Hi all, I have troubles installing (better: loading) BiocGenerics. See below [fn:1]. What am I to do here? Regards, Andreas [fn:1] sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=C [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C Footnotes: [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] andRstuff_1.0 devtools_1.3 tikzDevice_0.7.0 filehash_2.2-1 loaded via a namespace (and not attached): [1] digest_0.6.3 evaluate_0.4.7 grid_3.0.2 httr_0.2 memoise_0.1 [6] parallel_3.0.2 plyr_1.8 RCurl_1.95-4.1 stringr_0.6.2 tools_3.0.2 [11] whisker_0.3-2 > source("http://bioconductor.org/biocLite.R") Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help > biocLite("BiocGenerics") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. Installing package(s) 'BiocGenerics' trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/Bio cGenerics_0.8.0.tar.gz' Content type 'application/x-gzip' length 30969 bytes (30 Kb) opened URL ================================================== downloaded 30 Kb * installing *source* package ?BiocGenerics? ... ** R ** inst ** preparing package for lazy loading Warning: class "connection" is defined (with package slot ?filehash?) but no metadata object found to revise subclass information---not exported? Making a copy in package ?BiocGenerics? Warning: subclass "file" of class "connection" is not local and cannot be updated for new inheritance information; consider setClassUnion() Creating a new generic function for ?append? in package ?BiocGenerics? Creating a new generic function for ?as.data.frame? in package ?BiocGenerics? Creating a new generic function for ?as.vector? in package ?BiocGenerics? Creating a new generic function for ?cbind? in package ?BiocGenerics? Creating a new generic function for ?rbind? in package ?BiocGenerics? Creating a new generic function for ?duplicated? in package ?BiocGenerics? Creating a new generic function for ?anyDuplicated? in package ?BiocGenerics? Creating a new generic function for ?eval? in package ?BiocGenerics? Creating a new generic function for ?pmax? in package ?BiocGenerics? Creating a new generic function for ?pmin? in package ?BiocGenerics? Creating a new generic function for ?pmax.int? in package ?BiocGenerics? Creating a new generic function for ?pmin.int? in package ?BiocGenerics? Creating a new generic function for ?Reduce? in package ?BiocGenerics? Creating a new generic function for ?Filter? in package ?BiocGenerics? Creating a new generic function for ?Find? in package ?BiocGenerics? Creating a new generic function for ?Map? in package ?BiocGenerics? Creating a new generic function for ?Position? in package ?BiocGenerics? Creating a new generic function for ?get? in package ?BiocGenerics? Creating a new generic function for ?mget? in package ?BiocGenerics? Creating a new generic function for ?is.unsorted? in package ?BiocGenerics? Creating a new generic function for ?lapply? in package ?BiocGenerics? Creating a new generic function for ?sapply? in package ?BiocGenerics? Creating a new generic function for ?mapply? in package ?BiocGenerics? Creating a new generic function for ?match? in package ?BiocGenerics? Creating a new generic function for ?order? in package ?BiocGenerics? Creating a new generic function for ?paste? in package ?BiocGenerics? Creating a new generic function for ?rank? in package ?BiocGenerics? Creating a new generic function for ?rep.int? in package ?BiocGenerics? Creating a new generic function for ?rownames? in package ?BiocGenerics? Creating a new generic function for ?colnames? in package ?BiocGenerics? Creating a new generic function for ?union? in package ?BiocGenerics? Creating a new generic function for ?intersect? in package ?BiocGenerics? Creating a new generic function for ?setdiff? in package ?BiocGenerics? Creating a new generic function for ?sort? in package ?BiocGenerics? Creating a new generic function for ?table? in package ?BiocGenerics? Creating a new generic function for ?tapply? in package ?BiocGenerics? Creating a new generic function for ?unique? in package ?BiocGenerics? Creating a new generic function for ?unlist? in package ?BiocGenerics? Creating a new generic function for ?xtabs? in package ?BiocGenerics? Creating a new generic function for ?clusterCall? in package ?BiocGenerics? Creating a new generic function for ?clusterApply? in package ?BiocGenerics? Creating a new generic function for ?clusterApplyLB? in package ?BiocGenerics? Creating a new generic function for ?clusterEvalQ? in package ?BiocGenerics? Warning in getPackageName(environment(fdef)) : Created a package name, ?2014-01-20 01:16:35?, when none found Creating a new generic function for ?clusterExport? in package ?BiocGenerics? Creating a new generic function for ?clusterMap? in package ?BiocGenerics? Creating a new generic function for ?parLapply? in package ?BiocGenerics? Creating a new generic function for ?parSapply? in package ?BiocGenerics? Creating a new generic function for ?parApply? in package ?BiocGenerics? Creating a new generic function for ?parRapply? in package ?BiocGenerics? Creating a new generic function for ?parCapply? in package ?BiocGenerics? Creating a new generic function for ?parLapplyLB? in package ?BiocGenerics? Creating a new generic function for ?parSapplyLB? in package ?BiocGenerics? ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Error in namespaceExport(ns, exports) : undefined exports: .__C__file Error: loading failed * DONE (BiocGenerics) The downloaded source packages are in ?/tmp/Rtmp3P1KdF/downloaded_packages?

