load failed for 'Rlibstree'
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Paul Shannon ★ 1.1k
@paul-shannon-578
Last seen 10.2 years ago
While working my way through the rtracklayer pdf, I get stuck when library (microRNA) tries to load Rlibstree, with this error message: Loading required package: Rlibstree Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/Library/Frameworks/R.framework/Res ources/library/Rlibstree/libs/x86_64/Rlibstree.so': dlopen(/Library/Frameworks/R.framework/Resources/library/Rlibstree /libs/x86_64/Rlibstree.so, 6): Symbol not found: _lst_alg_longest_repeated_substring Referenced from: /Library/Frameworks/R.framework/Resources/library/ Rlibstree/libs/x86_64/Rlibstree.so Expected in: dynamic lookup Error: package 'Rlibstree' could not be loaded The package is installed (version 0.3-2) on my OS X 10.6.3 MacBook. Any suggestions? SessionInfo follows. Thanks - - Paul sessionInfo () R version 2.10.1 (2009-12-14) x86_64-apple-darwin9.8.0 locale: [1] 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] Biostrings_2.14.12 IRanges_1.4.8 limma_3.2.1 genefilter_1.28.2 humanStemCell_0.2.3 hgu133plus2.db_2.3.5 org.Hs.eg.db_2.3.6 [8] RSQLite_0.7-3 DBI_0.2-4 AnnotationDbi_1.8.0 Biobase_2.6.1 rtracklayer_1.6.0 RCurl_1.2-0 bitops_1.0-4.1 [15] RUnit_0.4.22 loaded via a namespace (and not attached): [1] annotate_1.24.1 BSgenome_1.14.2 splines_2.10.1 survival_2.35-8 tools_2.10.1 XML_2.6-0 xtable_1.5-6
hgu133plus2 rtracklayer hgu133plus2 rtracklayer • 1.7k views
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 10.2 years ago
Hi Paul, On 4/8/10 10:21 AM, Paul Shannon wrote: > While working my way through the rtracklayer pdf, I get stuck when > > library (microRNA) > > tries to load Rlibstree, with this error message: > > Loading required package: Rlibstree > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared library '/Library/Frameworks/R.framework/ Resources/library/Rlibstree/libs/x86_64/Rlibstree.so': > dlopen(/Library/Frameworks/R.framework/Resources/library/Rlibst ree/libs/x86_64/Rlibstree.so, 6): Symbol not found: _lst_alg_longest_repeated_substring > Referenced from: /Library/Frameworks/R.framework/Resources/libra ry/Rlibstree/libs/x86_64/Rlibstree.so > Expected in: dynamic lookup > > Error: package 'Rlibstree' could not be loaded > > The package is installed (version 0.3-2) on my OS X 10.6.3 MacBook. > > Any suggestions? SessionInfo follows. Have you tried reinstalling? I just did biocLite(c("microRNA", "Rlibstree")) And both packages load fine on my Mac where I'm building packages from source. + seth -- Seth Falcon Bioconductor Core Team | FHCRC
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Hi Paul, Seth Falcon wrote: > Hi Paul, > > On 4/8/10 10:21 AM, Paul Shannon wrote: >> While working my way through the rtracklayer pdf, I get stuck when >> >> library (microRNA) >> >> tries to load Rlibstree, with this error message: >> >> Loading required package: Rlibstree >> Error in dyn.load(file, DLLpath = DLLpath, ...) : >> unable to load shared library >> '/Library/Frameworks/R.framework/Resources/library/Rlibstree/libs/x 86_64/Rlibstree.so': >> >> >> dlopen(/Library/Frameworks/R.framework/Resources/library/Rlibstree/ libs/x86_64/Rlibstree.so, >> 6): Symbol not found: _lst_alg_longest_repeated_substring >> Referenced from: >> /Library/Frameworks/R.framework/Resources/library/Rlibstree/libs/x8 6_64/Rlibstree.so >> >> Expected in: dynamic lookup >> >> Error: package 'Rlibstree' could not be loaded >> >> The package is installed (version 0.3-2) on my OS X 10.6.3 MacBook. Mmmh, isn't 10.6 the OS version for Snow Leopard? What output is getOption("pkgType") giving you? I suspect it is "mac.binary.leopard", which means that you are installing the binaries we are producing for OS X 10.5 (Leopard). Those binaries are currently built on pelham (Mac OS X Leopard (10.5.8)): http://bioconductor.org/checkResults/2.5/bioc-LATEST/pelham- index.html and some of them are apparently not compatible with Snow Leopard. The good news is that we have plans to start building binaries for Snow Leopard