From huzimin9712 at 163.com Thu Jul 3 04:16:34 2014 From: huzimin9712 at 163.com (huzimin9712) Date: Thu, 3 Jul 2014 10:16:34 +0800 (CST) Subject: [adegenet-forum] Population DNA sequences input file for Adegenet analysis In-Reply-To: <2CB2DA8E426F3541AB1907F98ABA65709A12ED9C@icexch-m1.ic.ac.uk> References: <2fb82269.19e4b.146f5e394d0.Coremail.huzimin9712@163.com> <2CB2DA8E426F3541AB1907F98ABA65709A12ED9C@icexch-m1.ic.ac.uk> Message-ID: <7ca71c36.3a7e.146fa025249.Coremail.huzimin9712@163.com> Dear Adegenet users, Do anybody have experience to prepare the input file from DNA sequences of populations for Adegenet analysis? Any response or detailed intrustuctions will be appreciated. Thanks in advance -- Dr. Hu Zi-Min Institute of Oceanology, Chinese Academy of Sciences No. 7, Nanhai Road, Qingdao, 266071 P. R. China Tel: 0086-532-82898554 Fax: 0086-532-82898556 huzimin9712 at 163.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.jombart at imperial.ac.uk Thu Jul 3 12:20:16 2014 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Thu, 3 Jul 2014 10:20:16 +0000 Subject: [adegenet-forum] Population DNA sequences input file for Adegenet analysis In-Reply-To: <7ca71c36.3a7e.146fa025249.Coremail.huzimin9712@163.com> References: <2fb82269.19e4b.146f5e394d0.Coremail.huzimin9712@163.com> <2CB2DA8E426F3541AB1907F98ABA65709A12ED9C@icexch-m1.ic.ac.uk>, <7ca71c36.3a7e.146fa025249.Coremail.huzimin9712@163.com> Message-ID: <2CB2DA8E426F3541AB1907F98ABA65709A12F062@icexch-m1.ic.ac.uk> Hello, please look at the 'basics' tutorial for inputs into adegenet. Functions 'fasta2DNAbin' and 'DNAbin2genind' will be useful. More on: http://adegenet.r-forge.r-project.org/ Cheers Thibaut ________________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of huzimin9712 [huzimin9712 at 163.com] Sent: 03 July 2014 03:16 To: adegenet-forum at lists.r-forge.r-project.org Subject: [adegenet-forum] Population DNA sequences input file for Adegenet analysis Dear Adegenet users, Do anybody have experience to prepare the input file from DNA sequences of populations for Adegenet analysis? Any response or detailed intrustuctions will be appreciated. Thanks in advance -- Dr. Hu Zi-Min Institute of Oceanology, Chinese Academy of Sciences No. 7, Nanhai Road, Qingdao, 266071 P. R. China Tel: 0086-532-82898554 Fax: 0086-532-82898556 huzimin9712 at 163.com From francesco.montinaro at gmail.com Thu Jul 3 12:25:03 2014 From: francesco.montinaro at gmail.com (Francesco Montinaro) Date: Thu, 3 Jul 2014 11:25:03 +0100 Subject: [adegenet-forum] adegenet-forum Digest, Vol 71, Issue 1 In-Reply-To: References: Message-ID: Hi, Zun. You will just need fasta format files. Best, Francesco Montinaro On 3 July 2014 11:00, wrote: > Send adegenet-forum mailing list submissions to > adegenet-forum at lists.r-forge.r-project.org > > To subscribe or unsubscribe via the World Wide Web, visit > > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum > > or, via email, send a message with subject or body 'help' to > adegenet-forum-request at lists.r-forge.r-project.org > > You can reach the person managing the list at > adegenet-forum-owner at lists.r-forge.r-project.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of adegenet-forum digest..." > > > Today's Topics: > > 1. Population DNA sequences input file for Adegenet analysis > (huzimin9712) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 3 Jul 2014 10:16:34 +0800 (CST) > From: huzimin9712 > To: adegenet-forum at lists.r-forge.r-project.org > Subject: [adegenet-forum] Population DNA sequences input file for > Adegenet analysis > Message-ID: <7ca71c36.3a7e.146fa025249.Coremail.huzimin9712 at 163.com> > Content-Type: text/plain; charset="gbk" > > Dear Adegenet users, > Do anybody have experience to prepare the input file from DNA sequences of > populations for Adegenet analysis? Any response or detailed intrustuctions > will be appreciated. > > > Thanks in advance > > > -- > > > Dr. Hu Zi-Min > Institute of Oceanology, Chinese Academy of Sciences > No. 7, Nanhai Road, Qingdao, 266071 > P. R. China > Tel: 0086-532-82898554 > Fax: 0086-532-82898556 > huzimin9712 at 163.com > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20140703/54e2bb29/attachment-0001.html > > > > ------------------------------ > > _______________________________________________ > adegenet-forum mailing list > adegenet-forum at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum > > End of adegenet-forum Digest, Vol 71, Issue 1 > ********************************************* > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dacostaj at bu.edu Fri Jul 4 01:08:52 2014 From: dacostaj at bu.edu (Jeffrey DaCosta) Date: Thu, 3 Jul 2014 19:08:52 -0400 Subject: [adegenet-forum] Importing Z (X) linked data? Message-ID: <597CEF26-8015-4483-A12E-2E179091EBC3@bu.edu> I have a structure file for putative Z-linked loci for a set of birds. Since females are the heterogametic sex, they are coded as hemizygous (one allele and one ?-9?) whereas males are diploid. The read.structure function seems to ignore females, I?m guessing because each female has a missing allele for all loci. I can recode all individuals as haploid and use df2genind, but does anyone have a different/better solution for getting these data into adegenet for a DAPC? Thanks for any input, -Jeff -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.jombart at imperial.ac.uk Fri Jul 4 11:42:03 2014 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Fri, 4 Jul 2014 09:42:03 +0000 Subject: [adegenet-forum] Importing Z (X) linked data? In-Reply-To: <597CEF26-8015-4483-A12E-2E179091EBC3@bu.edu> References: <597CEF26-8015-4483-A12E-2E179091EBC3@bu.edu> Message-ID: <2CB2DA8E426F3541AB1907F98ABA65709A12F955@icexch-m1.ic.ac.uk> Hi there, if you have a mixture of haploid/diploid genotypes, then you'd need to recode all as diploid, and then convert the data to genind (e.g. using df2genind). Note that the allele frequencies at a population level will be wrong. But individual-level multivariate analyses (PCA, PCoA, DAPC etc) will be OK Cheers Thibaut ________________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Jeffrey DaCosta [dacostaj at bu.edu] Sent: 04 July 2014 00:08 To: adegenet-forum at r-forge.wu-wien.ac.at Subject: [adegenet-forum] Importing Z (X) linked data? I have a structure file for putative Z-linked loci for a set of birds. Since females are the heterogametic sex, they are coded as hemizygous (one allele and one ?-9?) whereas males are diploid. The read.structure function seems to ignore females, I?m guessing because each female has a missing allele for all loci. I can recode all individuals as haploid and use df2genind, but does anyone have a different/better solution for getting these data into adegenet for a DAPC? Thanks for any input, -Jeff From vojta at trapa.cz Wed Jul 9 12:34:47 2014 From: vojta at trapa.cz (=?utf-8?B?Vm9qdMSbY2g=?= Zeisek) Date: Wed, 09 Jul 2014 12:34:47 +0200 Subject: [adegenet-forum] Inconsistent DAPC Message-ID: <4287774.AlmuBrnSKg@veles.site> Hi, I was running DAPC on almost 500 individuals (over 60 populations) genotyped by 10 microsatellite primers as follows: kfind <- find.clusters(genind, n.pca=100, stat="BIC", choose.n.clust=FALSE, criterion="diffNgroup", max.n.clust=75, n.iter=100000000, n.start=10000, scale=FALSE, pca.select="nbEig", truenames=TRUE) table.value(table(pop(genind), kfind$grp), col.lab = paste("kfind", 1:length(kfind$size))) dapc <- dapc(genind, kfind$grp, n.pca=35, n.da=20, center=TRUE, scale=FALSE, var.contrib=TRUE, pca.info=TRUE, pca.select="nbEig", truenames=TRUE) scatter(dapc, main="DAPC", posi.da=?bottomleft?) When I did it for first time, I've got nice partitioning to 3 clusters, quiet similar to output of Structure and PCoA. When I tried it second time with same parameters, I've got division to 12 groups. So I wonder how is it possible and how to trace to make it reproducible and find out why it shifted so much. Sincerely, Vojt?ch -- Vojt?ch Zeisek http://trapa.cz/en/ Department of Botany, Faculty of Science Charles University in Prague Ben?tsk? 2, Prague, 12801, CZ http://botany.natur.cuni.cz/en/ Institute of Botany, Academy of Science Z?mek 1, Pr?honice, 25243, CZ http://www.ibot.cas.cz/en/ Czech Republic -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 490 bytes Desc: This is a digitally signed message part. URL: From t.jombart at imperial.ac.uk Wed Jul 9 12:49:04 2014 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Wed, 9 Jul 2014 10:49:04 +0000 Subject: [adegenet-forum] Inconsistent DAPC In-Reply-To: <4287774.AlmuBrnSKg@veles.site> References: <4287774.AlmuBrnSKg@veles.site> Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570A821D25E@icexch-m1.ic.ac.uk> Hello there, this is because you are using a fixed criteria to decide the group partitioning. This was only designed for simulated data analysis, or cases where one needs to analyse hundreds of datasets. Best for your to look at the BIC curves (over a couple of iterations) and assess which clustering solution you want to retain. Best Thibaut ________________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Vojt?ch Zeisek [vojta at trapa.cz] Sent: 09 July 2014 11:34 To: Adegenet R-Forum Subject: [adegenet-forum] Inconsistent DAPC Hi, I was running DAPC on almost 500 individuals (over 60 populations) genotyped by 10 microsatellite primers as follows: kfind <- find.clusters(genind, n.pca=100, stat="BIC", choose.n.clust=FALSE, criterion="diffNgroup", max.n.clust=75, n.iter=100000000, n.start=10000, scale=FALSE, pca.select="nbEig", truenames=TRUE) table.value(table(pop(genind), kfind$grp), col.lab = paste("kfind", 1:length(kfind$size))) dapc <- dapc(genind, kfind$grp, n.pca=35, n.da=20, center=TRUE, scale=FALSE, var.contrib=TRUE, pca.info=TRUE, pca.select="nbEig", truenames=TRUE) scatter(dapc, main="DAPC", posi.da=?bottomleft?) When I did it for first time, I've got nice partitioning to 3 clusters, quiet similar to output of Structure and PCoA. When I tried it second time with same parameters, I've got division to 12 groups. So I wonder how is it possible and how to trace to make it reproducible and find out why it shifted so much. Sincerely, Vojt?ch -- Vojt?ch Zeisek http://trapa.cz/en/ Department of Botany, Faculty of Science Charles University in Prague Ben?tsk? 2, Prague, 12801, CZ http://botany.natur.cuni.cz/en/ Institute of Botany, Academy of Science Z?mek 1, Pr?honice, 25243, CZ http://www.ibot.cas.cz/en/ Czech Republic From roberto at geodev.com.br Wed Jul 9 14:48:09 2014 From: roberto at geodev.com.br (Roberto Oliveira Santos) Date: Wed, 9 Jul 2014 13:48:09 +0100 Subject: [adegenet-forum] Workshop or training on spatial analysis of genetic data Message-ID: Dear all, Is there any plan for a workshop or training about spatial analysis of genetic data or adegenet? Best wishes, Roberto -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.jombart at imperial.ac.uk Wed Jul 9 16:07:21 2014 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Wed, 9 Jul 2014 14:07:21 +0000 Subject: [adegenet-forum] Workshop or training on spatial analysis of genetic data In-Reply-To: References: Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570A821D340@icexch-m1.ic.ac.uk> Dear Roberto, not that I am aware of at the moment, but I have been giving that kind of teaching more or less regularly in the past years. Feel free to email me off-list if you'd like to organize something. Cheers Thibaut ________________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Roberto Oliveira Santos [roberto at geodev.com.br] Sent: 09 July 2014 13:48 To: adegenet-forum at lists.r-forge.r-project.org Subject: [adegenet-forum] Workshop or training on spatial analysis of genetic data Dear all, Is there any plan for a workshop or training about spatial analysis of genetic data or adegenet? Best wishes, Roberto From vojta at trapa.cz Wed Jul 9 16:39:06 2014 From: vojta at trapa.cz (=?utf-8?B?Vm9qdMSbY2g=?