From sebastien.moretti at unil.ch Fri Mar 1 08:21:19 2013 From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?Moretti_S=E9bastien?=) Date: Fri, 01 Mar 2013 14:21:19 +0100 Subject: [EMBOSS] ./configure --prefix=/somewhere --destdir=/chroot/somewhere Message-ID: <5130AB4F.8010905@unil.ch> Hi I wonder if it is possible to define a prefix during configure step, used internally for library paths, AND a destination path, for the installation step, that can be different from the prefix one. Files will be installed in destdir but libraries will keep useful/internal paths (the one from prefix). I ask that because we install software through a chroot environment that cannot write directly in /somewhere -- S?bastien Moretti SIB Vital-IT EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4079/4221 http://www.vital-it.ch/ http://myhits.vital-it.ch/ From ricepeterm at yahoo.co.uk Fri Mar 1 13:37:46 2013 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Fri, 1 Mar 2013 18:37:46 +0000 (GMT) Subject: [EMBOSS] seqret segfault (refseq protein sequence, indexed with dbxflat) In-Reply-To: <20130228161359.GC4062@paxarchia.galaxy.uni> References: <20130228161359.GC4062@paxarchia.galaxy.uni> Message-ID: <1362163066.23833.YahooMailNeo@web171904.mail.ir2.yahoo.com> Dear Jan, > I've run into a weird problem with seqret after downloading the complete > protein refseq database and indexing that with dbxflat. The problem > seems to be triggered by a rare condition, so far I've only encountered > it with accession ZP_10312765: > > ? ? % seqret -feature -outseq=stdout -osformat=swiss ptest:ZP_10312765 > > Monitoring the seqret process using top, I noticed that the process > grows to a size of 2g before segfaulting. > > Trying the same with ZP_10312766, the next record in the file, causes > no problem. Also, -osformat=fasta and -osformat=genbank work with > ZP_10312765, so the problem seems to be with outputting the swiss format. I can reproduce the problem with the latest EMBOSS. The problem seems to be trying to wrap a feature line to 41 bytes per record when the coded_by location is longer than the available width. ? I will work on a patch for the latest release and also for the 6.4 release you were using. ? Many thanks for finding this one. ? Peter Rice EMBOSS Team From ricepeterm at yahoo.co.uk Fri Mar 1 14:03:44 2013 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Fri, 1 Mar 2013 19:03:44 +0000 (GMT) Subject: [EMBOSS] seqret segfault (refseq protein sequence, indexed with dbxflat) In-Reply-To: <20130228161359.GC4062@paxarchia.galaxy.uni> References: <20130228161359.GC4062@paxarchia.galaxy.uni> Message-ID: <1362164624.35157.YahooMailNeo@web171904.mail.ir2.yahoo.com> Dear Jan, ? > I've run into a weird problem with seqret after downloading the complete > protein refseq database and indexing that with dbxflat. The problem > seems to be triggered by a rare condition, so far I've only encountered > it with accession ZP_10312765: The problem is in ajax/core/ajfeatwrite.c in function featTagSwissWrapC (so it will only affect Swissprot format feature output). ? Variable j is declared ajulong but should be ajlong (signed, so it can have a value of -1 in this case). ? If you change the line to ? ??? ajlong j; ? and rebuild, that should fix it. ? I will check the other wrapping functions in case they have a similar problem with other inputs. ? Again, many thanks for finding it. ? Peter Rice EMBOSS Team From jttkim at googlemail.com Fri Mar 1 15:12:59 2013 From: jttkim at googlemail.com (Jan T Kim) Date: Fri, 1 Mar 2013 20:12:59 +0000 Subject: [EMBOSS] seqret segfault (refseq protein sequence, indexed with dbxflat) In-Reply-To: <1362164624.35157.YahooMailNeo@web171904.mail.ir2.yahoo.com> References: <20130228161359.GC4062@paxarchia.galaxy.uni> <1362164624.35157.YahooMailNeo@web171904.mail.ir2.yahoo.com> Message-ID: <20130301201256.GA4415@paxarchia.galaxy.uni> Dear Peter, this fixes the problem on my laptop so I'll roll this out on the Ubuntu box as well. Thank you for your quick reply, and apologies for forgetting the attachment. (I've been comparing the two records but I would not have guessed that the difference in length of the coded_by value is the problem -- not without using the source anyway.) Best regards, Jan On Fri, Mar 01, 2013 at 07:03:44PM +0000, Peter Rice wrote: > Dear Jan, > ? > > I've run into a weird problem with seqret after downloading the complete > > protein refseq database and indexing that with dbxflat. The problem > > seems to be triggered by a rare condition, so far I've only encountered > > it with accession ZP_10312765: > > The problem is in ajax/core/ajfeatwrite.c in function featTagSwissWrapC (so it will only affect Swissprot format feature output). > ? > Variable j is declared ajulong but should be ajlong (signed, so it can have a value of -1 in this case). > ? > If you change the line to > ? > ??? ajlong j; > ? > and rebuild, that should fix it. > ? > I will check the other wrapping functions in case they have a similar problem with other inputs. > ? > Again, many thanks for finding it. > ? > Peter Rice > EMBOSS Team -- +- Jan T. Kim -------------------------------------------------------+ | email: jttkim at gmail.com | | WWW: http://www.jtkim.dreamhosters.com/ | *-----=< hierarchical systems are for files, not for humans >=-----* From sebastien.moretti at unil.ch Fri Mar 15 08:02:40 2013 From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?Moretti_S=E9bastien?