Search
Question: Trouble installing BiocGenerics
0
gravatar for Andreas Leha
3.8 years ago by
Andreas Leha20
Andreas Leha20 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/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?
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Andreas Leha20
0
gravatar for Vincent J. Carey, Jr.
3.8 years ago by
United States
Vincent J. Carey, Jr.6.2k wrote:
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]]
ADD COMMENTlink written 3.8 years ago by Vincent J. Carey, Jr.6.2k
0
gravatar for Andreas Leha
3.8 years ago by
Andreas Leha20
Andreas Leha20 wrote:
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 COMMENTlink written 3.8 years ago by Andreas Leha20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 326 users visited in the last hour