= Zeisek) Date: Wed, 09 Jul 2014 16:39:06 +0200 Subject: [adegenet-forum] Inconsistent DAPC In-Reply-To: <2CB2DA8E426F3541AB1907F98ABA6570A821D25E@icexch-m1.ic.ac.uk> References: <4287774.AlmuBrnSKg@veles.site> <2CB2DA8E426F3541AB1907F98ABA6570A821D25E@icexch-m1.ic.ac.uk> Message-ID: <4422513.chP3QoNPfz@veles.site> Hello, thank You very much. Dne St 9. ?ervence 2014 10:49:04 jste napsal(a): > Hello there, > > this is because you are using a fixed criteria to decide the group > partitioning. This was only designed for simulated data analysis, or cases > where one needs to analyse hundreds of datasets. > > Best for your to look at the BIC curves (over a couple of iterations) and > assess which clustering solution you want to retain. Ah, right. When running it like this kfind <- find.clusters(genind, max.n.clust=75, stat="BIC", choose.n.clust=TRUE, n.iter=100000000, n.start=10000, scale=FALSE, truenames=TRUE) table.value(table(pop(genind), kfind$grp), col.lab=paste("Inferred cluster", 1:length(kfind$size)), grid=TRUE) I see there are more possible solutions... Interesting data set. :-) Sincerely, Vojt?ch > Best > Thibaut > ________________________________________ > From: adegenet-forum-bounces at lists.r-forge.r-project.org > [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Vojt?ch > Zeisek [vojta at trapa.cz] Sent: 09 July 2014 11:34 > To: Adegenet R-Forum > Subject: [adegenet-forum] Inconsistent DAPC > > Hi, > I was running DAPC on almost 500 individuals (over 60 populations) genotyped > by 10 microsatellite primers as follows: > kfind <- find.clusters(genind, n.pca=100, stat="BIC", choose.n.clust=FALSE, > criterion="diffNgroup", max.n.clust=75, n.iter=100000000, n.start=10000, > scale=FALSE, pca.select="nbEig", truenames=TRUE) > table.value(table(pop(genind), kfind$grp), col.lab = paste("kfind", > 1:length(kfind$size))) > dapc <- dapc(genind, kfind$grp, n.pca=35, n.da=20, center=TRUE, scale=FALSE, > var.contrib=TRUE, pca.info=TRUE, pca.select="nbEig", truenames=TRUE) > scatter(dapc, main="DAPC", posi.da=?bottomleft?) > When I did it for first time, I've got nice partitioning to 3 clusters, > quiet similar to output of Structure and PCoA. When I tried it second time > with same parameters, I've got division to 12 groups. So I wonder how is it > possible and how to trace to make it reproducible and find out why it > shifted so much. Sincerely, > Vojt?ch -- Vojt?ch Zeisek http://trapa.cz/en/ Department of Botany, Faculty of Science Charles University in Prague Ben?tsk? 2, Prague, 12801, CZ http://botany.natur.cuni.cz/en/ Institute of Botany, Academy of Science Z?mek 1, Pr?honice, 25243, CZ http://www.ibot.cas.cz/en/ Czech Republic -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 490 bytes Desc: This is a digitally signed message part. URL: From t.jombart at imperial.ac.uk Wed Jul 9 16:56:12 2014 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Wed, 9 Jul 2014 14:56:12 +0000 Subject: [adegenet-forum] Inconsistent DAPC In-Reply-To: <4422513.chP3QoNPfz@veles.site> References: <4287774.AlmuBrnSKg@veles.site> <2CB2DA8E426F3541AB1907F98ABA6570A821D25E@icexch-m1.ic.ac.uk>, <4422513.chP3QoNPfz@veles.site> Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570A821D3D9@icexch-m1.ic.ac.uk> Yes, that's pretty much a recurrent problem: often there is no single clustering solution capturing the biological reality perfectly. See other posts about "true K" on the forum. Best Thibaut ________________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Vojt?ch Zeisek [vojta at trapa.cz] Sent: 09 July 2014 15:39 To: Adegenet R-Forum Subject: Re: [adegenet-forum] Inconsistent DAPC Hello, thank You very much. Dne St 9. ?ervence 2014 10:49:04 jste napsal(a): > Hello there, > > this is because you are using a fixed criteria to decide the group > partitioning. This was only designed for simulated data analysis, or cases > where one needs to analyse hundreds of datasets. > > Best for your to look at the BIC curves (over a couple of iterations) and > assess which clustering solution you want to retain. Ah, right. When running it like this kfind <- find.clusters(genind, max.n.clust=75, stat="BIC", choose.n.clust=TRUE, n.iter=100000000, n.start=10000, scale=FALSE, truenames=TRUE) table.value(table(pop(genind), kfind$grp), col.lab=paste("Inferred cluster", 1:length(kfind$size)), grid=TRUE) I see there are more possible solutions... Interesting data set. :-) Sincerely, Vojt?ch > Best > Thibaut > ________________________________________ > From: adegenet-forum-bounces at lists.r-forge.r-project.org > [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Vojt?ch > Zeisek [vojta at trapa.cz] Sent: 09 July 2014 11:34 > To: Adegenet R-Forum > Subject: [adegenet-forum] Inconsistent DAPC > > Hi, > I was running DAPC on almost 500 individuals (over 60 populations) genotyped > by 10 microsatellite primers as follows: > kfind <- find.clusters(genind, n.pca=100, stat="BIC", choose.n.clust=FALSE, > criterion="diffNgroup", max.n.clust=75, n.iter=100000000, n.start=10000, > scale=FALSE, pca.select="nbEig", truenames=TRUE) > table.value(table(pop(genind), kfind$grp), col.lab = paste("kfind", > 1:length(kfind$size))) > dapc <- dapc(genind, kfind$grp, n.pca=35, n.da=20, center=TRUE, scale=FALSE, > var.contrib=TRUE, pca.info=TRUE, pca.select="nbEig", truenames=TRUE) > scatter(dapc, main="DAPC", posi.da=?bottomleft?) > When I did it for first time, I've got nice partitioning to 3 clusters, > quiet similar to output of Structure and PCoA. When I tried it second time > with same parameters, I've got division to 12 groups. So I wonder how is it > possible and how to trace to make it reproducible and find out why it > shifted so much. Sincerely, > Vojt?ch -- Vojt?ch Zeisek http://trapa.cz/en/ Department of Botany, Faculty of Science Charles University in Prague Ben?tsk? 2, Prague, 12801, CZ http://botany.natur.cuni.cz/en/ Institute of Botany, Academy of Science Z?mek 1, Pr?honice, 25243, CZ http://www.ibot.cas.cz/en/ Czech Republic From x.giroux.bougard at gmail.com Thu Jul 10 23:14:59 2014 From: x.giroux.bougard at gmail.com (Xavier Giroux-Bougard) Date: Thu, 10 Jul 2014 17:14:59 -0400 Subject: [adegenet-forum] testing sPCA differences Message-ID: Dear adegenet forum, does anybody know if there is a permutation test implemented in adegenet (or other R packages) that could differentiate the sPCA solutions of two (or more) subsets of a genetic dataset, for example to compare genetic structures across sexes or ages, etc... For example, Smouse et al. (2008) developed a heterogeneity test to differentiate two correlograms. I know there are the global and local statistics, but is there something similar that could help differentiate the spatial genetic structure between two groups in sPCA? Thanks, Xavier -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.jombart at imperial.ac.uk Fri Jul 11 11:14:36 2014 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Fri, 11 Jul 2014 09:14:36 +0000 Subject: [adegenet-forum] testing sPCA differences In-Reply-To: References: Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570A821F8E2@icexch-m1.ic.ac.uk> Hi Xavier, such a test will not be possible using approaches directly relating to the sPCA. This is because the range and null value of Moran's I (part of the optimized criteria, measuring the spatial structures) depend on the spatial weights. Therefore, Moran's I based approaches cannot compare spatial structures of different groups of locations/individuals. Cheers Thibaut ________________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Xavier Giroux-Bougard [x.giroux.bougard at gmail.com] Sent: 10 July 2014 22:14 To: adegenet-forum at lists.r-forge.r-project.org Subject: [adegenet-forum] testing sPCA differences Dear adegenet forum, does anybody know if there is a permutation test implemented in adegenet (or other R packages) that could differentiate the sPCA solutions of two (or more) subsets of a genetic dataset, for example to compare genetic structures across sexes or ages, etc... For example, Smouse et al. (2008) developed a heterogeneity test to differentiate two correlograms. I know there are the global and local statistics, but is there something similar that could help differentiate the spatial genetic structure between two groups in sPCA? Thanks, Xavier From samuel.k at gmx.de Sat Jul 12 20:50:23 2014 From: samuel.k at gmx.de (Samuel Knapp) Date: Sat, 12 Jul 2014 20:50:23 +0200 Subject: [adegenet-forum] Problem installation on Ubuntu Message-ID: <53C1836F.7030607@gmx.de> Dear all, I'm running R on Ubuntu and can't install the adegenet package. Versions: - Ubuntu: 14.04 (Trusty) - R.Version() $platform [1] "x86_64-pc-linux-gnu" $version.string [1] "R version 3.1.1 (2014-07-10)" In order to exclude other problems, I have reinstalled a clear R version and tried to install adegenet as the first package. I get the output below. Have tried to search for "Error in namespaceExport(ns, exports)" and "ERROR: lazy loading failed for package ?adegenet?", but can't find anything. Also I tried to install older versions of adegenet and got the same error report. The error occurs both, if I run R as sudo or as normal user. If anybody has an idea what the problem could be, please let me know. Thanks, Samuel ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// > install.packages("adegenet") Installing package into ?/home/samuel/R/x86_64-pc-linux-gnu-library/3.1? (as ?lib? is unspecified) trying URL 'http://ftp.igh.cnrs.fr/pub/CRAN/src/contrib/adegenet_1.4-2.tar.gz' Content type 'application/octet-stream' length 1588751 bytes (1.5 Mb) opened URL ================================================== downloaded 1.5 Mb * installing *source* package ?adegenet? ... ** package ?adegenet? successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c GLfunctions.c -o GLfunctions.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c adesub.c -o adesub.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c monmonier-utils.c -o monmonier-utils.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c sharedAll.c -o sharedAll.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c snpbin.c -o snpbin.o gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o adegenet.so GLfunctions.o adesub.o monmonier-utils.o sharedAll.o snpbin.o -L/usr/lib/R/lib -lR installing to /home/samuel/R/x86_64-pc-linux-gnu-library/3.1/adegenet/libs ** R ** data ** inst ** preparing package for lazy loading Warning: S3 methods ?[.igraph?, ?[[.igraph?, ?[<-.igraph?, ?+.igraph?, ?-.igraph?, ?$.igraph?, ?$<-.igraph?, ?$.igraph.vs?, ?[.igraph.vs?, ?[[.igraph.vs?, ?[<-.igraph.vs?, ?[[<-.igraph.vs?, ?$<-.igraph.vs?, ?$.igraph.es?, ?[.igraph.es?, ?[[.igraph.es?, ?[<-.igraph.es?, ?[[<-.igraph.es?, ?$<-.igraph.es?, ?print.igraph.vs?, ?print.igraph.es?, ?str.igraph?, ?print.communities?, ?modularity.communities?, ?length.communities?, ?as.dendrogram.communities?, ?as.hclust.communities?, ?asPhylo.communities?, ?modularity.igraph?, ?dendPlot.communities?, ?compare.communities?, ?compare.numeric?, ?compare.default?, ?rglplot.igraph?, ?layout.svd.igraph?, ?print.cohesiveBlocks?, ?summary.cohesiveBlocks?, ?plot.cohesiveBlocks?, ?length.cohesiveBlocks?, ?print.igraphHRG?, ?print.igraphHRGConsensus?, ?as.dendrogram.igraphHRG?, ?as.hclust.igraphHR [... truncated] Error in namespaceExport(ns, exports) : undefined exports: add.vertices, delete.edges, delete.vertices, ecount, neighbors, incident, get.edges, get.edge.ids, [.igraph, [[.igraph, [<-.igraph, edge, edges, vertex, vertices, path, +.igraph, -.igraph, get.graph.attribute, set.graph.attribute, graph.attributes, get.vertex.attribute, set.vertex.attribute, vertex.attributes, get.edge.attribute, set.edge.attribute, edge.attributes, list.graph.attributes, list.vertex.attributes, list.edge.attributes, remove.graph.attribute, remove.vertex.attribute, remove.edge.attribute, graph.attributes<-, vertex.attributes<-, edge.attributes<-, V, E, $.igraph.vs, $.igraph.es, [.igraph.vs, [[.igraph.vs, [.igraph.es, [[.igraph.es, [<-.igraph.vs, [<-.igraph.es, [[<-.igraph.vs, [[<-.igraph.es, $<-.igraph.vs, $<-.igraph.es, V<-, E<-, print.igraph.vs, print.igraph.es, %--%, %->%, %<-%, is.igraph, is.named, is.weighted, is.bipartite, are.connected, print.igraph, str.igraph, summary.igraph, is.directed, get.edge, graph, graph.adjacency, graph.star, graph.tree, graph.lattice, graph.ring, graph.full, graph.atlas, graph.data.frame, graph.edgelist, graph.extended.chordal.ring, line.graph, graph.de.bruijn, graph.kautz, graph.formula, graph.famous, erdos.renyi.game, random.graph.game, degree.sequence.game, aging.prefatt.game, aging.barabasi.game, aging.ba.game, growing.random.game, barabasi.game, ba.game, callaway.traits.game, establishment.game, grg.game, preference.game, asymmetric.preference.game, connect.neighborhood, rewire.edges, watts.strogatz.game, lastcit.game, cited.type.game, citing.cited.type.game, bipartite.random.game, edge.betweenness.community, spinglass.community, walktrap.community, edge.betweenness.community.merges, fastgreedy.community, community.to.membership, membership, modularity, sizes, algorithm, is.hierarchical, merges, cutat, communities, crossing, plot.communities, compare, compare.communities, showtrace, code.length, asPhylo, dendPlot, create.communities, get.adjacency, get.edgelist, as.directed, as.undirected, get.adjlist, get.adjedgelist, igraph.from.graphNEL, igraph.to.graphNEL, get.data.frame, power.law.fit, running.mean, igraph.sample, srand, read.graph, write.graph, graph.graphdb, layout.auto, layout.random, layout.circle, layout.spring, layout.kamada.kawai, layout.lgl, layout.fruchterman.reingold.grid, layout.sphere, layout.merge, layout.reingold.tilford, layout.norm, piecewise.layout, igraph.drl.default, igraph.drl.coarsen, igraph.drl.coarsest, igraph.drl.refine, igraph.drl.final, subgraph, degree, degree.distribution, diameter, subcomponent, betweenness, bibcoupling, cocitation, shortest.paths, minimum.spanning.tree, get.shortest.paths, average.path.length, transitivity, get.all.shortest.paths, get.diameter, farthest.nodes, constraint, page.rank, reciprocity, rewire