Question: ArrayExpressHTS fails to load
0
gravatar for Sean Rogers
8.0 years ago by
Sean Rogers10
Sean Rogers10 wrote:
Hello, I have recently installed the package ArrayExpressHTS. However it fails to load into R. Could someone tell me if this is something I can fix or is it perhaps a conflict related to Mac OS X Lion? Thanks for your help/suggestions. Regards Sean A. Rogers Ph. D. Research Associate, Department of Horticulture Michigan State University East Lansing, Michigan USA 48824 library("ArrayExpressHTS") Loading required package: sampling Loading required package: MASS Loading required package: lpSolve Loading required package: Rsamtools Loading required package: IRanges Attaching package: 'IRanges' The following object(s) are masked from 'package:base': Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, setdiff, table, union Loading required package: GenomicRanges Loading required package: Biostrings Loading required package: snow Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/ ArrayExpressHTS/libs/x86_64/ArrayExpressHTS.so': dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/libra ry/ ArrayExpressHTS/libs/x86_64/ArrayExpressHTS.so, 6): Symbol not found: _bam_aux2i Referenced from: /Library/Frameworks/R.framework/Versions/2.13/Resources/library/ ArrayExpressHTS/libs/x86_64/ArrayExpressHTS.so Expected in: dynamic lookup Error: package/namespace load failed for 'ArrayExpressHTS' sessionInfo() R version 2.13.2 (2011-09-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C/en_US.UTF-8/C/C/C/C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] snow_0.3-7 Rsamtools_1.4.3 Biostrings_2.20.4 [4] GenomicRanges_1.4.8 IRanges_1.10.6 sampling_2.4 [7] lpSolve_5.6.6 MASS_7.3-14 loaded via a namespace (and not attached): [1] AnnotationDbi_1.14.1 Biobase_2.12.2 DBI_0.2-5 ... [25] svMisc_0.9-63 tools_2.13.2 xtable_1.6-0
arrayexpresshts • 562 views
ADD COMMENTlink modified 8.0 years ago by Dan Tenenbaum8.2k • written 8.0 years ago by Sean Rogers10
Answer: ArrayExpressHTS fails to load
0
gravatar for Dan Tenenbaum
8.0 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
Hi Sean, On Tue, Oct 18, 2011 at 7:45 AM, Sean Rogers <srogers at="" msu.edu=""> wrote: > Hello, > > I have recently installed the package ArrayExpressHTS. However it fails > to load into R. Could someone tell me if this is something I can fix or > is it perhaps a conflict related to Mac OS X Lion? > > Thanks for your help/suggestions. > Regards > > Sean A. Rogers Ph. D. > > Research Associate, Department of Horticulture > Michigan State University > East Lansing, Michigan USA 48824 > > library("ArrayExpressHTS") > Loading required package: sampling > Loading required package: MASS > Loading required package: lpSolve > Loading required package: Rsamtools > Loading required package: IRanges > > Attaching package: 'IRanges' > > The following object(s) are masked from 'package:base': > > ? ?Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int, > ? ?pmin, pmin.int, rbind, rep.int, setdiff, table, union > > Loading required package: GenomicRanges > Loading required package: Biostrings > Loading required package: snow > Error in dyn.load(file, DLLpath = DLLpath, ...) : > ?unable to load shared object > '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/ > ArrayExpressHTS/libs/x86_64/ArrayExpressHTS.so': > ?dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/libr ary/ > ArrayExpressHTS/libs/x86_64/ArrayExpressHTS.so, 6): Symbol not found: _bam_aux2i > ?Referenced from: /Library/Frameworks/R.framework/Versions/2.13/Resources/library/ > ArrayExpressHTS/libs/x86_64/ArrayExpressHTS.so > ?Expected in: dynamic lookup > > Error: package/namespace load failed for 'ArrayExpressHTS' > It looks