in the near future (we recently purchased new hardware for this). >> >> Any suggestions? SessionInfo follows. > > Have you tried reinstalling? I just did > > biocLite(c("microRNA", "Rlibstree")) > > And both packages load fine on my Mac where I'm building packages from > source. Yep. Installing from source will solve the problem in the mean time. Cheers, H. > > + seth > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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Herve & Seth, Thanks for your replies. Yes, it must be the snow leopard binary problem. I've tried biocLite (c ('microRNA', 'Rlibstree')) a few times, always with the same problem. I should know this, but don't: what's the best way to install from source? An option or argument provided to install.packages? (I have been spoiled by the binary packages you provide...) - Paul On Apr 8, 2010, at 12:44 PM, Hervé Pagès wrote: > Hi Paul, > > Seth Falcon wrote: >> Hi Paul, >> On 4/8/10 10:21 AM, Paul Shannon wrote: >>> While working my way through the rtracklayer pdf, I get stuck when >>> >>> library (microRNA) >>> >>> tries to load Rlibstree, with this error message: >>> >>> Loading required package: Rlibstree >>> Error in dyn.load(file, DLLpath = DLLpath, ...) : >>> unable to load shared library '/Library/Frameworks/R.framework /Resources/library/Rlibstree/libs/x86_64/Rlibstree.so': >>> dlopen(/Library/Frameworks/R.framework/Resources/library/Rlibs tree/libs/x86_64/Rlibstree.so, 6): Symbol not found: _lst_alg_longest_repeated_substring >>> Referenced from: /Library/Frameworks/R.framework/Resources/libr ary/Rlibstree/libs/x86_64/Rlibstree.so >>> Expected in: dynamic lookup >>> >>> Error: package 'Rlibstree' could not be loaded >>> >>> The package is installed (version 0.3-2) on my OS X 10.6.3 MacBook. > > Mmmh, isn't 10.6 the OS version for Snow Leopard? What output > is getOption("pkgType") giving you? > I suspect it is "mac.binary.leopard", which means that you are > installing the binaries we are producing for OS X 10.5 (Leopard). > Those binaries are currently built on pelham (Mac OS X Leopard > (10.5.8)): > http://bioconductor.org/checkResults/2.5/bioc-LATEST/pelham- index.html > and some of them are apparently not compatible with Snow Leopard. > > The good news is that we have plans to start building binaries for > Snow Leopard in the near future (we recently purchased new hardware > for this). > >>> >>> Any suggestions? SessionInfo follows. >> Have you tried reinstalling? I just did >> biocLite(c("microRNA", "Rlibstree")) >> And both packages load fine on my Mac where I'm building packages from source. > > Yep. Installing from source will solve the problem in the mean time. > > Cheers, > H. > >> + seth > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages at fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319
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Paul Shannon wrote: > Herve & Seth, > > Thanks for your replies. Yes, it must be the snow leopard binary problem. > > I've tried biocLite (c ('microRNA', 'Rlibstree')) a few times, always with the same problem. > > I should know this, but don't: what's the best way to install from source? An option or argument provided to install.packages? biocLite() accepts the same extra args than install.packages(): biocLite(..., type="source") See ?install.packages for more information. Now of course this requires that you have Xcode installed on your machine. The primary source of information for installing source packages on Mac OS X is Section 5.3 of the "R for Mac OS X FAQ": http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html Cheers, H. > > (I have been spoiled by the binary packages you provide...) > > - Paul > > > On Apr 8, 2010, at 12:44 PM, Hervé Pagès wrote: > >> Hi Paul, >> >> Seth Falcon wrote: >>> Hi Paul, >>> On 4/8/10 10:21 AM, Paul Shannon wrote: >>>> While working my way through the rtracklayer pdf, I get stuck when >>>> >>>> library (microRNA) >>>> >>>> tries to load Rlibstree, with this error message: >>>> >>>> Loading required package: Rlibstree >>>> Error