Not able to install Bioconductor packages due to proxy
0
I am not able to install Bio-conductor packages due to proxy. I was having the same issue with CRAN packages also, and I fixed it by using
install.packages('package_name', dependencies=TRUE, repos='http://cran.rstudio.com/')
But Bio-conductor packages are giving me a tough time. I have set proxy and checked it using
Sys.getenv("http_proxy")
[1] "http://proxy.staff.ac.in:3128"
Sys.getenv("https_proxy")
[1] "https://proxy.staff.ac.in:3128"
Sys.getenv("ftp_proxy")
[1] "ftp://proxy.staff.ac.in:3128"
When I try to install the packages by BiocManager::install("affy"), I get the following error
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
Installing package(s) 'BiocVersion', 'affy'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/bioc/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/annotation/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/experiment/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/workflows/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/bioc/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/annotation/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/experiment/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/workflows/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
Warning message:
packages ‘BiocVersion’, ‘affy’ are not available (for R version 3.5.1)
Here is the session information:
sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS release 6.9 (Final)
Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_IN LC_NUMERIC=C LC_TIME=en_IN
[4] LC_COLLATE=en_IN LC_MONETARY=en_IN LC_MESSAGES=en_IN
[7] LC_PAPER=en_IN LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] BiocManager_1.30.4 compiler_3.5.1 tools_3.5.1
r proxy centos6 bioconductor
asked Nov 26 '18 at 9:08
HashimHashim
129214
add a comment |
0
I am not able to install Bio-conductor packages due to proxy. I was having the same issue with CRAN packages also, and I fixed it by using
install.packages('package_name', dependencies=TRUE, repos='http://cran.rstudio.com/')
But Bio-conductor packages are giving me a tough time. I have set proxy and checked it using
Sys.getenv("http_proxy")
[1] "http://proxy.staff.ac.in:3128"
Sys.getenv("https_proxy")
[1] "https://proxy.staff.ac.in:3128"
Sys.getenv("ftp_proxy")
[1] "ftp://proxy.staff.ac.in:3128"
When I try to install the packages by BiocManager::install("affy"), I get the following error
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
Installing package(s) 'BiocVersion', 'affy'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/bioc/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/annotation/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/experiment/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/workflows/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/bioc/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/annotation/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/experiment/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/workflows/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
Warning message:
packages ‘BiocVersion’, ‘affy’ are not available (for R version 3.5.1)
Here is the session information:
sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS release 6.9 (Final)
Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_IN LC_NUMERIC=C LC_TIME=en_IN
[4] LC_COLLATE=en_IN LC_MONETARY=en_IN LC_MESSAGES=en_IN
[7] LC_PAPER=en_IN LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] BiocManager_1.30.4 compiler_3.5.1 tools_3.5.1
r proxy centos6 bioconductor
asked Nov 26 '18 at 9:08
HashimHashim
129214
proxies are usually defined in the .Renviron file. If that is the case, removing .Renviron can resolve your issue. Although that might violate your institutions rules so you might want to check that first.
– Maylo
Nov 26 '18 at 9:22
@Maylo Thank your for your comment, that is not the solution.
