CODEWITHSUNDEEP
rpackagerstudiobioconductor
Edison
Edison

Reputation: 4291

package ‘GEOquery’ is not available (for R version 3.6.1)

In my windows 10 enviornment with latest version of R and RStudio, I am not able to download many of R packages like I mentioned, similarly R bioconductor package I am not being able to download,So whats the problem?

install.packages('GEOquery')
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/samer/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘GEOquery’ is not available (for R version 3.6.1)

install.packages('bioconductor')
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/samer/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘bioconductor’ is not available (for R version 3.6.1)

Update:

I downloaded and installed Rtools from the direct link instead from within the RStudio Environment.
Then I have following issues now.

BiocManager::install("GEOquery")
Bioconductor version 3.9 (BiocManager 1.30.7), R 3.6.1 (2019-07-05)
Installing package(s) 'BiocVersion', 'GEOquery'
also installing the dependencies ‘rlang’, ‘tidyselect’, ‘plogr’, ‘ellipsis’, ‘purrr’, ‘vctrs’, ‘lifecycle’, ‘Biobase’, ‘readr’, ‘xml2’, ‘dplyr’, ‘tidyr’, ‘limma’

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/rlang_0.4.0.zip'
Content type 'application/zip' length 1090422 bytes (1.0 MB)
downloaded 1.0 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/tidyselect_0.2.5.zip'
Content type 'application/zip' length 627063 bytes (612 KB)
downloaded 612 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/plogr_0.2.0.zip'
Content type 'application/zip' length 18873 bytes (18 KB)
downloaded 18 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/ellipsis_0.3.0.zip'
Content type 'application/zip' length 44553 bytes (43 KB)
downloaded 43 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/purrr_0.3.2.zip'
Content type 'application/zip' length 421098 bytes (411 KB)
downloaded 411 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/vctrs_0.2.0.zip'
Content type 'application/zip' length 828462 bytes (809 KB)
downloaded 809 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/lifecycle_0.1.0.zip'
Content type 'application/zip' length 84709 bytes (82 KB)
downloaded 82 KB

trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/Biobase_2.44.0.zip'
Content type 'application/zip' length 2421976 bytes (2.3 MB)
downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/readr_1.3.1.zip'
Content type 'application/zip' length 1589745 bytes (1.5 MB)
downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/xml2_1.2.2.zip'
Content type 'application/zip' length 3503035 bytes (3.3 MB)
downloaded 3.3 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/dplyr_0.8.3.zip'
Content type 'application/zip' length 3265027 bytes (3.1 MB)
downloaded 764 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/tidyr_1.0.0.zip'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/tidyr_1.0.0.zip'
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 782336 != reported length 3265027
2: In download.file(url, destfile, method, mode = "wb", ...) :
  InternetOpenUrl failed: 'The server returned an invalid or unrecognized response'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘tidyr’ failed
trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/limma_3.40.6.zip'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/limma_3.40.6.zip'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  InternetOpenUrl failed: 'The operation timed out'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘limma’ failed
trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/BiocVersion_3.9.0.zip'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/BiocVersion_3.9.0.zip'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  InternetOpenUrl failed: 'The operation timed out'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘BiocVersion’ failed
trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/GEOquery_2.52.0.zip'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/GEOquery_2.52.0.zip'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  InternetOpenUrl failed: 'The operation timed out'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘GEOquery’ failed
package ‘rlang’ successfully unpacked and MD5 sums checked
package ‘tidyselect’ successfully unpacked and MD5 sums checked
package ‘plogr’ successfully unpacked and MD5 sums checked
package ‘ellipsis’ successfully unpacked and MD5 sums checked
package ‘purrr’ successfully unpacked and MD5 sums checked
package ‘vctrs’ successfully unpacked and MD5 sums checked
package ‘lifecycle’ successfully unpacked and MD5 sums checked
package ‘Biobase’ successfully unpacked and MD5 sums checked
package ‘readr’ successfully unpacked and MD5 sums checked
package ‘xml2’ successfully unpacked and MD5 sums checked
Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : 
  cannot open the connection
In addition: Warning messages:
1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
2: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  cannot open compressed file 'dplyr/DESCRIPTION', probable reason 'No such file or directory'

Upvotes: 3

Views: 8830

Answers (1)

morgan121
morgan121

Reputation: 2253

To install bioconductor packages is not like normal R packages. To do so, follow the steps here:

Example Code:

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

BiocInstaller::biocLite(c("GEOquery"))

To install Rtools get the latest download from here and install it, then re-try the code.

Edit:

Apparently there are updated installation practices, so the correct code should be:

BiocManager::install("GEOquery")

Upvotes: 3

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