Question: lumi package
0
gravatar for Weiwei Shi
10.2 years ago by
Weiwei Shi1.2k
Weiwei Shi1.2k wrote:
Hi there I got the error from installing this package? Any suggestion? Thanks, Weiwei > source("http://www.bioconductor.org/biocLite.R") > biocLite("lumi") Running biocinstall version 2.1.11 with R version 2.6.1 Your version of R requires version 2.1 of BioConductor. trying URL ' http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib /2.6/lumi_1.4.0.tgz ' Content type 'application/x-gzip' length 5393927 bytes (5.1 Mb) opened URL ================================================== downloaded 5.1 Mb Error in sprintf(gettext(fmt, domain = domain), ...) : argument is missing, with no default tar: Skipping to next header tar: Archive contains obsolescent base-64 headers gzip: stdin: invalid compressed data--crc error gzip: stdin: invalid compressed data--length error tar: Child returned status 1 tar: Error exit delayed from previous errors > sessionInfo() R version 2.6.1 (2007-11-26) i386-apple-darwin8.10.1 locale: en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.6.1 -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III [[alternative HTML version deleted]]
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ADD COMMENTlink modified 10.2 years ago by Steve Lianoglou12k • written 10.2 years ago by Weiwei Shi1.2k
Answer: lumi package
0
gravatar for Steve Lianoglou
10.2 years ago by
Denali
Steve Lianoglou12k wrote:
Hi, On Sep 30, 2009, at 11:00 AM, Weiwei Shi wrote: > Hi there > I got the error from installing this package? Any suggestion? > > Thanks, > > Weiwei > >> source("http://www.bioconductor.org/biocLite.R") >> biocLite("lumi") > Running biocinstall version 2.1.11 with R version 2.6.1 > Your version of R requires version 2.1 of BioConductor. > trying URL ' > http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contr ib/2.6/lumi_1.4.0.tgz > ' > Content type 'application/x-gzip' length 5393927 bytes (5.1 Mb) > opened URL > ================================================== > downloaded 5.1 Mb > > Error in sprintf(gettext(fmt, domain = domain), ...) : > argument is missing, with no default > tar: Skipping to next header > tar: Archive contains obsolescent base-64 headers > > gzip: stdin: invalid compressed data--crc error > > gzip: stdin: invalid compressed data--length error > tar: Child returned status 1 > tar: Error exit delayed from previous errors > > >> sessionInfo() > R version 2.6.1 (2007-11-26) > i386-apple-darwin8.10.1 The first suggestion is to install the newest version of R and try again. http://cran.r-project.org/bin/macosx/ Let us know if you still have a problem after that. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
ADD COMMENTlink written 10.2 years ago by Steve Lianoglou12k
still not works. > source("http://www.bioconductor.org/biocLite.R") > biocLite("lumi") Using R version 2.9.2, biocinstall version 2.4.12. Installing Bioconductor version 2.4 packages: [1] "lumi" Please wait... Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contrib /2.9 trying URL ' http://bioconductor.org/packages/2.4/bioc/bin/macosx/universal/contrib /2.9/lumi_1.10.2.tgz ' Content type 'application/x-gzip' length 7082922 bytes (6.8 Mb) opened URL ================================================== downloaded 6.8 Mb tar: Skipping to next header tar: Archive contains obsolescent base-64 headers gzip: stdin: invalid compressed data--crc error gzip: stdin: invalid compressed data--length error tar: Child returned status 1 tar: Error exit delayed from previous errors Error in gzfile(file, "r") : cannot open the connection In addition: Warning messages: 1: 'tar' returned non-zero exit code 512 2: In gzfile(file, "r") : cannot open compressed file 'lumi/DESCRIPTION', probable reason 'No such file or directory' > sessionInfo() R version 2.9.2 (2009-08-24) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rpart_3.1-45 class_7.2-48 supclust_1.0-5 loaded via a namespace (and not attached): [1] tools_2.9.2 > version _ platform i386-apple-darwin8.11.1 arch i386 os darwin8.11.1 system i386, darwin8.11.1 status major 2 minor 9.2 year 2009 month 08 day 24 svn rev 49384 language R version.string R version 2.9.2 (2009-08-24) On Wed, Sep 30, 2009 at 11:10 PM, Steve Lianoglou < mailinglist.honeypot@gmail.com> wrote: > Hi, > > > On Sep 30, 2009, at 11:00 AM, Weiwei Shi wrote: > > Hi there >> I got the error from installing this package? Any suggestion? >> >> Thanks, >> >> Weiwei >> >> source("http://www.bioconductor.org/biocLite.R") >>> biocLite("lumi") >>> >> Running biocinstall version 2.1.11 with R version 2.6.1 >> Your version of R requires version 2.1 of BioConductor. >> trying URL ' >> >> http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/cont rib/2.6/lumi_1.4.0.tgz >> ' >> Content type 'application/x-gzip' length 5393927 bytes (5.1 Mb) >> opened URL >> ================================================== >> downloaded 5.1 Mb >> >> Error in sprintf(gettext(fmt, domain = domain), ...) : >> argument is missing, with no default >> tar: Skipping to next header >> tar: Archive contains obsolescent base-64 headers >> >> gzip: stdin: invalid compressed data--crc error >> >> gzip: stdin: invalid compressed data--length error >> tar: Child returned status 1 >> tar: Error exit delayed from previous errors >> >> >> sessionInfo() >>> >> R version 2.6.1 (2007-11-26) >> i386-apple-darwin8.10.1 >> > > The first suggestion is to install the newest version of R and try again. > > http://cran.r-project.org/bin/macosx/ > > Let us know if you still have a problem after that. > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact<http: cbio.mskc="" c.org="" %7elianos="" contact=""> > > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III [[alternative HTML version deleted]]
ADD REPLYlink written 10.2 years ago by Weiwei Shi1.2k
Hi, Wow ... weird: On Sep 30, 2009, at 1:25 PM, Weiwei Shi wrote: > still not works. > > > source("http://www.bioconductor.org/biocLite.R") > > biocLite("lumi") > Using R version 2.9.2, biocinstall version 2.4.12. > Installing Bioconductor version 2.4 packages: > [1] "lumi" > Please wait... > > Warning: unable to access index for repository http://brainarray.mbn i.med.umich.edu/bioc/bin/macosx/universal/contrib/2.9 > trying URL 'http://bioconductor.org/packages/2.4/bioc/bin/macosx/ > universal/contrib/2.9/lumi_1.10.2.tgz' > Content type 'application/x-gzip' length 7082922 bytes (6.8 Mb) > opened URL > ================================================== > downloaded 6.8 Mb > > tar: Skipping to next header > tar: Archive contains obsolescent base-64 headers > > gzip: stdin: invalid compressed data--crc error I'm not sure why this is happening, but it looks like it can't uncompress the downloaded tar correctly ... installing from both within R (via biocLite) and from the command line is working for me. Someone will likely have a better idea, but in the meantime, can you try to install the package from the command line? Like so: 1. Open Terminal.app 2. Download the package: $ curl -O http://bioconductor.org/packages/2.4/bioc/bin/macosx/univers al/contrib/2.9/lumi_1.10.2.tgz 3. Install into R $ R CMD INSTALL lumi_1.10.2.tgz Is it still breaking? If so, continue to 4, otherwise celebrate. 4. Can you you simply uncompress that file? eg. does this uncompress successfully? (From within Terminal, we're not in R) $ tar xvfz lumi_1.10.2.tgz 5. If that works, try to install the uncompressed file (it expanded to a "lumi" directory), but first remove the lumi*.tgz $ rm lumi_1.10.2.tgz $ R CMD INSTALL lumi Anything? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
