Recent changes to bugs

#252 Unable to deliver e-mail to help@treebase.org and bugs@treebase.org

Vimac Nolla — Mon, 11 Jan 2016 07:55:00 -0000

Thanks!

Unable to deliver e-mail to help@treebase.org and bugs@treebase.org

Vimac Nolla — Thu, 17 Dec 2015 08:40:16 -0000

Hi,
I'm new to Treebase and I'm not sure if this is the correct way to report this sort of problem.

I'm trying to contact Treebase through help@treebase.org and bugs@treebase.org but I keep on getting an automatic reply saying that the messages was not delivered. See below the error message:

Delivery to the following recipient failed permanently:

 help@treebase.org

Technical details of permanent failure:
The recipient server did not accept our requests to connect. Learn more at https://support.google.com/mail/answer/7720
[(10) isa.peabody.yale.edu.treebase.org. [67.159.80.239]:25: socket error]

I get the same message when I try sending the e-mail to bugs@treebase.org

Does any one know how I can contact Treebase for help regarding some of the data that I uploaded to Treebase.

Thanks.

treeBASE Proxy Error

Jorge Luis Sarmiento Villamil — Thu, 15 Oct 2015 15:29:39 -0000

Hi, i could not submit my nexus file, after i was tried to submit my nexus file, the charged page said

Proxy Error
The proxy server received an invalid response from an upstream server.
The proxy server could not handle the request POST /treebase-web/user/uploadFile.html.
Reason: Error reading from remote server

Apache Server at treebase.org Port 80

somebody could help me

study with empty tree

Mark Holder — Thu, 25 Jun 2015 14:21:46 -0000

The second tree in http://treebase.org/treebase-web/search/study/summary.html?id=14763
is empty in NEXUS and just has one node in NeXML.

#229 Unable to delete Study

Robin van Velzen — Mon, 06 Jan 2014 14:58:40 -0000

When will this bug finally be solved?

Manually deleting ALL trees and matrices is very cumbersome...

nexml export: lower case letters in molecular sequence matrices

Mark Holder — Sat, 04 Jan 2014 18:41:52 -0000

See http://treebase.org/treebase-web/search/downloadAStudy.html?id=10183&format=nexml
Affected IDs: S10183 S12267 S12471 S1874 S2168 S9977

nexml export: NEXUS-specific syntax in matrix

Mark Holder — Sat, 04 Jan 2014 18:39:14 -0000

Similar to the curly-brace bug ( https://sourceforge.net/p/treebase/bugs/245/ ) but this refers to other NEXUS syntax such as a "." I think the dots are probably from Mathchar="." imports. Some files have lots of colons. I"m not sure where they are coming from (could also be matchchar examples).
See http://treebase.org/treebase-web/search/downloadAStudy.html?id=1029&format=nexml

Other IDs: S1029 S10386 S10997 S11363 S1329 S1348 S1649 S1654 S1948 S2100 S230 S264 S320 S338 S352 S361 S648 S681 S742 S765 S792 S794 S925

nexml export: symbols added to DNA or AA type

Mark Holder — Sat, 04 Jan 2014 18:36:35 -0000

See:
http://treebase.org/treebase-web/search/downloadAStudy.html?id=1006&format=nexml

IDs: S1006 S1028 S10727 S11603 S12278 S13528 S1409 S1499 S1814 S672 S761 S888

nexml export: letters in seq element of standard datatype

Mark Holder — Sat, 04 Jan 2014 18:34:56 -0000

Several studies emit letters in the seq element for standard datatypes. As mentioned on https://sourceforge.net/mailarchive/message.php?msg_id=31802970
it is not clear if this should be allowed in NeXML.
Affected studies: S10004 S10039 S10051 S10090 S10092 S10137 S10153 S1016 S10186 S1018 S10191 S10192 S10208 S10243 S10272 S10279 S1051 S10549 S10601 S10867 S10905 S10917 S11167 S111 S1127 S1135 S1138 S1158 S1166 S116 S1174 S118 S1193 S11957 S120 S12298 S12319 S1238 S12681 S12816 S12890 S12904 S12910 S12922 S12925 S13149 S13223 S1322 S132 S13353 S13606 S1371 S1392 S1411 S1419 S1423 S1424 S1432 S1446 S1510 S1513 S1541 S154 S1556 S1570 S1611 S1624 S1640 S1666 S1681 S1697 S1705 S1739 S184 S1851 S1856 S1861 S1892 S1911 S193 S1942 S1958 S1996 S200 S2055 S2078 S2086 S2122 S2143 S2146 S2186 S2188 S2212 S226 S229 S231 S2372 S238 S274 S289 S299 S304 S307 S331 S332 S333 S336 S357 S363 S388 S395 S404 S421 S575 S592 S644 S647 S689 S695 S715 S725 S749 S791 S796 S828 S834 S85 S867 S883 S884 S893 S912 S913 S914 S958 S985 S988 S9939 S9949 S9953 S9974 S9990 S9998

nexml export: NEXUS-specific curly braces in matrix

Mark Holder — Sat, 04 Jan 2014 18:31:48 -0000

This is the ambiguity code in NEXUS. It should result in an uncertain state set in NeXML, not the use of the NEXUS syntax in a seq element.
See
http://treebase.org/treebase-web/search/downloadAStudy.html?id=10081&format=nexml
affected IDs:
S10081 S10108 S10135 S10146 S10350 S10466 S1050 S10553 S10667 S10671 S10676 S1070 S1094 S110 S1116 S1121 S1125 S11330 S11387 S1148 S11610 S11700 S11965 S11976 S1198 S12033 S12447 S12642 S12832 S12850 S12851 S12929 S12976 S12978 S12979 S12980 S12982 S12984 S12990 S12992 S12997 S12999 S13000 S13001 S13008 S13009 S13010 S13012 S13015 S13016 S13017 S13021 S13022 S13026 S13030 S13040 S13041 S13043 S13044 S13048 S13055 S13059 S13060 S13061 S13062 S13064 S13069 S13070 S13071 S13076 S13077 S13078 S13079 S13080 S13086 S13091 S13094 S13097 S13102 S13103 S13104 S13105 S13113 S13115 S13116 S13117 S13120 S13121 S13122 S13123 S13124 S13125 S13126 S13127 S13130 S13131 S13134 S13139 S13140 S13141 S13142 S13145 S13146 S13147 S13148 S13150 S13151 S13153 S13156 S13163 S13165 S13166 S13168 S13173 S13174 S13178 S13180 S13194 S13201 S13204 S13209 S13213 S13219 S13220 S13221 S13222 S13224 S13225 S13229 S13230 S13236 S13237 S13244 S13245 S1330 S13316 S13373 S13433 S1394 S1436 S145 S146 S1504 S1518 S1539 S156 S1585 S1601 S1688 S168 S1801 S1975 S2032 S2091 S2132 S2179 S225 S232 S2344 S255 S269 S270 S287 S295 S305 S334 S337 S341 S355 S356 S368 S384 S392 S396 S397 S409 S606 S615 S700 S733 S838 S874 S920 S991 S9941 S9944 S997