Hi I'm having troubles installing aroma.light (EDASeq dependency) l at np350v5c:~$ R Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help > biocLite("EDASeq", dep = TRUE) BioC_mirror: http://bioconductor.statistik.tu-dortmund.de Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version 3.1.0. Installing package(s) 'EDASeq' also installing the dependency ?aroma.light? provo con l'URL 'http://bioconductor.statistik.tu- dortmund.de/packages/2.14/bioc/src/contrib/aroma.light_2.0.0.tar.gz' Warning in download.file(url, destfile, method, mode = "wb", ...) : connesso a 'bioconductor.statistik.tu-dortmund.de' sulla porta 80. Warning in download.file(url, destfile, method, mode = "wb", ...) : -> GET /packages/2.14/bioc/src/contrib/aroma.light_2.0.0.tar.gz HTTP/1.0 Host: bioconductor.statistik.tu-dortmund.de User-Agent: R (3.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) Warning in download.file(url, destfile, method, mode = "wb", ...) : <- HTTP/1.1 200 OK Warning in download.file(url, destfile, method, mode = "wb", ...) : <- Date: Mon, 19 May 2014 00:05:41 GMT Warning in download.file(url, destfile, method, mode = "wb", ...) : <- Server: Apache/2.2.12 (Linux/SUSE) Warning in download.file(url, destfile, method, mode = "wb", ...) : <- Last-Modified: Sat, 12 Apr 2014 16:50:08 GMT Warning in download.file(url, destfile, method, mode = "wb", ...) : <- ETag: "37a1b3-5d1af-4f6db3e293000" Warning in download.file(url, destfile, method, mode = "wb", ...) : <- Accept-Ranges: bytes Warning in download.file(url, destfile, method, mode = "wb", ...) : <- Content-Length: 381359 Warning in download.file(url, destfile, method, mode = "wb", ...) : <- Connection: close Warning in download.file(url, destfile, method, mode = "wb", ...) : <- Content-Type: application/x-gzip Warning in download.file(url, destfile, method, mode = "wb", ...) : Code 200, content-type 'application/x-gzip' Content type 'application/x-gzip' length 381359 bytes (372 Kb) URL aperto ================================================== downloaded 372 Kb provo con l'URL 'http://bioconductor.statistik.tu- dortmund.de/packages/2.14/bioc/src/contrib/EDASeq_1.10.0.tar.gz' Warning in download.file(url, destfile, method, mode = "wb", ...) : connesso a 'bioconductor.statistik.tu-dortmund.de' sulla porta 80. Warning in download.file(url, destfile, method, mode = "wb", ...) : -> GET /packages/2.14/bioc/src/contrib/EDASeq_1.10.0.tar.gz HTTP/1.0 Host: bioconductor.statistik.tu-dortmund.de User-Agent: R (3.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) Warning in download.file(url, destfile, method, mode = "wb", ...) : <- HTTP/1.1 200 OK Warning in download.file(url, destfile, method, mode = "wb", ...) : <- Date: Mon, 19 May 2014 00:05:42 GMT Warning in download.file(url, destfile, method, mode = "wb", ...) : <- Server: Apache/2.2.12 (Linux/SUSE) Warning in download.file(url, destfile, method, mode = "wb", ...) : <- Last-Modified: Sat, 12 Apr 2014 16:50:41 GMT Warning in download.file(url, destfile, method, mode = "wb", ...) : <- ETag: "37a08e-15c662-4f6db4020ba40" Warning in download.file(url, destfile, method, mode = "wb", ...) : <- Accept-Ranges: bytes Warning in download.file(url, destfile, method, mode = "wb", ...) : <- Content-Length: 1427042 Warning in download.file(url, destfile, method, mode = "wb", ...) : <- Connection: close Warning in download.file(url, destfile, method, mode = "wb", ...) : <- Content-Type: application/x-gzip Warning in download.file(url, destfile, method, mode = "wb", ...) : Code 200, content-type 'application/x-gzip' Content type 'application/x-gzip' length 1427042 bytes (1.4 Mb) URL aperto ================================================== downloaded 1.4 Mb Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help > tools:::.install_packages() * installing *source* package ?aroma.light? ... ** R Warning in readLines(f, warn = FALSE) : input non valido trovato nella connessione di input '/tmp/RtmpjsSKWV /R.INSTALL4eda4bd24bdc/aroma.light/R/901.CalibrationAndNormalization.R ' Warning in readLines(f, warn = FALSE) : input non valido trovato nella connessione di input '/tmp/RtmpjsSKWV /R.INSTALL4eda4bd24bdc/aroma.light/R/normalizeCurveFit.R' ** inst ** preparing package for lazy loading Warning: metodo S3 ?weightedMedian.default? dichiarato in NAMESPACE ma non trovato Warning: metodi S3 ?