Search
Question: Problem with mzR and/or Rcpp?
0
gravatar for elabiead
14 months ago by
elabiead0
elabiead0 wrote:

Dear bioconductor team,

When I try to run the msPurity package on R (which is using the XCMS package) I run in the following warning message:

Warning message:
In fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.12.8)
than is installed on your system (0.12.11). 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.

I already tried to solve them according to the instructions on "

https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue" but it did not help. 

Here is also the sessionInfo which was mentioned in the warning message (hope I understood that right):

> sessionInfo("msPurity")
R version 3.3.1 (2016-06-21)
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  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
character(0)

other attached packages:
[1] msPurity_1.0.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.11         lattice_0.20-33      codetools_0.2-14     grDevices_3.3.1     
 [5] snow_0.4-2           foreach_1.4.3        grid_3.3.1           plyr_1.8.4          
 [9] magrittr_1.5         datasets_3.3.1       BiocInstaller_1.24.0 stringi_1.1.5       
[13] utils_3.3.1          reshape2_1.4.2       fastcluster_1.1.22   graphics_3.3.1      
[17] mzR_2.8.1            base_3.3.1           BiocParallel_1.8.2   RColorBrewer_1.1-2  
[21] iterators_1.0.8      tools_3.3.1          stringr_1.2.0        Biobase_2.34.0      
[25] ProtGenerics_1.6.0   parallel_3.3.1       BiocGenerics_0.20.0  stats_3.3.1         
[29] doSNOW_1.0.14        methods_3.3.1 
      
> sessionInfo("Rcpp")
R version 3.3.1 (2016-06-21)
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  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
character(0)

other attached packages:
[1] Rcpp_0.12.11

loaded via a namespace (and not attached):
 [1] lattice_0.20-33      codetools_0.2-14     grDevices_3.3.1      snow_0.4-2          
 [5] foreach_1.4.3        msPurity_1.0.0       grid_3.3.1           plyr_1.8.4          
 [9] magrittr_1.5         datasets_3.3.1       BiocInstaller_1.24.0 stringi_1.1.5       
[13] utils_3.3.1          reshape2_1.4.2       fastcluster_1.1.22   graphics_3.3.1      
[17] mzR_2.8.1            base_3.3.1           BiocParallel_1.8.2   RColorBrewer_1.1-2  
[21] iterators_1.0.8      tools_3.3.1          stringr_1.2.0        Biobase_2.34.0      
[25] ProtGenerics_1.6.0   parallel_3.3.1       BiocGenerics_0.20.0  stats_3.3.1         
[29] doSNOW_1.0.14        methods_3.3.1       
> sessionInfo("mzR")
R version 3.3.1 (2016-06-21)
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  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
character(0)

other attached packages:
[1] mzR_2.8.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.11         lattice_0.20-33      codetools_0.2-14     grDevices_3.3.1     
 [5] snow_0.4-2           foreach_1.4.3        msPurity_1.0.0       grid_3.3.1          
 [9] plyr_1.8.4           magrittr_1.5         datasets_3.3.1       BiocInstaller_1.24.0
[13] stringi_1.1.5        utils_3.3.1          reshape2_1.4.2       fastcluster_1.1.22  
[17] graphics_3.3.1       base_3.3.1           BiocParallel_1.8.2   RColorBrewer_1.1-2  
[21] iterators_1.0.8      tools_3.3.1          stringr_1.2.0        Biobase_2.34.0      
[25] ProtGenerics_1.6.0   parallel_3.3.1       BiocGenerics_0.20.0  stats_3.3.1         
[29] doSNOW_1.0.14        methods_3.3.1   

Do you know if there is a way to solve this problem or do I have to give you more information on it first? Anyway many thanks for your help in advance!

Greetings

Yasin

ADD COMMENTlink modified 14 months ago by Laurent Gatto1.0k • written 14 months ago by elabiead0
0
gravatar for Laurent Gatto
14 months ago by
Laurent Gatto1.0k
United Kingdom
Laurent Gatto1.0k wrote:

What you see is a warning that highlights the version mismatch. In most cases, it can be ignored and everything will work as expected. In the past, when Rcpp had more substantial changes, error happened. If this happens, please report back. Otherwise, enjoy mzR and msPurity.

ADD COMMENTlink written 14 months ago by Laurent Gatto1.0k

Note also that you are using a somewhat old version of R (current version is 3.4.1) and, as a result, the old release of Bioconductor. You won't be able to get the latest mzR (that is using the latest Rcpp) without a more recent R.

ADD REPLYlink written 14 months ago by Laurent Gatto1.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 180 users visited in the last hour