ADD REPLYlink written 10.2 years ago by Steve Lianoglou12k
The installation seems to work now but the loading got some error... > library(lumi) Loading required package: annotate 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: AnnotationDbi Loading required package: DBI Loading required package: RSQLite Loading required package: xtable Loading required package: affy Loading required package: affyio Loading required package: preprocessCore *** caught bus error *** address 0xc, cause 'non-existent physical address' Traceback: 1: dyn.load(file, DLLpath = DLLpath, ...) 2: library.dynam("preprocessCore", pkgname, libname, now = FALSE) 3: f(libname, pkgname) 4: firstlib(which.lib.loc, package) 5: doTryCatch(return(expr), name, parentenv, handler) 6: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 7: tryCatchList(expr, classes, parentenv, handlers) 8: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] if (14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") > LONG) prefix <- paste(prefix, "\n ", sep = "") } else prefix <- "Error : " msg <- paste(prefix, conditionMessage(e), "\n", sep = "") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error"))}) 9: try(firstlib(which.lib.loc, package)) 10: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) 11: .getRequiredPackages2(pkgInfo) 12: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) 13: .getRequiredPackages2(pkgInfo) 14: library(lumi) Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: On Thu, Oct 1, 2009 at 1:37 AM, Steve Lianoglou < mailinglist.honeypot@gmail.com> wrote: > Hi, > > Wow ... weird: > > On Sep 30, 2009, at 1:25 PM, Weiwei Shi wrote: > > still not works. >> >> > source("http://www.bioconductor.org/biocLite.R") >> > biocLite("lumi") >> Using R version 2.9.2, biocinstall version 2.4.12. >> Installing Bioconductor version 2.4 packages: >> [1] "lumi" >> Please wait... >> >> Warning: unable to access index for repository >> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/cont rib/2.9 >> trying URL 'http://bioconductor.org/packages/2.4/bioc/bin/macosx/ >> universal/contrib/2.9/lumi_1.10.2.tgz' >> Content type 'application/x-gzip' length 7082922 bytes (6.8 Mb) >> opened URL >> ================================================== >> downloaded 6.8 Mb >> >> tar: Skipping to next header >> tar: Archive contains obsolescent base-64 headers >> >> gzip: stdin: invalid compressed data--crc error >> > > I'm not sure why this is happening, but it looks like it can't uncompress > the downloaded tar correctly ... installing from both within R (via > biocLite) and from the command line is working for me. > > Someone will likely have a better idea, but in the meantime, can you try to > install the package from the command line? Like so: > > 1. Open Terminal.app > > 2. Download the package: > $ curl -O > http://bioconductor.org/packages/2.4/bioc/bin/macosx/universal/contr ib/2.9/lumi_1.10.2.tgz > > 3. Install into R > $ R CMD INSTALL lumi_1.10.2.tgz > > Is it still breaking? If so, continue to 4, otherwise celebrate. > > 4. Can you you simply uncompress that file? eg. does this uncompress > successfully? (From within Terminal, we're not in R) > $ tar xvfz lumi_1.10.2.tgz > > 5. If that works, try to install the uncompressed file (it expanded to a > "lumi" directory), but first remove the lumi*.tgz > > $ rm lumi_1.10.2.tgz > $ R CMD INSTALL lumi > > Anything? > > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact<http: cbio.mskc="" c.org="" %7elianos="" contact=""> > > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III [[alternative HTML version deleted]]
ADD REPLYlink written 10.2 years ago by Weiwei Shi1.2k
Weiwei Shi wrote: > The installation seems to work now but the loading got some error... try source('http://bioconductor.org/biocLite.R') old.packages(repos=biocinstallRepos()) update.packages(repos=biocinstallRepos(), ask=FALSE) Martin > > >> library(lumi) > Loading required package: annotate > 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: AnnotationDbi > Loading required package: DBI > Loading required package: RSQLite > Loading required package: xtable > Loading required package: affy > Loading required package: affyio > Loading required package: preprocessCore > > *** caught bus error *** > address 0xc, cause 'non-existent physical address' > > Traceback: > 1: dyn.load(file, DLLpath = DLLpath, ...) > 2: library.dynam("preprocessCore", pkgname, libname, now = FALSE) > 3: f(libname, pkgname) > 4: firstlib(which.lib.loc, package) > 5: doTryCatch(return(expr), name, parentenv, handler) > 6: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > 7: tryCatchList(expr, classes, parentenv, handlers) > 8: tryCatch(expr, error = function(e) { call <- conditionCall(e) if > (!is.null(call)) { if (identical(call[[1L]], > quote(doTryCatch))) call <- sys.call(-4L) dcall <- > deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") > LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, > "\n")[[1L]] if (14L + nchar(dcall, type = "w") + nchar(sm[1L], type = > "w") > LONG) prefix <- paste(prefix, "\n ", sep = > "") } else prefix <- "Error : " msg <- paste(prefix, > conditionMessage(e), "\n", sep = "") .Internal(seterrmessage(msg[1L])) > if (!silent && identical(getOption("show.error.messages"), TRUE)) > { cat(msg, file = stderr()) > .Internal(printDeferredWarnings()) } invisible(structure(msg, class = > "try-error"))}) > 9: try(firstlib(which.lib.loc, package)) > 10: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = > lib.loc) > 11: .getRequiredPackages2(pkgInfo) > 12: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = > lib.loc) > 13: .getRequiredPackages2(pkgInfo) > 14: library(lumi) > > Possible actions: > 1: abort (with core dump, if enabled) > 2: normal R exit > 3: exit R without saving workspace > 4: exit R saving workspace > Selection: > > > > On Thu, Oct 1, 2009 at 1:37 AM, Steve Lianoglou < > mailinglist.honeypot at gmail.com> wrote: > >> Hi, >> >> Wow ... weird: >> >> On Sep 30, 2009, at 1:25 PM, Weiwei Shi wrote: >> >> still not works. >>>> source("http://www.bioconductor.org/biocLite.R") >>>> biocLite("lumi") >>> Using R version 2.9.2, biocinstall version 2.4.12. >>> Installing Bioconductor version 2.4 packages: >>> [1] "lumi" >>> Please wait... >>> >>> Warning: unable