkNDRmYWZlZTI3YzI5 Yzc0YjNhZTQyNDdhZDAwNzViNDE3MjlkOWRjOTM1ZTJhODhkZTY2Ci1TSVpFIChtYWZmdC01Ljc0 My1zcmMudGd6KSA9IDI4MDIyNgorU0hBMjU2IChtYWZmdC02LjkwMy13aXRob3V0LWV4dGVuc2lv bnMtc3JjLnRneikgPSBkOTYzMjZhZWNkYjFmODZiNjM3NzkzMTJjNGE2ZDhmNzE5ZjMyNzg2Mzk2 NTY3YzFkMTgyOTM0MWZjNmRiY2M4CitTSVpFIChtYWZmdC02LjkwMy13aXRob3V0LWV4dGVuc2lv bnMtc3JjLnRneikgPSAzNTk1MzYKZGlmZiAtcnVOIG1hZmZ0Lm9yaWcvcGtnLWRlc2NyIG1hZmZ0 L3BrZy1kZXNjcgotLS0gbWFmZnQub3JpZy9wa2ctZGVzY3IJMjAxMi0wNy0xMyAxMzo0NzoyMC43 Nzc2OTgzNzQgLTA3MDAKKysrIG1hZmZ0L3BrZy1kZXNjcgkyMDEyLTA3LTEzIDE0OjI0OjA0Ljg2 NzY0MTY0MyAtMDcwMApAQCAtNSw4ICs1LDEyIEBACiBtb3N0IGFjY3VyYXRlIG1ldGhvZHMgY3Vy cmVudGx5IGF2YWlsYWJsZS4KIAogTUFGRlQgaGFzIGJlZW4gZGVzY3JpYmVkOgorCitLLiBLYXRv aCBhbmQgSC4gVG9oIDIwMDggKEJyaWVmaW5ncyBpbiBCaW9pbmZvcm1hdGljcyA5OjI4Ni0yOTgp CitSZWNlbnQgZGV2ZWxvcG1lbnRzIGluIHRoZSBNQUZGVCBtdWx0aXBsZSBzZXF1ZW5jZSBhbGln bm1lbnQgcHJvZ3JhbS4KKwogSy4gS2F0b2gsIEsuIE1pc2F3YSwgSy4gS3VtYSBhbmQgVC4gTWl5 YXRhIChOdWNsZWljIEFjaWRzIFJlcy4gMzA6CiAzMDU5LTMwNjYsIDIwMDIpIE1BRkZUOiBhIG5v dmVsIG1ldGhvZCBmb3IgcmFwaWQgbXVsdGlwbGUgc2VxdWVuY2UKIGFsaWdubWVudCBiYXNlZCBv biBmYXN0IEZvdXJpZXIgdHJhbnNmb3JtLiAKIAotV1dXOiBodHRwOi8vYWxpZ24uYm1yLmt5dXNo dS11LmFjLmpwL21hZmZ0CitXV1c6IGh0dHA6Ly9tYWZmdC5jYnJjLmpwL2FsaWdubWVudC9zb2Z0 d2FyZS8KZGlmZiAtcnVOIG1hZmZ0Lm9yaWcvcGtnLXBsaXN0IG1hZmZ0L3BrZy1wbGlzdAotLS0g bWFmZnQub3JpZy9wa2ctcGxpc3QJMjAxMi0wNy0xMyAxMzo0NzoyMC43Nzc2OTgzNzQgLTA3MDAK KysrIG1hZmZ0L3BrZy1wbGlzdAkyMDEyLTA3LTE2IDE1OjA0OjUyLjQ4MTY0MjMxMSAtMDcwMApA QCAtMSwzMSArMSw2OCBAQAotYmluL2R1bW15CitiaW4vZWluc2kKK2Jpbi9mZnRucworYmluL2Zm dG5zaQorYmluL2dpbnNpCitiaW4vbGluc2kKIGJpbi9tYWZmdAotYmluL2Rpc3R0YmZhc3QKLWJp bi9kbmRibGFzdAotYmluL2RuZGZhc3Q3Ci1iaW4vZG5kcHJlCi1iaW4vZG5kcHJlMgotYmluL2R2 dGRpdHIKLWJpbi9mMmNsCi1iaW4vZ2V0bGFnCitiaW4vbWFmZnQtZGlzdGFuY2UKK2Jpbi9tYWZm dC1laW5zaQorYmluL21hZmZ0LWZmdG5zCitiaW4vbWFmZnQtZmZ0bnNpCitiaW4vbWFmZnQtZ2lu c2kKK2Jpbi9tYWZmdC1ob21vbG9ncy5yYgorYmluL21hZmZ0LWxpbnNpCitiaW4vbWFmZnQtbndu cworYmluL21hZmZ0LW53bnNpCiBiaW4vbWFmZnQtcHJvZmlsZQotYmluL211bHRpMmhhdDNzCi1i aW4vcGFpcjJoYXQzcwotYmluL3BhaXJhbGlnbgotYmluL3BhaXJsb2NhbGFsaWduCi1iaW4vc2Nv cmUKLWJpbi9zZXRjb3JlCi1iaW4vc2V4dGV0NQotYmluL3NwbGl0c2VxCi1iaW4vdGJmYXN0Ci1i aW4vdGJmYXN0MgorYmluL21hZmZ0LXFpbnNpCitiaW4vbWFmZnQteGluc2kKK2Jpbi9ud25zCiti aW4vbnduc2kKK2xpYmV4ZWMvbWFmZnQvYWRkc2luZ2xlCitsaWJleGVjL21hZmZ0L2NvbnRyYWZv