=) Date: Fri, 15 Mar 2013 13:02:40 +0100 Subject: [EMBOSS] png support problem Message-ID: <51430DE0.7000306@unil.ch> Hi I try to compile EMBOSS 6.57, or EMBASSY tools, with png support but always get this from configure: checking for png_destroy_read_struct in -lpng... yes checking for gdImageCreateFromPng in -lgd... no need to upgrade gd for png driver for plplot No png driver will be made due to librarys missing/old. I read that at least gd 2.0.28 was required but use 2.0.35 (Linux x86_64 2.6.18, gcc 4.6.2) Do you have an idea what could cause this ? Regards -- S?bastien Moretti SIB Vital-IT EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4079/4221 http://www.vital-it.ch/ http://myhits.vital-it.ch/ From uludag at ebi.ac.uk Fri Mar 15 09:44:29 2013 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Fri, 15 Mar 2013 13:44:29 +0000 Subject: [EMBOSS] png support problem In-Reply-To: <51430DE0.7000306@unil.ch> References: <51430DE0.7000306@unil.ch> Message-ID: <514325BD.6000005@ebi.ac.uk> Hi Sebastien, I remember that recent EMBOSS versions doesn't need any configure options or environment settings for using the gd library. I have the same version (2.0.35) on my fedora desktop and doesn't get any errors at configure/compile time or when running the emboss programs that generates graphical output. If you were using the --with-pngdrive configure option, please retry without using that option. Mahmut > I try to compile EMBOSS 6.57, or EMBASSY tools, with png support but > always get this from configure: > checking for png_destroy_read_struct in -lpng... yes > checking for gdImageCreateFromPng in -lgd... no > need to upgrade gd for png driver for plplot > No png driver will be made due to librarys missing/old. > > I read that at least gd 2.0.28 was required but use 2.0.35 (Linux x86_64 > 2.6.18, gcc 4.6.2) From sebastien.moretti at unil.ch Fri Mar 15 10:25:54 2013 From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?Moretti_S=E9bastien?=) Date: Fri, 15 Mar 2013 15:25:54 +0100 Subject: [EMBOSS] png support problem In-Reply-To: <514325BD.6000005@ebi.ac.uk> References: <51430DE0.7000306@unil.ch> <514325BD.6000005@ebi.ac.uk> Message-ID: <51432F72.8000507@unil.ch> > Hi Sebastien, Hi Mahmut > I remember that recent EMBOSS versions doesn't need any configure > options or environment settings for using the gd library. I have the > same version (2.0.35) on my fedora desktop and doesn't get any errors at > configure/compile time or when running the emboss programs that > generates graphical output. > > If you were using the --with-pngdrive configure option, please retry > without using that option. I don't use this option > Mahmut > > >> I try to compile EMBOSS 6.57, or EMBASSY tools, with png support but >> always get this from configure: >> checking for png_destroy_read_struct in -lpng... yes >> checking for gdImageCreateFromPng in -lgd... no >> need to upgrade gd for png driver for plplot >> No png driver will be made due to librarys missing/old. >> >> I read that at least gd 2.0.28 was required but use 2.0.35 (Linux x86_64 >> 2.6.18, gcc 4.6.2) -- S?bastien Moretti SIB Vital-IT EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4079/4221 http://www.vital-it.ch/ http://myhits.vital-it.ch/ From ricepeterm at yahoo.co.uk Fri Mar 15 10:40:32 2013 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Fri, 15 Mar 2013 14:40:32 +0000 (GMT) Subject: [EMBOSS] png support problem In-Reply-To: <514325BD.6000005@ebi.ac.uk> References: <51430DE0.7000306@unil.ch> <514325BD.6000005@ebi.ac.uk> Message-ID: <1363358432.34669.YahooMailNeo@web171906.mail.ir2.yahoo.com> Hi Sebastien, > From: Mahmut Uludag >I remember that recent EMBOSS versions doesn't need any configure options or environment settings for using the gd library. I have the same version (2.0.35) on my fedora desktop and doesn't get any errors at configure/compile time or when running the emboss programs that generates graphical output. > >If you were using the --with-pngdrive configure option, please retry without using that option. The test in ./configure tries to compile a test program using gd to find the png library functions. You may have libgd installed but not the matching gd-devel header files and libraries. regards, Peter Rice EMBOSS Team From sebastien.moretti at unil.ch Fri Mar 15 10:48:58 2013 From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?Moretti_S=E9bastien?