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Question: Compiler/linker problem of mzR (and Rcpp)
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gravatar for cheng68
20 months ago by
cheng680
cheng680 wrote:

Hi everyone,

I have used the newest version of R (3.2.2 and 3.2.3) and Bioconductor (3.2), but I still could not successfully load the package mzR, it seems that it was one of the issues many people had mentioned -- compiler/linker. Below is the error message and the sessionInfo(). Note that I used R 3.2.3 first although the below was the output when I tried R 3.2.2.

 

> library(mzR)
Error : .onLoad failed in loadNamespace() for 'mzR', details:
  call: description[["RcppModules"]]
  error: subscript out of bounds
In addition: Warning messages:
1: In fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.12.1)
than is installed on your system (0.12.3). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
2: In packageDescription(pkg, lib.loc = lib) : no package 'mzR' was found
Error: package or namespace load failed for ‘mzR’
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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

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

other attached packages:
[1] Rcpp_0.12.3   limma_3.24.15

loaded via a namespace (and not attached):
[1] ProtGenerics_1.0.0  parallel_3.2.2      Biobase_2.28.0     
[4] BiocGenerics_0.14.0

 

I hope the output is not too messy to read. Look forward to hearing some helpful advice.

 

Many thanks in advance,

Mike C.

ADD COMMENTlink modified 20 months ago by Laurent Gatto840 • written 20 months ago by cheng680

This issue bothers me because these two are some of the dependencies needed for compiling our own r package.

ADD REPLYlink written 20 months ago by cheng680
0
gravatar for Laurent Gatto
20 months ago by
Laurent Gatto840
United Kingdom
Laurent Gatto840 wrote:

I don't think that the problem is the Rcpp version. The error is

Error : .onLoad failed in loadNamespace() for 'mzR', details:
  call: description[["RcppModules"]]
  error: subscript out of bounds

which is new however to me.

I have nevertheless committed a new mzR version 2.4.1, which will be build with Rcpp 0.12.3. Please try to install it in about 24 hours and let us know if this helps.
 

ADD COMMENTlink written 20 months ago by Laurent Gatto840

mzR 2.4.1, that has been rebuild with the latest Rcpp is now available through biocLite. Let us know if you still experience the error.

ADD REPLYlink modified 20 months ago by Dan Tenenbaum ♦♦ 8.2k • written 20 months ago by Laurent Gatto840

Unfortunately, I am still experiencing the same error, even in the case when I installed the package by the local source tar ball. However, everything works well when I run R in Linux.

ADD REPLYlink written 20 months ago by cheng680
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