Error: Bioconductor version cannot be validated; no internet connection?
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Elham • 0
@2368e910
Last seen 17 months ago
Germany

Hi, I am trying to install some packages but I keep getting this error, also I can't open the https://bioconductor.org/config.yaml. I would appreciate your help

The code should be placed in three backticks as shown below

BiocManager::install("DESeq2")

Error: Bioconductor version cannot be validated; no internet connection? See #troubleshooting section in vignette# please also include the results of running the following in an R session

sessionInfo( ) R version 4.3.1 (2023-06-16 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build 22621)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 [4] LC_NUMERIC=C LC_TIME=English_United States.utf8

time zone: Europe/Berlin tzcode source: internal

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] BiocManager_1.30.21 compiler_4.3.1 tools_4.3.1

```
scRNAseq • 6.2k views
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@james-w-macdonald-5106
Last seen 3 days ago
United States

If you can't open the YAML file using a browser then it's likely that your IT department is blocking you somehow. I'd talk to them.
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Hello, I encountered the same error. Can you find a solution for this?

sessionInfo()

R version 4.3.1 (2023-06-16 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

time zone: Asia/Tehran tzcode source: internal

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] BiocManager_1.30.21.1 compiler_4.3.1 tools_4.3.1
Warning message: R graphics engine version 16 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed.

library(BiocManager)

Bioconductor version cannot be validated; no internet connection? See #troubleshooting section in vignette Warning messages: 1: In file(con, "r") : URL 'https://bioconductor.org/config.yaml': status was 'SSL connect error' 2: In file(con, "r") : URL 'https://bioconductor.org/config.yaml': status was 'SSL connect error'

BiocManager::install("WGCNA")

Error: Bioconductor version cannot be validated; no internet connection? See #troubleshooting section in vignette

config <- readLines("https://bioconductor.org/config.yaml")

Error in file(con, "r") : cannot open the connection to 'https://bioconductor.org/config.yaml' In addition: Warning message: In file(con, "r") : URL 'https://bioconductor.org/config.yaml': status was 'SSL connect error'

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0
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Hi James, I can open the YAML file using a browser, no problem with that. But I am facing the problem below. I would appreciate any help.

BiocManager::install()

Error: Bioconductor version cannot be validated; no internet connection?

In addition: Warning messages:

1: In file(con, "r") : URL 'https://bioconductor.org/config.yaml': status was 'SSL connect error'

2: In file(con, "r") : URL 'https://bioconductor.org/config.yaml': status was 'SSL connect error'

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Does it help if you do this first (within R)?

options(download.file.method="curl", download.file.extra="--ssl-revoke-best-effort")
## or alternatively
Sys.setenv(R_LIBCURL_SSL_REVOKE_BEST_EFFORT=TRUE)
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Thanks. I did as you suggested. I am still having the same problem.

I am not under a proxy and I can install other packages without any problems.

I have the same problem with different R versions (4.3.2 and older ones).

I am running this on Windows 7, maybe that's the cause?

Any ideas?

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What do you get from

 readLines("https://bioconductor.org/config.yaml")
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I get:

Error in file(con, "r") : cannot open the connection to 'https://bioconductor.org/config.yaml'

In addition: Warning message: In file(con, "r") : URL 'https://bioconductor.org/config.yaml': status was 'SSL connect error'

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Can you get to that link using a browser?

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0
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Yes, I can.

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0
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Well, I don't know. It's always worked for me, so it's hard to diagnose. This might be of use however (from ?download.file)

Secure URLs:

     Methods which access 'https://' and (where supported) 'ftps://'
     URLs should try to verify the site certificates.  This is usually
     done using the CA root certificates installed by the OS (although
     we have seen instances in which these got removed rather than
     updated). For further information see
     <https://curl.se/docs/sslcerts.html>.

     On Windows with 'method = "libcurl"', the CA root certificates are
     provided by the OS when R was linked with 'libcurl' with
     'Schannel' enabled, which is the current default in Rtools.  This
     can be verified by checking that 'libcurlVersion()' returns a
     version string containing '"Schannel"'.  If it does not, for
     verification to be on the environment variable 'CURL_CA_BUNDLE'
     must be set to a path to a certificate bundle file, usually named
     'ca-bundle.crt' or 'curl-ca-bundle.crt'.  (This is normally done
     automatically for a binary installation of R, which installs
     'R_HOME/etc/curl-ca-bundle.crt' and sets 'CURL_CA_BUNDLE' to point
     to it if that environment variable is not already set.) For an
     updated certificate bundle, see
     <https://curl.se/docs/sslcerts.html>.  Currently one can download
     a copy from
     <https://raw.githubusercontent.com/bagder/ca-bundle/master/ca-bundle.crt>
     and set 'CURL_CA_BUNDLE' to the full path to the downloaded file.

     On Windows with 'method = "libcurl"', when R was linked with
     'libcurl' with 'Schannel' enabled, the connection fails if it
     cannot be established that the certificate has not been revoked.
     Some MITM proxies present particularly in corporate environments
     do not work with this behavior. It can be changed by setting
     environment variable 'R_LIBCURL_SSL_REVOKE_BEST_EFFORT' to 'TRUE',
     with the consequence of reducing security.

And I get

> libcurlVersion()
[1] "7.88.1"
attr(,"ssl_version")
[1] "OpenSSL/3.0.8 (Schannel)"
attr(,"libssh_version")
[1] "libssh2/1.10.0"
attr(,"protocols")
 [1] "dict"    "file"    "ftp"    
 [4] "ftps"    "gopher"  "gophers"
 [7] "http"    "https"   "imap"   
[10] "imaps"   "ldap"    "ldaps"  
[13] "mqtt"    "pop3"    "pop3s"  
[16] "rtsp"    "scp"     "sftp"   
[19] "smb"     "smbs"    "smtp"   
[22] "smtps"   "telnet"  "tftp"
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OK, thanks anyway. This is what I get:

> libcurlVersion()
[1] "7.88.1"
attr(,"ssl_version")
[1] "(OpenSSL/3.1.2) Schannel"
attr(,"libssh_version")
[1] "libssh2/1.10.0"
attr(,"protocols")
 [1] "dict"    "file"    "ftp"     "ftps"    "gopher"  "gophers" "http"   
 [8] "https"   "imap"    "imaps"   "ldap"    "ldaps"   "mqtt"    "pop3"   
[15] "pop3s"   "rtsp"    "scp"     "sftp"    "smb"     "smbs"    "smtp"   
[22] "smtps"   "telnet"  "tftp"
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