[BioC] Help with aroma.light install
Luca Braglia
lbraglia at gmail.com
Mon May 19 02:12:31 CEST 2014
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/aroma.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
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