like there is a problem with the way this package is built, there are some build errors here that do not show up as a failure in our build report: http://bioconductor.org/checkResults/release/bioc- LATEST/ArrayExpressHTS/pelham-buildbin.html We will look into this. In the meantime, you could try: R --arch i386 The 32-bit version seems to work. Dan > > sessionInfo() > R version 2.13.2 (2011-09-30) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C/en_US.UTF-8/C/C/C/C > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] snow_0.3-7 ? ? ? ? ?Rsamtools_1.4.3 ? ? Biostrings_2.20.4 > [4] GenomicRanges_1.4.8 IRanges_1.10.6 ? ? ?sampling_2.4 > [7] lpSolve_5.6.6 ? ? ? MASS_7.3-14 > > loaded via a namespace (and not attached): > ?[1] AnnotationDbi_1.14.1 Biobase_2.12.2 ? ? ? DBI_0.2-5 > ?... > [25] svMisc_0.9-63 ? ? ? ?tools_2.13.2 ? ? ? ? xtable_1.6-0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 8.0 years ago by Dan Tenenbaum8.2k
On 10/19/2011 10:30 PM, Dan Tenenbaum wrote: > Hi Sean, > > On Tue, Oct 18, 2011 at 7:45 AM, Sean Rogers<srogers at="" msu.edu=""> wrote: >> Hello, >> >> I have recently installed the package ArrayExpressHTS. However it fails >> to load into R. Could someone tell me if this is something I can fix or >> is it perhaps a conflict related to Mac OS X Lion? >> >> Thanks for your help/suggestions. >> Regards >> >> Sean A. Rogers Ph. D. >> >> Research Associate, Department of Horticulture >> Michigan State University >> East Lansing, Michigan USA 48824 >> >> library("ArrayExpressHTS") >> Loading required package: sampling >> Loading required package: MASS >> Loading required package: lpSolve >> Loading required package: Rsamtools >> Loading required package: IRanges >> >> Attaching package: 'IRanges' >> >> The following object(s) are masked from 'package:base': >> >> Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int, >> pmin, pmin.int, rbind, rep.int, setdiff, table, union >> >> Loading required package: GenomicRanges >> Loading required package: Biostrings >> Loading required package: snow >> Error in dyn.load(file, DLLpath = DLLpath, ...) : >> unable to load shared object >> '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/ >> ArrayExpressHTS/libs/x86_64/ArrayExpressHTS.so': >> dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/li brary/ >> ArrayExpressHTS/libs/x86_64/ArrayExpressHTS.so, 6): Symbol not found: _bam_aux2i >> Referenced from: /Library/Frameworks/R.framework/Versions/2.13/Resources/library/ >> ArrayExpressHTS/libs/x86_64/ArrayExpressHTS.so >> Expected in: dynamic lookup >> >> Error: package/namespace load failed for 'ArrayExpressHTS' >> > > It looks like there is a problem with the way this package is built, > there are some build errors here that do not show up as a failure in > our build report: > http://bioconductor.org/checkResults/release/bioc- LATEST/ArrayExpressHTS/pelham-buildbin.html > > We will look into this. > > In the meantime, you could try: > > R --arch i386 > > The 32-bit version seems to work. or (untested) build packages Rsamtools and ArrayExpressHTS from source. Martin > > Dan > > >> >> sessionInfo() >> R version 2.13.2 (2011-09-30) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] C/en_US.UTF-8/C/C/C/C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] snow_0.3-7 Rsamtools_1.4.3 Biostrings_2.20.4 >> [4] GenomicRanges_1.4.8 IRanges_1.10.6 sampling_2.4 >> [7] lpSolve_5.6.6 MASS_7.3-14 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.14.1 Biobase_2.12.2 DBI_0.2-5 >> ... >> [25] svMisc_0.9-63 tools_2.13.2 xtable_1.6-0 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD REPLYlink written 8.0 years ago by Martin Morgan ♦♦ 23k
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