Entering edit mode
Luca Braglia
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10
@luca-braglia-6560
Last seen 10.1 years ago
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