to access index for repository >>> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/con trib/2.9 >>> trying URL 'http://bioconductor.org/packages/2.4/bioc/bin/macosx/ >>> universal/contrib/2.9/lumi_1.10.2.tgz' >>> Content type 'application/x-gzip' length 7082922 bytes (6.8 Mb) >>> opened URL >>> ================================================== >>> downloaded 6.8 Mb >>> >>> tar: Skipping to next header >>> tar: Archive contains obsolescent base-64 headers >>> >>> gzip: stdin: invalid compressed data--crc error >>> >> I'm not sure why this is happening, but it looks like it can't uncompress >> the downloaded tar correctly ... installing from both within R (via >> biocLite) and from the command line is working for me. >> >> Someone will likely have a better idea, but in the meantime, can you try to >> install the package from the command line? Like so: >> >> 1. Open Terminal.app >> >> 2. Download the package: >> $ curl -O >> http://bioconductor.org/packages/2.4/bioc/bin/macosx/universal/cont rib/2.9/lumi_1.10.2.tgz >> >> 3. Install into R >> $ R CMD INSTALL lumi_1.10.2.tgz >> >> Is it still breaking? If so, continue to 4, otherwise celebrate. >> >> 4. Can you you simply uncompress that file? eg. does this uncompress >> successfully? (From within Terminal, we're not in R) >> $ tar xvfz lumi_1.10.2.tgz >> >> 5. If that works, try to install the uncompressed file (it expanded to a >> "lumi" directory), but first remove the lumi*.tgz >> >> $ rm lumi_1.10.2.tgz >> $ R CMD INSTALL lumi >> >> Anything? >> >> >> -steve >> >> -- >> Steve Lianoglou >> Graduate Student: Computational Systems Biology >> | Memorial Sloan-Kettering Cancer Center >> | Weill Medical College of Cornell University >> Contact Info: http://cbio.mskcc.org/~lianos/contact<http: cbio.msk="" cc.org="" %7elianos="" contact=""> >> >> > > -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD REPLYlink written 10.2 years ago by Martin Morgan ♦♦ 24k
Hi, On Sep 30, 2009, at 1:53 PM, Weiwei Shi wrote: > The installation seems to work now but the loading got some error... 1. What did you do to get the install to work? 2. It actually seems like your problems aren't really with the lumi package since it looks like you're having problems with some compiled code, given the bus error. As far as I can see lumi has no compiled code, which just means to say I think we should be trying to debug "greater" issues. After you installed your new R (2.9.2), you reinstalled your base bioconductor base packages, right? 3. Out of curiosity, what kind of machine are you running on? -steve > > > > library(lumi) > Loading required package: annotate > 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: AnnotationDbi > Loading required package: DBI > Loading required package: RSQLite > Loading required package: xtable > Loading required package: affy > Loading required package: affyio > Loading required package: preprocessCore > > *** caught bus error *** > address 0xc, cause 'non-existent physical address' > > Traceback: > 1: dyn.load(file, DLLpath = DLLpath, ...) > 2: library.dynam("preprocessCore", pkgname, libname, now = FALSE) > 3: f(libname, pkgname) > 4: firstlib(which.lib.loc, package) > 5: doTryCatch(return(expr), name, parentenv, handler) > 6: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > 7: tryCatchList(expr, classes, parentenv, handlers) > 8: tryCatch(expr, error = function(e) { call <- conditionCall > (e) if (!is.null(call)) { if (identical(call[[1L]], quote > (doTryCatch))) call <- sys.call(-4L) dcall <- > deparse(call)[1L] prefix <- paste("Error in", dcall, ": > ") LONG <- 75L msg <- conditionMessage(e) sm <- > strsplit(msg, "\n")[[1L]] if (14L + nchar(dcall, type = "w") > + nchar(sm[1L], type = "w") > LONG) prefix > <- paste(prefix, "\n ", sep = "") } else prefix <- "Error : > " msg <- paste(prefix, conditionMessage(e), "\n", sep = > "") .Internal(seterrmessage(msg[1L])) if (!silent && identical > (getOption("show.error.messages"), TRUE)) { cat(msg, > file = stderr()) .Internal(printDeferredWarnings()) } > invisible(structure(msg, class = "try-error"))}) > 9: try(firstlib(which.lib.loc, package)) > 10: library(pkg, character.only = TRUE, logical.return = TRUE, > lib.loc = lib.loc) > 11: .getRequiredPackages2(pkgInfo) > 12: library(pkg, character.only = TRUE, logical.return = TRUE, > lib.loc = lib.loc) > 13: .getRequiredPackages2(pkgInfo) > 14: library(lumi) > > Possible actions: > 1: abort (with core dump, if enabled) > 2: normal R exit > 3: exit R without saving workspace > 4: exit R saving workspace > Selection: > > > > On Thu, Oct 1, 2009 at 1:37 AM, Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> > wrote: > Hi, > > Wow ... weird: > > > On Sep 30, 2009, at 1:25 PM, Weiwei Shi wrote: > > still not works. > > > source("http://www.bioconductor.org/biocLite.R") > > biocLite("lumi") > Using R version 2.9.2, biocinstall version 2.4.12. > Installing Bioconductor version 2.4 packages: > [1] "lumi" > Please wait... > > Warning: unable to access index for repository http://brainarray.mbn i.med.umich.edu/bioc/bin/macosx/universal/contrib/2.9 > trying URL 'http://bioconductor.org/packages/2.4/bioc/bin/macosx/ > universal/contrib/2.9/lumi_1.10.2.tgz' > Content type 'application/x-gzip' length 7082922 bytes (6.8 Mb) > opened URL > ================================================== > downloaded 6.8 Mb > > tar: Skipping to next header > tar: Archive contains obsolescent base-64 headers > > gzip: stdin: invalid compressed data--crc error > > I'm not sure why this is happening, but it looks like it can't > uncompress the downloaded tar correctly ... installing from both > within R (via biocLite) and from the command line is working for me. > > Someone will likely have a better idea, but in the meantime, can you > try to install the package from the command line? Like so: > > 1. Open Terminal.app > > 2. Download the package: > $ curl -O http://bioconductor.org/packages/2.4/bioc/bin/macosx/unive rsal/contrib/2.9/lumi_1.10.2.tgz > > 3. Install into R > $ R CMD INSTALL lumi_1.10.2.tgz > > Is it still breaking? If so, continue to 4, otherwise celebrate. > > 4. Can you you simply uncompress that file? eg. does this uncompress > successfully? (From within Terminal, we're not in R) > $ tar xvfz lumi_1.10.2.tgz > > 5. If that works, try to install the uncompressed file (it expanded > to a "lumi" directory), but first remove the lumi*.tgz > > $ rm lumi_1.10.2.tgz > $ R CMD INSTALL lumi > > Anything? > > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > > > > > -- > Weiwei Shi, Ph.D > Research Scientist > GeneGO, Inc. > > "Did you always know?" > "No, I did not. But I believed..." > ---Matrix III -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
ADD REPLYlink written 10.2 years ago by Steve Lianoglou12k