in dyn.load(file, DLLpath = DLLpath, ...) : >>>> unable to load shared library '/Library/Frameworks/R.framewor k/Resources/library/Rlibstree/libs/x86_64/Rlibstree.so': >>>> dlopen(/Library/Frameworks/R.framework/Resources/library/Rlib stree/libs/x86_64/Rlibstree.so, 6): Symbol not found: _lst_alg_longest_repeated_substring >>>> Referenced from: /Library/Frameworks/R.framework/Resources/lib rary/Rlibstree/libs/x86_64/Rlibstree.so >>>> Expected in: dynamic lookup >>>> >>>> Error: package 'Rlibstree' could not be loaded >>>> >>>> The package is installed (version 0.3-2) on my OS X 10.6.3 MacBook. >> Mmmh, isn't 10.6 the OS version for Snow Leopard? What output >> is getOption("pkgType") giving you? >> I suspect it is "mac.binary.leopard", which means that you are >> installing the binaries we are producing for OS X 10.5 (Leopard). >> Those binaries are currently built on pelham (Mac OS X Leopard >> (10.5.8)): >> http://bioconductor.org/checkResults/2.5/bioc-LATEST/pelham- index.html >> and some of them are apparently not compatible with Snow Leopard. >> >> The good news is that we have plans to start building binaries for >> Snow Leopard in the near future (we recently purchased new hardware >> for this). >> >>>> Any suggestions? SessionInfo follows. >>> Have you tried reinstalling? I just did >>> biocLite(c("microRNA", "Rlibstree")) >>> And both packages load fine on my Mac where I'm building packages from source. >> Yep. Installing from source will solve the problem in the mean time. >> >> Cheers, >> H. >> >>> + seth >> -- >> Hervé Pagès >> >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, M2-B876 >> P.O. Box 19024 >> Seattle, WA 98109-1024 >> >> E-mail: hpages at fhcrc.org >> Phone: (206) 667-5791 >> Fax: (206) 667-1319 > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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Hi Paul, 2010/4/8 Paul Shannon <pshannon@systemsbiology.org> > Herve & Seth, > > Thanks for your replies. Yes, it must be the snow leopard binary problem. > > I've tried biocLite (c ('microRNA', 'Rlibstree')) a few times, always with > the same problem. > > I should know this, but don't: what's the best way to install from source? > An option or argument provided to install.packages? > > try biocLite(c(microRNA, Rlibstree), type="source") make sure you install the proper compilers from the Install DVD (in XCode tools) > (I have been spoiled by the binary packages you provide...) > > - Paul > > > On Apr 8, 2010, at 12:44 PM, Hervé Pagès wrote: > > > Hi Paul, > > > > Seth Falcon wrote: > >> Hi Paul, > >> On 4/8/10 10:21 AM, Paul Shannon wrote: > >>> While working my way through the rtracklayer pdf, I get stuck when > >>> > >>> library (microRNA) > >>> > >>> tries to load Rlibstree, with this error message: > >>> > >>> Loading required package: Rlibstree > >>> Error in dyn.load(file, DLLpath = DLLpath, ...) : > >>> unable to load shared library > '/Library/Frameworks/R.framework/Resources/library/Rlibstree/libs/x8 6_64/Rlibstree.so': > >>> > dlopen(/Library/Frameworks/R.framework/Resources/library/Rlibstree/l ibs/x86_64/Rlibstree.so, > 6): Symbol not found: _lst_alg_longest_repeated_substring > >>> Referenced from: > /Library/Frameworks/R.framework/Resources/library/Rlibstree/libs/x86 _64/Rlibstree.so > >>> Expected in: dynamic lookup > >>> > >>> Error: package 'Rlibstree' could not be loaded > >>> > >>> The package is installed (version 0.3-2) on my OS X 10.6.3 MacBook. > > > > Mmmh, isn't 10.6 the OS version for Snow Leopard? What output > > is getOption("pkgType") giving you? > > I suspect it is "mac.binary.leopard", which means that you are > > installing the binaries we are producing for OS X 10.5 (Leopard). > > Those binaries are currently built on pelham (Mac OS X Leopard > > (10.5.8)): > > http://bioconductor.org/checkResults/2.5/bioc-LATEST/pelham- index.html > > and some of them are apparently not compatible with Snow Leopard. > > > > The good news is that we have plans to start building binaries for > > Snow Leopard in the near future (we recently purchased new