, graph.density, neighborhood.size, neighborhood, graph.neighborhood, graph.coreness, topological.sort, girth, is.loop, is.multiple, count.multiple, plot.igraph, tkplot, tkplot.close, tkplot.off, tkplot.fit.to.screen, tkplot.reshape, tkplot.export.postscript, tkplot.getcoords, tkplot.center, tkplot.rotate, tkplot.canvas, tkplot.setcoords, rglplot.igraph, rglplot, autocurve.edges, vertex.shapes, add.vertex.shape, igraph.shape.noclip, igraph.shape.noplot, cluster.distribution, is.connected, decompose.graph, no.clusters, evcent, bonpow, alpha.centrality, subgraph.centrality, igraph.arpack.default, igraph.eigen.default, revolver.d, revolver.error.d, revolver.ad, revolver.error.ad, revolver.ade, revolver.error.ade, revolver.e, revolver.error.e, revolver.de, revolver.error.de, revolver.l, revolver.error.l, revolver.dl, revolver.error.dl, revolver.el, revolver.error.el, revolver.r, revolver.error.r, revolver.ar, revolver.error.ar, revolver.di, revolver.error.di, revolver.adi, revolver.error.adi, revolver.il, revolver.error.il, revolver.ir, revolver.error.ir, revolver.air, revolver.error.air, revolver.d.d, revolver.p.p, evolver.d, graph.isoclass, graph.isomorphic, graph.motifs, graph.motifs.est, graph.isocreate, graph.motifs.no, graph.isomorphic.vf2, graph.subisomorphic.vf2, graph.count.isomorphisms.vf2, graph.count.subisomorphisms.vf2, graph.get.isomorphisms.vf2, graph.get.subisomorphisms.vf2, graph.disjoint.union, %du%, graph.intersection, %s%, graph.union, %u%, graph.difference, %m%, graph.complementer, graph.compose, %c%, igraph.par, igraph.options, getIgraphOpt, igraphtest, igraph.version, igraph.console, .igraph.progress, .igraph.status, graph.mincut, vertex.connectivity, edge.connectivity, edge.disjoint.paths, vertex.disjoint.paths, graph.adhesion, graph.cohesion, cliques, largest.cliques, maximal.cliques, clique.number, independent.vertex.sets, largest.independent.vertex.sets, maximal.independent.vertex.sets, independence.number, layout.svd, blocks, blockGraphs, cohesion, hierarchy, parent, plotHierarchy, exportPajek, maxcohesion, arpack, tkigraph, igraphdemo, scg, nexus.get, nexus.list, nexus.info, nexus.search, as.igraph, graphlets, graphlets.project, plot.sir, time_bins, graph.empty, add.edges, vcount, graph.full.citation, graph.lcf, graph.adjlist, graph.full.bipartite, forest.fire.game, interconnected.islands.game, static.fitness.game, static.power.law.game, k.regular.game, sbm.game, closeness, closeness.estimate, betweenness.estimate, edge.betweenness, edge.betweenness.estimate, page.rank.old, induced.subgraph, subgraph.edges, path.length.hist, simplify, is.dag, is.simple, has.multiple, hub.score, authority.score, arpack.unpack.complex, unfold.tree, is.mutual, maximum.cardinality.search, is.chordal, graph.knn, graph.strength, centralize.scores, centralization.degree, centralization.degree.tmax, centralization.betweenness, centralization.betweenness.tmax, centralization.closeness, centralization.closeness.tmax, centralization.evcent, centralization.evcent.tmax, assortativity.nominal, assortativity, assortativity.degree, contract.vertices, eccentricity, radius, graph.diversity, is.degree.sequence, is.graphical.degree.sequence, graph.bfs, graph.dfs, bipartite.projection.size, bipartite.projection, graph.bipartite, graph.incidence, get.incidence, bipartite.mapping, graph.laplacian, clusters, articulation.points, biconnected.components, maximal.cliques.count, layout.star, layout.grid, layout.grid.3d, layout.fruchterman.reingold, layout.graphopt, layout.drl, layout.sugiyama, layout.mds, layout.bipartite, similarity.jaccard, similarity.dice, similarity.invlogweighted, community.le.to.membership, mod.matrix, leading.eigenvector.community, label.propagation.community, multilevel.community, optimal.community, hrg.fit, hrg.game, hrg.dendrogram, hrg.consensus, hrg.predict, hrg.create, infomap.community, graphlets.candidate.basis, get.stochastic, dyad.census, triad.census, adjacent.triangles, graph.maxflow, dominator.tree, stCuts, stMincuts, is.separator, is.minimal.separator, minimal.st.separators, minimum.size.separators, cohesive.blocks, graph.isoclass.subgraph, graph.isomorphic.34, canonical.permutation, permute.vertices, graph.isomorphic.bliss, graph.automorphisms, graph.subisomorphic.lad, scgGrouping, scgSemiProjectors, scgNormEps, is.matching, is.maximal.matching, maximum.bipartite.matching, graph.eigen, sir, convex.hull, revolver.ml.d, revolver.probs.d, revolver.ml.de, revolver.probs.de, revolver.ml.ade, revolver.probs.ade, revolver.ml.f, revolver.ml.df, revolver.ml.l, revolver.ml.ad, revolver.probs.ad, revolver.ml.D.alpha, revolver.ml.D.alpha.a, revolver.ml.DE.alpha.a, revolver.ml.AD.alpha.a.beta, revolver.ml.AD.dpareto, revolver.ml.AD.dpareto.eval, revolver.ml.ADE.alpha.a.beta, revolver.ml.ADE.dpareto, revolver.ml.ADE.dpareto.eval, revolver.ml.ADE.dpareto.evalf, revolver.probs.ADE.dpareto ERROR: lazy loading failed for package ?adegenet? * removing ?/home/samuel/R/x86_64-pc-linux-gnu-library/3.1/adegenet? The downloaded source packages are in ?/tmp/RtmpRguHDL/downloaded_packages? Warning message: In install.packages("adegenet") : installation of package ?adegenet? had non-zero exit status ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// From vojta at trapa.cz Sat Jul 12 20:57:32 2014 From: vojta at trapa.cz (=?utf-8?B?Vm9qdMSbY2g=?= Zeisek) Date: Sat, 12 Jul 2014 20:57:32 +0200 Subject: [adegenet-forum] Problem installation on Ubuntu In-Reply-To: <53C1836F.7030607@gmx.de> References: <53C1836F.7030607@gmx.de> Message-ID: <1823086.272X4meaJe@veles.site> Hello, generally, R packages have to be compiled on Linux. Do You have basic tools for compilation? See https://help.ubuntu.com/community/CompilingSoftware Might be You can try to install the package directly from Ubuntu binary package repository, see http://cran.r-project.org/bin/linux/ubuntu/README I don't use Ubuntu, so that I'm not sure about usability of that repository... And then try install.packages("adegenet", dependencies=TRUE) Good luck, Vojt?ch Dne So 12. ?ervence 2014 20:50:23, Samuel Knapp napsal(a): > Dear all, > > I'm running R on Ubuntu and can't install the adegenet package. > > Versions: > - Ubuntu: 14.04 (Trusty) > - R.Version() > $platform > [1] "x86_64-pc-linux-gnu" > $version.string > [1] "R version 3.1.1 (2014-07-10)" > > In order to exclude other problems, I have reinstalled a clear R version > and tried to install adegenet as the first package. I get the output below. > > Have tried to search for "Error in namespaceExport(ns, exports)" and > "ERROR: lazy loading failed for package ?adegenet?", but can't find > anything. > Also I tried to install older versions of adegenet and got the same > error report. The error occurs both, if I run R as sudo or as normal user. > > If anybody has an idea what the problem could be, please let me know. > > Thanks, > Samuel > > //////////////////////////////////////////////////////////////////////////// > //////////////////////////////////////////////////////////////////////////// > ////////////////////////////////////////////////////////////// > > install.packages("adegenet") > > Installing package into ?/home/samuel/R/x86_64-pc-linux-gnu-library/3.1? > (as ?lib? is unspecified) > trying URL > 'http://ftp.igh.cnrs.fr/pub/CRAN/src/contrib/adegenet_1.4-2.tar.gz' > Content type 'application/octet-stream' length 1588751 bytes (1.5 Mb) > opened URL > ================================================== > downloaded 1.5 Mb > > * installing *source* package ?adegenet? ... > ** package ?adegenet? successfully unpacked and MD5 sums checked > ** libs > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 > -fstack-protector --param=ssp-buffer-size=4 -Wformat > -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c GLfunctions.c -o > GLfunctions.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 > -fstack-protector --param=ssp-buffer-size=4 -Wformat > -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c adesub.c -o adesub.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 > -fstack-protector --param=ssp-buffer-size=4 -Wformat > -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c monmonier-utils.c -o > monmonier-utils.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 > -fstack-protector --param=ssp-buffer-size=4 -Wformat > -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c sharedAll.c -o sharedAll.o > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 > -fstack-protector --param=ssp-buffer-size=4 -Wformat > -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c snpbin.c -o snpbin.o > gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o > adegenet.so GLfunctions.o adesub.o monmonier-utils.o sharedAll.o > snpbin.o -L/usr/lib/R/lib -lR > installing to /home/samuel/R/x86_64-pc-linux-gnu-library/3.1/adegenet/libs > ** R > ** data > ** inst > ** preparing package for lazy loading > Warning: S3 methods ?[.igraph?, ?[[.igraph?, ?[<-.igraph?, ?+.igraph?, > ?-.igraph?, ?$.igraph?, ?$<-.igraph?, ?$.igraph.vs?, ?[.igraph.vs?, > ?[[.igraph.vs?, ?[<-.igraph.vs?, ?[[<-.igraph.vs?, ?$<-.igraph.vs?, > ?$.igraph.es?, ?[.igraph.es?, ?[[.igraph.es?, ?[<-.igraph.es?, > ?[[<-.igraph.es?, ?$<-.igraph.es?, ?print.igraph.vs?, ?print.igraph.es?, > ?str.igraph?, ?print.communities?, ?modularity.communities?, > ?length.communities?, ?as.dendrogram.communities?, > ?as.hclust.communities?, ?asPhylo.communities?, ?modularity.igraph?, > ?dendPlot.communities?, ?compare.communities?, ?compare.numeric?, > ?compare.default?, ?rglplot.igraph?, ?layout.svd.igraph?, > ?print.cohesiveBlocks?, ?summary.cohesiveBlocks?, ?plot.cohesiveBlocks?, > ?length.cohesiveBlocks?, ?print.igraphHRG?, ?print.igraphHRGConsensus?, > ?as.dendrogram.igraphHRG?, ?as.hclust.igraphHR [... truncated] > Error in namespaceExport(ns, exports) : > undefined exports: add.vertices, delete.edges, delete.vertices, ecount, > neighbors, incident, get.edges, get.edge.ids, [.igraph, [[.igraph, > [<-.igraph, edge, edges, vertex, vertices, path, +.igraph, -.igraph, > get.graph.attribute, set.graph.attribute, graph.attributes, > get.vertex.attribute, set.vertex.attribute, vertex.attributes, > get.edge.attribute, set.edge.attribute, edge.attributes, > list.graph.attributes, list.vertex.attributes, list.edge.attributes, > remove.graph.attribute, remove.vertex.attribute, remove.edge.attribute, > graph.attributes<-, vertex.attributes<-, edge.attributes<-, V, E, > $.igraph.vs, $.igraph.es, [.igraph.vs, [[.igraph.vs, [.igraph.es, > [[.igraph.es, [<-.igraph.vs, [<-.igraph.es, [[<-.igraph.vs, > [[<-.igraph.es, $<-.igraph.vs, $<-.igraph.es, V<-, E<-, print.igraph.vs, > print.igraph.es, %--%, %->%, %<-%, is.igraph, is.named, is.weighted, > is.bipartite, are.connected, print.igraph, str.igraph, summary.igraph, > is.directed, get.edge, graph, graph.adjacency, graph.star, graph.tree, > graph.lattice, graph.ring, graph.full, graph.atlas, graph.data.frame, > graph.edgelist, graph.extended.chordal.ring, line.graph, > graph.de.bruijn, graph.kautz, graph.formula, graph.famous, > erdos.renyi.game, random.graph.game, degree.sequence.game, > aging.prefatt.game, aging.barabasi.game, aging.ba.game, > growing.random.game, barabasi.game, ba.game, callaway.traits.game, > establishment.game, grg.game, preference.game, > asymmetric.preference.game, connect.neighborhood, rewire.edges, > watts.strogatz.game, lastcit.game, cited.type.game, > citing.cited.type.game, bipartite.random.game, > edge.betweenness.community, spinglass.community, walktrap.community, > edge.betweenness.community.merges, fastgreedy.community, > community.to.membership, membership, modularity, sizes, algorithm, > is.hierarchical, merges, cutat, communities, crossing, plot.communities, > compare, compare.communities, showtrace, code.length, asPhylo, dendPlot, > create.communities, get.adjacency, get.edgelist, as.directed, > as.undirected, get.adjlist, get.adjedgelist, igraph.from.graphNEL, > igraph.to.graphNEL, get.data.frame, power.law.fit, running.mean, > igraph.sample, srand, read.graph, write.graph, graph.graphdb, > layout.auto, layout.random, layout.circle, layout.spring, > layout.kamada.kawai, layout.lgl, layout.fruchterman.reingold.grid, > layout.sphere, layout.merge, layout.reingold.tilford, layout.norm, > piecewise.layout, igraph.drl.default, igraph.drl.coarsen, > igraph.drl.coarsest, igraph.drl.refine, igraph.drl.final, subgraph, > degree, degree.distribution, diameter, subcomponent, betweenness, > bibcoupling, cocitation, shortest.paths, minimum.spanning.tree, > get.shortest.paths, average.path.length, transitivity, > get.all.shortest.paths, get.diameter, farthest.nodes, constraint, > page.rank, reciprocity, rewire, graph.density, neighborhood.size, > neighborhood, graph.neighborhood, graph.coreness, topological.sort, > girth, is.loop, is.multiple, count.multiple, plot.igraph, tkplot, > tkplot.close, tkplot.off, tkplot.fit.to.screen, tkplot.reshape, > tkplot.export.postscript, tkplot.getcoords, tkplot.center, > tkplot.rotate, tkplot.canvas, tkplot.setcoords, rglplot.igraph, rglplot, > autocurve