=) Date: Fri, 15 Mar 2013 15:48:58 +0100 Subject: [EMBOSS] png support problem In-Reply-To: <51432F72.8000507@unil.ch> References: <51430DE0.7000306@unil.ch> <514325BD.6000005@ebi.ac.uk> <51432F72.8000507@unil.ch> Message-ID: <514334DA.50307@unil.ch> >> Hi Sebastien, > > Hi Mahmut > >> I remember that recent EMBOSS versions doesn't need any configure >> options or environment settings for using the gd library. I have the >> same version (2.0.35) on my fedora desktop and doesn't get any errors at >> configure/compile time or when running the emboss programs that >> generates graphical output. >> >> If you were using the --with-pngdrive configure option, please retry >> without using that option. > > I don't use this option But tried and got the same >> Mahmut >> >> >>> I try to compile EMBOSS 6.57, or EMBASSY tools, with png support but >>> always get this from configure: >>> checking for png_destroy_read_struct in -lpng... yes >>> checking for gdImageCreateFromPng in -lgd... no >>> need to upgrade gd for png driver for plplot >>> No png driver will be made due to librarys missing/old. >>> >>> I read that at least gd 2.0.28 was required but use 2.0.35 (Linux x86_64 >>> 2.6.18, gcc 4.6.2) -- S?bastien Moretti SIB Vital-IT EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4079/4221 http://www.vital-it.ch/ http://myhits.vital-it.ch/ From sebastien.moretti at unil.ch Fri Mar 15 11:13:51 2013 From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?Moretti_S=E9bastien?=) Date: Fri, 15 Mar 2013 16:13:51 +0100 Subject: [EMBOSS] png support problem In-Reply-To: <1363358432.34669.YahooMailNeo@web171906.mail.ir2.yahoo.com> References: <51430DE0.7000306@unil.ch> <514325BD.6000005@ebi.ac.uk> <1363358432.34669.YahooMailNeo@web171906.mail.ir2.yahoo.com> Message-ID: <51433AAF.7050701@unil.ch> > Hi Sebastien, > > >> From: Mahmut Uludag >> I remember that recent EMBOSS versions doesn't need any configure options or environment settings for using the gd library. I have the same version (2.0.35) on my fedora desktop and doesn't get any errors at configure/compile time or when running the emboss programs that generates graphical output. >> >> If you were using the --with-pngdrive configure option, please retry without using that option. > > > The test in ./configure tries to compile a test program using gd to find the png library functions. > > You may have libgd installed but not the matching gd-devel header files and libraries. I use this to "force" searches there CXXFLAGS='-I/software/include' CFLAGS='-I/software/include' LDFLAGS='-L/software/lib64' ./configure I have libgd.so in one of these paths. I've just noticed that libgd.a is missing. Is this particular one used for static builds ? > regards, > > Peter Rice > EMBOSS Team -- S?bastien Moretti SIB Vital-IT EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4079/4221 http://www.vital-it.ch/ http://myhits.vital-it.ch/ From uludag at ebi.ac.uk Fri Mar 15 11:47:56 2013 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Fri, 15 Mar 2013 15:47:56 +0000 Subject: [EMBOSS] png support problem In-Reply-To: <51433AAF.7050701@unil.ch> References: <51430DE0.7000306@unil.ch> <514325BD.6000005@ebi.ac.uk> <1363358432.34669.YahooMailNeo@web171906.mail.ir2.yahoo.com> <51433AAF.7050701@unil.ch> Message-ID: <514342AC.6060105@ebi.ac.uk> > I've just noticed that libgd.a is missing. > Is this particular one used for static builds ? I think it should be. Mahmut From sebastien.moretti at unil.ch Fri Mar 15 11:50:04 2013 From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?Moretti_S=E9bastien?=) Date: Fri, 15 Mar 2013 16:50:04 +0100 Subject: [EMBOSS] png support problem In-Reply-To: <514342AC.6060105@ebi.ac.uk> References: <51430DE0.7000306@unil.ch> <514325BD.6000005@ebi.ac.uk> <1363358432.34669.YahooMailNeo@web171906.mail.ir2.yahoo.com> <51433AAF.7050701@unil.ch> <514342AC.6060105@ebi.ac.uk> Message-ID: <5143432C.2000702@unil.ch> I will check why we don't have this file and retry configure. Will let you know. Regards >> I've just noticed that libgd.a is missing. >> Is this particular one used for static builds ? > > I think it should be. > > Mahmut -- S?bastien Moretti SIB Vital-IT EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4079/4221 http://www.vital-it.ch/ http://myhits.vital-it.ch/ From uludag at ebi.ac.uk Fri Mar 15 12:19:04 2013 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Fri, 15 Mar 2013 16:19:04 +0000 Subject: [EMBOSS] png support problem In-Reply-To: <5143432C.2000702@unil.ch> References: <51430DE0.7000306@unil.ch> <514325BD.6000005@ebi.ac.uk> <1363358432.34669.YahooMailNeo@web171906.mail.ir2.yahoo.com> <51433AAF.7050701@unil.ch> <514342AC.6060105@ebi.ac.uk> <5143432C.2000702@unil.ch> Message-ID: <514349F8.6040903@ebi.ac.uk> I apologise for my email. I didn't pay attention that you were saying "I have libgd.so in one of these paths.". I