hardware > > for this). > > > >>> > >>> Any suggestions? SessionInfo follows. > >> Have you tried reinstalling? I just did > >> biocLite(c("microRNA", "Rlibstree")) > >> And both packages load fine on my Mac where I'm building packages from > source. > > > > Yep. Installing from source will solve the problem in the mean time. > > > > Cheers, > > H. > > > >> + seth > > > > -- > > Hervé Pagès > > > > Program in Computational Biology > > Division of Public Health Sciences > > Fred Hutchinson Cancer Research Center > > 1100 Fairview Ave. N, M2-B876 > > P.O. Box 19024 > > Seattle, WA 98109-1024 > > > > E-mail: hpages@fhcrc.org > > Phone: (206) 667-5791 > > Fax: (206) 667-1319 > > _______________________________________________ > 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 > [[alternative HTML version deleted]]
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biocLite (c ("microRNA", "Rlibstree"), type='source') worked like a charm! Thanks you all! - Paul On Apr 8, 2010, at 1:37 PM, Tony Chiang wrote: > Hi Paul, > > 2010/4/8 Paul Shannon <pshannon at="" systemsbiology.org=""> > Herve & Seth, > > Thanks for your replies. Yes, it must be the snow leopard binary problem. > > I've tried biocLite (c ('microRNA', 'Rlibstree')) a few times, always with the same problem. > > I should know this, but don't: what's the best way to install from source? An option or argument provided to install.packages? > > > try biocLite(c(microRNA, Rlibstree), type="source") > > make sure you install the proper compilers from the Install DVD (in XCode tools) > > (I have been spoiled by the binary packages you provide...) > > - Paul > > > On Apr 8, 2010, at 12:44 PM, Hervé Pagès wrote: > > > Hi Paul, > > > > Seth Falcon wrote: > >> Hi Paul, > >> On 4/8/10 10:21 AM, Paul Shannon wrote: > >>> While working my way through the rtracklayer pdf, I get stuck when > >>> > >>> library (microRNA) > >>> > >>> tries to load Rlibstree, with this error message: > >>> > >>> Loading required package: Rlibstree > >>> Error in dyn.load(file, DLLpath = DLLpath, ...) : > >>> unable to load shared library '/Library/Frameworks/R.framewo rk/Resources/library/Rlibstree/libs/x86_64/Rlibstree.so': > >>> dlopen(/Library/Frameworks/R.framework/Resources/library/Rli bstree/libs/x86_64/Rlibstree.so, 6): Symbol not found: _lst_alg_longest_repeated_substring > >>> Referenced from: /Library/Frameworks/R.framework/Resources/li brary/Rlibstree/libs/x86_64/Rlibstree.so > >>> Expected in: dynamic lookup > >>> > >>> Error: package 'Rlibstree' could not be loaded > >>> > >>> The package is installed (version 0.3-2) on my OS X 10.6.3 MacBook. > > > > Mmmh, isn't 10.6 the OS version for Snow Leopard? What output > > is getOption("pkgType") giving you? > > I suspect it is "mac.binary.leopard", which means that you are > > installing the binaries we are producing for OS X 10.5 (Leopard). > > Those binaries are currently built on pelham (Mac OS X Leopard > > (10.5.8)): > > http://bioconductor.org/checkResults/2.5/bioc-LATEST/pelham- index.html > > and some of them are apparently not compatible with Snow Leopard. > > > > The good news is that we have plans to start building binaries for > > Snow Leopard in the near future (we recently purchased new hardware > > for this). > > > >>> > >>> Any suggestions? SessionInfo follows. > >> Have you tried reinstalling? I just did > >> biocLite(c("microRNA", "Rlibstree")) > >> And both packages load fine on my Mac where I'm building packages from source. > > > > Yep. Installing from source will solve the problem in the mean time. > > > > Cheers, > > H. > > > >> + seth > > > > -- > > Hervé Pagès > > > > Program in Computational Biology > > Division of Public Health Sciences > > Fred Hutchinson Cancer Research Center > > 1100 Fairview Ave. N, M2-B876 > > P.O. Box 19024 > > Seattle, WA 98109-1024 > > > > E-mail: hpages at fhcrc.org > > Phone: (206) 667-5791 > > Fax: (206) 667-1319 > > _______________________________________________ > 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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