From uludag at ebi.ac.uk Mon Mar 4 12:05:02 2013 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Mon, 04 Mar 2013 17:05:02 +0000 Subject: [emboss-dev] cpgplot, feature output file Message-ID: <5134D43E.6000409@ebi.ac.uk> As far as i can see cpgplot always generates gff feature output file. I can't see any option to disable it. Please let me know if i'm missing it. Mahmut From uludag at ebi.ac.uk Tue Mar 5 06:04:31 2013 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Tue, 05 Mar 2013 11:04:31 +0000 Subject: [emboss-dev] emboss cvs broken? Message-ID: <5135D13F.3040802@ebi.ac.uk> If i'm not wrong emboss cvs is broken? I get errors similar to the following. restrict.c:813:59: error: ?EmbOMatMatch? has no member named ?len4? Mahmut (Michael, i don't know you are in emboss-dev so i cc to you) From sebastien.moretti at unil.ch Tue Mar 5 06:14:36 2013 From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?Moretti_S=E9bastien?=) Date: Tue, 05 Mar 2013 12:14:36 +0100 Subject: [emboss-dev] ./configure --prefix=/somewhere --destdir=/chroot/somewhere Message-ID: <5135D39C.7090908@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 Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4079 http://selectome.unil.ch/ http://bgee.unil.ch/ From uludag at ebi.ac.uk Tue Mar 5 06:49:32 2013 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Tue, 05 Mar 2013 11:49:32 +0000 Subject: [emboss-dev] ./configure --prefix=/somewhere --destdir=/chroot/somewhere In-Reply-To: <5135D39C.7090908@unil.ch> References: <5135D39C.7090908@unil.ch> Message-ID: <5135DBCC.2050104@ebi.ac.uk> Hi Sebastien, I don't know about the chroot environments and has poor knowledge of configure system EMBOSS have. I write just in case you are not aware of the configure script --help option. > ./configure --help It has a section called "Fine tuning of the installation directories" that i thought can be used to address the problem you described. Picked below few options that might be relevant to your query. --bindir=DIR user executables [EPREFIX/bin] --sbindir=DIR system admin executables [EPREFIX/sbin] --libexecdir=DIR program executables [EPREFIX/libexec] --libdir=DIR object code libraries [EPREFIX/lib] Mahmut On 05/03/13 11:14, Moretti S?bastien wrote: > 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 > > From sebastien.moretti at unil.ch Tue Mar 5 08:00:40 2013 From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?Moretti_S=E9bastien?=) Date: Tue, 05 Mar 2013 14:00:40 +0100 Subject: [emboss-dev] ./configure --prefix=/somewhere --destdir=/chroot/somewhere In-Reply-To: <5135DBCC.2050104@ebi.ac.uk> References: <5135D39C.7090908@unil.ch> <5135DBCC.2050104@ebi.ac.uk> Message-ID: <5135EC78.6030602@unil.ch> Hi Mahmut Thanks for your answer. I already use bindir and libdir but they have the same drawback than prefix. At the end binaries and libraries are linked to /somewhere but I cannot directly install them there. Or they are linked to /chroot/somewhere and I need to use $LD_LIBRAY_PATH to run them, and compilation of EMBASSY tools fail. Regards S?bastien > Hi Sebastien, > > I don't know about the chroot environments and has poor knowledge of > configure system EMBOSS have. I write just in case you are not aware of > the configure script --help option. > > > ./configure --help > > It has a section called "Fine tuning of the installation directories" > that i thought can be used to address the problem you described. > > Picked below few options that might be relevant to your query. > > --bindir=DIR user executables [EPREFIX/bin] > --sbindir=DIR system admin executables [EPREFIX/sbin] > --libexecdir=DIR program executables [EPREFIX/libexec] > --libdir=DIR object code libraries [EPREFIX/lib] > > Mahmut > > > > On 05/03/13 11:14, Moretti S?bastien wrote: >> 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 Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4079 http://selectome.unil.ch/ http://bgee.unil.ch/ From peterhendler at hushmail.com Fri Mar 22 16:04:24 2013 From: peterhendler at hushmail.com (peterhendler at hushmail.com) Date: Fri, 22 Mar 2013 16:04:24 -0400 Subject: [emboss-dev] Biggest Fake Conference in Computer Science Message-ID: <20130322200424.6AE7D10E2D3@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 