just have tried a static build and my emboss executables are not linked to libgd.a but linked to libgd.so. Mahmut On 15/03/13 15:50, Moretti S?bastien wrote: > I will check why we don't have this file and retry configure. > Will let you know. > > Regards > >>> I've just noticed that libgd.a is missing. >>> Is this particular one used for static builds ? >> >> I think it should be. >> >> Mahmut > From peterhendler at hushmail.com Fri Mar 22 16:04:37 2013 From: peterhendler at hushmail.com (peterhendler at hushmail.com) Date: Fri, 22 Mar 2013 16:04:37 -0400 Subject: [EMBOSS] Biggest Fake Conference in Computer Science Message-ID: <20130322200437.D1E9810E2D3@smtp.hushmail.com> I graduated from University of Florida (UFL) and am currently running a computer firm in Florida. I have attended WORLDCOMP conference (see http://sites.google.com/site/worlddump1 for details) in 2010. Except for few keynote speeches and presentations, the conference was very disappointing due to a large number of poor quality papers and cancellation of some sessions. I was instantly suspicious of this conference. Me and my friends started a study on WORLDCOMP. We submitted a fake paper to WORLDCOMP 2011 and again (the same paper with a modified title) to WORLDCOMP 2012. This paper had numerous fundamental mistakes. Sample statements from that paper include: (1). Binary logic is fuzzy logic and vice versa (2). Pascal developed fuzzy logic (3). Object oriented languages do not exhibit any polymorphism or inheritance (4). TCP and IP are synonyms and are part of OSI model (5). Distributed systems deal with only one computer (6). Laptop is an example for a super computer (7). Operating system is an example for computer hardware Also, our paper did not express any conceptual meaning. However, it was accepted both the times without any modifications (and without any reviews) and we were invited to submit the final paper and a payment of $500+ fee to present the paper. We decided to use the fee for better purposes than making Prof. Hamid Arabnia (Chairman of WORLDCOMP) rich. After that, we received few reminders from WORLDCOMP to pay the fee but we never responded. We MUST say that you should look at the website http://sites.google.com/site/worlddump1 if you have any thoughts to submit a paper to WORLDCOMP. DBLP and other indexing agencies have stopped indexing WORLDCOMP?s proceedings since 2011 due to its fakeness. The status of your WORLDCOMP papers can be changed from ?scientific? to ?other? (i.e., junk or non-technical) at anytime. See the comments http://www.mail-archive.com/tccc at lists.cs.columbia.edu/msg05168.html of a respected researcher on this. Better not to have a paper than having it in WORLDCOMP and spoil the resume and peace of mind forever! Our study revealed that WORLDCOMP is a money making business, using University of Georgia mask, for Prof. Hamid Arabnia. He is throwing out a small chunk of that money (around 20 dollars per paper published in WORLDCOMP?s proceedings) to his puppet who publicizes WORLDCOMP and also defends it at various forums, using fake/anonymous names. The puppet uses fake names and defames other conferences/people to divert traffic to WORLDCOMP. That is, the puppet does all his best to get a maximum number of papers published at WORLDCOMP to get more money into his (and Prof. Hamid Arabnia?s) pockets. Monte Carlo Resort (the venue of WORLDCOMP until 2012) has refused to provide the venue for WORLDCOMP?13 because of the fears of their image being tarnished due to WORLDCOMP?s fraudulent activities. WORLDCOMP will not be held after 2013. The paper submission deadline for WORLDCOMP?13 was March 18 and it is extended to April 6 (it will be extended many times, as usual) but still there are no committee members, no reviewers, and there is no conference Chairman. The only contact details available on WORLDCOMP?s website is just an email address! What bothers us the most is that Prof. Hamid Arabnia never posted an apology for the damage he has done to the research community. He is still trying to defend WORLDCOMP. Let us make a direct request to him: publish all reviews for all the papers (after blocking identifiable details) since 2000 conference. Reveal the names and affiliations of all the reviewers (for each year) and how many papers each reviewer had reviewed on average. We also request him to look at the Open Challenge at http://sites.google.com/site/dumpconf We think that it is our professional obligation to spread this message to alert the computer science community. Sorry for posting to multiple lists. Spreading the word is the only way to stop this bogus conference. Please forward this message to other mailing lists and people. We are shocked with Prof. Hamid Arabnia and his puppet?s activities http://worldcomp-fake-bogus.blogspot.com Search Google using the keywords ?worldcomp, fake? for additional links. Sincerely, Peter From sebastien.moretti at unil.ch Fri Mar 1 13:21:19 2013 From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?Moretti_S=E9bastien?