Question: Lumi failed to load
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gravatar for Hitoshi Okada
6.0 years ago by
Hitoshi Okada30 wrote:
Hi, I have installed R version 3.0.2 (Mac version, MacOS is 10.8.5)and lumi (2.12), and tried to load but failed with the message at bottom. I appreciate any suggestions to solve this problem. I have updated Bioconductor packages are updated. Thank you Hitoshi > library(lumi) Loading required package: Biobase Loading required package: BiocGenerics Loading required package: parallel Attaching package: ?BiocGenerics? The following objects are masked from ?package:parallel?: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ?package:stats?: xtabs The following objects are masked from ?package:base?: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ?minfi? In addition: Warning message: replacing previous import by ?graphics::image? when loading ?methylumi? Error: package or namespace load failed for ?lumi?
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ADD COMMENTlink modified 6.0 years ago by Pan Du440 • written 6.0 years ago by Hitoshi Okada30
Answer: Lumi failed to load
0
gravatar for Pan Du
6.0 years ago by
Pan Du440
Pan Du440 wrote:
Hi Hitoshi Based on the information you provided. I believe the problem happens when you loading the methylumi package. So please check whether methylumi package was properly installed. If the problem still exists, please provide your sessionInfo(). Pan On Fri, Oct 11, 2013 at 3:00 AM, <bioconductor-request@r-project.org> wrote: > > > Date: Thu, 10 Oct 2013 19:12:51 -0400 > From: Hitoshi Okada <hokada0421@gmail.com> > To: bioconductor@r-project.org > Subject: [BioC] Lumi failed to load > Message-ID: <cc3d6769-98d2-4705-bd34-59ed0ccb3f1a@gmail.com> > Content-Type: text/plain; charset=windows-1252 > > Hi, > > I have installed R version 3.0.2 (Mac version, MacOS is 10.8.5)and lumi > (2.12), and tried to load but failed with the message at bottom. > > I appreciate any suggestions to solve this problem. I have updated > Bioconductor packages are updated. > > Thank you > > Hitoshi > > > > library(lumi) > Loading required package: Biobase > Loading required package: BiocGenerics > Loading required package: parallel > > Attaching package: ?BiocGenerics? > > The following objects are masked from ?package:parallel?: > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, > clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, > parSapply, parSapplyLB > > The following object is masked from ?package:stats?: > > xtabs > > The following objects are masked from ?package:base?: > > anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, > duplicated, > eval, Filter, Find, get, intersect, lapply, Map, mapply, match, mget, > order, > paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, > rep.int, rownames, sapply, setdiff, sort, table, tapply, union, > unique, > unlist > > Welcome to Bioconductor > > Vignettes contain introductory material; view with > 'browseVignettes()'. To > cite Bioconductor, see 'citation("Biobase")', and for packages > 'citation("pkgname")'. > > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck > = vI[[j]]) : > there is no package called ?minfi? > In addition: Warning message: > replacing previous import by ?graphics::image? when loading ?methylumi? > Error: package or namespace load failed for ?lumi? > > > > [[alternative HTML version deleted]]
ADD COMMENTlink written 6.0 years ago by Pan Du440
This is presumably my fault. Will fix and commit. --t *He that would live in peace and at ease, * *Must not speak all he knows, nor judge all he sees.* * * Benjamin Franklin, Poor Richard's Almanack<http: archive.org="" details="" poorrichardsalma00franrich=""> On Fri, Oct 11, 2013 at 4:04 AM, Pan Du <dupan.mail@gmail.com> wrote: > Hi Hitoshi > > Based on the information you provided. I believe the problem happens when > you loading the methylumi package. So please check whether methylumi > package was properly installed. If the problem still exists, please provide > your sessionInfo(). > > > Pan > > > On Fri, Oct 11, 2013 at 3:00 AM, <bioconductor- request@r-project.org=""> > wrote: > > > > > > > Date: Thu, 10 Oct 2013 19:12:51 -0400 > > From: Hitoshi Okada <hokada0421@gmail.com> > > To: bioconductor@r-project.org > > Subject: [BioC] Lumi failed to load > > Message-ID: <cc3d6769-98d2-4705-bd34-59ed0ccb3f1a@gmail.com> > > Content-Type: text/plain; charset=windows-1252 > > > > Hi, > > > > I have installed R version 3.0.2 (Mac version, MacOS is 10.8.5)and lumi > > (2.12), and tried to load but failed with the message at