.edges, vertex.shapes, add.vertex.shape, igraph.shape.noclip, > igraph.shape.noplot, cluster.distribution, is.connected, > decompose.graph, no.clusters, evcent, bonpow, alpha.centrality, > subgraph.centrality, igraph.arpack.default, igraph.eigen.default, > revolver.d, revolver.error.d, revolver.ad, revolver.error.ad, > revolver.ade, revolver.error.ade, revolver.e, revolver.error.e, > revolver.de, revolver.error.de, revolver.l, revolver.error.l, > revolver.dl, revolver.error.dl, revolver.el, revolver.error.el, > revolver.r, revolver.error.r, revolver.ar, revolver.error.ar, > revolver.di, revolver.error.di, revolver.adi, revolver.error.adi, > revolver.il, revolver.error.il, revolver.ir, revolver.error.ir, > revolver.air, revolver.error.air, revolver.d.d, revolver.p.p, evolver.d, > graph.isoclass, graph.isomorphic, graph.motifs, graph.motifs.est, > graph.isocreate, graph.motifs.no, graph.isomorphic.vf2, > graph.subisomorphic.vf2, graph.count.isomorphisms.vf2, > graph.count.subisomorphisms.vf2, graph.get.isomorphisms.vf2, > graph.get.subisomorphisms.vf2, graph.disjoint.union, %du%, > graph.intersection, %s%, graph.union, %u%, graph.difference, %m%, > graph.complementer, graph.compose, %c%, igraph.par, igraph.options, > getIgraphOpt, igraphtest, igraph.version, igraph.console, > .igraph.progress, .igraph.status, graph.mincut, vertex.connectivity, > edge.connectivity, edge.disjoint.paths, vertex.disjoint.paths, > graph.adhesion, graph.cohesion, cliques, largest.cliques, > maximal.cliques, clique.number, independent.vertex.sets, > largest.independent.vertex.sets, maximal.independent.vertex.sets, > independence.number, layout.svd, blocks, blockGraphs, cohesion, > hierarchy, parent, plotHierarchy, exportPajek, maxcohesion, arpack, > tkigraph, igraphdemo, scg, nexus.get, nexus.list, nexus.info, > nexus.search, as.igraph, graphlets, graphlets.project, plot.sir, > time_bins, graph.empty, add.edges, vcount, graph.full.citation, > graph.lcf, graph.adjlist, graph.full.bipartite, forest.fire.game, > interconnected.islands.game, static.fitness.game, static.power.law.game, > k.regular.game, sbm.game, closeness, closeness.estimate, > betweenness.estimate, edge.betweenness, edge.betweenness.estimate, > page.rank.old, induced.subgraph, subgraph.edges, path.length.hist, > simplify, is.dag, is.simple, has.multiple, hub.score, authority.score, > arpack.unpack.complex, unfold.tree, is.mutual, > maximum.cardinality.search, is.chordal, graph.knn, graph.strength, > centralize.scores, centralization.degree, centralization.degree.tmax, > centralization.betweenness, centralization.betweenness.tmax, > centralization.closeness, centralization.closeness.tmax, > centralization.evcent, centralization.evcent.tmax, > assortativity.nominal, assortativity, assortativity.degree, > contract.vertices, eccentricity, radius, graph.diversity, > is.degree.sequence, is.graphical.degree.sequence, graph.bfs, graph.dfs, > bipartite.projection.size, bipartite.projection, graph.bipartite, > graph.incidence, get.incidence, bipartite.mapping, graph.laplacian, > clusters, articulation.points, biconnected.components, > maximal.cliques.count, layout.star, layout.grid, layout.grid.3d, > layout.fruchterman.reingold, layout.graphopt, layout.drl, > layout.sugiyama, layout.mds, layout.bipartite, similarity.jaccard, > similarity.dice, similarity.invlogweighted, community.le.to.membership, > mod.matrix, leading.eigenvector.community, label.propagation.community, > multilevel.community, optimal.community, hrg.fit, hrg.game, > hrg.dendrogram, hrg.consensus, hrg.predict, hrg.create, > infomap.community, graphlets.candidate.basis, get.stochastic, > dyad.census, triad.census, adjacent.triangles, graph.maxflow, > dominator.tree, stCuts, stMincuts, is.separator, is.minimal.separator, > minimal.st.separators, minimum.size.separators, cohesive.blocks, > graph.isoclass.subgraph, graph.isomorphic.34, canonical.permutation, > permute.vertices, graph.isomorphic.bliss, graph.automorphisms, > graph.subisomorphic.lad, scgGrouping, scgSemiProjectors, scgNormEps, > is.matching, is.maximal.matching, maximum.bipartite.matching, > graph.eigen, sir, convex.hull, revolver.ml.d, revolver.probs.d, > revolver.ml.de, revolver.probs.de, revolver.ml.ade, revolver.probs.ade, > revolver.ml.f, revolver.ml.df, revolver.ml.l, revolver.ml.ad, > revolver.probs.ad, revolver.ml.D.alpha, revolver.ml.D.alpha.a, > revolver.ml.DE.alpha.a, revolver.ml.AD.alpha.a.beta, > revolver.ml.AD.dpareto, revolver.ml.AD.dpareto.eval, > revolver.ml.ADE.alpha.a.beta, revolver.ml.ADE.dpareto, > revolver.ml.ADE.dpareto.eval, revolver.ml.ADE.dpareto.evalf, > revolver.probs.ADE.dpareto > ERROR: lazy loading failed for package ?adegenet? > * removing ?/home/samuel/R/x86_64-pc-linux-gnu-library/3.1/adegenet? > > The downloaded source packages are in > ?/tmp/RtmpRguHDL/downloaded_packages? > Warning message: > In install.packages("adegenet") : > installation of package ?adegenet? had non-zero exit status > //////////////////////////////////////////////////////////////////////////// > //////////////////////////////////////////////////////////////////////////// > ////////////////////////////////////////////////////////////// -- Vojt?ch Zeisek http://trapa.cz/en/ Department of Botany, Faculty of Science Charles University in Prague Ben?tsk? 2, Prague, 12801, CZ http://botany.natur.cuni.cz/en/ Institute of Botany, Academy of Science Z?mek 1, Pr?honice, 25243, CZ http://www.ibot.cas.cz/en/ Czech Republic -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 490 bytes Desc: This is a digitally signed message part. URL: From samuel.k at gmx.de Sat Jul 12 22:21:09 2014 From: samuel.k at gmx.de (Samuel Knapp) Date: Sat, 12 Jul 2014 22:21:09 +0200 Subject: [adegenet-forum] Problem installation on Ubuntu In-Reply-To: References: Message-ID: <53C198B5.1040803@gmx.de> Thanks Vojte(ch/,/ I normally install packages through the normal CRAN server. And all other packages work fine. R is installed through the Ubuntu repo. But there is only a limited collection of other R packages (not including adegenet). Also "/install.packages("adegenet", dependencies=TRUE)//"/ produces the same error./ / Under linux, the source is downloaded and compiled during installation (see the lines starting with gcc). This seems to go all fine. Also when downloading the "adegenet_1.4-2.tar.gz" file and installing that, the same error occurs. I have no idea, what else I could try. Other ideas? On 12.07.2014 20:57, adegenet-forum-request at lists.r-forge.r-project.org wrote: > Date: Sat, 12 Jul 2014 20:57:32 +0200 > From: Vojt?ch Zeisek > To: adegenet-forum at lists.r-forge.r-project.org > Subject: Re: [adegenet-forum] Problem installation on Ubuntu > Message-ID: <1823086.272X4meaJe at veles.site> > Content-Type: text/plain; charset="utf-8" > > Hello, > generally, R packages have to be compiled on Linux. Do You have basic tools > for compilation? See https://help.ubuntu.com/community/CompilingSoftware Might > be You can try to install the package directly from Ubuntu binary package > repository, see http://cran.r-project.org/bin/linux/ubuntu/README I don't use > Ubuntu, so that I'm not sure about usability of that repository... And then > try install.packages("adegenet", dependencies=TRUE) > Good luck, > Vojt?ch > > Dne So 12. ?ervence 2014 20:50:23, Samuel Knapp napsal(a): >> Dear all, >> >> I'm running R on Ubuntu and can't install the adegenet package. >> >> Versions: >> - Ubuntu: 14.04 (Trusty) >> - R.Version() >> $platform >> [1] "x86_64-pc-linux-gnu" >> $version.string >> [1] "R version 3.1.1 (2014-07-10)" >> >> In order to exclude other problems, I have reinstalled a clear R version >> and tried to install adegenet as the first package. I get the output below. >> >> Have tried to search for "Error in namespaceExport(ns, exports)" and >> "ERROR: lazy loading failed for package ?adegenet?", but can't find >> anything. >> Also I tried to install older versions of adegenet and got the same >> error report. The error occurs both, if I run R as sudo or as normal user. >> >> If anybody has an idea what the problem could be, please let me know. >> >> Thanks, >> Samuel >> >> //////////////////////////////////////////////////////////////////////////// >> //////////////////////////////////////////////////////////////////////////// >> ////////////////////////////////////////////////////////////// >> > install.packages("adegenet") >> >> Installing package into ?/home/samuel/R/x86_64-pc-linux-gnu-library/3.1? >> (as ?lib? is unspecified) >> trying URL >> 'http://ftp.igh.cnrs.fr/pub/CRAN/src/contrib/adegenet_1.4-2.tar.gz' >> Content type 'application/octet-stream' length 1588751 bytes (1.5 Mb) >> opened URL >> ================================================== >> downloaded 1.5 Mb >> >> * installing *source* package ?adegenet? ... >> ** package ?adegenet? successfully unpacked and MD5 sums checked >> ** libs >> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 >> -fstack-protector --param=ssp-buffer-size=4 -Wformat >> -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c GLfunctions.c -o >> GLfunctions.o >> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 >> -fstack-protector --param=ssp-buffer-size=4 -Wformat >> -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c adesub.c -o adesub.o >> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 >> -fstack-protector --param=ssp-buffer-size=4 -Wformat >> -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c monmonier-utils.c -o >> monmonier-utils.o >> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 >> -fstack-protector --param=ssp-buffer-size=4 -Wformat >> -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c sharedAll.c -o sharedAll.o >> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 >> -fstack-protector --param=ssp-buffer-size=4 -Wformat >> -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c snpbin.c -o snpbin.o >> gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o >> adegenet.so GLfunctions.o adesub.o monmonier-utils.o sharedAll.o >> snpbin.o -L/usr/lib/R/lib -lR >> installing to /home/samuel/R/x86_64-pc-linux-gnu-library/3.1/adegenet/libs >> ** R >> ** data >> ** inst >> ** preparing package for lazy loading >> Warning: S3 methods ?[.igraph?, ?[[.igraph?, ?[<-.igraph?, ?+.igraph?, >> ?-.igraph?, ?$.igraph?, ?$<-.igraph?, ?$.igraph.vs?, ?[.igraph.vs?, >> ?[[.igraph.vs?, ?[<-.igraph.vs?, ?[[<-.igraph.vs?, ?$<-.igraph.vs?, >> ?$.igraph.es?, ?[.igraph.es?, ?[[.igraph.es?, ?[<-.igraph.es?, >> ?[[<-.igraph.es?, ?$<-.igraph.es?, ?print.igraph.vs?, ?print.igraph.es?, >> ?str.igraph?, ?print.communities?, ?modularity.communities?, >> ?length.communities?, ?as.dendrogram.communities?, >> ?as.hclust.communities?, ?asPhylo.communities?, ?modularity.igraph?, >> ?dendPlot.communities?, ?compare.communities?, ?compare.numeric?, >> ?compare.default?, ?rglplot.igraph?, ?layout.svd.igraph?, >> ?print.cohesiveBlocks?, ?summary.cohesiveBlocks?, ?plot.cohesiveBlocks?, >> ?length.cohesiveBlocks?, ?print.igraphHRG?, ?print.igraphHRGConsensus?, >> ?as.dendrogram.igraphHRG?, ?as.hclust.igraphHR [... truncated] >> Error in namespaceExport(ns, exports) : >> undefined exports: add.vertices, delete.edges, delete.vertices, ecount, >> neighbors, incident, get.edges, get.edge.ids, [.igraph, [[.igraph, >> [<-.igraph, edge, edges, vertex, vertices, path, +.igraph, -.igraph, >> get.graph.attribute, set.graph.attribute, graph.attributes, >> get.vertex.attribute, set.vertex.attribute, vertex.attributes, >> get.edge.attribute, set.edge.attribute, edge.attributes, >> list.graph.attributes, list.vertex.attributes, list.edge.attributes, >> remove.graph.attribute, remove.vertex.attribute, remove.edge.attribute, >> graph.attributes<-, vertex.attributes<-, edge.attributes<-, V, E, >> $.igraph.vs, $.igraph.es, [.igraph.vs, [[.igraph.vs, [.igraph.es, >> [[.igraph.es, [<-.igraph.vs, [<-.igraph.es, [[<-.igraph.vs, >> [[<-.igraph.es, $<-.igraph.vs, $<-.igraph.es, V<-, E<-, print.igraph.vs, >> print.igraph.es, %--%, %->%, %<-%, is.igraph, is.named, is.weighted, >> is.bipartite, are.connected, print.igraph, str.igraph, summary.igraph, >> is.directed, get.edge, graph, graph.adjacency, graph.star, graph.tree, >> graph.lattice, graph.ring, graph.full, graph.atlas, graph.data.frame, >> graph.edgelist, graph.extended.chordal.ring, line.graph, >> graph.de.bruijn, graph.kautz, graph.formula, graph.famous, >> erdos.renyi.game, random.graph.game, degree.sequence.game, >> aging.prefatt.game, aging.barabasi.game, aging.ba.game, >> growing.random.game, barabasi.game, ba.game, callaway.traits.game, >> establishment.game, grg.game, preference.game, >> asymmetric.preference.game, connect.neighborhood, rewire.edges, >> watts.strogatz.game, lastcit.game, cited.type.game, >> citing.cited.type.game, bipartite.random.game, >> edge.betweenness.community, spinglass.community, walktrap.community, >> edge.betweenness.community.merges, fastgreedy.community, >> community.to.membership, membership, modularity, sizes, algorithm, >> is.hierarchical, merges, cutat, communities, crossing, plot.communities, >> compare, compare.communities, showtrace, code.length, asPhylo, dendPlot, >> create.communities, get.adjacency, get.edgelist, as.directed, >> as.undirected, get.adjlist, get.adjedgelist, igraph.from.graphNEL, >> igraph.to.graphNEL, get.data.frame, power.law.fit, running.mean, >> igraph.sample, srand, read.graph, write.graph, graph.graphdb, >> layout.auto, layout.random, layout.circle, layout.spring, >> layout.kamada.kawai, layout.lgl, layout.fruchterman.reingold.grid, >> layout.sphere, layout.merge, layout.reingold.tilford, layout.norm, >> piecewise.layout, igraph.drl.default, igraph.drl.coarsen, >> igraph.drl.coarsest, igraph.drl.refine, igraph.drl.final, subgraph, >> degree, degree.distribution, diameter, subcomponent, betweenness, >> bibcoupling, cocitation, shortest.paths, minimum.spanning.tree, >> get.shortest.paths, average.path.length, transitivity, >> get.all.shortest.paths, get.diameter, farthest.nodes, constraint, >> page.rank, reciprocity, rewire, graph.density, neighborhood.size, >> neighborhood, graph.neighborhood, graph.coreness, topological.sort, >> girth, is.loop, is.multiple, count.multiple, plot.igraph, tkplot, >> tkplot.close, tkplot.off, tkplot.fit.to.screen, tkplot.reshape, >> tkplot.export.postscript, tkplot.getcoords, tkplot.center, >> tkplot.rotate, tkplot.canvas, tkplot.setcoords, rglplot.igraph, rglplot, >> autocurve.edges, vertex.shapes, add.vertex.shape, igraph.shape.noclip, >> igraph.shape.noplot, cluster.distribution, is.connected, >> decompose.graph, no.clusters, evcent, bonpow, alpha.centrality, >> subgraph.centrality, igraph.arpack.default, igraph.eigen.default, >> revolver.d, revolver.error.d, revolver.ad, revolver.error.ad, >> revolver.ade, revolver.error.ade, revolver.e, revolver.error.e, >> revolver.de, revolver.error.de, revolver.l, revolver.error.l, >> revolver.dl, revolver.error.dl, revolver.el, revolver.error.el, >> revolver.r, revolver.error.r, revolver.ar, revolver.error.ar, >> revolver.di, revolver.error.di, revolver.adi, revolver.error.adi, >> revolver.il, revolver.error.il, revolver.ir, revolver.error.ir, >> revolver.air, revolver.error.air, revolver.d.d, revolver.p.p, evolver.d, >> graph.isoclass, graph.isomorphic, graph.motifs, graph.motifs.est, >> graph.isocreate, graph.motifs.no, graph.isomorphic.vf2, >> graph.subisomorphic.vf2, graph.count.isomorphisms.vf2, >> graph.count.subisomorphisms.vf2, graph.get.isomorphisms.vf2, >> graph.get.subisomorphisms.vf2, graph.disjoint.union, %du%, >> graph.intersection, %s%, graph.union, %u%, graph.difference, %m%, >> graph.complementer, graph.compose, %c%, igraph.par, igraph.options, >> getIgraphOpt, igraphtest, igraph.version, igraph.console, >> .igraph.progress, .igraph.status, graph.mincut, vertex.connectivity, >> edge.connectivity, edge.disjoint.paths, vertex.disjoint.paths, >> graph.adhesion, graph.cohesion, cliques, largest.cliques, >> maximal.cliques, clique.number, independent.vertex.sets, >> largest.independent.vertex.sets, maximal.independent.vertex.sets, >> independence.number, layout.svd, blocks, blockGraphs, cohesion, >> hierarchy, parent, plotHierarchy, exportPajek, maxcohesion, arpack, >> tkigraph, igraphdemo, scg, nexus.get, nexus.list, nexus.info, >> nexus.search, as.igraph, graphlets, graphlets.project, plot.sir, >> time_bins, graph.empty, add.edges, vcount, graph.full.citation, >> graph.lcf, graph.adjlist, graph.full.bipartite, forest.fire.game, >> interconnected.islands.game, static.fitness.game, static.power.law.game, >> k.regular.game, sbm.game, closeness, closeness.estimate, >> betweenness.estimate, edge.betweenness, edge.betweenness.estimate, >> page.rank.old, induced.subgraph, subgraph.edges, path.length.hist, >> simplify, is.dag, is.simple, has.multiple, hub.score, authority.score, >> arpack.unpack.complex, unfold.tree, is.mutual, >> maximum.cardinality.search, is.chordal, graph.knn, graph.strength, >> centralize.scores, centralization.degree, centralization.degree.tmax, >> centralization.betweenness, centralization.betweenness.tmax, >> centralization.closeness, centralization.closeness.tmax, >> centralization.evcent, centralization.evcent.tmax, >> assortativity.nominal, assortativity, assortativity.degree, >> contract.vertices, eccentricity, radius, graph.diversity, >> is.degree.sequence, is.graphical.degree.sequence, graph.bfs, graph.dfs, >> bipartite.projection.size, bipartite.projection, graph.bipartite, >> graph.incidence, get.incidence, bipartite.mapping, graph.laplacian, >> clusters, articulation.points, biconnected.components, >> maximal.cliques.count, layout.star, layout.grid, layout.grid.3d, >> layout.fruchterman.reingold, layout.graphopt, layout.drl, >> layout.sugiyama, layout.mds, layout.bipartite, similarity.jaccard, >> similarity.dice, similarity.invlogweighted, community.le.to.membership, >> mod.matrix, leading.eigenvector.community, label.propagation.community, >> multilevel.community, optimal.community, hrg.fit, hrg.game, >> hrg.dendrogram, hrg.consensus, hrg.predict, hrg.create, >> infomap.community, graphlets.candidate.basis, get.stochastic, >> dyad.census, triad.census, adjacent.triangles, graph.maxflow, >> dominator.tree, stCuts, stMincuts, is.separator, is.minimal.separator, >> minimal.st.separators, minimum.size.separators, cohesive.blocks, >> graph.isoclass.subgraph, graph.isomorphic.34, canonical.permutation, >> permute.vertices, graph.isomorphic.bliss, graph.automorphisms, >> graph.subisomorphic.lad, scgGrouping, scgSemiProjectors, scgNormEps, >> is.matching, is.maximal.matching, maximum.bipartite.matching, >> graph.eigen, sir, convex.hull, revolver.ml.d, revolver.probs.d, >> revolver.ml.de, revolver.probs.de, revolver.ml.ade, revolver.probs.ade, >> revolver.ml.f, revolver.ml.df, revolver.ml.l, revolver.ml.ad, >> revolver.probs.ad, revolver.ml.D.alpha, revolver.ml.D.alpha.a, >> revolver.ml.DE.alpha.a, revolver.ml.AD.alpha.a.beta, >> revolver.ml.AD.dpareto, revolver.ml.AD.dpareto.eval, >> revolver.ml.ADE.alpha.a.beta, revolver.ml.ADE.dpareto, >> revolver.ml.ADE.dpareto.eval, revolver.ml.ADE.dpareto.evalf, >> revolver.probs.ADE.dpareto >> ERROR: lazy loading failed for package ?adegenet? >> * removing ?/home/samuel/R/x86_64-pc-linux-gnu-library/3.1/adegenet? >> >> The downloaded source packages are in >> ?/tmp/RtmpRguHDL/downloaded_packages? >> Warning message: >> In install.packages("adegenet") : >> installation of package ?adegenet? had non-zero exit status >> //////////////////////////////////////////////////////////////////////////// >> //////////////////////////////////////////////////////////////////////////// >> ////////////////////////////////////////////////////////////// -------------- next part -------------- An HTML attachment was scrubbed... URL: From samuel.k at gmx.de Sat Jul 12 23:06:51 2014 From: samuel.k at gmx.de (Samuel Knapp) Date: Sat, 12 Jul 2014 23:06:51 +0200 Subject: [adegenet-forum] Problem installation on Ubuntu Message-ID: <53C1A36B.1020207@gmx.de> I could now narrow down the problem: After commenting out the importFrom(igraph,.. [see below] in the NAMESPACE file, I could install adegenet without any problem. #importFrom(igraph, "graph.data.frame", "V", "V<-", "E", "E<-", # "layout.fruchterman.reingold", # "as.igraph", "plot.igraph", "print.igraph", "graph.adjacency", "clusters") So, this error must be due to the igraph package. When loading igraph with library("igraph") the long error message was also produced. After install.packages("igraph"), I can also load it normally and install adegenet without commenting out the above. Probably this should rather be reported to igraph... From vojta at trapa.cz Sun Jul 13 22:18:10 2014 From: vojta at trapa.cz (=?utf-8?B?Vm9qdMSbY2g=?= Zeisek) Date: Sun, 13 Jul 2014 22:18:10 +0200 Subject: [adegenet-forum] Not working Monmonier Message-ID: <1554139.ks4H6062Ct@veles.site> Hello, I tried Monmonier analysis as described in Adegent tutorial. I'm not familiar with that method (for similar question I used IMa2 last time), so I was curious what it does. :-) I tried with relatively relatively large dataset. Individuals from one locality usually have same coordinates. The code: > monmonier <- monmonier(xy=genind$other$xy, dist=dist(genind$tab), cn=chooseCN(genind$other$xy, ask=FALSE, type=5, d1=0, d2=2.5, plot.nb=FALSE, edit.nb=FALSE), nrun=1) Indicate the threshold ('d' for default): d > coords.monmonier(monmonier) Error in output[[runname]]$dir1[i, ] <- halfway[which(eval.x == TRUE & : number of items to replace is not a multiple of replacement length Calls: coords.monmonier > plot(monmonier) Warning messages: 1: In arrows(obj$dir1$path[1:(nrow(obj$dir1$path) - 1), 1], obj$dir1$path[1: (nrow(obj$dir1$path) - : zero-length arrow is of indeterminate angle and so skipped 2: In arrows(obj$dir1$path[1:(nrow(obj$dir1$path) - 1), 1], obj$dir1$path[1: (nrow(obj$dir1$path) - : zero-length arrow is of indeterminate angle and so skipped 3: In arrows(obj$dir2$path[1:(nrow(obj$dir2$path) - 1), 1], obj$dir2$path[1: (nrow(obj$dir2$path) - : zero-length arrow is of indeterminate angle and so skipped 4: In arrows(obj$dir2$path[1:(nrow(obj$dir2$path) - 1), 1], obj$dir2$path[1: (nrow(obj$dir2$path) - : zero-length arrow is of indeterminate angle and so skipped genind$other$xy contains geographical coordinates in WGS 84 (from GPS). The only problem coming to my mind are those repetitive coordinates (for individuals from one locality) - because of that, chooseCN practically allows only methods 5 and 6. Might be, I could try it with populations, but then I'm afraid to get little bit different information... Or might be I could add some little uncertainty to the coordinates...? I was also thinking if it could be because of missing data, but when I tried with genind object corrected for missing data, I ended up with same errors. Any ideas? Sincerely, Vojt?ch -- Vojt?ch Zeisek http://trapa.cz/en/ Department of Botany, Faculty of Science Charles University in Prague Ben?tsk? 2, Prague, 12801, CZ http://botany.natur.cuni.cz/en/ Institute of Botany, Academy of Science Z?mek 1, Pr?honice, 25243, CZ http://www.ibot.cas.cz/en/ Czech Republic -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 490 bytes Desc: This is a digitally signed message part. URL: From t.jombart at imperial.ac.uk Mon Jul 14 11:42:16 2014 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Mon, 14 Jul 2014 09:42:16 +0000 Subject: [adegenet-forum] testing sPCA differences In-Reply-To: References: <2CB2DA8E426F3541AB1907F98ABA6570A821F8E2@icexch-m1.ic.ac.uk>, Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570A822737F@icexch-m1.ic.ac.uk> Hi Xavier, yes, it makes sense. I think St?phane Dray (Cced) did something along these lines a while back. The basic idea is to use a spatial grid to define new spatial units which can be compared across different categories of individuals. Building up a test for this should not be too complicated, if we're talking about one single variable. You can just use the (possibly standardized) difference in Moran'I values, and use permutations to generate the reference distribution. Type I error will (by construction) be OK, you'll only have to assess the power of the test. When considering more than one variable, things get complicated as basic tests are already becoming more scarce. As for sPCA PCs, the problem is that they are already optimized, so most simple tests are circular. The non-independence of the tests of different PCs also is a problem. Valeria Montano started working on such issues and may be interested in this discussion. Last time I checked she was on this ML but I'll Cc her to bully her into the discussion. Best Thibaut ________________________________________ From: Xavier Giroux-Bougard [x.giroux.bougard at gmail.com] Sent: 11 July 2014 17:40 To: Jombart, Thibaut Subject: Re: [adegenet-forum] testing sPCA differences Thanks for the answer Thibault, I too had thought of varying spatial locations as a problem. However, there is a way to circumvent this problem if we move away from an individual based approach, which of course requires a species with more discrete groupings. In this case, if we build two 'genpop' objects using individuals seperated from their initial population based on some other characteristic (ie sex, age, morph, etc...), then the connection network remains identical if we use the population locations. While the spatial weights remain constant, we are left with two distinct allelic frequency tables. Admittedly we are losing power by moving away from and individual based network, but then we could stand to gain a useful comparative method. Let me know if you think that makes sense, and if you think there would be an easy way to implement this. Merci pour votre aide, et votre temps! Xavier Giroux-Bougard PS If the concept holds, I would be glad to share my coding explorations (as amateur as they might be!) On Fri, Jul 11, 2014 at 5:14 AM, Jombart, Thibaut > wrote: Hi Xavier, such a test will not be possible using approaches directly relating to the sPCA. This