can i suggest that you start with a fresh R --vanilla session? -- you have some packages such as filehash attached that seem to be causing some conflicts. On Sun, Jan 19, 2014 at 7:21 PM, Andreas Leha < andreas.leha@med.uni-goettingen.de> wrote: > Hi all, > > I have troubles installing (better: loading) BiocGenerics. See below > [fn:1]. > > What am I to do here? > > Regards, > Andreas > > > [fn:1] > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C > [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 > [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=C > [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > Footnotes: > > [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] andRstuff_1.0 devtools_1.3 tikzDevice_0.7.0 filehash_2.2-1 > > loaded via a namespace (and not attached): > [1] digest_0.6.3 evaluate_0.4.7 grid_3.0.2 httr_0.2 > memoise_0.1 > [6] parallel_3.0.2 plyr_1.8 RCurl_1.95-4.1 stringr_0.6.2 > tools_3.0.2 > [11] whisker_0.3-2 > > source("http://bioconductor.org/biocLite.R") > Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help > > biocLite("BiocGenerics") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. > Installing package(s) 'BiocGenerics' > trying URL ' > http://bioconductor.org/packages/2.13/bioc/src/contrib/BiocGenerics_ 0.8.0.tar.gz > ' > Content type 'application/x-gzip' length 30969 bytes (30 Kb) > opened URL > ================================================== > downloaded 30 Kb > > * installing *source* package ‘BiocGenerics’ ... > ** R > ** inst > ** preparing package for lazy loading > Warning: class "connection" is defined (with package slot ‘filehash’) but > no metadata object found to revise subclass information---not exported? > Making a copy in package ‘BiocGenerics’ > Warning: subclass "file" of class "connection" is not local and cannot be > updated for new inheritance information; consider setClassUnion() > Creating a new generic function for ‘append’ in package ‘BiocGenerics’ > Creating a new generic function for ‘as.data.frame’ in package > ‘BiocGenerics’ > Creating a new generic function for ‘as.vector’ in package ‘BiocGenerics’ > Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’ > Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’ > Creating a new generic function for ‘duplicated’ in package ‘BiocGenerics’ > Creating a new generic function for ‘anyDuplicated’ in package > ‘BiocGenerics’ > Creating a new generic function for ‘eval’ in package ‘BiocGenerics’ > Creating a new generic function for ‘pmax’ in package ‘BiocGenerics’ > Creating a new generic function for ‘pmin’ in package ‘BiocGenerics’ > Creating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’ > Creating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’ > Creating a new generic function for ‘Reduce’ in package ‘BiocGenerics’ > Creating a new generic function for ‘Filter’ in package ‘BiocGenerics’ > Creating a new generic function for ‘Find’ in package ‘BiocGenerics’ > Creating a new generic function for ‘Map’ in package ‘BiocGenerics’ > Creating a new generic function for ‘Position’ in package ‘BiocGenerics’ > Creating a new generic function for ‘get’ in package ‘BiocGenerics’ > Creating a new generic function for ‘mget’ in package ‘BiocGenerics’ > Creating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’ > Creating a new generic function for ‘lapply’ in package ‘BiocGenerics’ > Creating a new generic function for ‘sapply’ in package ‘BiocGenerics’ > Creating a new generic function for ‘mapply’ in package ‘BiocGenerics’ > Creating a new generic function for ‘match’ in package ‘BiocGenerics’ > Creating a new generic function for ‘order’ in package ‘BiocGenerics’ > Creating a new generic function for ‘paste’ in package ‘BiocGenerics’ > Creating a new generic function for ‘rank’ in package ‘BiocGenerics’ > Creating a new generic function for ‘rep.int’ in package ‘BiocGenerics’ > Creating a new generic function for ‘rownames’ in package ‘BiocGenerics’ > Creating a new generic function for ‘colnames’ in package ‘BiocGenerics’ > Creating a new generic function for ‘union’ in package ‘BiocGenerics’ > Creating a new generic function for ‘intersect’ in package ‘BiocGenerics’ > Creating a new generic function for ‘setdiff’ in package ‘BiocGenerics’ > Creating a new generic function for ‘sort’ in package ‘BiocGenerics’ > Creating a new generic function for ‘table’ in package ‘BiocGenerics’ > Creating a new generic function for ‘tapply’ in package ‘BiocGenerics’ > Creating a new generic function for ‘unique’ in package ‘BiocGenerics’ > Creating a new generic function for ‘unlist’ in package ‘BiocGenerics’ > Creating a new generic function for ‘xtabs’ in package ‘BiocGenerics’ > Creating a new generic function for ‘clusterCall’ in package ‘BiocGenerics’ > Creating a new generic function for ‘clusterApply’ in package > ‘BiocGenerics’ > Creating a new generic function for ‘clusterApplyLB’ in package > ‘BiocGenerics’ > Creating a new generic function for ‘clusterEvalQ’ in package > ‘BiocGenerics’ > Warning in getPackageName(environment(fdef)) : > Created a package name, ‘2014-01-20 01:16:35’, when none found > Creating a new generic function for ‘clusterExport’ in package > ‘BiocGenerics’ > Creating a new generic function for ‘clusterMap’ in package ‘BiocGenerics’ > Creating a new generic function for ‘parLapply’ in package ‘BiocGenerics’ > Creating a new generic function for ‘parSapply’ in package ‘BiocGenerics’ > Creating a new generic function for ‘parApply’ in package ‘BiocGenerics’ > Creating a new generic function for ‘parRapply’ in package ‘BiocGenerics’ > Creating a new generic function for ‘parCapply’ in package ‘BiocGenerics’ > Creating a new generic function for ‘parLapplyLB’ in package ‘BiocGenerics’ > Creating a new generic function for ‘parSapplyLB’ in package ‘BiocGenerics’ > ** help > *** installing help indices > ** building package indices > ** testing if installed package can be loaded > Error in namespaceExport(ns, exports) : undefined exports: .__C__file > Error: loading failed > * DONE (BiocGenerics) > > The downloaded source packages are in > ‘/tmp/Rtmp3P1KdF/downloaded_packages’ > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

Hi Vincent, Vincent Carey <stvjc at="" channing.harvard.edu=""> writes: > can i suggest that you start with a fresh R --vanilla session? -- you have > some packages such as filehash attached that seem to be causing some > conflicts. > that did the trick. Should have tried before posting. Thanks a lot! Regards, Andreas > > On Sun, Jan 19, 2014 at 7:21 PM, Andreas Leha < > andreas.leha at med.uni-goettingen.de> wrote: > >> Hi all, >> >> I have troubles installing (better: loading) BiocGenerics. See below >> [fn:1]. >> >> What am I to do here? >> >> Regards, >> Andreas >> >> >> [fn:1] >> >> sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 >> [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=C >> [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> Footnotes: >> >> [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] andRstuff_1.0 devtools_1.3 tikzDevice_0.7.0 filehash_2.2-1 >> >> loaded via a namespace (and not attached): >> [1] digest_0.6.3 evaluate_0.4.7 grid_3.0.2 httr_0.2 >> memoise_0.1 >> [6] parallel_3.0.2 plyr_1.8 RCurl_1.95-4.1 stringr_0.6.2 >> tools_3.0.2 >> [11] whisker_0.3-2 >> > source("http://bioconductor.org/biocLite.R") >> Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help >> > biocLite("BiocGenerics") >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. >> Installing package(s) 'BiocGenerics' >> trying URL ' >> http://bioconductor.org/packages/2.13/bioc/src/contrib/BiocGenerics _0.8.0.tar.gz >> ' >> Content type 'application/x-gzip' length 30969 bytes (30 Kb) >> opened URL >> ================================================== >> downloaded 30 Kb >> >> * installing *source* package ?BiocGenerics? ... >> ** R >> ** inst >> ** preparing package for lazy loading >> Warning: class "connection" is defined (with package slot ?filehash?) but >> no metadata object found to revise subclass information---not exported? >> Making a copy in package ?BiocGenerics? >> Warning: subclass "file" of class "connection" is not local and cannot be >> updated for new inheritance information; consider setClassUnion() >> Creating a new generic function for ?append? in package ?BiocGenerics? >> Creating a new generic function for ?as.data.frame? in package >> ?BiocGenerics? >> Creating a new generic function for ?as.vector? in package ?BiocGenerics? >> Creating a new generic function for ?cbind? in package ?BiocGenerics? >> Creating a new generic function