=) Date: Fri, 01 Mar 2013 14:21:19 +0100 Subject: [EMBOSS] ./configure --prefix=/somewhere --destdir=/chroot/somewhere Message-ID: <5130AB4F.8010905@unil.ch> Hi I wonder if it is possible to define a prefix during configure step, used internally for library paths, AND a destination path, for the installation step, that can be different from the prefix one. Files will be installed in destdir but libraries will keep useful/internal paths (the one from prefix). I ask that because we install software through a chroot environment that cannot write directly in /somewhere -- S?bastien Moretti SIB Vital-IT EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4079/4221 http://www.vital-it.ch/ http://myhits.vital-it.ch/ From ricepeterm at yahoo.co.uk Fri Mar 1 18:37:46 2013 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Fri, 1 Mar 2013 18:37:46 +0000 (GMT) Subject: [EMBOSS] seqret segfault (refseq protein sequence, indexed with dbxflat) In-Reply-To: <20130228161359.GC4062@paxarchia.galaxy.uni> References: <20130228161359.GC4062@paxarchia.galaxy.uni> Message-ID: <1362163066.23833.YahooMailNeo@web171904.mail.ir2.yahoo.com> Dear Jan, > I've run into a weird problem with seqret after downloading the complete > protein refseq database and indexing that with dbxflat. The problem > seems to be triggered by a rare condition, so far I've only encountered > it with accession ZP_10312765: > > ? ? % seqret -feature -outseq=stdout -osformat=swiss ptest:ZP_10312765 > > Monitoring the seqret process using top, I noticed that the process > grows to a size of 2g before segfaulting. > > Trying the same with ZP_10312766, the next record in the file, causes > no problem. Also, -osformat=fasta and -osformat=genbank work with > ZP_10312765, so the problem seems to be with outputting the swiss format. I can reproduce the problem with the latest EMBOSS. The problem seems to be trying to wrap a feature line to 41 bytes per record when the coded_by location is longer than the available width. ? I will work on a patch for the latest release and also for the 6.4 release you were using. ? Many thanks for finding this one. ? Peter Rice EMBOSS Team From ricepeterm at yahoo.co.uk Fri Mar 1 19:03:44 2013 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Fri, 1 Mar 2013 19:03:44 +0000 (GMT) Subject: [EMBOSS] seqret segfault (refseq protein sequence, indexed with dbxflat) In-Reply-To: <20130228161359.GC4062@paxarchia.galaxy.uni> References: <20130228161359.GC4062@paxarchia.galaxy.uni> Message-ID: <1362164624.35157.YahooMailNeo@web171904.mail.ir2.yahoo.com> Dear Jan, ? > I've run into a weird problem with seqret after downloading the complete > protein refseq database and indexing that with dbxflat. The problem > seems to be triggered by a rare condition, so far I've only encountered > it with accession ZP_10312765: The problem is in ajax/core/ajfeatwrite.c in function featTagSwissWrapC (so it will only affect Swissprot format feature output). ? Variable j is declared ajulong but should be ajlong (signed, so it can have a value of -1 in this case). ? If you change the line to ? ??? ajlong j; ? and rebuild, that should fix it. ? I will check the other wrapping functions in case they have a similar problem with other inputs. ? Again, many thanks for finding it. ? Peter Rice EMBOSS Team From jttkim at googlemail.com Fri Mar 1 20:12:59 2013 From: jttkim at googlemail.com (Jan T Kim) Date: Fri, 1 Mar 2013 20:12:59 +0000 Subject: [EMBOSS] seqret segfault (refseq protein sequence, indexed with dbxflat) In-Reply-To: <1362164624.35157.YahooMailNeo@web171904.mail.ir2.yahoo.com> References: <20130228161359.GC4062@paxarchia.galaxy.uni> <1362164624.35157.YahooMailNeo@web171904.mail.ir2.yahoo.com> Message-ID: <20130301201256.GA4415@paxarchia.galaxy.uni> Dear Peter, this fixes the problem on my laptop so I'll roll this out on the Ubuntu box as well. Thank you for your quick reply, and apologies for forgetting the attachment. (I've been comparing the two records but I would not have guessed that the difference in length of the coded_by value is the problem -- not without using the source anyway.) Best regards, Jan On Fri, Mar 01, 2013 at 07:03:44PM +0000, Peter Rice wrote: > Dear Jan, > ? > > I've run into a weird problem with seqret after downloading the complete > > protein refseq database and indexing that with dbxflat. The problem > > seems to be triggered by a rare condition, so far I've only encountered > > it with accession ZP_10312765: > > The problem is in ajax/core/ajfeatwrite.c in function featTagSwissWrapC (so it will only affect Swissprot format feature output). > ? > Variable j is declared ajulong but should be ajlong (signed, so it can have a value of -1 in this case). > ? > If you change the line to > ? > ??? ajlong j; > ? > and rebuild, that should fix it. > ? > I will check the other wrapping functions in case they have a similar problem with other inputs. > ? > Again, many thanks for finding it. > ? > Peter Rice > EMBOSS Team -- +- Jan T. Kim -------------------------------------------------------+ | email: jttkim at gmail.com | | WWW: http://www.jtkim.dreamhosters.com/ | *-----=< hierarchical systems are for files, not for humans >=-----* From sebastien.moretti at unil.ch Fri Mar 15 12:02:40 2013 From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?Moretti_S=E9bastien?