– Hashim
Nov 26 '18 at 9:52
add a comment |
0
0
0
I am not able to install Bio-conductor packages due to proxy. I was having the same issue with CRAN packages also, and I fixed it by using
install.packages('package_name', dependencies=TRUE, repos='http://cran.rstudio.com/')
But Bio-conductor packages are giving me a tough time. I have set proxy and checked it using
Sys.getenv("http_proxy")
[1] "http://proxy.staff.ac.in:3128"
Sys.getenv("https_proxy")
[1] "https://proxy.staff.ac.in:3128"
Sys.getenv("ftp_proxy")
[1] "ftp://proxy.staff.ac.in:3128"
When I try to install the packages by BiocManager::install("affy"), I get the following error
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
Installing package(s) 'BiocVersion', 'affy'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/bioc/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/annotation/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/experiment/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/workflows/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/bioc/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/annotation/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/experiment/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/workflows/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
Warning message:
packages ‘BiocVersion’, ‘affy’ are not available (for R version 3.5.1)
Here is the session information:
sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS release 6.9 (Final)
Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_IN LC_NUMERIC=C LC_TIME=en_IN
[4] LC_COLLATE=en_IN LC_MONETARY=en_IN LC_MESSAGES=en_IN
[7] LC_PAPER=en_IN LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] BiocManager_1.30.4 compiler_3.5.1 tools_3.5.1
r proxy centos6 bioconductor
asked Nov 26 '18 at 9:08
HashimHashim
129214
I am not able to install Bio-conductor packages due to proxy. I was having the same issue with CRAN packages also, and I fixed it by using
install.packages('package_name', dependencies=TRUE, repos='http://cran.rstudio.com/')
But Bio-conductor packages are giving me a tough time. I have set proxy and checked it using
Sys.getenv("http_proxy")
[1] "http://proxy.staff.ac.in:3128"
Sys.getenv("https_proxy")
[1] "https://proxy.staff.ac.in:3128"
Sys.getenv("ftp_proxy")
[1] "ftp://proxy.staff.ac.in:3128"
When I try to install the packages by BiocManager::install("affy"), I get the following error
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
Installing package(s) 'BiocVersion', 'affy'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/bioc/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/annotation/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/experiment/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/workflows/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/bioc/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/annotation/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/experiment/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/workflows/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
Warning message:
packages ‘BiocVersion’, ‘affy’ are not available (for R version 3.5.1)
Here is the session information:
sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS release 6.9 (Final)
Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_IN LC_NUMERIC=C LC_TIME=en_IN
[4] LC_COLLATE=en_IN LC_MONETARY=en_IN LC_MESSAGES=en_IN
[7] LC_PAPER=en_IN LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] BiocManager_1.30.4 compiler_3.5.1 tools_3.5.1
r proxy centos6 bioconductor
r proxy centos6 bioconductor
asked Nov 26 '18 at 9:08
HashimHashim
129214
asked Nov 26 '18 at 9:08
HashimHashim
129214
asked Nov 26 '18 at 9:08
HashimHashim
129214
asked Nov 26 '18 at 9:08
HashimHashim
129214
asked Nov 26 '18 at 9:08
HashimHashim
129214
129214
proxies are usually defined in the .Renviron file. If that is the case, removing .Renviron can resolve your issue. Although that might violate your institutions rules so you might want to check that first.
– Maylo
Nov 26 '18 at 9:22
@Maylo Thank your for your comment, that is not the solution.
– Hashim
Nov 26 '18 at 9:52
add a comment |
proxies are usually defined in the .Renviron file. If that is the case, removing .Renviron can resolve your issue. Although that might violate your institutions rules so you might want to check that first.
– Maylo
Nov 26 '18 at 9:22
@Maylo Thank your for your comment, that is not the solution.
– Hashim
Nov 26 '18 at 9:52
proxies are usually defined in the .Renviron file. If that is the case, removing .Renviron can resolve your issue. Although that might violate your institutions rules so you might want to check that first.
– Maylo
Nov 26 '18 at 9:22
proxies are usually defined in the .Renviron file. If that is the case, removing .Renviron can resolve your issue. Although that might violate your institutions rules so you might want to check that first.
– Maylo
Nov 26 '18 at 9:22
@Maylo Thank your for your comment, that is not the solution.
– Hashim
Nov 26 '18 at 9:52
@Maylo Thank your for your comment, that is not the solution.
– Hashim
Nov 26 '18 at 9:52
add a comment |
0
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proxies are usually defined in the .Renviron file. If that is the case, removing .Renviron can resolve your issue. Although that might violate your institutions rules so you might want to check that first.
– Maylo
Nov 26 '18 at 9:22
@Maylo Thank your for your comment, that is not the solution.
– Hashim
Nov 26 '18 at 9:52