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Question: Weird error when installing VariantAnnotation and/or snpStats (whether from SVN or using biocLite)
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gravatar for Tim Triche
6.8 years ago by
Tim Triche4.2k
United States
Tim Triche4.2k wrote:
This is after trying to reinstall snpStats, which was the first thing I tried. That fails with the same error message ("error: argument "lib.loc" is missing, with no default") I didn't have this problem previously... should I rebuild R and see if it was some sort of a transient issue with HEAD? BiocInstaller version 1.1.28, ?biocLite for help * installing *source* package ‘VariantAnnotation’ ... ** R ** data ** inst ** preparing package for lazy loading Warning: replacing previous import ‘ls’ when loading ‘AnnotationDbi’ Error : .onLoad failed in loadNamespace() for 'snpStats', details: call: library.dynam("snpStats", package) error: argument "lib.loc" is missing, with no default ERROR: lazy loading failed for package ‘VariantAnnotation’ * removing ‘/usr/lib/R/library/VariantAnnotation’ * restoring previous ‘/usr/lib/R/library/VariantAnnotation’ Session info: > sessionInfo() R Under development (unstable) (2011-10-04 r57169) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices datasets utils methods [8] base other attached packages: [1] Rsubread_1.2.1 [2] methylumi_1.9.12 [3] matrixStats_0.2.2 [4] R.methodsS3_1.2.1 [5] MASS_7.3-15 [6] ggplot2_0.8.9 [7] proto_0.3-9.2 [8] reshape_0.8.4 [9] plyr_1.6 [10] IlluminaHumanMethylation450kprobe_1.9.12 [11] IlluminaHumanMethylation450k.db_1.4.9 [12] org.Hs.eg.db_2.6.2 [13] RSQLite_0.10.0 [14] DBI_0.2-5 [15] AnnotationDbi_1.15.29 [16] Biobase_2.13.10 [17] BiocInstaller_1.1.28 [18] gtools_2.6.2 loaded via a namespace (and not attached): [1] annotate_1.31.1 digest_0.5.1 IRanges_1.11.30 lattice_0.19-33 [5] RColorBrewer_1.0-5 tools_2.15.0 xtable_1.5-6 -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is.John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> [[alternative HTML version deleted]]
ADD COMMENTlink modified 6.8 years ago by Martin Morgan ♦♦ 22k • written 6.8 years ago by Tim Triche4.2k
0
gravatar for Martin Morgan
6.8 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:
On 10/11/2011 10:02 AM, Tim Triche, Jr. wrote: > This is after trying to reinstall snpStats, which was the first thing I > tried. That fails with the same error message ("error: argument "lib.loc" > is missing, with no default") Hi Tim -- This is a bleeding-edge issue, associated with using R-devel. The maintainer will undoubtedly address this, but if you're desperate to make progress either use R-2-14 alpha (where the 'error' is just a warning) or download the source code and edit it as: - remove zzz.R -- these paradigms aren't needed any more - edit DESCRIPTION Collate: to exclude zzz.R - edit NAMESPACE to useDynLib("snpStats") then R CMD build snpStats && R CMD INSTALL snpStats_*gz Martin > I didn't have this problem previously... should I rebuild R and see if it > was some sort of a transient issue with HEAD? > > BiocInstaller version 1.1.28, ?biocLite for help > * installing *source* package ?VariantAnnotation? ... > ** R > ** data > ** inst > ** preparing package for lazy loading > Warning: replacing previous import ?ls? when loading ?AnnotationDbi? > Error : .onLoad failed in loadNamespace() for 'snpStats', details: > call: library.dynam("snpStats", package) > error: argument "lib.loc" is missing, with no default > ERROR: lazy loading failed for package ?VariantAnnotation? > * removing ?/usr/lib/R/library/VariantAnnotation? > * restoring previous ?