=) Date: Fri, 15 Mar 2013 13:02:40 +0100 Subject: [EMBOSS] png support problem Message-ID: <51430DE0.7000306@unil.ch> Hi I try to compile EMBOSS 6.57, or EMBASSY tools, with png support but always get this from configure: checking for png_destroy_read_struct in -lpng... yes checking for gdImageCreateFromPng in -lgd... no need to upgrade gd for png driver for plplot No png driver will be made due to librarys missing/old. I read that at least gd 2.0.28 was required but use 2.0.35 (Linux x86_64 2.6.18, gcc 4.6.2) Do you have an idea what could cause this ? Regards -- S?bastien Moretti SIB Vital-IT EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4079/4221 http://www.vital-it.ch/ http://myhits.vital-it.ch/ From uludag at ebi.ac.uk Fri Mar 15 13:44:29 2013 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Fri, 15 Mar 2013 13:44:29 +0000 Subject: [EMBOSS] png support problem In-Reply-To: <51430DE0.7000306@unil.ch> References: <51430DE0.7000306@unil.ch> Message-ID: <514325BD.6000005@ebi.ac.uk> Hi Sebastien, I remember that recent EMBOSS versions doesn't need any configure options or environment settings for using the gd library. I have the same version (2.0.35) on my fedora desktop and doesn't get any errors at configure/compile time or when running the emboss programs that generates graphical output. If you were using the --with-pngdrive configure option, please retry without using that option. Mahmut > I try to compile EMBOSS 6.57, or EMBASSY tools, with png support but > always get this from configure: > checking for png_destroy_read_struct in -lpng... yes > checking for gdImageCreateFromPng in -lgd... no > need to upgrade gd for png driver for plplot > No png driver will be made due to librarys missing/old. > > I read that at least gd 2.0.28 was required but use 2.0.35 (Linux x86_64 > 2.6.18, gcc 4.6.2) From sebastien.moretti at unil.ch Fri Mar 15 14:25:54 2013 From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?Moretti_S=E9bastien?=) Date: Fri, 15 Mar 2013 15:25:54 +0100 Subject: [EMBOSS] png support problem In-Reply-To: <514325BD.6000005@ebi.ac.uk> References: <51430DE0.7000306@unil.ch> <514325BD.6000005@ebi.ac.uk> Message-ID: <51432F72.8000507@unil.ch> > Hi Sebastien, Hi Mahmut > I remember that recent EMBOSS versions doesn't need any configure > options or environment settings for using the gd library. I have the > same version (2.0.35) on my fedora desktop and doesn't get any errors at > configure/compile time or when running the emboss programs that > generates graphical output. > > If you were using the --with-pngdrive configure option, please retry > without using that option. I don't use this option > Mahmut > > >> I try to compile EMBOSS 6.57, or EMBASSY tools, with png support but >> always get this from configure: >> checking for png_destroy_read_struct in -lpng... yes >> checking for gdImageCreateFromPng in -lgd... no >> need to upgrade gd for png driver for plplot >> No png driver will be made due to librarys missing/old. >> >> I read that at least gd 2.0.28 was required but use 2.0.35 (Linux x86_64 >> 2.6.18, gcc 4.6.2) -- S?bastien Moretti SIB Vital-IT EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4079/4221 http://www.vital-it.ch/ http://myhits.vital-it.ch/ From ricepeterm at yahoo.co.uk Fri Mar 15 14:40:32 2013 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Fri, 15 Mar 2013 14:40:32 +0000 (GMT) Subject: [EMBOSS] png support problem In-Reply-To: <514325BD.6000005@ebi.ac.uk> References: <51430DE0.7000306@unil.ch> <514325BD.6000005@ebi.ac.uk> Message-ID: <1363358432.34669.YahooMailNeo@web171906.mail.ir2.yahoo.com> Hi Sebastien, > From: Mahmut Uludag >I remember that recent EMBOSS versions doesn't need any configure options or environment settings for using the gd library. I have the same version (2.0.35) on my fedora desktop and doesn't get any errors at configure/compile time or when running the emboss programs that generates graphical output. > >If you were using the --with-pngdrive configure option, please retry without using that option. The test in ./configure tries to compile a test program using gd to find the png library functions. You may have libgd installed but not the matching gd-devel header files and libraries. regards, Peter Rice EMBOSS Team From sebastien.moretti at unil.ch Fri Mar 15 14:48:58 2013 From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?Moretti_S=E9bastien?