bottom. > > > > I appreciate any suggestions to solve this problem. I have updated > > Bioconductor packages are updated. > > > > Thank you > > > > Hitoshi > > > > > > > library(lumi) > > Loading required package: Biobase > > Loading required package: BiocGenerics > > Loading required package: parallel > > > > Attaching package: ?BiocGenerics? > > > > The following objects are masked from ?package:parallel?: > > > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, > clusterExport, > > clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, > > parSapply, parSapplyLB > > > > The following object is masked from ?package:stats?: > > > > xtabs > > > > The following objects are masked from ?package:base?: > > > > anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, > > duplicated, > > eval, Filter, Find, get, intersect, lapply, Map, mapply, match, mget, > > order, > > paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, > Reduce, > > rep.int, rownames, sapply, setdiff, sort, table, tapply, union, > > unique, > > unlist > > > > Welcome to Bioconductor > > > > Vignettes contain introductory material; view with > > 'browseVignettes()'. To > > cite Bioconductor, see 'citation("Biobase")', and for packages > > 'citation("pkgname")'. > > > > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), > versionCheck > > = vI[[j]]) : > > there is no package called ?minfi? > > In addition: Warning message: > > replacing previous import by ?graphics::image? when loading ?methylumi? > > Error: package or namespace load failed for ?lumi? > > > > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 6.0 years ago by Tim Triche4.2k
----- Original Message ----- > From: "Tim Triche, Jr." <tim.triche at="" gmail.com=""> > To: "Pan Du" <dupan.mail at="" gmail.com=""> > Cc: "Hitoshi Okada" <hokada0421 at="" gmail.com="">, bioconductor at r-project.org > Sent: Friday, October 11, 2013 10:15:22 AM > Subject: Re: [BioC] Lumi failed to load > > This is presumably my fault. Will fix and commit. > > --t > > *He that would live in peace and at ease, * > *Must not speak all he knows, nor judge all he sees.* > * > * > Benjamin Franklin, Poor Richard's > Almanack<http: archive.org="" details="" poorrichardsalma00franrich=""> > > > On Fri, Oct 11, 2013 at 4:04 AM, Pan Du <dupan.mail at="" gmail.com=""> wrote: > > > Hi Hitoshi > > > > Based on the information you provided. I believe the problem > > happens when > > you loading the methylumi package. So please check whether > > methylumi > > package was properly installed. If the problem still exists, please > > provide > > your sessionInfo(). > > I don't think this is really a methyLumi problem. I think the problem is that we flushed our repositories and then minfi failed to build, We are working on this and it should be fixed by tomorrow morning Seattle time. Dan > > > > Pan > > > > > > On Fri, Oct 11, 2013 at 3:00 AM, > > <bioconductor-request at="" r-project.org=""> > > wrote: > > > > > > > > > > > Date: Thu, 10 Oct 2013 19:12:51 -0400 > > > From: Hitoshi Okada <hokada0421 at="" gmail.com=""> > > > To: bioconductor at r-project.org > > > Subject: [BioC] Lumi failed to load > > > Message-ID: <cc3d6769-98d2-4705-bd34-59ed0ccb3f1a at="" gmail.com=""> > > > Content-Type: text/plain; charset=windows-1252 > > > > > > Hi, > > > > > > I have installed R version 3.0.2 (Mac version, MacOS is > > > 10.8.5)and lumi > > > (2.12), and tried to load but failed with the message at bottom. > > > > > > I appreciate any suggestions to solve this problem. I have > > > updated > > > Bioconductor packages are updated. > > > > > > Thank you > > > > > > Hitoshi > > > > > > > > > > library(lumi) > > > Loading required package: Biobase > > > Loading required package: BiocGenerics > > > Loading required package: parallel > > > > > > Attaching package: ?BiocGenerics? > > > > > > The following objects are masked from ?package:parallel?: > > > > > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, > > clusterExport, > > > clusterMap, parApply, parCapply, parLapply, parLapplyLB, > > > parRapply, > > > parSapply, parSapplyLB > > > > > > The following object is masked from ?package:stats?: > > > > > > xtabs > > > > > > The following objects are masked from ?package:base?: > > > > > > anyDuplicated, append, as.data.frame, as.vector, cbind, > > > colnames, > > > duplicated, > > > eval, Filter, Find, get, intersect, lapply, Map, mapply, > > > match, mget, > > > order, > > > paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, > > Reduce, > > > rep.int, rownames, sapply, setdiff, sort, table, tapply, > > > union, > > > unique, > > > unlist > > > > > > Welcome to Bioconductor > > > > > > Vignettes contain introductory material; view with > > > 'browseVignettes()'. To > > > cite Bioconductor, see 'citation("Biobase")', and for > > > packages > > > 'citation("pkgname")'. > > > > > > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), > > versionCheck > > > = vI[[j]]) : > > > there is no package called ?minfi? > > > In addition: Warning message: > > > replacing previous import by ?graphics::image? when loading > > > ?methylumi? > > > Error: package or namespace load failed for ?lumi? > > > > > > > > > > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 6.0 years ago by Dan Tenenbaum8.2k
