Question

Problem installing CRISPRseek

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ldumas9 • 0

@ldumas9-17689

Last seen 6.2 years ago

Dear support staff,

I have been trying to install CRISPRseek. I've tried it on several systems, using the commands specified on the Bioconductor page. There always seems to be packages that are not installed correctly (non-zero exit status), including CRISPRseek.

Below is the session info for the location I would like to install the package to:

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.4 (Maipo)

Matrix products: default
BLAS/LAPACK: /ssoft/spack/external/intel/2018.2/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.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

loaded via a namespace (and not attached):
[1] compiler_3.5.0

Bioconductor looks like it's installed correctly and the packages that are there are valid:

> library(BiocInstaller)
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
> biocValid()
[1] TRUE

However, CRISPRseek is absent:

> library(CRISPRseek)
Error in library(CRISPRseek) : there is no package called ‘CRISPRseek’

I've also tried using install.packages:

> install.packages("CRISPRseek")
Installing package into ‘/home/ldumas/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors

...

Selection: 55
Warning message:
package ‘CRISPRseek’ is not available (for R version 3.5.0)

I'm not sure how to proceed, any help would be appreciated!

Thank you,

Louis Dumas

crisprseek • 1.6k views

ADD COMMENT • link updated 6.2 years ago by Julie Zhu ★ 4.3k • written 6.2 years ago by ldumas9 • 0

score 0 · Answer 1 · 2018-10-08

Hi Louis,

BiocInstaller is the name of the package and biocLite() is the function in the package that does the installing. It looks like you haven't called biocLite("CRISPRseek").

FYI, BiocInstaller::biocLite() is being phased out and replaced by BiocManager::install():

install.packages("BiocManager")

library(BiocManager)

BiocManager::install("CRISPRseek")

The reason install.packages() did not work for installing CRISPRseek is because the package is in the Bioconductor repository (not CRAN). install.packages() can install packages from the Bioconductor repos but you need to provide the appropriate url as the 'repos' argument. BiocManager::install() (and the older BiocInstaller::biocLite()) both work 'out-of-the-box' because they look in both Bioconductor and CRAN repos by default.

> BiocManager::repositories()
                                               BioCsoft
           "https://bioconductor.org/packages/3.8/bioc"
                                                BioCann
"https://bioconductor.org/packages/3.8/data/annotation"
                                                BioCexp
"https://bioconductor.org/packages/3.8/data/experiment"
                                          BioCworkflows
      "https://bioconductor.org/packages/3.8/workflows"
                                                   CRAN
                        "https://cran.cnr.berkeley.edu"

More details on the man page:

> ?install

Valerie

score 0 · Answer 2 · 2018-10-08

Please try to install the CRISPRseek using source("http://bioconductor.org/biocLite.R") biocLite("CRISPRseek") Best regards, Julie On Oct 8, 2018, at 8:47 AM, ldumas9 [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: urldefense.proofpoint.com="" v2="" url?u="<a href=" http:="" <a="" href="http://https-3A__support.bioconductor.org" rel="nofollow">https-3A__support.bioconductor.org"="" rel="nofollow">https-3A__support.bioconductor.org&d=DwMDaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=tj2Ek7ZCE17iV0Hv3ywndQwqqS83dn2maL_5TF1ylqA&s=uWEw82FqyLuwxdgih6cHnGO00b5o2WHXNFukYmzx6iA&e="> User ldumas9<https: urldefense.proofpoint.com="" v2="" url?u="https-3A__support.bioconductor.org_u_17689_&d=DwMDaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=tj2Ek7ZCE17iV0Hv3ywndQwqqS83dn2maL_5TF1ylqA&s=ceuX15w1c4s23zXF7KA4LcQk3bpzCxeAO6a4k-mMDqo&e="> wrote Question: Problem installing CRISPRseek<https: urldefense.proofpoint.com="" v2="" url?u="https-3A__support.bioconductor.org_p_113742_&d=DwMDaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=tj2Ek7ZCE17iV0Hv3ywndQwqqS83dn2maL_5TF1ylqA&s=v8SHeOGXkzQZyTA6Na9SIic6h_29ZjOgzbXHC0dAS_A&e=">: Dear support staff, I have been trying to install CRISPRseek. I've tried it on several systems, using the commands specified on the Bioconductor page. There always seems to be packages that are not installed correctly (non-zero exit status), including CRISPRseek. Below is the session info for the location I would like to install the package to: > sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server 7.4 (Maipo) Matrix products: default BLAS/LAPACK: /ssoft/spack/external/intel/2018.2/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so<https: urldefense.proofpoint.com="" v2="" url?u="<a href=" http:="" <a="" href="<a href=" http:="" http-3A__libmkl-5Fintel-5Flp64.so"="" rel="nofollow">http://http-3A__libmkl-5Fintel-5Flp64.so" rel="nofollow">http-3A__libmkl-5Fintel-5Flp64.so"="" rel="nofollow">http-3A__libmkl-5Fintel-5Flp64.so&d=DwQDaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=tj2Ek7ZCE17iV0Hv3ywndQwqqS83dn2maL_5TF1ylqA&s=rF-xF6t_UVl-P73YnupsIPlL6P0eIpJHa3YsGe3ERtU&e="> 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 loaded via a namespace (and not attached): [1] compiler_3.5.0 Bioconductor looks like it's installed correctly and the packages that are there are valid: > library(BiocInstaller) Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help > biocValid() [1] TRUE However, CRISPRseek is absent: > library(CRISPRseek) Error in library(CRISPRseek) : there is no package called �CRISPRseek� I've also tried using install.packages: > install.packages("CRISPRseek") Installing package into �/home/ldumas/R/x86_64-pc-linux-gnu-library/3.5� (as �lib� is unspecified) --- Please select a CRAN mirror for use in this session --- Secure CRAN mirrors ... Selection: 55 Warning message: package �CRISPRseek� is not available (for R version 3.5.0) I'm not sure how to proceed, any help would be appreciated! Thank you, Louis Dumas ________________________________ Post tags: crisprseek You may reply via email or visit Problem installing CRISPRseek<https: urldefense.proofpoint.com="" v2="" url?u="https-3A__support.bioconductor.org_p_113742_&d=DwQDaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=tj2Ek7ZCE17iV0Hv3ywndQwqqS83dn2maL_5TF1ylqA&s=v8SHeOGXkzQZyTA6Na9SIic6h_29ZjOgzbXHC0dAS_A&e=">