=) Date: Fri, 15 Mar 2013 15:48:58 +0100 Subject: [EMBOSS] png support problem In-Reply-To: <51432F72.8000507@unil.ch> References: <51430DE0.7000306@unil.ch> <514325BD.6000005@ebi.ac.uk> <51432F72.8000507@unil.ch> Message-ID: <514334DA.50307@unil.ch> >> Hi Sebastien, > > Hi Mahmut > >> I remember that recent EMBOSS versions doesn't need any configure >> options or environment settings for using the gd library. I have the >> same version (2.0.35) on my fedora desktop and doesn't get any errors at >> configure/compile time or when running the emboss programs that >> generates graphical output. >> >> If you were using the --with-pngdrive configure option, please retry >> without using that option. > > I don't use this option But tried and got the same >> Mahmut >> >> >>> I try to compile EMBOSS 6.57, or EMBASSY tools, with png support but >>> always get this from configure: >>> checking for png_destroy_read_struct in -lpng... yes >>> checking for gdImageCreateFromPng in -lgd... no >>> need to upgrade gd for png driver for plplot >>> No png driver will be made due to librarys missing/old. >>> >>> I read that at least gd 2.0.28 was required but use 2.0.35 (Linux x86_64 >>> 2.6.18, gcc 4.6.2) -- S?bastien Moretti SIB Vital-IT EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4079/4221 http://www.vital-it.ch/ http://myhits.vital-it.ch/ From sebastien.moretti at unil.ch Fri Mar 15 15:13:51 2013 From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?Moretti_S=E9bastien?=) Date: Fri, 15 Mar 2013 16:13:51 +0100 Subject: [EMBOSS] png support problem In-Reply-To: <1363358432.34669.YahooMailNeo@web171906.mail.ir2.yahoo.com> References: <51430DE0.7000306@unil.ch> <514325BD.6000005@ebi.ac.uk> <1363358432.34669.YahooMailNeo@web171906.mail.ir2.yahoo.com> Message-ID: <51433AAF.7050701@unil.ch> > Hi Sebastien, > > >> From: Mahmut Uludag >> I remember that recent EMBOSS versions doesn't need any configure options or environment settings for using the gd library. I have the same version (2.0.35) on my fedora desktop and doesn't get any errors at configure/compile time or when running the emboss programs that generates graphical output. >> >> If you were using the --with-pngdrive configure option, please retry without using that option. > > > The test in ./configure tries to compile a test program using gd to find the png library functions. > > You may have libgd installed but not the matching gd-devel header files and libraries. I use this to "force" searches there CXXFLAGS='-I/software/include' CFLAGS='-I/software/include' LDFLAGS='-L/software/lib64' ./configure I have libgd.so in one of these paths. I've just noticed that libgd.a is missing. Is this particular one used for static builds ? > regards, > > Peter Rice > EMBOSS Team -- S?bastien Moretti SIB Vital-IT EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4079/4221 http://www.vital-it.ch/ http://myhits.vital-it.ch/ From uludag at ebi.ac.uk Fri Mar 15 15:47:56 2013 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Fri, 15 Mar 2013 15:47:56 +0000 Subject: [EMBOSS] png support problem In-Reply-To: <51433AAF.7050701@unil.ch> References: <51430DE0.7000306@unil.ch> <514325BD.6000005@ebi.ac.uk> <1363358432.34669.YahooMailNeo@web171906.mail.ir2.yahoo.com> <51433AAF.7050701@unil.ch> Message-ID: <514342AC.6060105@ebi.ac.uk> > I've just noticed that libgd.a is missing. > Is this particular one used for static builds ? I think it should be. Mahmut From sebastien.moretti at unil.ch Fri Mar 15 15:50:04 2013 From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?Moretti_S=E9bastien?=) Date: Fri, 15 Mar 2013 16:50:04 +0100 Subject: [EMBOSS] png support problem In-Reply-To: <514342AC.6060105@ebi.ac.uk> References: <51430DE0.7000306@unil.ch> <514325BD.6000005@ebi.ac.uk> <1363358432.34669.YahooMailNeo@web171906.mail.ir2.yahoo.com> <51433AAF.7050701@unil.ch> <514342AC.6060105@ebi.ac.uk> Message-ID: <5143432C.2000702@unil.ch> I will check why we don't have this file and retry configure. Will let you know. Regards >> I've just noticed that libgd.a is missing. >> Is this particular one used for static builds ? > > I think it should be. > > Mahmut -- S?bastien Moretti SIB Vital-IT EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4079/4221 http://www.vital-it.ch/ http://myhits.vital-it.ch/ From uludag at ebi.ac.uk Fri Mar 15 16:19:04 2013 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Fri, 15 Mar 2013 16:19:04 +0000 Subject: [EMBOSS] png support problem In-Reply-To: <5143432C.2000702@unil.ch> References: <51430DE0.7000306@unil.ch> <514325BD.6000005@ebi.ac.uk> <1363358432.34669.YahooMailNeo@web171906.mail.ir2.yahoo.com> <51433AAF.7050701@unil.ch> <514342AC.6060105@ebi.ac.uk> <5143432C.2000702@unil.ch> Message-ID: <514349F8.6040903@ebi.ac.uk> I apologise for my email. I didn't pay attention that you were saying "I have libgd.so in one of these paths.". I