Actually both 3 and 5 method work. I found that issue too. It could be because the upgrade since to save my previous packages, I just copy my previous packages from Library/Framework/R.framework/.../2.6/resources/library to 2.9's library. Do you think that cause the problem? I did not reinstall base bioconductor base packages, let me try that too. The machine I am using is Macbook Pro, 2.2 GHz 4GB..., and OSX 10.5.5 thanks, Weiwei On Thu, Oct 1, 2009 at 1:59 AM, Steve Lianoglou < mailinglist.honeypot@gmail.com> wrote: > Hi, > > On Sep 30, 2009, at 1:53 PM, Weiwei Shi wrote: > > The installation seems to work now but the loading got some error... >> > > 1. What did you do to get the install to work? > > 2. It actually seems like your problems aren't really with the lumi package > since it looks like you're having problems with some compiled code, given > the bus error. As far as I can see lumi has no compiled code, which just > means to say I think we should be trying to debug "greater" issues. > > After you installed your new R (2.9.2), you reinstalled your base > bioconductor base packages, right? > > 3. Out of curiosity, what kind of machine are you running on? > > -steve > > > >> >> > library(lumi) >> Loading required package: annotate >> 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: AnnotationDbi >> Loading required package: DBI >> Loading required package: RSQLite >> Loading required package: xtable >> Loading required package: affy >> Loading required package: affyio >> Loading required package: preprocessCore >> >> *** caught bus error *** >> address 0xc, cause 'non-existent physical address' >> >> Traceback: >> 1: dyn.load(file, DLLpath = DLLpath, ...) >> 2: library.dynam("preprocessCore", pkgname, libname, now = FALSE) >> 3: f(libname, pkgname) >> 4: firstlib(which.lib.loc, package) >> 5: doTryCatch(return(expr), name, parentenv, handler) >> 6: tryCatchOne(expr, names, parentenv, handlers[[1L]]) >> 7: tryCatchList(expr, classes, parentenv, handlers) >> 8: tryCatch(expr, error = function(e) { call <- conditionCall(e) if >> (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) >> call <- sys.call(-4L) dcall <- deparse(call)[1L] >> prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- >> conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] if (14L + >> nchar(dcall, type = "w") + nchar(sm[1L], type = "w") > LONG) >> prefix <- paste(prefix, "\n ", sep = "") } else prefix <- >> "Error : " msg <- paste(prefix, conditionMessage(e), "\n", sep = "") >> .Internal(seterrmessage(msg[1L])) if (!silent && >> identical(getOption("show.error.messages"), TRUE)) { cat(msg, >> file = stderr()) .Internal(printDeferredWarnings()) } >> invisible(structure(msg, class = "try-error"))}) >> 9: try(firstlib(which.lib.loc, package)) >> 10: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = >> lib.loc) >> 11: .getRequiredPackages2(pkgInfo) >> 12: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = >> lib.loc) >> 13: .getRequiredPackages2(pkgInfo) >> 14: library(lumi) >> >> Possible actions: >> 1: abort (with core dump, if enabled) >> 2: normal R exit >> 3: exit R without saving workspace >> 4: exit R saving workspace >> Selection: >> >> >> >> On Thu, Oct 1, 2009 at 1:37 AM, Steve Lianoglou < >> mailinglist.honeypot@gmail.com> wrote: >> Hi, >> >> Wow ... weird: >> >> >> On Sep 30, 2009, at 1:25 PM, Weiwei Shi wrote: >> >> still not works. >> >> > source("http://www.bioconductor.org/biocLite.R") >> > biocLite("lumi") >> Using R version 2.9.2, biocinstall version 2.4.12. >> Installing Bioconductor version 2.4 packages: >> [1] "lumi" >> Please wait... >> >> Warning: unable to access index for repository >> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/cont rib/2.9 >> trying URL 'http://bioconductor.org/packages/2.4/bioc/bin/macosx/ >> universal/contrib/2.9/lumi_1.10.2.tgz' >> Content type 'application/x-gzip' length 7082922 bytes (6.8 Mb) >> opened URL >> ================================================== >> downloaded 6.8 Mb >> >> tar: Skipping to next header >> tar: Archive contains obsolescent base-64 headers >> >> gzip: stdin: invalid compressed data--crc error >> >> I'm not sure why this is happening, but it looks like it can't uncompress >> the downloaded tar correctly ... installing from both within R (via >> biocLite) and from the command line is working for me. >> >> Someone will likely have a better idea, but in the meantime, can you try >> to install the package from the command line? Like so: >> >> 1. Open Terminal.app >> >> 2. Download the package: >> $ curl -O >> http://bioconductor.org/packages/2.4/bioc/bin/macosx/universal/cont rib/2.9/lumi_1.10.2.tgz >> >> 3. Install into R >> $ R CMD INSTALL lumi_1.10.2.tgz >> >> Is it still breaking? If so, continue to 4, otherwise celebrate. >> >> 4. Can you you simply uncompress that file? eg. does this uncompress >> successfully? (From within Terminal, we're not in R) >> $ tar xvfz lumi_1.10.2.tgz >> >> 5. If that works, try to install the uncompressed file (it expanded to a >> "lumi" directory), but first remove the lumi*.tgz >> >> $ rm lumi_1.10.2.tgz >> $ R CMD INSTALL lumi >> >> Anything? >> >> >> -steve >> >> -- >> Steve Lianoglou >> Graduate Student: Computational Systems Biology >> | Memorial Sloan-Kettering Cancer Center >> | Weill Medical College of Cornell University >> Contact Info: http://cbio.mskcc.org/~lianos/contact<http: cbio.msk="" cc.org="" %7elianos="" contact=""> >> >> >> >> >> -- >> Weiwei Shi, Ph.D >> Research Scientist >> GeneGO, Inc. >> >> "Did you always know?" >> "No, I did not. But I believed..." >> ---Matrix III >> > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact<http: cbio.mskc="" c.org="" %7elianos="" contact=""> > > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III [[alternative HTML version deleted]]
ADD REPLYlink written 10.2 years ago by Weiwei Shi1.2k
Hi, On Sep 30, 2009, at 2:07 PM, Weiwei Shi wrote: > Actually both 3 and 5 method work. > > I found that issue too. It could be because the upgrade since to > save my previous packages, I just copy my previous packages from > Library/Framework/R.framework/.../2.6/resources/library to 2.9's > library. Do you think that cause the problem? > > I did not reinstall base bioconductor base packages, let me try that > too. Right, as Martin just pointed out, this is it. Once you reinstall (you can follow his instructions), everything should be back to normal. -steve > > The machine I am using is Macbook Pro, 2.2 GHz 4GB..., and OSX 10.5.5 > > thanks, > > Weiwei > > On Thu, Oct 1, 2009 at 1:59 AM, Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> > wrote: > Hi, > > > On Sep 30, 2009, at 1:53 PM, Weiwei Shi wrote: > > The installation seems to work now but the loading got some error... > > 1. What did you do to get the install to work? > > 2. It actually seems like your problems aren't really with the lumi > package since it looks like you're having problems with some > compiled code, given the bus error. As far as I can see lumi has no > compiled code, which just means to say I think we should be trying > to debug "greater" issues. > > After