$.BasicObject?, ?$<-.BasicObject?, ?[[.BasicObject?, ?[[<-.BasicObject?, ?as.character.BasicObject?, ?attach.BasicObject?, ?detach.BasicObject?, ?equals.BasicObject?, ?extend.BasicObject?, ?getFields.BasicObject?, ?getInstantiationTime.BasicObject?, ?hasField.BasicObject?, ?hashCode.BasicObject?, ?isReferable.BasicObject?, ?newInstance.BasicObject?, ?objectSize.BasicObject?, ?print.BasicObject?, ?uses.character?, ?$.Class?, ?$<-.Class?, ?[[.Class?, ?[[<-.Class?, ?argsToString.Class?, ?as.character.Class?, ?forName.Class?, ?getDetails.Class?, ?getFields.Class?, ?getKnownSubclasses.Class?, ?getMethods.Class?, ?getName.Class?, ?getPackage.Class?, ?getRdDeclaration.Class?, ?getRdHierarchy.Class?, ?getRdMethods.Class?, ?getStaticInstance.Class?, ?getSuperclasses.Class?, ?isAbstract.Class?, ?isBeingCreated.Class?, ?isDeprecated.C [... truncated] Error : object ?Package? is not exported by 'namespace:R.oo' ERROR: lazy loading failed for package ?aroma.light? * removing ?/home/l/R/x86_64-pc-linux-gnu-library/3.1/aroma.light? Warning in install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ?aroma.light? had non-zero exit status Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help > tools:::.install_packages() ERROR: dependency ?aroma.light? is not available for package ?EDASeq? * removing ?/home/l/R/x86_64-pc-linux-gnu-library/3.1/EDASeq? Warning in install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ?EDASeq? had non-zero exit status The downloaded source packages are in ?/tmp/RtmpVNXmMp/downloaded_packages? Freely translating back to english not valid input found in '/tmp/RtmpjsSKWV/R.INSTALL4eda4bd24bdc/aro ma.light/R/901.CalibrationAndNormalization.R' Warning: S3 method ?weightedMedian.default? declared in NAMESPACE but not found my session Info is > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=it_IT.UTF-8 LC_NUMERIC=C [3] LC_TIME=it_IT.UTF-8 LC_COLLATE=it_IT.UTF-8 [5] LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=it_IT.UTF-8 [7] LC_PAPER=it_IT.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] datasets grDevices graphics utils stats methods base other attached packages: [1] BiocInstaller_1.14.2 loaded via a namespace (and not attached): [1] tools_3.1.0 I have R.oo installed and when i "library" it > library(R.oo) Carico il pacchetto richiesto: R.methodsS3 R.methodsS3 v1.6.1 (2014-01-04) successfully loaded. See ?R.methodsS3 for help. Warning: metodi S3 ?$.BasicObject?, ?$<-.BasicObject?, ?[[.BasicObject?, ?[[<-.BasicObject?, ?as.character.BasicObject?, ?attach.BasicObject?, ?detach.BasicObject?, ?equals.BasicObject?, ?extend.BasicObject?, ?getFields.BasicObject?, ?getInstantiationTime.BasicObject?, ?hasField.BasicObject?, ?hashCode.BasicObject?, ?isReferable.BasicObject?, ?newInstance.BasicObject?, ?objectSize.BasicObject?, ?print.BasicObject?, ?uses.character?, ?$.Class?, ?$<-.Class?, ?[[.Class?, ?[[<-.Class?, ?argsToString.Class?, ?as.character.Class?, ?forName.Class?, ?getDetails.Class?, ?getFields.Class?, ?getKnownSubclasses.Class?, ?getMethods.Class?, ?getName.Class?, ?getPackage.Class?, ?getRdDeclaration.Class?, ?getRdHierarchy.Class?, ?getRdMethods.Class?, ?getStaticInstance.Class?, ?getSuperclasses.Class?, ?isAbstract.Class?, ?isBeingCreated.Class?, ?isDeprecated.C [... truncated] Attaching package: ?R.oo? The following objects are masked from ?package:methods?: getClasses, getMethods The following objects are masked from ?package:base?: attach, detach, gc, load, save any hint? thanks luca