just have tried a static build and my emboss executables are not linked to libgd.a but linked to libgd.so. Mahmut On 15/03/13 15:50, Moretti S?bastien wrote: > I will check why we don't have this file and retry configure. > Will let you know. > > Regards > >>> I've just noticed that libgd.a is missing. >>> Is this particular one used for static builds ? >> >> I think it should be. >> >> Mahmut > From peterhendler at hushmail.com Fri Mar 22 20:04:37 2013 From: peterhendler at hushmail.com (peterhendler at hushmail.com) Date: Fri, 22 Mar 2013 16:04:37 -0400 Subject: [EMBOSS] Biggest Fake Conference in Computer Science Message-ID: <20130322200437.D1E9810E2D3@smtp.hushmail.com> I graduated from University of Florida (UFL) and am currently running a computer firm in Florida. I have attended WORLDCOMP conference (see http://sites.google.com/site/worlddump1 for details) in 2010. Except for few keynote speeches and presentations, the conference was very disappointing due to a large number of poor quality papers and cancellation of some sessions. I was instantly suspicious of this conference. Me and my friends started a study on WORLDCOMP. We submitted a fake paper to WORLDCOMP 2011 and again (the same paper with a modified title) to WORLDCOMP 2012. This paper had numerous fundamental mistakes. Sample statements from that paper include: (1). Binary logic is fuzzy logic and vice versa (2). Pascal developed fuzzy logic (3). Object oriented languages do not exhibit any polymorphism or inheritance (4). TCP and IP are synonyms and are part of OSI model (5). Distributed systems deal with only one computer (6). Laptop is an example for a super computer (7). Operating system is an example for computer hardware Also, our paper did not express any conceptual meaning. However, it was accepted both the times without any modifications (and without any reviews) and we were invited to submit the final paper and a payment of $500+ fee to present the paper. We decided to use the fee for better purposes than making Prof. Hamid Arabnia (Chairman of WORLDCOMP) rich. After that, we received few reminders from WORLDCOMP to pay the fee but we never responded. We MUST say that you should look at the website http://sites.google.com/site/worlddump1 if you have any thoughts to submit a paper to WORLDCOMP. DBLP and other indexing agencies have stopped indexing WORLDCOMP?s proceedings since 2011 due to its fakeness. The status of your WORLDCOMP papers can be changed from ?scientific? to ?other? (i.e., junk or non-technical) at anytime. See the comments http://www.mail-archive.com/tccc at lists.cs.columbia.edu/msg05168.html of a respected researcher on this. Better not to have a paper than having it in WORLDCOMP and spoil the resume and peace of mind forever! Our study revealed that WORLDCOMP is a money making business, using University of Georgia mask, for Prof. Hamid Arabnia. He is throwing out a small chunk of that money (around 20 dollars per paper published in WORLDCOMP?s proceedings) to his puppet who publicizes WORLDCOMP and also defends it at various forums, using fake/anonymous names. The puppet uses fake names and defames other conferences/people to divert traffic to WORLDCOMP. That is, the puppet does all his best to get a maximum number of papers published at WORLDCOMP to get more money into his (and Prof. Hamid Arabnia?s) pockets. Monte Carlo Resort (the venue of WORLDCOMP until 2012) has refused to provide the venue for WORLDCOMP?13 because of the fears of their image being tarnished due to WORLDCOMP?s fraudulent activities. WORLDCOMP will not be held after 2013. The paper submission deadline for WORLDCOMP?13 was March 18 and it is extended to April 6 (it will be extended many times, as usual) but still there are no committee members, no reviewers, and there is no conference Chairman. The only contact details available on WORLDCOMP?s website is just an email address! What bothers us the most is that Prof. Hamid Arabnia never posted an apology for the damage he has done to the research community. He is still trying to defend WORLDCOMP. Let us make a direct request to him: publish all reviews for all the papers (after blocking identifiable details) since 2000 conference. Reveal the names and affiliations of all the reviewers (for each year) and how many papers each reviewer had reviewed on average. We also request him to look at the Open Challenge at http://sites.google.com/site/dumpconf We think that it is our professional obligation to spread this message to alert the computer science community. Sorry for posting to multiple lists. Spreading the word is the only way to stop this bogus conference. Please forward this message to other mailing lists and people. We are shocked with Prof. Hamid Arabnia and his puppet?s activities http://worldcomp-fake-bogus.blogspot.com Search Google using the keywords ?worldcomp, fake? for additional links. Sincerely, Peter