Yes, I changed a ton in the last couple of days in minfi, including new name for the annotation package and new version of minfiData. This is what is being complained about. Kasper On Fri, Oct 11, 2013 at 1:17 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > > > ----- Original Message ----- > > From: "Tim Triche, Jr." <tim.triche@gmail.com> > > To: "Pan Du" <dupan.mail@gmail.com> > > Cc: "Hitoshi Okada" <hokada0421@gmail.com>, bioconductor@r-project.org > > Sent: Friday, October 11, 2013 10:15:22 AM > > Subject: Re: [BioC] Lumi failed to load > > > > This is presumably my fault. Will fix and commit. > > > > --t > > > > *He that would live in peace and at ease, * > > *Must not speak all he knows, nor judge all he sees.* > > * > > * > > Benjamin Franklin, Poor Richard's > > Almanack<http: archive.org="" details="" poorrichardsalma00franrich=""> > > > > > > On Fri, Oct 11, 2013 at 4:04 AM, Pan Du <dupan.mail@gmail.com> wrote: > > > > > Hi Hitoshi > > > > > > Based on the information you provided. I believe the problem > > > happens when > > > you loading the methylumi package. So please check whether > > > methylumi > > > package was properly installed. If the problem still exists, please > > > provide > > > your sessionInfo(). > > > > > I don't think this is really a methyLumi problem. I think the problem is > that we flushed our repositories and then minfi failed to build, We are > working on this and it should be fixed by tomorrow morning Seattle time. > > Dan > > > > > > > > Pan > > > > > > > > > On Fri, Oct 11, 2013 at 3:00 AM, > > > <bioconductor-request@r-project.org> > > > wrote: > > > > > > > > > > > > > > > Date: Thu, 10 Oct 2013 19:12:51 -0400 > > > > From: Hitoshi Okada <hokada0421@gmail.com> > > > > To: bioconductor@r-project.org > > > > Subject: [BioC] Lumi failed to load > > > > Message-ID: <cc3d6769-98d2-4705-bd34-59ed0ccb3f1a@gmail.com> > > > > Content-Type: text/plain; charset=windows-1252 > > > > > > > > Hi, > > > > > > > > I have installed R version 3.0.2 (Mac version, MacOS is > > > > 10.8.5)and lumi > > > > (2.12), and tried to load but failed with the message at bottom. > > > > > > > > I appreciate any suggestions to solve this problem. I have > > > > updated > > > > Bioconductor packages are updated. > > > > > > > > Thank you > > > > > > > > Hitoshi > > > > > > > > > > > > > library(lumi) > > > > Loading required package: Biobase > > > > Loading required package: BiocGenerics > > > > Loading required package: parallel > > > > > > > > Attaching package: ?BiocGenerics? > > > > > > > > The following objects are masked from ?package:parallel?: > > > > > > > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, > > > clusterExport, > > > > clusterMap, parApply, parCapply, parLapply, parLapplyLB, > > > > parRapply, > > > > parSapply, parSapplyLB > > > > > > > > The following object is masked from ?package:stats?: > > > > > > > > xtabs > > > > > > > > The following objects are masked from ?package:base?: > > > > > > > > anyDuplicated, append, as.data.frame, as.vector, cbind, > > > > colnames, > > > > duplicated, > > > > eval, Filter, Find, get, intersect, lapply, Map, mapply, > > > > match, mget, > > > > order, > > > > paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, > > > Reduce, > > > > rep.int, rownames, sapply, setdiff, sort, table, tapply, > > > > union, > > > > unique, > > > > unlist > > > > > > > > Welcome to Bioconductor > > > > > > > > Vignettes contain introductory material; view with > > > > 'browseVignettes()'. To > > > > cite Bioconductor, see 'citation("Biobase")', and for > > > > packages > > > > 'citation("pkgname")'. > > > > > > > > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), > > > versionCheck > > > > = vI[[j]]) : > > > > there is no package called ?minfi? > > > > In addition: Warning message: > > > > replacing previous import by ?graphics::image? when loading > > > > ?methylumi? > > > > Error: package or namespace load failed for ?lumi? > > > > > > > > > > > > > > > > > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@r-project.org > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 6.0 years ago by Kasper Daniel Hansen6.4k