you installed your new R (2.9.2), you reinstalled your base > bioconductor base packages, right? > > 3. Out of curiosity, what kind of machine are you running on? > > -steve > > > > > > library(lumi) > Loading required package: annotate > 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: AnnotationDbi > Loading required package: DBI > Loading required package: RSQLite > Loading required package: xtable > Loading required package: affy > Loading required package: affyio > Loading required package: preprocessCore > > *** caught bus error *** > address 0xc, cause 'non-existent physical address' > > Traceback: > 1: dyn.load(file, DLLpath = DLLpath, ...) > 2: library.dynam("preprocessCore", pkgname, libname, now = FALSE) > 3: f(libname, pkgname) > 4: firstlib(which.lib.loc, package) > 5: doTryCatch(return(expr), name, parentenv, handler) > 6: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > 7: tryCatchList(expr, classes, parentenv, handlers) > 8: tryCatch(expr, error = function(e) { call <- conditionCall > (e) if (!is.null(call)) { if (identical(call[[1L]], quote > (doTryCatch))) call <- sys.call(-4L) dcall <- > deparse(call)[1L] prefix <- paste("Error in", dcall, ": > ") LONG <- 75L msg <- conditionMessage(e) sm <- > strsplit(msg, "\n")[[1L]] if (14L + nchar(dcall, type = "w") > + nchar(sm[1L], type = "w") > LONG) prefix > <- paste(prefix, "\n ", sep = "") } else prefix <- "Error : > " msg <- paste(prefix, conditionMessage(e), "\n", sep = > "") .Internal(seterrmessage(msg[1L])) if (!silent && identical > (getOption("show.error.messages"), TRUE)) { cat(msg, > file = stderr()) .Internal(printDeferredWarnings()) } > invisible(structure(msg, class = "try-error"))}) > 9: try(firstlib(which.lib.loc, package)) > 10: library(pkg, character.only = TRUE, logical.return = TRUE, > lib.loc = lib.loc) > 11: .getRequiredPackages2(pkgInfo) > 12: library(pkg, character.only = TRUE, logical.return = TRUE, > lib.loc = lib.loc) > 13: .getRequiredPackages2(pkgInfo) > 14: library(lumi) > > Possible actions: > 1: abort (with core dump, if enabled) > 2: normal R exit > 3: exit R without saving workspace > 4: exit R saving workspace > Selection: > > > > On Thu, Oct 1, 2009 at 1:37 AM, Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> > wrote: > Hi, > > Wow ... weird: > > > On Sep 30, 2009, at 1:25 PM, Weiwei Shi wrote: > > still not works. > > > source("http://www.bioconductor.org/biocLite.R") > > biocLite("lumi") > Using R version 2.9.2, biocinstall version 2.4.12. > Installing Bioconductor version 2.4 packages: > [1] "lumi" > Please wait... > > Warning: unable to access index for repository http://brainarray.mbn i.med.umich.edu/bioc/bin/macosx/universal/contrib/2.9 > trying URL 'http://bioconductor.org/packages/2.4/bioc/bin/macosx/ > universal/contrib/2.9/lumi_1.10.2.tgz' > Content type 'application/x-gzip' length 7082922 bytes (6.8 Mb) > opened URL > ================================================== > downloaded 6.8 Mb > > tar: Skipping to next header > tar: Archive contains obsolescent base-64 headers > > gzip: stdin: invalid compressed data--crc error > > I'm not sure why this is happening, but it looks like it can't > uncompress the downloaded tar correctly ... installing from both > within R (via biocLite) and from the command line is working for me. > > Someone will likely have a better idea, but in the meantime, can you > try to install the package from the command line? Like so: > > 1. Open Terminal.app > > 2. Download the package: > $ curl -O http://bioconductor.org/packages/2.4/bioc/bin/macosx/unive rsal/contrib/2.9/lumi_1.10.2.tgz > > 3. Install into R > $ R CMD INSTALL lumi_1.10.2.tgz > > Is it still breaking? If so, continue to 4, otherwise celebrate. > > 4. Can you you simply uncompress that file? eg. does this uncompress > successfully? (From within Terminal, we're not in R) > $ tar xvfz lumi_1.10.2.tgz > > 5. If that works, try to install the uncompressed file (it expanded > to a "lumi" directory), but first remove the lumi*.tgz > > $ rm lumi_1.10.2.tgz > $ R CMD INSTALL lumi > > Anything? > > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > > > > > -- > Weiwei Shi, Ph.D > Research Scientist > GeneGO, Inc. > > "Did you always know?" > "No, I did not. But I believed..." > ---Matrix III > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > > > > > -- > Weiwei Shi, Ph.D > Research Scientist > GeneGO, Inc. > > "Did you always know?" > "No, I did not. But I believed..." > ---Matrix III -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
ADD REPLYlink written 10.2 years ago by Steve Lianoglou12k
On Wed, Sep 30, 2009 at 2:07 PM, Weiwei Shi <helprhelp at="" gmail.com=""> wrote: > Actually both 3 and 5 method work. > > I found that issue too. It could be because the upgrade since to save my > previous packages, I just copy my previous packages from > Library/Framework/R.framework/.../2.6/resources/library to 2.9's library. Do > you think that cause the problem? You shouldn't do that, and that is likely the cause of at least parts of the problem. > I did not reinstall base bioconductor base packages, let me try that too. Each time you re-install a new version of R, it is best to reinstall all packages, in general, preferably using biocLite(). > The machine I am using is Macbook Pro, 2.2 GHz 4GB..., and OSX 10.5.5 > > thanks, > > Weiwei > > On Thu, Oct 1, 2009 at 1:59 AM, Steve Lianoglou < > mailinglist.honeypot at gmail.com> wrote: > >> Hi, >> >> On Sep 30, 2009, at 1:53 PM, Weiwei Shi wrote: >> >> ?The installation seems to work now but the loading got some error... >>> >> >> 1. What did you do to get the install to work? >> >> 2. It actually seems like your problems aren't really with the lumi package >> since it looks like you're having problems with some compiled code, given >> the bus error. As far as I can see lumi has no compiled code, which just >> means to say I think we should be trying to debug "greater" issues. >> >> After you installed your new R (2.9.2), you reinstalled your base >> bioconductor base packages, right? >> >> 3. Out of curiosity, what kind of machine are you running on? >> >> -steve >> >> >> >>> >>> > library(lumi) >>> Loading required package: annotate >>> 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: AnnotationDbi >>> Loading required package: DBI >>> Loading required package: RSQLite >>> Loading required package: xtable >>> Loading required package: affy >>> Loading required package: affyio >>> Loading required package: preprocessCore >>> >>> ?