is because the range and null value of Moran's I (part of the optimized criteria, measuring the spatial structures) depend on the spatial weights. Therefore, Moran's I based approaches cannot compare spatial structures of different groups of locations/individuals. Cheers Thibaut ________________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Xavier Giroux-Bougard [x.giroux.bougard at gmail.com] Sent: 10 July 2014 22:14 To: adegenet-forum at lists.r-forge.r-project.org Subject: [adegenet-forum] testing sPCA differences Dear adegenet forum, does anybody know if there is a permutation test implemented in adegenet (or other R packages) that could differentiate the sPCA solutions of two (or more) subsets of a genetic dataset, for example to compare genetic structures across sexes or ages, etc... For example, Smouse et al. (2008) developed a heterogeneity test to differentiate two correlograms. I know there are the global and local statistics, but is there something similar that could help differentiate the spatial genetic structure between two groups in sPCA? Thanks, Xavier From t.jombart at imperial.ac.uk Mon Jul 14 11:50:11 2014 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Mon, 14 Jul 2014 09:50:11 +0000 Subject: [adegenet-forum] Problem installation on Ubuntu In-Reply-To: <53C198B5.1040803@gmx.de> References: , <53C198B5.1040803@gmx.de> Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570A82283D8@icexch-m1.ic.ac.uk> Hi there, I suspect a problem specific to your settings, as CRAN says adegenet is relatively well-behaved these days: http://cran.r-project.org/web/checks/check_results_adegenet.html The error message you report looks like a possible broken dependency with igraph. Can you install this package and load it? It may also be worth checking that you're not loading any related library in your .Rprofile. Cheers Thibaut ============================== Dr Thibaut Jombart MRC Centre for Outbreak Analysis and Modelling Department of Infectious Disease Epidemiology Imperial College - School of Public Health Norfolk Place, London W2 1PG, UK Tel. : 0044 (0)20 7594 3658 http://sites.google.com/site/thibautjombart/ http://sites.google.com/site/therepiproject/ http://adegenet.r-forge.r-project.org/ Twitter: @thibautjombart ________________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Samuel Knapp [samuel.k at gmx.de] Sent: 12 July 2014 21:21 To: adegenet-forum at lists.r-forge.r-project.org Subject: Re: [adegenet-forum] Problem installation on Ubuntu Thanks Vojt?ch, I normally install packages through the normal CRAN server. And all other packages work fine. R is installed through the Ubuntu repo. But there is only a limited collection of other R packages (not including adegenet). Also "install.packages("adegenet", dependencies=TRUE)" produces the same error. Under linux, the source is downloaded and compiled during installation (see the lines starting with gcc). This seems to go all fine. Also when downloading the "adegenet_1.4-2.tar.gz" file and installing that, the same error occurs. I have no idea, what else I could try. Other ideas? On 12.07.2014 20:57, adegenet-forum-request at lists.r-forge.r-project.org wrote: Date: Sat, 12 Jul 2014 20:57:32 +0200 From: Vojt?ch Zeisek To: adegenet-forum at lists.r-forge.r-project.org Subject: Re: [adegenet-forum] Problem installation on Ubuntu Message-ID: <1823086.272X4meaJe at veles.site> Content-Type: text/plain; charset="utf-8" Hello, generally, R packages have to be compiled on Linux. Do You have basic tools for compilation? See https://help.ubuntu.com/community/CompilingSoftware Might be You can try to install the package directly from Ubuntu binary package repository, see http://cran.r-project.org/bin/linux/ubuntu/README I don't use Ubuntu, so that I'm not sure about usability of that repository... And then try install.packages("adegenet", dependencies=TRUE) Good luck, Vojt?ch Dne So 12. ?ervence 2014 20:50:23, Samuel Knapp napsal(a): Dear all, I'm running R on Ubuntu and can't install the adegenet package. Versions: - Ubuntu: 14.04 (Trusty) - R.Version() $platform [1] "x86_64-pc-linux-gnu" $version.string [1] "R version 3.1.1 (2014-07-10)" In order to exclude other problems, I have reinstalled a clear R version and tried to install adegenet as the first package. I get the output below. Have tried to search for "Error in namespaceExport(ns, exports)" and "ERROR: lazy loading failed for package ?adegenet?", but can't find anything. Also I tried to install older versions of adegenet and got the same error report. The error occurs both, if I run R as sudo or as normal user. If anybody has an idea what the problem could be, please let me know. Thanks, Samuel //////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////// > install.packages("adegenet") Installing package into ?/home/samuel/R/x86_64-pc-linux-gnu-library/3.1? (as ?lib? is unspecified) trying URL 'http://ftp.igh.cnrs.fr/pub/CRAN/src/contrib/adegenet_1.4-2.tar.gz' Content type 'application/octet-stream' length 1588751 bytes (1.5 Mb) opened URL ================================================== downloaded 1.5 Mb * installing *source* package ?adegenet? ... ** package ?adegenet? successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c GLfunctions.c -o GLfunctions.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c adesub.c -o adesub.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c monmonier-utils.c -o monmonier-utils.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c sharedAll.c -o sharedAll.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c snpbin.c -o snpbin.o gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o adegenet.so GLfunctions.o adesub.o monmonier-utils.o sharedAll.o snpbin.o -L/usr/lib/R/lib -lR installing to /home/samuel/R/x86_64-pc-linux-gnu-library/3.1/adegenet/libs ** R ** data ** inst ** preparing package for lazy loading Warning: S3 methods ?[.igraph?, ?[[.igraph?, ?[<-.igraph?, ?+.igraph?, ?-.igraph?, ?$.igraph?, ?$<-.igraph?, ?$.igraph.vs?, ?[.igraph.vs?, ?[[.igraph.vs?, ?[<-.igraph.vs?, ?[[<-.igraph.vs?, ?$<-.igraph.vs?, ?$.igraph.es?, ?[.igraph.es?, ?[[.igraph.es?, ?[<-.igraph.es?, ?[[<-.igraph.es?, ?$<-.igraph.es?, ?print.igraph.vs?, ?print.igraph.es?, ?str.igraph?, ?print.communities?, ?modularity.communities?, ?length.communities?, ?as.dendrogram.communities?, ?as.hclust.communities?, ?asPhylo.communities?, ?modularity.igraph?, ?dendPlot.communities?, ?compare.communities?, ?compare.numeric?, ?compare.default?, ?rglplot.igraph?, ?layout.svd.igraph?, ?print.cohesiveBlocks?, ?summary.cohesiveBlocks?, ?plot.cohesiveBlocks?, ?length.cohesiveBlocks?, ?print.igraphHRG?, ?print.igraphHRGConsensus?, ?as.dendrogram.igraphHRG?, ?as.hclust.igraphHR [... truncated] Error in namespaceExport(ns, exports) : undefined exports: add.vertices, delete.edges, delete.vertices, ecount, neighbors, incident, get.edges, get.edge.ids, [.igraph, [[.igraph, [<-.igraph, edge, edges, vertex, vertices, path, +.igraph, -.igraph, get.graph.attribute, set.graph.attribute, graph.attributes, get.vertex.attribute, set.vertex.attribute, vertex.attributes, get.edge.attribute, set.edge.attribute, edge.attributes, list.graph.attributes, list.vertex.attributes, list.edge.attributes, remove.graph.attribute, remove.vertex.attribute, remove.edge.attribute, graph.attributes<-, vertex.attributes<-, edge.attributes<-, V, E, $.igraph.vs, $.igraph.es, [.igraph.vs, [[.igraph.vs, [.igraph.es, [[.igraph.es, [<-.igraph.vs, [<-.igraph.es, [[<-.igraph.vs, [[<-.igraph.es, $<-.igraph.vs, $<-.igraph.es, V<-, E<-, print.igraph.vs, print.igraph.es, %--%, %->%, %<-%, is.igraph, is.named, is.weighted, is.bipartite, are.connected, print.igraph, str.igraph, summary.igraph, is.directed, get.edge, graph, graph.adjacency, graph.star, graph.tree, graph.lattice, graph.ring, graph.full, graph.atlas, graph.data.frame, graph.edgelist, graph.extended.chordal.ring, line.graph, graph.de.bruijn, graph.kautz, graph.formula, graph.famous, erdos.renyi.game, random.graph.game, degree.sequence.game, aging.prefatt.game, aging.barabasi.game, aging.ba.game, growing.random.game, barabasi.game, ba.game, callaway.traits.game, establishment.game, grg.game, preference.game, asymmetric.preference.game, connect.neighborhood, rewire.edges, watts.strogatz.game, lastcit.game, cited.type.game, citing.cited.type.game, bipartite.random.game, edge.betweenness.community, spinglass.community, walktrap.community, edge.betweenness.community.merges, fastgreedy.community, community.to.membership, membership, modularity, sizes, algorithm, is.hierarchical, merges, cutat, communities, crossing, plot.communities, compare, compare.communities, showtrace, code.length, asPhylo, dendPlot, create.communities, get.adjacency, get.edgelist, as.directed, as.undirected, get.adjlist, get.adjedgelist, igraph.from.graphNEL, igraph.to.graphNEL, get.data.frame, power.law.fit, running.mean, igraph.sample, srand, read.graph, write.graph, graph.graphdb, layout.auto, layout.random, layout.circle, layout.spring, layout.kamada.kawai, layout.lgl, layout.fruchterman.reingold.grid, layout.sphere, layout.merge, layout.reingold.tilford, layout.norm, piecewise.layout, igraph.drl.default, igraph.drl.coarsen, igraph.drl.coarsest, igraph.drl.refine, igraph.drl.final, subgraph, degree, degree.distribution, diameter, subcomponent, betweenness, bibcoupling, cocitation, shortest.paths, minimum.spanning.tree, get.shortest.paths, average.path.length, transitivity, get.all.shortest.paths, get.diameter, farthest.nodes, constraint, page.rank, reciprocity, rewire, graph.density, neighborhood.size, neighborhood, graph.neighborhood, graph.coreness, topological.sort, girth, is.loop, is.multiple, count.multiple, plot.igraph, tkplot, tkplot.close, tkplot.off, tkplot.fit.to.screen, tkplot.reshape, tkplot.export.postscript, tkplot.getcoords, tkplot.center, tkplot.rotate, tkplot.canvas, tkplot.setcoords, rglplot.igraph, rglplot, autocurve.edges, vertex.shapes, add.vertex.shape, igraph.shape.noclip, igraph.shape.noplot, cluster.distribution, is.connected, decompose.graph, no.clusters, evcent, bonpow, alpha.centrality, subgraph.centrality, igraph.arpack.default, igraph.eigen.default, revolver.d, revolver.error.d, revolver.ad, revolver.error.ad, revolver.ade, revolver.error.ade, revolver.e, revolver.error.e, revolver.de, revolver.error.de, revolver.l, revolver.error.l, revolver.dl, revolver.error.dl, revolver.el, revolver.error.el, revolver.r, revolver.error.r, revolver.ar, revolver.error.ar, revolver.di, revolver.error.di, revolver.adi, revolver.error.adi, revolver.il, revolver.error.il, revolver.ir, revolver.error.ir, revolver.air, revolver.error.air, revolver.d.d, revolver.p.p, evolver.d, graph.isoclass, graph.isomorphic, graph.motifs, graph.motifs.est, graph.isocreate, graph.motifs.no, graph.isomorphic.vf2, graph.subisomorphic.vf2, graph.count.isomorphisms.vf2, graph.count.subisomorphisms.vf2, graph.get.isomorphisms.vf2, graph.get.subisomorphisms.vf2, graph.disjoint.union, %du%, graph.intersection, %s%, graph.union, %u%, graph.difference, %m%, graph.complementer, graph.compose, %c%, igraph.par, igraph.options, getIgraphOpt, igraphtest, igraph.version, igraph.console, .igraph.progress, .igraph.status, graph.mincut, vertex.connectivity, edge.connectivity, edge.disjoint.paths, vertex.disjoint.paths, graph.adhesion, graph.cohesion, cliques, largest.cliques, maximal.cliques, clique.number, independent.vertex.sets, largest.independent.vertex.sets, maximal.independent.vertex.sets, independence.number, layout.svd, blocks, blockGraphs, cohesion, hierarchy, parent, plotHierarchy, exportPajek, maxcohesion, arpack, tkigraph, igraphdemo, scg, nexus.get, nexus.list, nexus.info, nexus.search, as.igraph, graphlets, graphlets.project, plot.sir, time_bins, graph.empty, add.edges, vcount, graph.full.citation, graph.lcf, graph.adjlist, graph.full.bipartite, forest.fire.game, interconnected.islands.game, static.fitness.game, static.power.law.game, k.regular.game, sbm.game, closeness, closeness.estimate, betweenness.estimate, edge.betweenness, edge.betweenness.estimate, page.rank.old, induced.subgraph, subgraph.edges, path.length.hist, simplify, is.dag, is.simple, has.multiple, hub.score, authority.score, arpack.unpack.complex, unfold.tree, is.mutual, maximum.cardinality.search, is.chordal, graph.knn, graph.strength, centralize.scores, centralization.degree, centralization.degree.tmax, centralization.betweenness, centralization.betweenness.tmax, centralization.closeness, centralization.closeness.tmax, centralization.evcent, centralization.evcent.tmax, assortativity.nominal, assortativity, assortativity.degree, contract.vertices, eccentricity, radius, graph.diversity, is.degree.sequence, is.graphical.degree.sequence, graph.bfs, graph.dfs, bipartite.projection.size, bipartite.projection, graph.bipartite, graph.incidence, get.incidence, bipartite.mapping, graph.laplacian, clusters, articulation.points, biconnected.components, maximal.cliques.count, layout.star, layout.grid, layout.grid.3d, layout.fruchterman.reingold, layout.graphopt, layout.drl, layout.sugiyama, layout.mds, layout.bipartite, similarity.jaccard, similarity.dice, similarity.invlogweighted, community.le.to.membership, mod.matrix, leading.eigenvector.community, label.propagation.community, multilevel.community, optimal.community, hrg.fit, hrg.game, hrg.dendrogram, hrg.consensus, hrg.predict, hrg.create, infomap.community, graphlets.candidate.basis, get.stochastic, dyad.census, triad.census, adjacent.triangles, graph.maxflow, dominator.tree, stCuts, stMincuts, is.separator, is.minimal.separator, minimal.st.separators, minimum.size.separators, cohesive.blocks, graph.isoclass.subgraph, graph.isomorphic.34, canonical.permutation, permute.vertices, graph.isomorphic.bliss, graph.automorphisms, graph.subisomorphic.lad, scgGrouping, scgSemiProjectors, scgNormEps, is.matching, is.maximal.matching, maximum.bipartite.matching, graph.eigen, sir, convex.hull, revolver.ml.d, revolver.probs.d, revolver.ml.de, revolver.probs.de, revolver.ml.ade, revolver.probs.ade, revolver.ml.f, revolver.ml.df, revolver.ml.l, revolver.ml.ad, revolver.probs.ad, revolver.ml.D.alpha, revolver.ml.D.alpha.a, revolver.ml.DE.alpha.a, revolver.ml.AD.alpha.a.beta, revolver.ml.AD.dpareto, revolver.ml.AD.dpareto.eval, revolver.ml.ADE.alpha.a.beta, revolver.ml.ADE.dpareto, revolver.ml.ADE.dpareto.eval, revolver.ml.ADE.dpareto.evalf, revolver.probs.ADE.dpareto ERROR: lazy loading failed for package ?adegenet? * removing ?