В моей среде Windows 10 с последней версией R и RStudio я не могу загрузить многие из пакетов R, как я упоминал, аналогично пакет R bioconductor, который я не могу загрузить, так в чем же проблема?
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)
Обновление :
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'