Question: Why package "BiocLite" is not available (for R version 3.6.1)
0
gravatar for 3076782769
29 days ago by
30767827690
30767827690 wrote:

Hi All,

Sorry to disturb,

I am following bioconductor website,source("http://www.bioconductor.org/biocLite.R")

Below is my commands:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
##:
> install.packages("BiocManager")
Installing package into ‘C:/Users/Administrator/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/BiocManager_1.30.9.zip'
Content type 'application/zip' length 100320 bytes (97 KB)
downloaded 97 KB

package ‘BiocManager’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\Administrator\AppData\Local\Temp\RtmpmUMeyD\downloaded_packages

BiocManager::install()
##:
> BiocManager::install()
Bioconductor version 3.10 (BiocManager 1.30.9), R 3.6.1 (2019-07-05)


BiocManager::install(c("GenomicFeatures", "AnnotationDbi"))
##:
> BiocManager::install(c("GenomicFeatures", "AnnotationDbi"))
Bioconductor version 3.10 (BiocManager 1.30.9), R 3.6.1 (2019-07-05)
Installing package(s) 'GenomicFeatures', 'AnnotationDbi'
trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/windows/contrib/3.6/GenomicFeatures_1.38.0.zip'
Content type 'application/zip' length 2242939 bytes (2.1 MB)
downloaded 2.1 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/windows/contrib/3.6/AnnotationDbi_1.48.0.zip'
Content type 'application/zip' length 5226197 bytes (5.0 MB)
downloaded 5.0 MB

package ‘GenomicFeatures’ successfully unpacked and MD5 sums checked
package ‘AnnotationDbi’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\Administrator\AppData\Local\Temp\RtmpmUMeyD\downloaded_packages

BiocManager::install("biocLite")
##:
> BiocManager::install("biocLite")
Bioconductor version 3.10 (BiocManager 1.30.9), R 3.6.1 (2019-07-05)
Installing package(s) 'biocLite'
Warning message:
package ‘biocLite’ is not available (for R version 3.6.1) 

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936 
[2] LC_CTYPE=Chinese (Simplified)_China.936   
[3] LC_MONETARY=Chinese (Simplified)_China.936
[4] LC_NUMERIC=C                              
[5] LC_TIME=Chinese (Simplified)_China.936    

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.9 compiler_3.6.1     tools_3.6.1       

So is there anyone can help me, what I am supposed to do now?

Thank you very much!

Regards, Huihui

bioclite • 477 views
ADD COMMENTlink modified 29 days ago by shepherl ♦♦ 1.7k • written 29 days ago by 30767827690
Answer: C: Why package "BiocLite" is not available (for R version 3.6.1)
2
gravatar for Lluís Revilla Sancho
29 days ago by
European Union
Lluís Revilla Sancho530 wrote:

The biocLite script was deprecated as it could induce to errors and installing malicious code. If you are using R 3.6.1 you don't need it any more, with BiocManager you can do the same you previously did with biocLite and BiocInstaller.

For completeness, you see that BiocInstaller was removed on Bioconductor version 3.9

ADD COMMENTlink modified 29 days ago • written 29 days ago by Lluís Revilla Sancho530
Answer: Why package "BiocLite" is not available (for R version 3.6.1)
2
gravatar for shepherl
29 days ago by
shepherl ♦♦ 1.7k
United States
shepherl ♦♦ 1.7k wrote:

What Lluís says is correct. For R versions > 3.5.0 the new way to install Bioconductor and related packages is through BiocManager as documented on our install page. biocLite was a function not a package and as Lluís stated had security risks. Please install all Bioconductor (and CRAN if you like) packages using BiocManager::install( ).

ADD COMMENTlink written 29 days ago by shepherl ♦♦ 1.7k
2

You can even install GitHub packages using BiocManager::install, so there really is no reason to use anything else to install packages.

ADD REPLYlink written 29 days ago by James W. MacDonald52k
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