/home/samuel/R/x86_64-pc-linux-gnu-library/3.1/adegenet? The downloaded source packages are in ?/tmp/RtmpRguHDL/downloaded_packages? Warning message: In install.packages("adegenet") : installation of package ?adegenet? had non-zero exit status //////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////// From t.jombart at imperial.ac.uk Mon Jul 14 11:51:27 2014 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Mon, 14 Jul 2014 09:51:27 +0000 Subject: [adegenet-forum] Problem installation on Ubuntu In-Reply-To: <53C1A36B.1020207@gmx.de> References: <53C1A36B.1020207@gmx.de> Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570A82283E8@icexch-m1.ic.ac.uk> Argh, just seeing this one. Well done on nailing it. Yep, probably best reporting this to the igraph maintainer. You may not be the only one going through this issue. Cheers Thibaut ________________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Samuel Knapp [samuel.k at gmx.de] Sent: 12 July 2014 22:06 To: adegenet-forum at lists.r-forge.r-project.org Subject: Re: [adegenet-forum] Problem installation on Ubuntu I could now narrow down the problem: After commenting out the importFrom(igraph,.. [see below] in the NAMESPACE file, I could install adegenet without any problem. #importFrom(igraph, "graph.data.frame", "V", "V<-", "E", "E<-", # "layout.fruchterman.reingold", # "as.igraph", "plot.igraph", "print.igraph", "graph.adjacency", "clusters") So, this error must be due to the igraph package. When loading igraph with library("igraph") the long error message was also produced. After install.packages("igraph"), I can also load it normally and install adegenet without commenting out the above. Probably this should rather be reported to igraph... _______________________________________________ adegenet-forum mailing list adegenet-forum at lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum From t.jombart at imperial.ac.uk Mon Jul 14 11:54:47 2014 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Mon, 14 Jul 2014 09:54:47 +0000 Subject: [adegenet-forum] Not working Monmonier In-Reply-To: <1554139.ks4H6062Ct@veles.site> References: <1554139.ks4H6062Ct@veles.site> Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570A8228414@icexch-m1.ic.ac.uk> Hi Vojt?ch Monmonier is not designed for spatial distribution with duplicate locations. Problem is, if you jitter the data, you'll get a different boundary every time you run the analysis. If you're looking for spatial structures, sPCA may be more useful there. Cheers Thibaut ________________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Vojt?ch Zeisek [vojta at trapa.cz] Sent: 13 July 2014 21:18 To: Adegenet R-Forum Subject: [adegenet-forum] Not working Monmonier Hello, I tried Monmonier analysis as described in Adegent tutorial. I'm not familiar with that method (for similar question I used IMa2 last time), so I was curious what it does. :-) I tried with relatively relatively large dataset. Individuals from one locality usually have same coordinates. The code: > monmonier <- monmonier(xy=genind$other$xy, dist=dist(genind$tab), cn=chooseCN(genind$other$xy, ask=FALSE, type=5, d1=0, d2=2.5, plot.nb=FALSE, edit.nb=FALSE), nrun=1) Indicate the threshold ('d' for default): d > coords.monmonier(monmonier) Error in output[[runname]]$dir1[i, ] <- halfway[which(eval.x == TRUE & : number of items to replace is not a multiple of replacement length Calls: coords.monmonier > plot(monmonier) Warning messages: 1: In arrows(obj$dir1$path[1:(nrow(obj$dir1$path) - 1), 1], obj$dir1$path[1: (nrow(obj$dir1$path) - : zero-length arrow is of indeterminate angle and so skipped 2: In arrows(obj$dir1$path[1:(nrow(obj$dir1$path) - 1), 1], obj$dir1$path[1: (nrow(obj$dir1$path) - : zero-length arrow is of indeterminate angle and so skipped 3: In arrows(obj$dir2$path[1:(nrow(obj$dir2$path) - 1), 1], obj$dir2$path[1: (nrow(obj$dir2$path) - : zero-length arrow is of indeterminate angle and so skipped 4: In arrows(obj$dir2$path[1:(nrow(obj$dir2$path) - 1), 1], obj$dir2$path[1: (nrow(obj$dir2$path) - : zero-length arrow is of indeterminate angle and so skipped genind$other$xy contains geographical coordinates in WGS 84 (from GPS). The only problem coming to my mind are those repetitive coordinates (for individuals from one locality) - because of that, chooseCN practically allows only methods 5 and 6. Might be, I could try it with populations, but then I'm afraid to get little bit different information... Or might be I could add some little uncertainty to the coordinates...? I was also thinking if it could be because of missing data, but when I tried with genind object corrected for missing data, I ended up with same errors. Any ideas? Sincerely, Vojt?ch -- Vojt?ch Zeisek http://trapa.cz/en/ Department of Botany, Faculty of Science Charles University in Prague Ben?tsk? 2, Prague, 12801, CZ http://botany.natur.cuni.cz/en/ Institute of Botany, Academy of Science Z?mek 1, Pr?honice, 25243, CZ http://www.ibot.cas.cz/en/ Czech Republic From samuel.k at gmx.de Mon Jul 14 12:27:58 2014 From: samuel.k at gmx.de (Samuel Knapp) Date: Mon, 14 Jul 2014 12:27:58 +0200 Subject: [adegenet-forum] Problem installation on Ubuntu In-Reply-To: <2CB2DA8E426F3541AB1907F98ABA6570A82283E8@icexch-m1.ic.ac.uk> References: <53C1A36B.1020207@gmx.de> <2CB2DA8E426F3541AB1907F98ABA6570A82283E8@icexch-m1.ic.ac.uk> Message-ID: <53C3B0AE.5090204@gmx.de> Hi Thibaut, I tried to reproduce the problem. Complete removal of the igraph package and R. Then after installing R, installing adegenet. igraph is then also installed as dependency and adegenet goes fine as well. So, I'm guessing that I had either an old or somehow corrupted version of igraph. When installing adegenet, this old/corrupted version of igraph could not be loaded properly and thus adegenet could not be installed. Let's hope that nobody else is experiencing this problem or than at least finds this threat. Cheers, Samuel On 14.07.2014 11:51, Jombart, Thibaut wrote: > Argh, just seeing this one. Well done on nailing it. > Yep, probably best reporting this to the igraph maintainer. You may not be the only one going through this issue. > Cheers > Thibaut > > ________________________________________ > From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Samuel Knapp [samuel.k at gmx.de] > Sent: 12 July 2014 22:06 > To: adegenet-forum at lists.r-forge.r-project.org > Subject: Re: [adegenet-forum] Problem installation on Ubuntu > > I could now narrow down the problem: > > After commenting out the importFrom(igraph,.. [see below] in the > NAMESPACE file, I could install adegenet without any problem. > > #importFrom(igraph, "graph.data.frame", "V", "V<-", "E", "E<-", > # "layout.fruchterman.reingold", > # "as.igraph", "plot.igraph", "print.igraph", "graph.adjacency", > "clusters") > > So, this error must be due to the igraph package. When loading igraph > with library("igraph") the long error message was also produced. After > install.packages("igraph"), I can also load it normally and install > adegenet without commenting out the above. > > Probably this should rather be reported to igraph... > _______________________________________________ > adegenet-forum mailing list > adegenet-forum at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum From t.jombart at imperial.ac.uk Mon Jul 14 12:52:36 2014 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Mon, 14 Jul 2014 10:52:36 +0000 Subject: [adegenet-forum] Problem installation on Ubuntu In-Reply-To: <53C3B0AE.5090204@gmx.de> References: <53C1A36B.1020207@gmx.de> <2CB2DA8E426F3541AB1907F98ABA6570A82283E8@icexch-m1.ic.ac.uk>, <53C3B0AE.5090204@gmx.de> Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570A822B698@icexch-m2.ic.ac.uk> Makes sense. In general, an 'update.packages(ask=FALSE)' is good policy before installing new stuff. Bear in mind, though, that attached packages won't generally be updated. Cheers Thibaut ________________________________________ From: Samuel Knapp [samuel.k at gmx.de] Sent: 14 July 2014 11:27 To: Jombart, Thibaut; adegenet-forum at lists.r-forge.r-project.org Subject: Re: [adegenet-forum] Problem installation on Ubuntu Hi Thibaut, I tried to reproduce the problem. Complete removal of the igraph package and R. Then after installing R, installing adegenet. igraph is then also installed as dependency and adegenet goes fine as well. So, I'm guessing that I had either an old or somehow corrupted version of igraph. When installing adegenet, this old/corrupted version of igraph could not be loaded properly and thus adegenet could not be installed. Let's hope that nobody else is experiencing this problem or than at least finds this threat. Cheers, Samuel On 14.07.2014 11:51, Jombart, Thibaut wrote: > Argh, just seeing this one. Well done on nailing it. > Yep, probably best reporting this to the igraph maintainer. You may not be the only one going through this issue. > Cheers > Thibaut > > ________________________________________ > From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Samuel Knapp [samuel.k at gmx.de] > Sent: 12 July 2014 22:06 > To: adegenet-forum at lists.r-forge.r-project.org > Subject: Re: [adegenet-forum] Problem installation on Ubuntu > > I could now narrow down the problem: > > After commenting out the importFrom(igraph,.. [see below] in the > NAMESPACE file, I could install adegenet without any problem. > > #importFrom(igraph, "graph.data.frame", "V", "V<-", "E", "E<-", > # "layout.fruchterman.reingold", > # "as.igraph", "plot.igraph", "print.igraph", "graph.adjacency", > "clusters") > > So, this error must be due to the igraph package. When loading igraph > with library("igraph") the long error message was also produced. After > install.packages("igraph"), I can also load it normally and install > adegenet without commenting out the above. > > Probably this should rather be reported to igraph... > _______________________________________________ > adegenet-forum mailing list > adegenet-forum at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum From crypticlineage at gmail.com Mon Jul 14 15:01:03 2014 From: crypticlineage at gmail.com (Vikram Chhatre) Date: Mon, 14 Jul 2014 09:01:03 -0400 Subject: [adegenet-forum] Per locus pairwise Fst Message-ID: Good morning. I would like to estimate per locus pairwise Fst for populations, but it appears that Adegenet only estimates this over all loci (i.e. single matrix). What I would like is one matrix per locus. Has anyone modified the functions or know of alternative programs that can do this? Thanks Vikram -------------- next part -------------- An HTML attachment was scrubbed... URL: From vojta at trapa.cz Mon Jul 14 15:09:34 2014 From: vojta at trapa.cz (=?utf-8?B?Vm9qdMSbY2g=?