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Question: not able to install bioconductor packages
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gravatar for farahqureshi5
9 months ago by
farahqureshi50 wrote:

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

ADD COMMENTlink modified 9 months ago • written 9 months ago by farahqureshi50

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 REPLYlink written 9 months ago by Lluís R300

 ## 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 REPLYlink written 9 months ago by farahqureshi50

Then you need to install GenomicRanges too and zlibbioc

ADD REPLYlink written 9 months ago by Lluís R300
0
gravatar for farahqureshi5
9 months ago by
farahqureshi50 wrote:

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 COMMENTlink modified 9 months ago by Martin Morgan ♦♦ 20k • written 9 months ago by farahqureshi50

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 REPLYlink written 9 months ago by Martin Morgan ♦♦ 20k
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 REPLYlink written 9 months ago by farahqureshi50
0
gravatar for farahqureshi5
9 months ago by
farahqureshi50 wrote:

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 COMMENTlink written 9 months ago by farahqureshi50

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 REPLYlink modified 9 months ago • written 9 months ago by Martin Morgan ♦♦ 20k
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