Thank, Dan, Kasper, and Pan. I will wait. Hitoshi On 2013-10-11, at 1:19 PM, Kasper Daniel Hansen <kasperdanielhansen@gmail.com> wrote: > Yes, I changed a ton in the last couple of days in minfi, including new name for the annotation package and new version of minfiData. This is what is being complained about. > > Kasper > > > On Fri, Oct 11, 2013 at 1:17 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > > > ----- Original Message ----- > > From: "Tim Triche, Jr." <tim.triche@gmail.com> > > To: "Pan Du" <dupan.mail@gmail.com> > > Cc: "Hitoshi Okada" <hokada0421@gmail.com>, bioconductor@r-project.org > > Sent: Friday, October 11, 2013 10:15:22 AM > > Subject: Re: [BioC] Lumi failed to load > > > > This is presumably my fault. Will fix and commit. > > > > --t > > > > *He that would live in peace and at ease, * > > *Must not speak all he knows, nor judge all he sees.* > > * > > * > > Benjamin Franklin, Poor Richard's > > Almanack<http: archive.org="" details="" poorrichardsalma00franrich=""> > > > > > > On Fri, Oct 11, 2013 at 4:04 AM, Pan Du <dupan.mail@gmail.com> wrote: > > > > > Hi Hitoshi > > > > > > Based on the information you provided. I believe the problem > > > happens when > > > you loading the methylumi package. So please check whether > > > methylumi > > > package was properly installed. If the problem still exists, please > > > provide > > > your sessionInfo(). > > > > > I don't think this is really a methyLumi problem. I think the problem is that we flushed our repositories and then minfi failed to build, We are working on this and it should be fixed by tomorrow morning Seattle time. > > Dan > > > > > > > > Pan > > > > > > > > > On Fri, Oct 11, 2013 at 3:00 AM, > > > <bioconductor-request@r-project.org> > > > wrote: > > > > > > > > > > > > > > > Date: Thu, 10 Oct 2013 19:12:51 -0400 > > > > From: Hitoshi Okada <hokada0421@gmail.com> > > > > To: bioconductor@r-project.org > > > > Subject: [BioC] Lumi failed to load > > > > Message-ID: <cc3d6769-98d2-4705-bd34-59ed0ccb3f1a@gmail.com> > > > > Content-Type: text/plain; charset=windows-1252 > > > > > > > > Hi, > > > > > > > > I have installed R version 3.0.2 (Mac version, MacOS is > > > > 10.8.5)and lumi > > > > (2.12), and tried to load but failed with the message at bottom. > > > > > > > > I appreciate any suggestions to solve this problem. I have > > > > updated > > > > Bioconductor packages are updated. > > > > > > > > Thank you > > > > > > > > Hitoshi > > > > > > > > > > > > > library(lumi) > > > > Loading required package: Biobase > > > > Loading required package: BiocGenerics > > > > Loading required package: parallel > > > > > > > > Attaching package: ?BiocGenerics? > > > > > > > > The following objects are masked from ?package:parallel?: > > > > > > > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, > > > clusterExport, > > > > clusterMap, parApply, parCapply, parLapply, parLapplyLB, > > > > parRapply, > > > > parSapply, parSapplyLB > > > > > > > > The following object is masked from ?package:stats?: > > > > > > > > xtabs > > > > > > > > The following objects are masked from ?package:base?: > > > > > > > > anyDuplicated, append, as.data.frame, as.vector, cbind, > > > > colnames, > > > > duplicated, > > > > eval, Filter, Find, get, intersect, lapply, Map, mapply, > > > > match, mget, > > > > order, > > > > paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, > > > Reduce, > > > > rep.int, rownames, sapply, setdiff, sort, table, tapply, > > > > union, > > > > unique, > > > > unlist > > > > > > > > Welcome to Bioconductor > > > > > > > > Vignettes contain introductory material; view with > > > > 'browseVignettes()'. To > > > > cite Bioconductor, see 'citation("Biobase")', and for > > > > packages > > > > 'citation("pkgname")'. > > > > > > > > Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), > > > versionCheck > > > > = vI[[j]]) : > > > > there is no package called ?minfi? > > > > In addition: Warning message: > > > > replacing previous import by ?graphics::image? when loading > > > > ?methylumi? > > > > Error: package or namespace load failed for ?lumi? > > > > > > > > > > > > > > > > > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@r-project.org > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 6.0 years ago by Hitoshi Okada30
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