Installation failed: error setting certificate verify locations

[fruce-ki]

I am failing to install wasabi, and I don't understand why.

> biocLite("COMBINE-lab/wasabi")

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).
Installing github package(s) ‘COMBINE-lab/wasabi’
Installation failed: error setting certificate verify locations:
  CAfile: microsoft-r-cacert.pem
  CApath: none

Why would there be a microsoft certificate error on a linux system?

> sessionInfo()

R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.8 (Final)

Matrix products: default
BLAS: /homes/kfroussios/local_installs/miniconda3/envs/mybasics/lib/R/lib/libRblas.so
LAPACK: /homes/kfroussios/local_installs/miniconda3/envs/mybasics/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] BiocInstaller_1.28.0 RevoUtils_10.0.8     RevoUtilsMath_10.0.1

loaded via a namespace (and not attached):
 [1] httr_1.3.1      compiler_3.4.3  R6_2.2.2        tools_3.4.3    
 [5] withr_2.1.2     curl_3.2        memoise_1.1.0   git2r_0.21.0   
 [9] digest_0.6.15   devtools_1.13.5

My R is installed and accessed through a miniconda environment. It is located in my home directory. So far I have had no problems with any other packages, from CRAN or Bioconductor. Wasabi is the only one that refuses to install.

[fruce-ki]

Although it repeatedly failed yesterday, today I was unable to recreate the issue from a different node of our cluster. Must be yet another inconsistency in the setup of our nodes... You can probably ignore this issue, although it is still weird that only wasabi was affected by whatever caused this.

[channsoden]

Myself as well. I'm using an Anaconda install.

> biocLite("COMBINE-lab/wasabi")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).
Installing github package(s) ‘COMBINE-lab/wasabi’
Installation failed: error setting certificate verify locations:
  CAfile: microsoft-r-cacert.pem
  CApath: none

Unfortunately this is my local machine, so I can't just try another node.

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /home/christopher/anaconda3/lib/R/lib/libRblas.so
LAPACK: /home/christopher/anaconda3/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] BiocInstaller_1.28.0 RevoUtils_10.0.8     RevoUtilsMath_10.0.1

loaded via a namespace (and not attached):
 [1] httr_1.3.1      compiler_3.4.3  R6_2.2.2        tools_3.4.3    
 [5] withr_2.1.1     curl_3.1        memoise_1.1.0   git2r_0.21.0   
 [9] digest_0.6.13   devtools_1.13.5

On a related note, using conda to install wasabi also fails.

$ conda install --channel bioconda r-wasabi
Solving environment: failed

UnsatisfiableError: The following specifications were found to be in conflict:
  - r-wasabi
Use "conda info <package>" to see the dependencies for each package.

[rob-p]

Hi @channsoden,

Can you give this solution a try? It seems it may be due to R-curl.

[channsoden]

Hi @rob-p,

Thanks for your response! I've found a way around using wasabi, so I'm not going to put any more effort into troubleshooting the install. Hopefully this helps someone else later.