*** caught bus error *** >>> address 0xc, cause 'non-existent physical address' >>> >>> Traceback: >>> ?1: dyn.load(file, DLLpath = DLLpath, ...) >>> ?2: library.dynam("preprocessCore", pkgname, libname, now = FALSE) >>> ?3: f(libname, pkgname) >>> ?4: firstlib(which.lib.loc, package) >>> ?5: doTryCatch(return(expr), name, parentenv, handler) >>> ?6: tryCatchOne(expr, names, parentenv, handlers[[1L]]) >>> ?7: tryCatchList(expr, classes, parentenv, handlers) >>> ?8: tryCatch(expr, error = function(e) { ? ?call <- conditionCall(e) ? ?if >>> (!is.null(call)) { ? ? ? ?if (identical(call[[1L]], quote(doTryCatch))) >>> ? ? ? ? call <- sys.call(-4L) ? ? ? ?dcall <- deparse(call)[1L] >>> ?prefix <- paste("Error in", dcall, ": ") ? ? ? ?LONG <- 75L ? ? ? ?msg <- >>> conditionMessage(e) ? ? ? ?sm <- strsplit(msg, "\n")[[1L]] ? ? ? ?if (14L + >>> nchar(dcall, type = "w") + nchar(sm[1L], type = "w") > ? ? ? ? ? ? LONG) >>> ? ? ? ? prefix <- paste(prefix, "\n ?", sep = "") ? ?} ? ?else prefix <- >>> "Error : " ? ?msg <- paste(prefix, conditionMessage(e), "\n", sep = "") >>> ?.Internal(seterrmessage(msg[1L])) ? ?if (!silent && >>> identical(getOption("show.error.messages"), ? ? ? ? TRUE)) { ? ? ? ?cat(msg, >>> file = stderr()) ? ? ? ?.Internal(printDeferredWarnings()) ? ?} >>> ?invisible(structure(msg, class = "try-error"))}) >>> ?9: try(firstlib(which.lib.loc, package)) >>> 10: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = >>> lib.loc) >>> 11: .getRequiredPackages2(pkgInfo) >>> 12: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = >>> lib.loc) >>> 13: .getRequiredPackages2(pkgInfo) >>> 14: library(lumi) >>> >>> Possible actions: >>> 1: abort (with core dump, if enabled) >>> 2: normal R exit >>> 3: exit R without saving workspace >>> 4: exit R saving workspace >>> Selection: >>> >>> >>> >>> On Thu, Oct 1, 2009 at 1:37 AM, Steve Lianoglou < >>> mailinglist.honeypot at gmail.com> wrote: >>> Hi, >>> >>> Wow ... weird: >>> >>> >>> On Sep 30, 2009, at 1:25 PM, Weiwei Shi wrote: >>> >>> still not works. >>> >>> > source("http://www.bioconductor.org/biocLite.R") >>> > biocLite("lumi") >>> Using R version 2.9.2, biocinstall version 2.4.12. >>> Installing Bioconductor version 2.4 packages: >>> [1] "lumi" >>> Please wait... >>> >>> Warning: unable to access index for repository >>> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/con trib/2.9 >>> trying URL 'http://bioconductor.org/packages/2.4/bioc/bin/macosx/ >>> universal/contrib/2.9/lumi_1.10.2.tgz' >>> Content type 'application/x-gzip' length 7082922 bytes (6.8 Mb) >>> opened URL >>> ================================================== >>> downloaded 6.8 Mb >>> >>> tar: Skipping to next header >>> tar: Archive contains obsolescent base-64 headers >>> >>> gzip: stdin: invalid compressed data--crc error >>> >>> I'm not sure why this is happening, but it looks like it can't uncompress >>> the downloaded tar correctly ... installing from both within R (via >>> biocLite) and from the command line is working for me. >>> >>> Someone will likely have a better idea, but in the meantime, can you try >>> to install the package from the command line? Like so: >>> >>> 1. Open Terminal.app >>> >>> 2. Download the package: >>> $ curl -O >>> http://bioconductor.org/packages/2.4/bioc/bin/macosx/universal/con trib/2.9/lumi_1.10.2.tgz >>> >>> 3. Install into R >>> $ R CMD INSTALL lumi_1.10.2.tgz >>> >>> Is it still breaking? If so, continue to 4, otherwise celebrate. >>> >>> 4. Can you you simply uncompress that file? eg. does this uncompress >>> successfully? (From within Terminal, we're not in R) >>> $ tar xvfz lumi_1.10.2.tgz >>> >>> 5. If that works, try to install the uncompressed file (it expanded to a >>> "lumi" directory), but first remove the lumi*.tgz >>> >>> $ rm lumi_1.10.2.tgz >>> $ R CMD INSTALL lumi >>> >>> Anything? >>> >>> >>> -steve >>> >>> -- >>> Steve Lianoglou >>> Graduate Student: Computational Systems Biology >>> ?| ?Memorial Sloan-Kettering Cancer Center >>> ?| ?Weill Medical College of Cornell University >>> Contact Info: http://cbio.mskcc.org/~lianos/contact<http: cbio.ms="" kcc.org="" %7elianos="" contact=""> >>> >>> >>> >>> >>> -- >>> Weiwei Shi, Ph.D >>> Research Scientist >>> GeneGO, Inc. >>> >>> "Did you always know?" >>> "No, I did not. But I believed..." >>> ---Matrix III >>> >> >> -- >> Steve Lianoglou >> Graduate Student: Computational Systems Biology >> ?| ?Memorial Sloan-Kettering Cancer Center >> ?| ?Weill Medical College of Cornell University >> Contact Info: http://cbio.mskcc.org/~lianos/contact<http: cbio.msk="" cc.org="" %7elianos="" contact=""> >> >> > > > -- > Weiwei Shi, Ph.D > Research Scientist > GeneGO, Inc. > > "Did you always know?" > "No, I did not. But I believed..." > ---Matrix III > > ? ? ? ?[[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 >
ADD REPLYlink written 10.2 years ago by Sean Davis21k
Thanks for all advice! Last time, I upgrade from 2.5 to 2.6, I remember it works in that way; maybe this time, there is some change. I want to make sure of my understanding, so if I follow Martin's suggestion, each time I upgrade my R, those 3 lines of codes can help me re- install all of my previous packages? I checked some previous posts and it seems that there is some other way since I have too many packages installed and re-installation might take really long time... Any suggestion about a quick re-installation? On Thu, Oct 1, 2009 at 2:10 AM, Sean Davis <seandavi@gmail.com> wrote: > On Wed, Sep 30, 2009 at 2:07 PM, Weiwei Shi <helprhelp@gmail.com> wrote: > > Actually both 3 and 5 method work. > > > > I found that issue too. It could be because the upgrade since to save my > > previous packages, I just copy my previous packages from > > Library/Framework/R.framework/.../2.6/resources/library to 2.9's library. > Do > > you think that cause the problem? > > You shouldn't do that, and that is likely the cause of at least parts > of the problem. > > > I did not reinstall base bioconductor base packages, let me try that too. > > Each time you re-install a new version of R, it is best to reinstall > all packages, in general, preferably using biocLite(). > > > The machine I am using is Macbook Pro, 2.2 GHz 4GB..., and OSX 10.5.5 > > > > thanks, > > > > Weiwei > > > > On Thu, Oct 1, 2009 at 1:59 AM, Steve Lianoglou < > > mailinglist.honeypot@gmail.com> wrote: > > > >> Hi, > >> > >> On Sep 30, 2009, at 1:53 PM, Weiwei Shi wrote: > >> > >> The installation seems to work now but the loading got some error... > >>> > >> > >> 1. What did you do to get the install to work? > >> > >> 2. It actually seems like your problems aren't really with the lumi > package > >> since it looks like you're having problems with some compiled code, > given > >> the bus error. As far as I can see lumi has no compiled code, which just > >> means to say I think we should be trying to debug "greater" issues. > >> > >> After you installed your new R (2.9.2), you reinstalled your base > >> bioconductor base packages, right? > >> > >> 3. Out of curiosity, what kind of machine are you running on? > >> > >> -steve > >> > >> > >> > >>> > >>> > library(lumi) > >>> Loading required package: annotate > >>> 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: AnnotationDbi > >>> Loading required package: DBI > >>> Loading required package: RSQLite > >>> Loading required package: xtable > >>> Loading required