uludag at ebi.ac.uk Mon Mar 4 17:05:02 2013 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Mon, 04 Mar 2013 17:05:02 +0000 Subject: [emboss-dev] cpgplot, feature output file Message-ID: <5134D43E.6000409@ebi.ac.uk> As far as i can see cpgplot always generates gff feature output file. I can't see any option to disable it. Please let me know if i'm missing it. Mahmut From uludag at ebi.ac.uk Tue Mar 5 11:04:31 2013 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Tue, 05 Mar 2013 11:04:31 +0000 Subject: [emboss-dev] emboss cvs broken? Message-ID: <5135D13F.3040802@ebi.ac.uk> If i'm not wrong emboss cvs is broken? I get errors similar to the following. restrict.c:813:59: error: ?EmbOMatMatch? has no member named ?len4? Mahmut (Michael, i don't know you are in emboss-dev so i cc to you) From sebastien.moretti at unil.ch Tue Mar 5 11:14:36 2013 From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?Moretti_S=E9bastien?=) Date: Tue, 05 Mar 2013 12:14:36 +0100 Subject: [emboss-dev] ./configure --prefix=/somewhere --destdir=/chroot/somewhere Message-ID: <5135D39C.7090908@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 Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4079 http://selectome.unil.ch/ http://bgee.unil.ch/ From uludag at ebi.ac.uk Tue Mar 5 11:49:32 2013 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Tue, 05 Mar 2013 11:49:32 +0000 Subject: [emboss-dev] ./configure --prefix=/somewhere --destdir=/chroot/somewhere In-Reply-To: <5135D39C.7090908@unil.ch> References: <5135D39C.7090908@unil.ch> Message-ID: <5135DBCC.2050104@ebi.ac.uk> Hi Sebastien, I don't know about the chroot environments and has poor knowledge of configure system EMBOSS have. I write just in case you are not aware of the configure script --help option. > ./configure --help It has a section called "Fine tuning of the installation directories" that i thought can be used to address the problem you described. Picked below few options that might be relevant to your query. --bindir=DIR user executables [EPREFIX/bin] --sbindir=DIR system admin executables [EPREFIX/sbin] --libexecdir=DIR program executables [EPREFIX/libexec] --libdir=DIR object code libraries [EPREFIX/lib] Mahmut On 05/03/13 11:14, Moretti S?bastien wrote: > 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 > > From sebastien.moretti at unil.ch Tue Mar 5 13:00:40 2013 From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?Moretti_S=E9bastien?=) Date: Tue, 05 Mar 2013 14:00:40 +0100 Subject: [emboss-dev] ./configure --prefix=/somewhere --destdir=/chroot/somewhere In-Reply-To: <5135DBCC.2050104@ebi.ac.uk> References: <5135D39C.7090908@unil.ch> <5135DBCC.2050104@ebi.ac.uk> Message-ID: <5135EC78.6030602@unil.ch> Hi Mahmut Thanks for your answer. I already use bindir and libdir but they have the same drawback than prefix. At the end binaries and libraries are linked to /somewhere but I cannot directly install them there. Or they are linked to /chroot/somewhere and I need to use $LD_LIBRAY_PATH to run them, and compilation of EMBASSY tools fail. Regards S?bastien > Hi Sebastien, > > I don't know about the chroot environments and has poor knowledge of > configure system EMBOSS have. I write just in case you are not aware of > the configure script --help option. > > > ./configure --help > > It has a section called "Fine tuning of the installation directories" > that i thought can be used to address the problem you described. > > Picked below few options that might be relevant to your query. > > --bindir=DIR user executables [EPREFIX/bin] > --sbindir=DIR system admin executables [EPREFIX/sbin] > --libexecdir=DIR program executables [EPREFIX/libexec] > --libdir=DIR object code libraries [EPREFIX/lib] > > Mahmut > > > > On 05/03/13 11:14, Moretti S?bastien wrote: >> 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 Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4079 http://selectome.unil.ch/ http://bgee.unil.ch/ From peterhendler at hushmail.com Fri Mar 22 20:04:24 2013 From: peterhendler at hushmail.com (peterhendler at hushmail.com) Date: Fri, 22 Mar 2013 16:04:24 -0400 Subject: [emboss-dev] Biggest Fake Conference in Computer Science Message-ID: <20130322200424.6AE7D10E2D3@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