/usr/lib/R/library/VariantAnnotation? > > Session info: > >> sessionInfo() > R Under development (unstable) (2011-10-04 r57169) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] grid stats graphics grDevices datasets utils methods > [8] base > > other attached packages: > [1] Rsubread_1.2.1 > [2] methylumi_1.9.12 > [3] matrixStats_0.2.2 > [4] R.methodsS3_1.2.1 > [5] MASS_7.3-15 > [6] ggplot2_0.8.9 > [7] proto_0.3-9.2 > [8] reshape_0.8.4 > [9] plyr_1.6 > [10] IlluminaHumanMethylation450kprobe_1.9.12 > [11] IlluminaHumanMethylation450k.db_1.4.9 > [12] org.Hs.eg.db_2.6.2 > [13] RSQLite_0.10.0 > [14] DBI_0.2-5 > [15] AnnotationDbi_1.15.29 > [16] Biobase_2.13.10 > [17] BiocInstaller_1.1.28 > [18] gtools_2.6.2 > > loaded via a namespace (and not attached): > [1] annotate_1.31.1 digest_0.5.1 IRanges_1.11.30 lattice_0.19-33 > > [5] RColorBrewer_1.0-5 tools_2.15.0 xtable_1.5-6 > > > > > _______________________________________________ > 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 COMMENTlink written 6.8 years ago by Martin Morgan ♦♦ 22k
Cool, solved the problems. Thanks! On Tue, Oct 11, 2011 at 11:35 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 10/11/2011 10:02 AM, Tim Triche, Jr. wrote: > >> This is after trying to reinstall snpStats, which was the first thing I >> tried. That fails with the same error message ("error: argument "lib.loc" >> is missing, with no default") >> > > Hi Tim -- > > This is a bleeding-edge issue, associated with using R-devel. The > maintainer will undoubtedly address this, but if you're desperate to make > progress either use R-2-14 alpha (where the 'error' is just a warning) or > download the source code and edit it as: > > - remove zzz.R -- these paradigms aren't needed any more > - edit DESCRIPTION Collate: to exclude zzz.R > - edit NAMESPACE to useDynLib("snpStats") > > then R CMD build snpStats && R CMD INSTALL snpStats_*gz > > Martin > > I didn't have this problem previously... should I rebuild R and see if >> it >> was some sort of a transient issue with HEAD? >> >> BiocInstaller version 1.1.28, ?biocLite for help >> * installing *source* package ‘VariantAnnotation’ ... >> ** R >> ** data >> ** inst >> ** preparing package for lazy loading >> Warning: replacing previous import ‘ls’ when loading ‘AnnotationDbi’ >> Error : .onLoad failed in loadNamespace() for 'snpStats', details: >> call: library.dynam("snpStats", package) >> error: argument "lib.loc" is missing, with no default >> ERROR: lazy loading failed for package ‘VariantAnnotation’ >> * removing ‘/usr/lib/R/library/**VariantAnnotation’ >> * restoring previous ‘/usr/lib/R/library/**VariantAnnotation’ >> >> Session info: >> >> sessionInfo() >>> >> R Under development (unstable) (2011-10-04 r57169) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] grid stats graphics grDevices datasets utils methods >> [8] base >> >> other attached packages: >> [1] Rsubread_1.2.1 >> [2] methylumi_1.9.12 >> [3] matrixStats_0.2.2 >> [4] R.methodsS3_1.2.1 >> [5] MASS_7.3-15 >> [6] ggplot2_0.8.9 >> [7] proto_0.3-9.2 >> [8] reshape_0.8.4 >> [9] plyr_1.6 >> [10] IlluminaHumanMethylation450kpr**obe_1.9.12 >> [11] IlluminaHumanMethylation450k.**db_1.4.9 >> [12] org.Hs.eg.db_2.6.2 >> [13] RSQLite_0.10.0 >> [14] DBI_0.2-5 >> [15] AnnotationDbi_1.15.29 >> [16] Biobase_2.13.10 >> [17] BiocInstaller_1.1.28 >> [18] gtools_2.6.2 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.31.1 digest_0.5.1 IRanges_1.11.30 >> lattice_0.19-33 >> >> [5] RColorBrewer_1.0-5 tools_2.15.0 xtable_1.5-6 >> >> >> >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<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 > -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> [[alternative HTML version deleted]]
ADD REPLYlink written 6.8 years ago by Tim Triche4.2k
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