= Zeisek) Date: Mon, 14 Jul 2014 15:09:34 +0200 Subject: [adegenet-forum] Per locus pairwise Fst In-Reply-To: References: Message-ID: <11156573.phF7SWq2xW@veles.site> Good afternoon. :-P Dne Po 14. ?ervence 2014 09:01:03, Vikram Chhatre napsal(a): > Good morning. > > I would like to estimate per locus pairwise Fst for populations, but it > appears that Adegenet only estimates this over all loci (i.e. single > matrix). What I would like is one matrix per locus. Has anyone modified > the functions or know of alternative programs that can do this? Try package diveRsity. It requires genepop file and works only for haploid and diploid data (as far as I know), but otherwise it should do what You wish. ;-) > Thanks > Vikram Sincerely, Vojt?ch -- Vojt?ch Zeisek http://trapa.cz/en/ Department of Botany, Faculty of Science Charles University in Prague Ben?tsk? 2, Prague, 12801, CZ http://botany.natur.cuni.cz/en/ Institute of Botany, Academy of Science Z?mek 1, Pr?honice, 25243, CZ http://www.ibot.cas.cz/en/ Czech Republic -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 490 bytes Desc: This is a digitally signed message part. URL: From t.jombart at imperial.ac.uk Mon Jul 14 15:13:38 2014 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Mon, 14 Jul 2014 13:13:38 +0000 Subject: [adegenet-forum] Per locus pairwise Fst In-Reply-To: References: Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570A8233A2D@icexch-m1.ic.ac.uk> Hi there, you can use seploc to separate loci, and lapply over the resulting list using your prefered fst function. Cheers Thibaut ________________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Vikram Chhatre [crypticlineage at gmail.com] Sent: 14 July 2014 14:01 To: adegenet-forum at lists.r-forge.r-project.org Subject: [adegenet-forum] Per locus pairwise Fst Good morning. I would like to estimate per locus pairwise Fst for populations, but it appears that Adegenet only estimates this over all loci (i.e. single matrix). What I would like is one matrix per locus. Has anyone modified the functions or know of alternative programs that can do this? Thanks Vikram From crypticlineage at gmail.com Mon Jul 14 15:16:59 2014 From: crypticlineage at gmail.com (Vikram Chhatre) Date: Mon, 14 Jul 2014 09:16:59 -0400 Subject: [adegenet-forum] Per locus pairwise Fst In-Reply-To: <2CB2DA8E426F3541AB1907F98ABA6570A8233A2D@icexch-m1.ic.ac.uk> References: <2CB2DA8E426F3541AB1907F98ABA6570A8233A2D@icexch-m1.ic.ac.uk> Message-ID: Perfect! Thank you for both solutions. V On Mon, Jul 14, 2014 at 9:13 AM, Jombart, Thibaut wrote: > > Hi there, > > you can use seploc to separate loci, and lapply over the resulting list > using your prefered fst function. > > Cheers > Thibaut > ________________________________________ > From: adegenet-forum-bounces at lists.r-forge.r-project.org [ > adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Vikram > Chhatre [crypticlineage at gmail.com] > Sent: 14 July 2014 14:01 > To: adegenet-forum at lists.r-forge.r-project.org > Subject: [adegenet-forum] Per locus pairwise Fst > > Good morning. > > I would like to estimate per locus pairwise Fst for populations, but it > appears that Adegenet only estimates this over all loci (i.e. single > matrix). What I would like is one matrix per locus. Has anyone modified > the functions or know of alternative programs that can do this? > > Thanks > Vikram > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.jombart at imperial.ac.uk Wed Jul 30 11:45:27 2014 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Wed, 30 Jul 2014 09:45:27 +0000 Subject: [adegenet-forum] read.PLINK error In-Reply-To: References: , <2CB2DA8E426F3541AB1907F98ABA657087BEF8DB@icexch-m1.ic.ac.uk>, Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570A8239EA1@icexch-m1.ic.ac.uk> Hi there, I confess I never use vcftools so I'm not sure what it's been doing to your data, but it looks like the format might have been altered. I Cc Emmanuel Paradis (ape, pegas, ...) who I think might have been developing something for this kind of data recently. Best Thibaut ________________________________________ From: ADAM PETER CARDILINI [apcar at deakin.edu.au] Sent: 08 June 2014 23:24 To: Jombart, Thibaut Cc: adegenet-forum at lists.r-forge.r-project.org Subject: Re: read.PLINK error G'day Thibaut, Sorry I should have included that in the original email. The code I use to read the data was: dat <- read.PLINK('myfiltered_plinkconvertedfile.raw', map.file = 'myfiltered_plinkconvertedfile.map') This command line worked on the unfiltered data files, just not the ones I got after filtering in vcftools. Cheers, Adam Sent from my iPad > On 9 Jun 2014, at 3:42 am, "Jombart, Thibaut" wrote: > > > Hello, > > what command line did you use to read the data? > > Cheers > Thibaut > ________________________________________ > From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of ADAM PETER CARDILINI [apcar at deakin.edu.au] > Sent: 06 June 2014 03:44 > To: adegenet-forum at lists.r-forge.r-project.org > Subject: [adegenet-forum] read.PLINK error > > G?day Everyone, > > I have recently produced a .vcf file for a set of SNPs obtained using Genotype-by-sequencing. The .vcf file is the final output from the TASSEL pipeline which takes in fastq sequence files. I converted my .vcf file to a .ped and .map files using vcftools and then converted the .ped file to .raw so that I could load it into R using ?adegenet? function ?read.PLINK?. The linux vcftools and plink code was as follows: > > vcftools --vcf myfile.vcf --out myfile.plink --plink > plink --file myfile.plink --out myfile.plink --recodeA > > I successfully loaded my unaltered file into R using ?adegenet?, however it has way many SNPs that I am not interested in (because it has only been sequenced for a couple of individuals) so I thought I would filter my .vcf snp file using vcftools. I filtered my original file so that only SNPs that were sequenced from >90% of samples remained. This significantly reduced the number of SNPs I had and produced a new .vcf file. I then converted this file to .ped and .map, and then .ped to .raw so I could bring it into R and have a quick look. > > When I tried to import the new, filtered .raw file using ?read.PLINK? I got the following error: > > > Reading PLINK raw format into a genlight object... > > Reading loci information... > > Reading and converting genotypes... > .Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function ?nLoc? for signature ?"try-error"? > In addition: Warning message: > In mclapply(txt, function(e) new("SNPbin", snp = e, ploidy = 2), : > 9 function calls resulted in an error > > > > It seems as if something has gone wrong when I have produced the new .vcf file during filtering. I was wondering if anyone might know what I have done wrong, what these error messages mean and whether there is a fix I can try? > > Thanks in advance for your time and help, I appreciate it. > > Kind regards, > > Adam Cardilini > PhD Candidate > Schools of Life and Environmental Sciences, > Deakin University, 75 Pigdons Rd, > Waurn Ponds, Vic, Australia, 3217 > Mob: 0431 566 340 > Email: apcar at deakin.edu.au > From emmanuel.paradis at ird.fr Wed Jul 30 17:41:13 2014 From: emmanuel.paradis at ird.fr (Emmanuel Paradis) Date: Wed, 30 Jul 2014 17:41:13 +0200 Subject: [adegenet-forum] read.PLINK error In-Reply-To: <2CB2DA8E426F3541AB1907F98ABA6570A8239EA1@icexch-m1.ic.ac.uk> References: Message-ID: Hi Thibaut, The last version of pegas (0.6) includes a function read.vcf to read VCF files. Together with the genotypes, it reads only the basic extra fields (POS, CHROM, FILTER, QUAL); the genotype likelihoods are not read (this could be changed in future releases). The purpose of this function is not to process very big VCF files, but rather to read files for downstream analyses with pegas or adegenet. By default, the first 1000 loci are read (this can be controlled by options). pegas 0.6 is available as a pre-release here: http://ape-package.ird.fr/ ADAM PETER CARDILINI wrote: > I successfully loaded my unaltered file into R using ?adegenet?, So why don't you filter your data in R? Best, Emmanuel Wed, 30 Jul 2014 09:45:27 +0000 "Jombart, Thibaut" : > > Hi there, > > I confess I never use vcftools so I'm not sure what it's been doing >to your data, but it looks like the format might have been altered. > > I Cc Emmanuel Paradis (ape, pegas, ...) who I think might have been >developing something for this kind of data recently. > > Best > Thibaut > > > > > ________________________________________ >From: ADAM PETER CARDILINI [apcar at deakin.edu.au] > Sent: 08 June 2014 23:24 > To: Jombart, Thibaut > Cc: adegenet-forum at lists.r-forge.r-project.org > Subject: Re: read.PLINK error > > G'day Thibaut, > > Sorry I should have included that in the original email. > > The code I use to read the data was: > > dat <- read.PLINK('myfiltered_plinkconvertedfile.raw', map.file = >'myfiltered_plinkconvertedfile.map') > > This command line worked on the unfiltered data files, just not the >ones I got after filtering in vcftools. > > Cheers, > Adam > > Sent from my iPad > >> On 9 Jun 2014, at 3:42 am, "Jombart, Thibaut" >> wrote: >> >> >> Hello, >> >> what command line did you use to read the data? >> >> Cheers >> Thibaut >> ________________________________________ >> From: adegenet-forum-bounces at lists.r-forge.r-project.org >>[adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of >>ADAM PETER CARDILINI [apcar at deakin.edu.au] >> Sent: 06 June 2014 03:44 >> To: adegenet-forum at lists.r-forge.r-project.org >> Subject: [adegenet-forum] read.PLINK error >> >> G?day Everyone, >> >> I have recently produced a .vcf file for a set of SNPs obtained >>using Genotype-by-sequencing. The .vcf file is the final output from >>the TASSEL pipeline which takes in fastq sequence files. I converted >>my .vcf file to a .ped and .map files using vcftools and then >>converted the .ped file to .raw so that I could load it into R using >>?adegenet? function ?read.PLINK?. The linux vcftools and plink code >>was as follows: >> >> vcftools --vcf myfile.vcf --out myfile.plink --plink >> plink --file myfile.plink --out myfile.plink --recodeA >> >> I successfully loaded my unaltered file into R using ?adegenet?, >>however it has way many SNPs that I am not interested in (because it >>has only been sequenced for a couple of individuals) so I thought I >>would filter my .vcf snp file using vcftools. I filtered my original >>file so that only SNPs that were sequenced from >90% of samples >>remained. This significantly reduced the number of SNPs I had and >>produced a new .vcf file. I then converted this file to .ped and >>.map, and then .ped to .raw so I could bring it into R and have a >>quick look. >> >> When I tried to import the new, filtered .raw file using >>?read.PLINK? I got the following error: >> >> >> Reading PLINK raw format into a genlight object... >> >> Reading loci information... >> >> Reading and converting genotypes... >> .Error in (function (classes, fdef, mtable) : >> unable to find an inherited method for function ?nLoc? for >>signature ?"try-error"? >> In addition: Warning message: >> In mclapply(txt, function(e) new("SNPbin", snp = e, ploidy = 2), : >> 9 function calls resulted in an error >> >> >> >> It seems as if something has gone wrong when I have produced the new >>.vcf file during filtering. I was wondering if anyone might know what >>I have done wrong, what these error messages mean and whether there >>is a fix I can try? >> >> Thanks in advance for your time and help, I appreciate it. >> >> Kind regards, >> >> Adam Cardilini >> PhD Candidate >> Schools of Life and Environmental Sciences, >> Deakin University, 75 Pigdons Rd, >> Waurn Ponds, Vic, Australia, 3217 >> Mob: 0431 566 340 >> Email: apcar at deakin.edu.au >> From tohamyy at yahoo.com Wed Jul 30 18:26:24 2014 From: tohamyy at yahoo.com (Tohamy Yousef) Date: Wed, 30 Jul 2014 09:26:24 -0700 Subject: [adegenet-forum] Number for DAPC Message-ID: <1406737584.13239.YahooMailNeo@web121103.mail.ne1.yahoo.com> Dear all, I have used dapc in my study and it gives me five clusters (with find.cluster function). But this five clusters have no any biological meaning. the biological meaning is 2 clustres. So, what the conclusion should be? ? Best, Tohamy -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.jombart at imperial.ac.uk Thu Jul 31 12:59:23 2014 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Thu, 31 Jul 2014 10:59:23 +0000 Subject: [adegenet-forum] Number for DAPC In-Reply-To: <1406737584.13239.YahooMailNeo@web121103.mail.ne1.yahoo.com> References: <1406737584.13239.YahooMailNeo@web121103.mail.ne1.yahoo.com> Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570A823B311@icexch-m1.ic.ac.uk> Hello, there has been a number of discussions on the 'true K' on this forum, so you probably want to look at these. Without a BIC curve and a bit more detail about what your 2 biological clusters are, it is hard to make an educated reply. Cheers Thibaut ============================== Dr Thibaut Jombart MRC Centre for Outbreak Analysis and Modelling Department of Infectious Disease Epidemiology Imperial College - School of Public Health Norfolk Place, London W2 1PG, UK Tel. : 0044 (0)20 7594 3658 http://sites.google.com/site/thibautjombart/ http://sites.google.com/site/therepiproject/ http://adegenet.r-forge.r-project.org/ Twitter: @thibautjombart ________________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Tohamy Yousef [tohamyy at yahoo.com] Sent: 30 July 2014 17:26 To: adegenet-forum at lists.r-forge.r-project.org Subject: [adegenet-forum] Number for DAPC Dear all, I have used dapc in my study and it gives me five clusters (with find.cluster function). But this five clusters have no any biological meaning. the biological meaning is 2 clustres. So, what the conclusion should be? Best, Tohamy