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Error inR load libary

Error inR load libary

by Youdong Hu - Number of replies: 2

Hello, I meet a problem when run the 6 step, where show a error for TCGAbiolinks shown below, but looks it already in the r-bib. I tried with remove the r-bib shortcut and re-run steps 1-5 and looks no problem. Not sure how to fix that, did any one have any experience for that? Thanks!^_^


R[write to console]: Error: package or namespace load failed for ‘TCGAbiolinks’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘Rcpp’

Error: package or namespace load failed for ‘TCGAbiolinks’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘Rcpp’
---------------------------------------------------------------------------
RRuntimeError                             Traceback (most recent call last)
/usr/local/lib/python3.7/dist-packages/rpy2/ipython/rmagic.py in eval(self, code)
    267                 # Need the newline in case the last line in code is a comment.
--> 268                 value, visible = ro.r("withVisible({%s\n})" % code)
    269             except (ri.embedded.RRuntimeError, ValueError) as exception:


10 frames
RRuntimeError: Error: package or namespace load failed for ‘TCGAbiolinks’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘Rcpp’

During handling of the above exception, another exception occurred:

RInterpreterError                         Traceback (most recent call last)
<decorator-gen-119> in R(self, line, cell, local_ns)

/usr/local/lib/python3.7/dist-packages/rpy2/ipython/rmagic.py in eval(self, code)
    271                 warning_or_other_msg = self.flush()
    272                 raise RInterpreterError(code, str(exception),
--> 273                                         warning_or_other_msg)
    274             text_output = self.flush()
    275             return text_output, value, visible[0]

RInterpreterError: Failed to parse and evaluate line 'library(scales)\nlibrary(BiocManager)\nlibrary(TCGAbiolinks)\nlibrary(SummarizedExperiment)\nlibrary(DT)\nlibrary(NOISeq)\nlibrary(ComplexHeatmap)\nlibrary(EDASeq)\n\nprint(sessionInfo())'.
R error message: 'Error: package or namespace load failed for ‘TCGAbiolinks’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):\n there is no package called ‘Rcpp’'

In reply to Youdong Hu

Re: Error inR load libary

by Noelia Dasilva Freire -
I don't know if it's a little bit late, but I had the same problem and after repeating the process for more than hour getting the same result I started to run the code into R and it's working well for me. Hope it still helps!!! Good luck! 😊
In reply to Noelia Dasilva Freire

Re: Error inR load libary

by Youdong Hu -
Thanks Noelia, The package dependence of python makes me crazy. So I did not install R on my computer, so I try with the google lab one. Anyway, still thanks your experience. Maybe I need to try with it after installation.^_^