Trouble installing BiocGenerics
2
0
Entering edit mode
Andreas Leha ▴ 30
@andreas-leha-6343
Last seen 4.7 years ago
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?
BiocGenerics BiocGenerics • 2.1k views
ADD COMMENT
0
Entering edit mode
@vincent-j-carey-jr-4
Last seen 15 days ago
United States
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]]
0
Entering edit mode
Andreas Leha ▴ 30
@andreas-leha-6343
Last seen 4.7 years ago
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
ADD COMMENT

Login before adding your answer.

Traffic: 211 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6