package: affy > >>> Loading required package: affyio > >>> Loading required package: preprocessCore > >>> > >>> *** caught bus error *** > >>> address 0xc, cause 'non-existent physical address' > >>> > >>> Traceback: > >>> 1: dyn.load(file, DLLpath = DLLpath, ...) > >>> 2: library.dynam("preprocessCore", pkgname, libname, now = FALSE) > >>> 3: f(libname, pkgname) > >>> 4: firstlib(which.lib.loc, package) > >>> 5: doTryCatch(return(expr), name, parentenv, handler) > >>> 6: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > >>> 7: tryCatchList(expr, classes, parentenv, handlers) > >>> 8: tryCatch(expr, error = function(e) { call <- conditionCall(e) > if > >>> (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) > >>> call <- sys.call(-4L) dcall <- deparse(call)[1L] > >>> prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg > <- > >>> conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] if > (14L + > >>> nchar(dcall, type = "w") + nchar(sm[1L], type = "w") > > LONG) > >>> prefix <- paste(prefix, "\n ", sep = "") } else prefix > <- > >>> "Error : " msg <- paste(prefix, conditionMessage(e), "\n", sep = "") > >>> .Internal(seterrmessage(msg[1L])) if (!silent && > >>> identical(getOption("show.error.messages"), TRUE)) { > cat(msg, > >>> file = stderr()) .Internal(printDeferredWarnings()) } > >>> invisible(structure(msg, class = "try-error"))}) > >>> 9: try(firstlib(which.lib.loc, package)) > >>> 10: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc > = > >>> lib.loc) > >>> 11: .getRequiredPackages2(pkgInfo) > >>> 12: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc > = > >>> lib.loc) > >>> 13: .getRequiredPackages2(pkgInfo) > >>> 14: library(lumi) > >>> > >>> Possible actions: > >>> 1: abort (with core dump, if enabled) > >>> 2: normal R exit > >>> 3: exit R without saving workspace > >>> 4: exit R saving workspace > >>> Selection: > >>> > >>> > >>> > >>> On Thu, Oct 1, 2009 at 1:37 AM, Steve Lianoglou < > >>> mailinglist.honeypot@gmail.com> wrote: > >>> Hi, > >>> > >>> Wow ... weird: > >>> > >>> > >>> On Sep 30, 2009, at 1:25 PM, Weiwei Shi wrote: > >>> > >>> still not works. > >>> > >>> > source("http://www.bioconductor.org/biocLite.R") > >>> > biocLite("lumi") > >>> Using R version 2.9.2, biocinstall version 2.4.12. > >>> Installing Bioconductor version 2.4 packages: > >>> [1] "lumi" > >>> Please wait... > >>> > >>> Warning: unable to access index for repository > >>> > http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/contr ib/2.9 > >>> trying URL 'http://bioconductor.org/packages/2.4/bioc/bin/macosx/ > >>> universal/contrib/2.9/lumi_1.10.2.tgz' > >>> Content type 'application/x-gzip' length 7082922 bytes (6.8 Mb) > >>> opened URL > >>> ================================================== > >>> downloaded 6.8 Mb > >>> > >>> tar: Skipping to next header > >>> tar: Archive contains obsolescent base-64 headers > >>> > >>> gzip: stdin: invalid compressed data--crc error > >>> > >>> I'm not sure why this is happening, but it looks like it can't > uncompress > >>> the downloaded tar correctly ... installing from both within R (via > >>> biocLite) and from the command line is working for me. > >>> > >>> Someone will likely have a better idea, but in the meantime, can you > try > >>> to install the package from the command line? Like so: > >>> > >>> 1. Open Terminal.app > >>> > >>> 2. Download the package: > >>> $ curl -O > >>> > http://bioconductor.org/packages/2.4/bioc/bin/macosx/universal/contr ib/2.9/lumi_1.10.2.tgz > >>> > >>> 3. Install into R > >>> $ R CMD INSTALL lumi_1.10.2.tgz > >>> > >>> Is it still breaking? If so, continue to 4, otherwise celebrate. > >>> > >>> 4. Can you you simply uncompress that file? eg. does this uncompress > >>> successfully? (From within Terminal, we're not in R) > >>> $ tar xvfz lumi_1.10.2.tgz > >>> > >>> 5. If that works, try to install the uncompressed file (it expanded to > a > >>> "lumi" directory), but first remove the lumi*.tgz > >>> > >>> $ rm lumi_1.10.2.tgz > >>> $ R CMD INSTALL lumi > >>> > >>> Anything? > >>> > >>> > >>> -steve > >>> > >>> -- > >>> Steve Lianoglou > >>> Graduate Student: Computational Systems Biology > >>> | Memorial Sloan-Kettering Cancer Center > >>> | Weill Medical College of Cornell University > >>> Contact Info: http://cbio.mskcc.org/~lianos/contact<http: cbio.="" mskcc.org="" %7elianos="" contact=""> > <http: cbio.mskcc.org="" %7elianos="" contact=""> > >>> > >>> > >>> > >>> > >>> -- > >>> Weiwei Shi, Ph.D > >>> Research Scientist > >>> GeneGO, Inc. > >>> > >>> "Did you always know?" > >>> "No, I did not. But I believed..." > >>> ---Matrix III > >>> > >> > >> -- > >> Steve Lianoglou > >> Graduate Student: Computational Systems Biology > >> | Memorial Sloan-Kettering Cancer Center > >> | Weill Medical College of Cornell University > >> Contact Info: http://cbio.mskcc.org/~lianos/contact<http: cbio.m="" skcc.org="" %7elianos="" contact=""> > <http: cbio.mskcc.org="" %7elianos="" contact=""> > >> > >> > > > > > > -- > > Weiwei Shi, Ph.D > > Research Scientist > > GeneGO, Inc. > > > > "Did you always know?" > > "No, I did not. But I believed..." > > ---Matrix III > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III [[alternative HTML version deleted]]
ADD REPLYlink written 10.2 years ago by Weiwei Shi1.2k
I like Florian's solution (sometime earlier this year, which I post here a somewhat differently): - before installing the new R: writeLines(installed.packages()[,1], con="~/packages.dump") - install R packs <- readLines("~/packages.dump") biocLite(packs) b On Sep 30, 2009, at 3:15 PM, Weiwei Shi wrote: > Thanks for all advice! > > Last time, I upgrade from 2.5 to 2.6, I remember it works in that > way; maybe > this time, there is some change. > > I want to make sure of my understanding, so if I follow Martin's > suggestion, > each time I upgrade my R, those 3 lines of codes can help me re- > install all > of my previous packages? > > I checked some previous posts and it seems that there is some other > way > since I have too many packages installed and re-installation might > take > really long time... > > Any suggestion about a quick re-installation? > > On Thu, Oct 1, 2009 at 2:10 AM, Sean Davis <seandavi at="" gmail.com=""> wrote: > >> On Wed, Sep 30, 2009 at 2:07 PM, Weiwei Shi <helprhelp at="" gmail.com=""> >> wrote: >>> Actually both 3 and 5 method work. >>> >>> I found that issue too. It could be because the upgrade since to >>> save my >>> previous packages, I just copy my previous packages from >>> Library/Framework/R.framework/.../2.6/resources/library to 2.9's >>> library. >> Do >>> you think that cause the problem? >> >> You shouldn't do that, and that is likely the cause of at least parts >> of the problem. >> >>> I did not reinstall base bioconductor base packages, let me try >>> that too. >> >> Each time you re-install a new version of R, it is best to reinstall >> all packages, in general, preferably using