for ?rbind? in package ?BiocGenerics? >> Creating a new generic function for ?duplicated? in package ?BiocGenerics? >> Creating a new generic function for ?anyDuplicated? in package >> ?BiocGenerics? >> Creating a new generic function for ?eval? in package ?BiocGenerics? >> Creating a new generic function for ?pmax? in package ?BiocGenerics? >> Creating a new generic function for ?pmin? in package ?BiocGenerics? >> Creating a new generic function for ?pmax.int? in package ?BiocGenerics? >> Creating a new generic function for ?pmin.int? in package ?BiocGenerics? >> Creating a new generic function for ?Reduce? in package ?BiocGenerics? >> Creating a new generic function for ?Filter? in package ?BiocGenerics? >> Creating a new generic function for ?Find? in package ?BiocGenerics? >> Creating a new generic function for ?Map? in package ?BiocGenerics? >> Creating a new generic function for ?Position? in package ?BiocGenerics? >> Creating a new generic function for ?get? in package ?BiocGenerics? >> Creating a new generic function for ?mget? in package ?BiocGenerics? >> Creating a new generic function for ?is.unsorted? in package ?BiocGenerics? >> Creating a new generic function for ?lapply? in package ?BiocGenerics? >> Creating a new generic function for ?sapply? in package ?BiocGenerics? >> Creating a new generic function for ?mapply? in package ?BiocGenerics? >> Creating a new generic function for ?match? in package ?BiocGenerics? >> Creating a new generic function for ?order? in package ?BiocGenerics? >> Creating a new generic function for ?paste? in package ?BiocGenerics? >> Creating a new generic function for ?rank? in package ?BiocGenerics? >> Creating a new generic function for ?rep.int? in package ?BiocGenerics? >> Creating a new generic function for ?rownames? in package ?BiocGenerics? >> Creating a new generic function for ?colnames? in package ?BiocGenerics? >> Creating a new generic function for ?union? in package ?BiocGenerics? >> Creating a new generic function for ?intersect? in package ?BiocGenerics? >> Creating a new generic function for ?setdiff? in package ?BiocGenerics? >> Creating a new generic function for ?sort? in package ?BiocGenerics? >> Creating a new generic function for ?table? in package ?BiocGenerics? >> Creating a new generic function for ?tapply? in package ?BiocGenerics? >> Creating a new generic function for ?unique? in package ?BiocGenerics? >> Creating a new generic function for ?unlist? in package ?BiocGenerics? >> Creating a new generic function for ?xtabs? in package ?BiocGenerics? >> Creating a new generic function for ?clusterCall? in package ?BiocGenerics? >> Creating a new generic function for ?clusterApply? in package >> ?BiocGenerics? >> Creating a new generic function for ?clusterApplyLB? in package >> ?BiocGenerics? >> Creating a new generic function for ?clusterEvalQ? in package >> ?BiocGenerics? >> Warning in getPackageName(environment(fdef)) : >> Created a package name, ?2014-01-20 01:16:35?, when none found >> Creating a new generic function for ?clusterExport? in package >> ?BiocGenerics? >> Creating a new generic function for ?clusterMap? in package ?BiocGenerics? >> Creating a new generic function for ?parLapply? in package ?BiocGenerics? >> Creating a new generic function for ?parSapply? in package ?BiocGenerics? >> Creating a new generic function for ?parApply? in package ?BiocGenerics? >> Creating a new generic function for ?parRapply? in package ?BiocGenerics? >> Creating a new generic function for ?parCapply? in package ?BiocGenerics? >> Creating a new generic function for ?parLapplyLB? in package ?BiocGenerics? >> Creating a new generic function for ?parSapplyLB? in package ?BiocGenerics? >> ** help >> *** installing help indices >> ** building package indices >> ** testing if installed package can be loaded >> Error in namespaceExport(ns, exports) : undefined exports: .__C__file >> Error: loading failed >> * DONE (BiocGenerics) >> >> The downloaded source packages are in >> ?/tmp/Rtmp3P1KdF/downloaded_packages? >> >> _______________________________________________ >> 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 > > [[alternative HTML version deleted]] > > _______________________________________________ > 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