bGR3cmFwCitsaWJleGVjL21hZmZ0L2NvdW50bGVuCitsaWJleGVjL21hZmZ0L2Rpc3R0YmZhc3QK K2xpYmV4ZWMvbWFmZnQvZG5kYmxhc3QKK2xpYmV4ZWMvbWFmZnQvZG5kZmFzdDcKK2xpYmV4ZWMv bWFmZnQvZG5kcHJlCitsaWJleGVjL21hZmZ0L2RuZHByZTIKK2xpYmV4ZWMvbWFmZnQvZHZ0ZGl0 cgorbGliZXhlYy9tYWZmdC9mMmNsCitsaWJleGVjL21hZmZ0L2dldGxhZworbGliZXhlYy9tYWZm dC9tYWZmdC1kaXN0YW5jZQorbGliZXhlYy9tYWZmdC9tYWZmdC1wcm9maWxlCitsaWJleGVjL21h ZmZ0L21ha2VkaXJlY3Rpb25saXN0CitsaWJleGVjL21hZmZ0L21jY2Fza2lsbHdyYXAKK2xpYmV4 ZWMvbWFmZnQvbXVsdGkyaGF0M3MKK2xpYmV4ZWMvbWFmZnQvcGFpcjJoYXQzcworbGliZXhlYy9t YWZmdC9wYWlyYXNoCitsaWJleGVjL21hZmZ0L3BhaXJsb2NhbGFsaWduCitsaWJleGVjL21hZmZ0 L3JlZ3RhYmxlMnNlcQorbGliZXhlYy9tYWZmdC9yZXBsYWNldQorbGliZXhlYy9tYWZmdC9yZXN0 b3JldQorbGliZXhlYy9tYWZmdC9ybmF0ZXN0CitsaWJleGVjL21hZmZ0L3Njb3JlCitsaWJleGVj L21hZmZ0L3NlcTJyZWd0YWJsZQorbGliZXhlYy9tYWZmdC9zZXRjb3JlCitsaWJleGVjL21hZmZ0 L3NldGRpcmVjdGlvbgorbGliZXhlYy9tYWZmdC9zZXh0ZXQ1CitsaWJleGVjL21hZmZ0L3NwbGl0 dGJmYXN0CitsaWJleGVjL21hZmZ0L3RiZmFzdAorbGliZXhlYy9tYWZmdC92ZXJzaW9uCislJVBP UlRET0NTJSUlJURPQ1NESVIlJS9saWNlbnNlCiAlJVBPUlRET0NTJSUlJURPQ1NESVIlJS9yZWFk bWUKLSUlRVhBTVBMRVNESVIlJS9zYW1wbGUKLSUlRVhBTVBMRVNESVIlJS9zYW1wbGUuZmZ0bnMy Ci0lJUVYQU1QTEVTRElSJSUvc2FtcGxlLmZmdG5zaQotJSVFWEFNUExFU0RJUiUlL3NhbXBsZS5n aW5zMQotJSVFWEFNUExFU0RJUiUlL3NhbXBsZS5naW5zaQotJSVFWEFNUExFU0RJUiUlL3NhbXBs ZS5saW5zMQotJSVFWEFNUExFU0RJUiUlL3NhbXBsZS5saW5zaQorJSVQT1JURVhBTVBMRVMlJSUl RVhBTVBMRVNESVIlJS9zYW1wbGUKKyUlUE9SVEVYQU1QTEVTJSUlJUVYQU1QTEVTRElSJSUvc2Ft cGxlLmRwcGFydHRyZWUKKyUlUE9SVEVYQU1QTEVTJSUlJUVYQU1QTEVTRElSJSUvc2FtcGxlLmZm dG5zMgorJSVQT1JURVhBTVBMRVMlJSUlRVhBTVBMRVNESVIlJS9zYW1wbGUuZmZ0bnNpCislJVBP UlRFWEFNUExFUyUlJSVFWEFNUExFU0RJUiUlL3NhbXBsZS5naW5zMQorJSVQT1JURVhBTVBMRVMl JSUlRVhBTVBMRVNESVIlJS9zYW1wbGUuZ2luc2kKKyUlUE9SVEVYQU1QTEVTJSUlJUVYQU1QTEVT RElSJSUvc2FtcGxlLmxpbnMxCislJVBPUlRFWEFNUExFUyUlJSVFWEFNUExFU0RJUiUlL3NhbXBs ZS5saW5zaQorJSVQT1JURVhBTVBMRVMlJSUlRVhBTVBMRVNESVIlJS9zYW1wbGUucGFydHRyZWUK KyUlUE9SVEVYQU1QTEVTJSUlJUVYQU1QTEVTRElSJSUvc2FtcGxlcm5hCislJVBPUlRFWEFNUExF UyUlJSVFWEFNUExFU0RJUiUlL3NhbXBsZXJuYS5xaW5zaQorJSVQT1JURVhBTVBMRVMlJSUlRVhB TVBMRVNESVIlJS9zYW1wbGVybmEueGluc2kKKyUlUE9SVEVYQU1QTEVTJSVAZGlycm0gJSVFWEFN UExFU0RJUiUlCiAlJVBPUlRET0NTJSVAZGlycm0gJSVET0NTRElSJSUKLUBkaXJybSAlJUVYQU1Q TEVTRElSJSUKK0BkaXJybSBsaWJleGVjL21hZmZ0Cg== --e89a8f3ba6b73ae30104c66594eb--
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?201208040020.q740KBA2091133>