biocLite(). >> >>> The machine I am using is Macbook Pro, 2.2 GHz 4GB..., and OSX >>> 10.5.5 >>> >>> thanks, >>> >>> Weiwei >>> >>> On Thu, Oct 1, 2009 at 1:59 AM, Steve Lianoglou < >>> mailinglist.honeypot at gmail.com> wrote: >>> >>>> Hi, >>>> >>>> On Sep 30, 2009, at 1:53 PM, Weiwei Shi wrote: >>>> >>>> The installation seems to work now but the loading got some >>>> error... >>>>> >>>> >>>> 1. What did you do to get the install to work? >>>> >>>> 2. It actually seems like your problems aren't really with the lumi >> package >>>> since it looks like you're having problems with some compiled code, >> given >>>> the bus error. As far as I can see lumi has no compiled code, >>>> which just >>>> means to say I think we should be trying to debug "greater" issues. >>>> >>>> After you installed your new R (2.9.2), you reinstalled your base >>>> bioconductor base packages, right? >>>> >>>> 3. Out of curiosity, what kind of machine are you running on? >>>> >>>> -steve >>>> >>>> >>>> >>>>> >>>>>> library(lumi) >>>>> Loading required package: annotate >>>>> 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: AnnotationDbi >>>>> Loading required package: DBI >>>>> Loading required package: RSQLite >>>>> Loading required package: xtable >>>>> Loading required package: affy >>>>> Loading required package: affyio >>>>> Loading required package: preprocessCore >>>>> >>>>> *** caught bus error *** >>>>> address 0xc, cause 'non-existent physical address' >>>>> >>>>> Traceback: >>>>> 1: dyn.load(file, DLLpath = DLLpath, ...) >>>>> 2: library.dynam("preprocessCore", pkgname, libname, now = FALSE) >>>>> 3: f(libname, pkgname) >>>>> 4: firstlib(which.lib.loc, package) >>>>> 5: doTryCatch(return(expr), name, parentenv, handler) >>>>> 6: tryCatchOne(expr, names, parentenv, handlers[[1L]]) >>>>> 7: tryCatchList(expr, classes, parentenv, handlers) >>>>> 8: tryCatch(expr, error = function(e) { call <- >>>>> conditionCall(e) >> if >>>>> (!is.null(call)) { if (identical(call[[1L]], >>>>> quote(doTryCatch))) >>>>> call <- sys.call(-4L) dcall <- deparse(call)[1L] >>>>> prefix <- paste("Error in", dcall, ": ") LONG <- >>>>> 75L msg >> <- >>>>> conditionMessage(e) sm <- strsplit(msg, "\n") >>>>> [[1L]] if >> (14L + >>>>> nchar(dcall, type = "w") + nchar(sm[1L], type = "w") > >> LONG) >>>>> prefix <- paste(prefix, "\n ", sep = "") } else >>>>> prefix >> <- >>>>> "Error : " msg <- paste(prefix, conditionMessage(e), "\n", >>>>> sep = "") >>>>> .Internal(seterrmessage(msg[1L])) if (!silent && >>>>> identical(getOption("show.error.messages"), TRUE)) { >> cat(msg, >>>>> file = stderr()) .Internal(printDeferredWarnings()) } >>>>> invisible(structure(msg, class = "try-error"))}) >>>>> 9: try(firstlib(which.lib.loc, package)) >>>>> 10: library(pkg, character.only = TRUE, logical.return = TRUE, >>>>> lib.loc >> = >>>>> lib.loc) >>>>> 11: .getRequiredPackages2(pkgInfo) >>>>> 12: library(pkg, character.only = TRUE, logical.return = TRUE, >>>>> lib.loc >> = >>>>> lib.loc) >>>>> 13: .getRequiredPackages2(pkgInfo) >>>>> 14: library(lumi) >>>>> >>>>> Possible actions: >>>>> 1: abort (with core dump, if enabled) >>>>> 2: normal R exit >>>>> 3: exit R without saving workspace >>>>> 4: exit R saving workspace >>>>> Selection: >>>>> >>>>> >>>>> >>>>> On Thu, Oct 1, 2009 at 1:37 AM, Steve Lianoglou < >>>>> mailinglist.honeypot at gmail.com> wrote: >>>>> Hi, >>>>> >>>>> Wow ... weird: >>>>> >>>>> >>>>> On Sep 30, 2009, at 1:25 PM, Weiwei Shi wrote: >>>>> >>>>> still not works. >>>>> >>>>>> source("http://www.bioconductor.org/biocLite.R") >>>>>> biocLite("lumi") >>>>> Using R version 2.9.2, biocinstall version 2.4.12. >>>>> Installing Bioconductor version 2.4 packages: >>>>> [1] "lumi" >>>>> Please wait... >>>>> >>>>> Warning: unable to access index for repository >>>>> >> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/universal/cont rib/2.9 >>>>> trying URL 'http://bioconductor.org/packages/2.4/bioc/bin/macosx/ >>>>> universal/contrib/2.9/lumi_1.10.2.tgz' >>>>> Content type 'application/x-gzip' length 7082922 bytes (6.8 Mb) >>>>> opened URL >>>>> ================================================== >>>>> downloaded 6.8 Mb >>>>> >>>>> tar: Skipping to next header >>>>> tar: Archive contains obsolescent base-64 headers >>>>> >>>>> gzip: stdin: invalid compressed data--crc error >>>>> >>>>> I'm not sure why this is happening, but it looks like it can't >> uncompress >>>>> the downloaded tar correctly ... installing from both within R >>>>> (via >>>>> biocLite) and from the command line is working for me. >>>>> >>>>> Someone will likely have a better idea, but in the meantime, can >>>>> you >> try >>>>> to install the package from the command line? Like so: >>>>> >>>>> 1. Open Terminal.app >>>>> >>>>> 2. Download the package: >>>>> $ curl -O >>>>> >> http://bioconductor.org/packages/2.4/bioc/bin/macosx/universal/cont rib/2.9/lumi_1.10.2.tgz >>>>> >>>>> 3. Install into R >>>>> $ R CMD INSTALL lumi_1.10.2.tgz >>>>> >>>>> Is it still breaking? If so, continue to 4, otherwise celebrate. >>>>> >>>>> 4. Can you you simply uncompress that file? eg. does this >>>>> uncompress >>>>> successfully? (From within Terminal, we're not in R) >>>>> $ tar xvfz lumi_1.10.2.tgz >>>>> >>>>> 5. If that works, try to install the uncompressed file (it >>>>> expanded to >> a >>>>> "lumi" directory), but first remove the lumi*.tgz >>>>> >>>>> $ rm lumi_1.10.2.tgz >>>>> $ R CMD INSTALL lumi >>>>> >>>>> Anything? >>>>> >>>>> >>>>> -steve >>>>> >>>>> -- >>>>> Steve Lianoglou >>>>> Graduate Student: Computational Systems Biology >>>>> | Memorial Sloan-Kettering Cancer Center >>>>> | Weill Medical College of Cornell University >>>>> Contact Info: http://cbio.mskcc.org/~lianos/contact<http: cbio.="" mskcc.org="" %7elianos="" contact="">>>>> > >> <http: cbio.mskcc.org="" %7elianos="" contact=""> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Weiwei Shi, Ph.D >>>>> Research Scientist >>>>> GeneGO, Inc. >>>>> >>>>> "Did you always know?" >>>>> "No, I did not. But I believed..." >>>>> ---Matrix III >>>>> >>>> >>>> -- >>>> Steve Lianoglou >>>> Graduate Student: Computational Systems Biology >>>> | Memorial Sloan-Kettering Cancer Center >>>> | Weill Medical College of Cornell University >>>> Contact Info: http://cbio.mskcc.org/~lianos/contact<http: cbio.m="" skcc.org="" %7elianos="" contact="">>>> > >> <http: cbio.mskcc.org="" %7elianos="" contact=""> >>>> >>>> >>> >>> >>> -- >>> Weiwei Shi, Ph.D >>> Research Scientist >>> GeneGO, Inc. >>> >>> "Did you always know?" >>> "No, I did not. But I believed..." >>> ---Matrix III >>> >>> [[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 >>> >> > > > > -- > Weiwei Shi, Ph.D > Research Scientist > GeneGO, Inc. > > "Did you always know?" > "No, I did not. But I believed..." > ---Matrix III > > [[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
ADD REPLYlink written 10.2 years ago by Benilton Carvalho4.3k
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