Question

package instalation

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dartehyaw • 0

@e359093b

Last seen 2.8 years ago

U.S.A

How do I download and install "RTCGA.clinical" package? I have tried the following command to no avail. if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("RTCGA.clinical")

Thanks ```

Clinical • 1.7k views

ADD COMMENT • link 2.8 years ago dartehyaw • 0

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Please provide you output/error, since those lines of code work for me:

(note that I included force=TRUE because I had the package already installed, and this argument is needed for a reinstall).

> if (!require("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
> 
> BiocManager::install("RTCGA.clinical", force=TRUE)
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.1 Patched (2021-09-28
  r80981)
Installing package(s) 'RTCGA.clinical'
installing the source package ‘RTCGA.clinical’

trying URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/RTCGA.clinical_20151101.24.0.tar.gz'
Content type 'application/x-gzip' length 14652323 bytes (14.0 MB)
downloaded 14.0 MB

* installing *source* package 'RTCGA.clinical' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RTCGA.clinical'
    finding HTML links ... done
    clinical                                html  
REDIRECT:topic   ACC.clinical,BLCA.clinical,BRCA.clinical,CESC.clinical,CHOL.clinical,COAD.clinical,COADREAD.clinical,DLBC.clinical,ESCA.clinical,FPPP.clinical,GBM.clinical,GBMLGG.clinical,HNSC.clinical,KICH.clinical,KIPAN.clinical,KIRC.clinical,KIRP.clinical,LAML.clinical,LGG.clinical,LIHC.clinical,LUAD.clinical,LUSC.clinical,MESO.clinical,OV.clinical,PAAD.clinical,PCPG.clinical,PRAD.clinical,READ.clinical,SARC.clinical,SKCM.clinical,STAD.clinical,STES.clinical,TGCT.clinical,THCA.clinical,THYM.clinical,UCEC.clinical,UCS.clinical,UVM.clinical -> clinical.html [ FAIL ]
    finding level-2 HTML links ... done

** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RTCGA.clinical)

The downloaded source packages are in
        ‘C:\TMP_R\Rtmp6pR6ad\downloaded_packages’
> 
> 
> library(RTCGA.clinical)
Loading required package: RTCGA
Welcome to the RTCGA (version: 1.24.0).
> 




> sessionInfo()
R version 4.1.1 Patched (2021-09-28 r80981)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

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

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

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

other attached packages:
[1] RTCGA.clinical_20151101.24.0 RTCGA_1.24.0                
[3] BiocManager_1.30.16

ADD REPLY • link 2.8 years ago Guido Hooiveld ★ 4.1k

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Thanks for the response. I am installing it for the first time. Could not break through with what you gave. Thanks anyway

ADD REPLY • link 2.8 years ago dartehyaw • 0

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It is not clear to me what you mean...

If you copy the code below, and paste it in a freshly opened R session, then the package should install. The remainder of my output was to show you that the installation procedure ran, and finally that the package could be loaded in the R session (by using library(RTCGA.clinical) ) .

if (!require("BiocManager", quietly = TRUE))
     install.packages("BiocManager")

BiocManager::install("RTCGA.clinical", force=TRUE)

ADD REPLY • link 2.8 years ago Guido Hooiveld ★ 4.1k

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if (!require("BiocManager", quietly = TRUE))

install.packages("BiocManager") Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
BiocManager::install("RTCGA.clinical", force=TRUE) 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://cran.rstudio.com/

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01) Installing package(s) 'RTCGA.clinical' installing the source package ‘RTCGA.clinical’

trying URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/RTCGA.clinical_20151101.24.0.tar.gz' Content type 'application/x-gzip' length 14652323 bytes (14.0 MB) downloaded 14.0 MB

installing source package 'RTCGA.clinical' ... using staged installation R data * moving datasets to lazyload DB inst byte-compile and prepare package for lazy loading Error: package or namespace load failed for 'RTCGA' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): namespace 'rlang' 0.4.12 is being loaded, but >= 1.0.0 is required Execution halted ERROR: lazy loading failed for package 'RTCGA.clinical'
removing 'C:/Users/HP/Documents/R/win-library/4.1/RTCGA.clinical'

The downloaded source packages are in ‘C:\Users\HP\AppData\Local\Temp\Rtmp69JU9M\downloaded_packages’ Installation paths not writeable, unable to update packages path: C:/Program Files/R/R-4.1.2/library packages: class, foreign, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial Old packages: 'fansi', 'glue', 'magrittr', 'rlang', 'survival' Update all/some/none? [a/s/n]:

Above is the output from the command you sent.

ADD REPLY • link 2.8 years ago dartehyaw • 0

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OK, note this error message:

Error: package or namespace load failed for 'RTCGA' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): namespace 'rlang' 0.4.12 is being loaded, but >= 1.0.0 is required

It basically states the installed version of the package rlang does not meet the requirements, and you should update it.

Next note this message:

> Installation paths not writeable, unable to update packages

This means you started R on your Win10 machine with insufficient user rights; or you did start R as a different user that installed R (that obviously had installation rights). Although R should be able to handle this types of setups, when i need to install or update packages, I always run R on my Win10 machine as local administrator.

Lastly, if you could solve the 2nd issue then you would simply say a[ll] to this (last) question (and then install the package RTCGA.clinical again):

Update all/some/none? [a/s/n]:

ADD REPLY • link 2.8 years ago Guido Hooiveld ★ 4.1k

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Thank you very much. Installation completed.

ADD REPLY • link 2.8 years ago dartehyaw • 0

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Entering edit mode

Thanks for the response. I am installing it for the first time. Could not break through with what you gave. Thanks anyway

ADD REPLY • link 2.8 years ago dartehyaw • 0