installation of affycoretools
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@james-anderson-1641
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@sean-davis-490
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Hi Sean and James, I just wanted to note that biocLite() _will_ install dependencies of dependencies (and on down the dependency tree), otherwise it would be a pretty worthless install script for the BioC packages. To ensure that what I state above is true, I downloaded and built a brand new R-devel, and the first and only thing I did upon starting it was to run biocLite("affycoretools"). OK. I lied -- I ran install.packages("rcompgen") first, because my Rprofile file loads that package and doesn't like it if it is missing, but that is peripheral to this discussion. The result: > library(affycoretools) Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: affyio Loading required package: preprocessCore Loading required package: limma Loading required package: GOstats Loading required package: graph Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: DBI Loading required package: RSQLite Loading required package: annotate Loading required package: xtable Loading required package: RBGL Loading required package: Category Loading required package: genefilter Loading required package: survival Loading required package: splines Loading required package: biomaRt Loading required package: RCurl Attaching package: 'biomaRt' The following object(s) are masked from package:annotate : getGO Loading required package: gcrma Loading required package: matchprobes Loading required package: annaffy Loading required package: GO Attaching package: 'GO' The following object(s) are masked from package:GO.db : GOBPANCESTOR, GOBPCHILDREN, GOBPOFFSPRING, GOBPPARENTS, GOCCANCESTOR, GOCCCHILDREN, GOCCOFFSPRING, GOCCPARENTS, GOMAPCOUNTS, GOMFANCESTOR, GOMFCHILDREN, GOMFOFFSPRING, GOMFPARENTS, GOOBSOLETE, GOSYNONYM, GOTERM Loading required package: KEGG Attaching package: 'annaffy' The following object(s) are masked from package:RCurl : getURL > sessionInfo() R version 2.7.0 Under development (unstable) (2007-12-20 r43739) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] splines tools stats graphics grDevices datasets utils [8] methods base other attached packages: [1] affycoretools_1.11.2 annaffy_1.11.1 KEGG_2.0.1 [4] GO_2.0.1 gcrma_2.11.1 matchprobes_1.11.0 [7] biomaRt_1.13.6 RCurl_0.8-1 GOstats_2.5.0 [10] Category_2.5.0 genefilter_1.17.7 survival_2.34 [13] RBGL_1.15.6 annotate_1.17.3 xtable_1.5-2 [16] GO.db_2.0.2 AnnotationDbi_1.1.6 RSQLite_0.6-4 [19] DBI_0.2-4 graph_1.17.14 limma_2.13.1 [22] affy_1.17.3 preprocessCore_1.1.5 affyio_1.7.6 [25] Biobase_1.17.7 rcompgen_0.1-17 loaded via a namespace (and not attached): [1] cluster_1.11.9 XML_1.9-0 So all you should ever have to do is run biocLite() to install things. However, it may come to pass that certain packages for whatever reason don't get installed correctly (or at all, although barring the occasional missing package on BioC, I have never personally seen such a thing), in which case you may need an additional biocLite("TheMissingPackage"). Best, Jim Sean Davis wrote: > On Dec 19, 2007 5:06 PM, James Anderson <janderson_net at="" yahoo.com=""> wrote: > >> Sean, >> >> Thanks for your advice. I followed your suggestion and typed >> >> source("http://bioconductor.org/biocLite.R") >> biocLite() >> biocLite("affycoretools") >> >> and there is nothing abnormal. However, when I type >> library(affycoretools), it pops up the following lines: >> >> Loading required package: affy >> Loading required package: Biobase >> Loading required package: tools >> >> Welcome to Bioconductor >> >> Vignettes contain introductory material. To view, type >> 'openVignette()'. To cite Bioconductor, see >> 'citation("Biobase")' and for packages 'citation(pkgname)'. >> >> Loading required package: affyio >> Loading required package: preprocessCore >> Loading required package: limma >> Loading required package: GOstats >> Loading required package: graph >> Loading required package: GO.db >> Loading required package: AnnotationDbi >> Loading required package: DBI >> Loading required package: RSQLite >> Loading required package: annotate >> Loading required package: xtable >> Loading required package: RBGL >> Loading required package: Category >> Loading required package: genefilter >> Loading required package: survival >> Loading required package: splines >> Loading required package: biomaRt >> Loading required package: RCurl >> Error: package 'RCurl' could not be loaded >> In addition: Warning message: >> In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = >> lib.loc) : >> there is no package called 'RCurl' >> >> Below is what I got from using sessionInfo() for diagnose >> >> R version 2.6.1 (2007-11-26) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] splines tools stats graphics grDevices utils datasets >> [8] methods base >> >> other attached packages: >> [1] GOstats_2.4.0 Category_2.4.0 genefilter_1.16.0 >> [4] survival_2.34 RBGL_1.14.0 annotate_1.16.1 >> [7] xtable_1.5-2 GO.db_2.0.2 AnnotationDbi_1.0.6 >> [10] RSQLite_0.6-4 DBI_0.2-4 graph_1.16.1 >> [13] limma_2.12.0 affy_1.16.0 preprocessCore_1.0.0 >> [16] affyio_1.6.1 Biobase_1.16.2 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.9 >> >> Seems that it still can not find the package Rcurl. >> > > Unfortunately, biocLite() does not find dependencies of dependencies (and I > believe RCurl is a dependency of biomaRt). My guess is that you have > installed other packages without using biocLite() in the past and have > missed installing the RCurl dependency for one of them. Therefore, I would > suggest using biocLite() to install ALL PACKAGES ALL THE TIME so that this > doesn't occur in the future. However, in the short term, you might try: > > biocLite('RCurl') > library(affycoretools) > > Hope that helps. > > Sean > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
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I think what is more correct to say has to do with dependency checking. Say we have a dependency tree like A requires B requires C and that someone install B without install C. When you then do biocLite("A") it checks whether B is installed and if that is the case, I believe it stops. It does not check whether C exists. Kasper On Dec 20, 2007, at 7:51 AM, James W. MacDonald wrote: > Hi Sean and James, > > I just wanted to note that biocLite() _will_ install dependencies of > dependencies (and on down the dependency tree), otherwise it would > be a > pretty worthless install script for the BioC packages. > > To ensure that what I state above is true, I downloaded and built a > brand new R-devel, and the first and only thing I did upon starting it > was to run biocLite("affycoretools"). > > OK. I lied -- I ran install.packages("rcompgen") first, because my > Rprofile file loads that package and doesn't like it if it is missing, > but that is peripheral to this discussion. > > The result: > >> library(affycoretools) > Loading required package: affy > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: affyio > Loading required package: preprocessCore > Loading required package: limma > Loading required package: GOstats > Loading required package: graph > Loading required package: GO.db > Loading required package: AnnotationDbi > Loading required package: DBI > Loading required package: RSQLite > Loading required package: annotate > Loading required package: xtable > Loading required package: RBGL > Loading required package: Category > Loading required package: genefilter > Loading required package: survival > Loading required package: splines > Loading required package: biomaRt > Loading required package: RCurl > > Attaching package: 'biomaRt' > > > The following object(s) are masked from package:annotate : > > getGO > > Loading required package: gcrma > Loading required package: matchprobes > Loading required package: annaffy > Loading required package: GO > > Attaching package: 'GO' > > > The following object(s) are masked from package:GO.db : > > GOBPANCESTOR, > GOBPCHILDREN, > GOBPOFFSPRING, > GOBPPARENTS, > GOCCANCESTOR, > GOCCCHILDREN, > GOCCOFFSPRING, > GOCCPARENTS, > GOMAPCOUNTS, > GOMFANCESTOR, > GOMFCHILDREN, > GOMFOFFSPRING, > GOMFPARENTS, > GOOBSOLETE, > GOSYNONYM, > GOTERM > > Loading required package: KEGG > > Attaching package: 'annaffy' > > > The following object(s) are masked from package:RCurl : > > getURL > >> sessionInfo() > R version 2.7.0 Under development (unstable) (2007-12-20 r43739) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] splines tools stats graphics grDevices datasets utils > [8] methods base > > other attached packages: > [1] affycoretools_1.11.2 annaffy_1.11.1 KEGG_2.0.1 > [4] GO_2.0.1 gcrma_2.11.1 matchprobes_1.11.0 > [7] biomaRt_1.13.6 RCurl_0.8-1 GOstats_2.5.0 > [10] Category_2.5.0 genefilter_1.17.7 survival_2.34 > [13] RBGL_1.15.6 annotate_1.17.3 xtable_1.5-2 > [16] GO.db_2.0.2 AnnotationDbi_1.1.6 RSQLite_0.6-4 > [19] DBI_0.2-4 graph_1.17.14 limma_2.13.1 > [22] affy_1.17.3 preprocessCore_1.1.5 affyio_1.7.6 > [25] Biobase_1.17.7 rcompgen_0.1-17 > > loaded via a namespace (and not attached): > [1] cluster_1.11.9 XML_1.9-0 > > So all you should ever have to do is run biocLite() to install things. > However, it may come to pass that certain packages for whatever reason > don't get installed correctly (or at all, although barring the > occasional missing package on BioC, I have never personally seen > such a > thing), in which case you may need an additional > biocLite("TheMissingPackage"). > > Best, > > Jim > > > > Sean Davis wrote: >> On Dec 19, 2007 5:06 PM, James Anderson <janderson_net at="" yahoo.com=""> >> wrote: >> >>> Sean, >>> >>> Thanks for your advice. I followed your suggestion and typed >>> >>> source("http://bioconductor.org/biocLite.R") >>> biocLite() >>> biocLite("affycoretools") >>> >>> and there is nothing abnormal. However, when I type >>> library(affycoretools), it pops up the following lines: >>> >>> Loading required package: affy >>> Loading required package: Biobase >>> Loading required package: tools >>> >>> Welcome to Bioconductor >>> >>> Vignettes contain introductory material. To view, type >>> 'openVignette()'. To cite Bioconductor, see >>> 'citation("Biobase")' and for packages 'citation(pkgname)'. >>> >>> Loading required package: affyio >>> Loading required package: preprocessCore >>> Loading required package: limma >>> Loading required package: GOstats >>> Loading required package: graph >>> Loading required package: GO.db >>> Loading required package: AnnotationDbi >>> Loading required package: DBI >>> Loading required package: RSQLite >>> Loading required package: annotate >>> Loading required package: xtable >>> Loading required package: RBGL >>> Loading required package: Category >>> Loading required package: genefilter >>> Loading required package: survival >>> Loading required package: splines >>> Loading required package: biomaRt >>> Loading required package: RCurl >>> Error: package 'RCurl' could not be loaded >>> In addition: Warning message: >>> In library(pkg, character.only = TRUE, logical.return = TRUE, >>> lib.loc = >>> lib.loc) : >>> there is no package called 'RCurl' >>> >>> Below is what I got from using sessionInfo() for diagnose >>> >>> R version 2.6.1 (2007-11-26) >>> i386-pc-mingw32 >>> >>> locale: >>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >>> States.1252;LC_MONETARY=English_United >>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >>> >>> attached base packages: >>> [1] splines tools stats graphics grDevices utils >>> datasets >>> [8] methods base >>> >>> other attached packages: >>> [1] GOstats_2.4.0 Category_2.4.0 genefilter_1.16.0 >>> [4] survival_2.34 RBGL_1.14.0 annotate_1.16.1 >>> [7] xtable_1.5-2 GO.db_2.0.2 AnnotationDbi_1.0.6 >>> [10] RSQLite_0.6-4 DBI_0.2-4 graph_1.16.1 >>> [13] limma_2.12.0 affy_1.16.0 preprocessCore_1.0.0 >>> [16] affyio_1.6.1 Biobase_1.16.2 >>> >>> loaded via a namespace (and not attached): >>> [1] cluster_1.11.9 >>> >>> Seems that it still can not find the package Rcurl. >>> >> >> Unfortunately, biocLite() does not find dependencies of >> dependencies (and I >> believe RCurl is a dependency of biomaRt). My guess is that you have >> installed other packages without using biocLite() in the past and >> have >> missed installing the RCurl dependency for one of them. >> Therefore, I would >> suggest using biocLite() to install ALL PACKAGES ALL THE TIME so >> that this >> doesn't occur in the future. However, in the short term, you >> might try: >> >> biocLite('RCurl') >> library(affycoretools) >> >> Hope that helps. >> >> Sean >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/ >> gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor
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@james-w-macdonald-5106
