not able to install bioconductor packages
2
0
Entering edit mode
@farahqureshi5-12184
Last seen 7.1 years ago

i am working on i

R version 3.3.2 (2016-10-31)
nickname       Sincere Pumpkin Patch   

initially i was able to access the airway package of bioconductor. but now wen i use the library(airway) it tells me that this package is not available. and when i again install it, it shows that package airway doesnt work with R version 3.3.2

install.packages("airway")

Warning in install.packages :
  package ‘airway’ is not available (for R version 3.3.2)

looking forward for your help

thanking in anticipation

package bioconductor new version • 7.0k views
ADD COMMENT
0
Entering edit mode

To install packages of Bioconductor use biocLite instead of install.packages to look for the right version in the right repository:

source("https://bioconductor.org/biocLite.R")
biocLite("airway")

Which error message appears when you call library("airway")?

ADD REPLY
0
Entering edit mode

 ## try http:// if https:// URLs are not supported
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite("airway")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘airway’
installing the source package ‘airway’

trying URL 'https://bioconductor.org/packages/3.4/data/experiment/src/contrib/airway_0.108.0.tar.gz'
Content type 'application/x-gzip' length 11755934 bytes (11.2 MB)
downloaded 11.2 MB

* installing *source* package 'airway' ...
** data
** inst
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called 'zlibbioc'
Error : package 'GenomicRanges' could not be loaded
Error: loading failed
Execution halted
ERROR: loading failed
* removing 'C:/Users/Farah Qureshi/Documents/R/win-library/3.3/airway'

The downloaded source packages are in
    ‘C:\Users\Farah Qureshi\AppData\Local\Temp\RtmpCyjOjg\downloaded_packages’
installation path not writeable, unable to update packages: Matrix, mgcv, nlme, survival
Warning messages:
1: running command '"C:/PROGRA~1/R/R-33~1.2/bin/i386/R" CMD INSTALL -l "C:\Users\Farah Qureshi\Documents\R\win-library\3.3" C:\Users\FARAHQ~1\AppData\Local\Temp\RtmpCyjOjg/downloaded_packages/airway_0.108.0.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘airway’ had non-zero exit status

ADD REPLY
0
Entering edit mode

Then you need to install GenomicRanges too and zlibbioc

ADD REPLY
0
Entering edit mode
@farahqureshi5-12184
Last seen 7.1 years ago

i dont know how to debug it. 

biocLite("airway")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘airway’
installing the source package ‘airway’

trying URL 'https://bioconductor.org/packages/3.4/data/experiment/src/contrib/airway_0.108.0.tar.gz'
Content type 'application/x-gzip' length 11755934 bytes (11.2 MB)
downloaded 7.4 MB

Error in untar2(tarfile, files, list, exdir, restore_times) : 
  incomplete block on file

The downloaded source packages are in
    ‘C:\Users\Farah Qureshi\AppData\Local\Temp\RtmpWUIuwn\downloaded_packages’
installation path not writeable, unable to update packages: Matrix, mgcv, nlme, survival
Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 7729152 != reported length 11755934
2: running command '"C:/PROGRA~1/R/R-33~1.2/bin/i386/R" CMD INSTALL -l "C:\Users\Farah Qureshi\Documents\R\win-library\3.3" C:\Users\FARAHQ~1\AppData\Local\Temp\RtmpWUIuwn/downloaded_packages/airway_0.108.0.tar.gz' had status 1 
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘airway’ had non-zero exit status
ADD COMMENT
0
Entering edit mode

The line

1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 7729152 != reported length 11755934

says that the download was incomplete. The solution is to try again, perhaps from a location with a faster or more reliable internet connection.

ADD REPLY
0
Entering edit mode
biocLite("airway") BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31). Installing package(s) ‘airway’ installing the source package ‘airway’ trying URL 'https://bioconductor.org/packages/3.4/data/experiment/src/contrib/airway_0.108.0.tar.gz' Content type 'application/x-gzip' length 11755934 bytes (11.2 MB) downloaded 11.2 MB * installing *source* package 'airway' ... ** data ** inst ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (airway) The downloaded source packages are in ‘C:\Users\Farah Qureshi\AppData\Local\Temp\RtmpWUIuwn\downloaded_packages’ installation path not writeable, unable to update packages: Matrix, mgcv, nlme, survival > On 2/16/17, Martin Morgan [bioc] <noreply@bioconductor.org> wrote: > Martin Morgan posted the Comment: "not able to install bioconductor > packages": > > The line 1: In download.file(url, destfile, method, mode = "wb", ...) : > downloaded length 7729152 != reported length 11755934 says that the download > was incomplete. The solution is to try again, perhaps from a location with a > faster or more reliable internet connection. > > --- > See the full post at: C: not able to install bioconductor packages > Replying to this email will post a comment to the answer above. >
ADD REPLY
0
Entering edit mode
@farahqureshi5-12184
Last seen 7.1 years ago

biocLite("airway")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘airway’
installing the source package ‘airway’

trying URL 'https://bioconductor.org/packages/3.4/data/experiment/src/contrib/airway_0.108.0.tar.gz'
Content type 'application/x-gzip' length 11755934 bytes (11.2 MB)
downloaded 11.2 MB

* installing *source* package 'airway' ...
** data
** inst
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (airway)

The downloaded source packages are in
    ‘C:\Users\Farah Qureshi\AppData\Local\Temp\RtmpWUIuwn\downloaded_packages’
installation path not writeable, unable to update packages: Matrix, mgcv, nlme, survival
> library(airway)
Loading required package: SummarizedExperiment
> dir <- system.file("extdata", package="airway", mustWork=TRUE)
> filenames <- file.path(dir, paste0(sampleTable$Run, "_subset.bam"))
Error in paste0(sampleTable$Run, "_subset.bam") : 
  object 'sampleTable' not found

ADD COMMENT
0
Entering edit mode

This is a different question, so start a new support site question. But review first the error message -- an object 'sampleTable' is not found in your R session -- and the script that I guess you are trying to follow, and ask how R should know about the object sampleTable.

ADD REPLY

Login before adding your answer.

Traffic: 675 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