TCGAbiolinks installation error because of R.oo installation error
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Talip Zengin ▴ 10
@talip-zengin-14290
Last seen 11 months ago
Mugla, Turkiye

Hi, I tried to install TCGAbiolinks for both R-4.0.1 and R-4.0.2 but I got R.oo installation error below while installing TCGAbiolinks package. It is very surprising to get R package installation error in itself. How can I solve this problem?

    BiocManager::install("BioinformaticsFMRP/TCGAbiolinks", dependencies=TRUE)

> ...  
> installing source package ‘R.oo’ ... * package ‘R.oo’
> successfully unpacked and MD5 sums checked * using staged installation
> * R * inst ** byte-compile and prepare package for lazy loading Error in RccViolationException("Class names must begin with a letter: ", : 
> "RccViolationException" function can not be found Error: unable to
> load R code in package ‘R.oo’ Stopped working ERROR: lazy loading
> failed for package ‘R.oo’ * removing
> ‘/truba/home/tzengin/R/lib64/R/library/R.oo’ Error: Failed to install
> 'TCGAbiolinks' from GitHub: installation of package ‘R.oo’ had
> non-zero exit status

    install.packages("R.oo")

> URL 'https://cran.rstudio.com/src/contrib/R.oo_1.23.0.tar.gz' trying
> Content type 'application/x-gzip' length 381285 bytes (372 KB)
> ================================================== downloaded 372 KB
> 
> installing source package ‘R.oo’ ... package ‘R.oo’ successfully
> unpacked and MD5 sums checked using staged installation R inst
> byte-compile and prepare package for lazy loading Error in
> RccViolationException("Class names must begin with a letter: ", : 
> "RccViolationException" command not found Error: unable to load R code
> in package ‘R.oo’ Stop working ERROR: lazy loading failed for package
> ‘R.oo’ * removing ‘/truba/home/tzengin/R/lib64/R/library/R.oo’
> 
> The downloaded source packages are in
> ‘/tmp/RtmpL6TpHe/downloaded_packages’ Updating HTML index of packages
> in '.Library' Making 'packages.html' ... done Warning message: In
> install.packages("R.oo") : installation of package ‘R.oo’ had non-zero
> exit status

    sessionInfo()

> R version 4.0.1 (2020-06-06) Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: CentOS Linux 7 (Core)
> 
> Matrix products: default BLAS: 
> /truba/home/tzengin/R/lib64/R/lib/libRblas.so LAPACK:
> /truba/home/tzengin/R/lib64/R/lib/libRlapack.so
> 
> locale: [1] LCCTYPE=trTR.UTF-8 LCNUMERIC=C  [3] LCTIME=trTR.UTF-8
> LCCOLLATE=trTR.UTF-8 [5] LCMONETARY=trTR.UTF-8 LCMESSAGES=trTR.UTF-8
> [7] LCPAPER=trTR.UTF-8 LCNAME=C [9] LCADDRESS=C LCTELEPHONE=C [11]
> LCMEASUREMENT=trTR.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages: [1] stats graphics grDevices utils  datasets
> methods base
> 
> other attached packages: [1] remotes_2.2.0
> 
> loaded via a namespace (and not attached): [1] BiocManager1.30.10
> compiler4.0.1 tools4.0.1 [4] curl4.3
TCGAbiolinks R.oo • 196 views
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@james-w-macdonald-5106
Last seen 9 hours ago
United States

That's weird. I can install R.oo without problems. Can you try installing it directly?

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How? I have tried install.packages("R.oo") and installation from source package but got same error. Can it be because of missing of linux packages at Centos7 system or because of installing R locally?

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> library(BiocManager)
Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help
> install("R.oo")
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
Installing package(s) 'R.oo'
trying URL 'https://cran.rstudio.com/src/contrib/R.oo_1.23.0.tar.gz'
Content type 'application/x-gzip' length 381285 bytes (372 KB)
==================================================
downloaded 372 KB

* installing *source* package  R.oo  ...
** package  R.oo  successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (R.oo)

The downloaded source packages are in
     /tmp/RtmpnPxLen/downloaded_packages 
Installation path not writeable, unable to update packages: boot, class,
  foreign, KernSmooth, MASS, nlme, nnet, spatial, survival

> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /share/apps/MKL/mkl-2019.3/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64_lin/libmkl_gf_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     

other attached packages:
[1] BiocManager_1.30.10

loaded via a namespace (and not attached):
[1] compiler_4.0.0 tools_4.0.0   

> system("cat /etc/redhat-release")
CentOS Linux release 7.6.1810 (Core) 

So I doubt it's an OS problem. Maybe something weird about your R install?

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Hi, I have installed R as below. Only difference is --with-pcre1 option because ./configure --prefix=$HOME/R gives an error as pcre2 is needed. --with-pcre1 is recommended as alternative.

wget http://cran.rstudio.com/src/base/R-4/R-4.0.1.tar.gz
tar xvf R-4.0.1.tar.gz 
cd R-4.0.1/
./configure --prefix=$HOME/R --with-pcre1
make && make install
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