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James Anderson wrote: > Dear list, > > Is there any specific requirement for installation of affycoretools? like the version of R, etc. I am trying to install affycoretools, but there is always some error msg like: > > Error: package 'GO.db' required by 'GOstats' could not be found. > After I fix the above error, there is some new error: > > Error: package 'DBI' required by 'AnnotationDbi' could not be found > I fix this one there is some new one and seems that it will never end. This question is astonishingly similar to a question of yours that was answered just seven days ago: https://stat.ethz.ch/pipermail/bioconductor/2007-December/020480.html > > So what should I do in order to install affycoretools? As in the last response, and to any future question about installing packages -- please use biocLite() to install BioC packages. The dependencies for almost all of these packages are such that you will endure no amount of anguish by ignoring this advice and attempting to install packages one by one. > In addition, the function affystart in affycoretools can be used to plot the distribution of intensity, what is the corresponding function in package affy to perform the same task? I am trying to plot the intensity distribution from two batches of data. > > Thanks a lot! Happy holidays, > > James > > > > > --------------------------------- > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
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@martin-morgan-1513
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Try RCurl, with a capital C. Also once successful try the directions for updating packages http://www.bioconductor.org/docs/install-howto.html (the link Sean mentioned earlier and the one above should, but do not, point to the same text; expect this to change shortly). Martin James Anderson <janderson_net at="" yahoo.com=""> writes: > Sean, > > Thanks for your reply. I actually rebooted machine and restarted R. Then I typed biocLite() after sourcing it, after that I found there is no package named affycoretools, I type biocLite("affycoretools") and it seems to be working fine. The error I reported is because it can not find package Rcurl when I type library(affycoretools). > > I typed biocLite("Rcurl") and below is the response: > Running biocinstall version 2.1.8 with R version 2.6.1 > Your version of R requires version 2.1 of Bioconductor. > Warning message: > package ?Rcurl? is not available > > It still does not work. > > James > > > > > Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > > On Dec 19, 2007 5:06 PM, James Anderson <janderson_net at="" yahoo.com=""> wrote: > Sean, > > Thanks for your advice. I followed your suggestion and typed > > source("http://bioconductor.org/biocLite.R") > biocLite() > biocLite("affycoretools") > > and there is nothing abnormal. However, when I type > library(affycoretools), it pops up the following lines: > > Loading required package: affy > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: affyio > Loading required package: preprocessCore > Loading required package: limma > Loading required package: GOstats > Loading required package: graph > Loading required package: GO.db > Loading required package: AnnotationDbi > Loading required package: DBI > Loading required package: RSQLite > Loading required package: annotate > Loading required package: xtable > Loading required package: RBGL > Loading required package: Category > Loading required package: genefilter > Loading required package: survival > Loading required package: splines > Loading required package: biomaRt > Loading required package: RCurl > Error: package 'RCurl' could not be loaded > In addition: Warning message: > In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : > there is no package called 'RCurl' > > Below is what I got from using sessionInfo() for diagnose > > R version 2.6.1 (2007-11-26) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] GOstats_2.4.0 Category_2.4.0 genefilter_1.16.0 > [4] survival_2.34 RBGL_1.14.0 annotate_1.16.1 > [7] xtable_1.5-2 GO.db_2.0.2 AnnotationDbi_1.0.6 > [10] RSQLite_0.6-4 DBI_0.2-4 graph_1.16.1 > [13] limma_2.12.0 affy_1.16.0 preprocessCore_1.0.0 > [16] affyio_1.6.1 Biobase_1.16.2 > > loaded via a namespace (and not attached): > [1] cluster_1.11.9 > > Seems that it still can not find the package Rcurl. > > Unfortunately, biocLite() does not find dependencies of dependencies (and I believe RCurl is a dependency of biomaRt). My guess is that you have installed other packages without using biocLite() in the past and have missed installing the RCurl dependency for one of them. Therefore, I would suggest using biocLite() to install ALL PACKAGES ALL THE TIME so that this doesn't occur in the future. However, in the short term, you might try: > > biocLite('RCurl') > library(affycoretools) > > Hope that helps. > > Sean > > > > > > > --------------------------------- > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793
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