[Bioc-devel] FW: Package build error

[Ioannis Vardaxis]

Hey,


Ok, I have made the changes to the DESCRIPTION file adding the c++11 you
suggested, and also fixed the Rd files. I will try to push the package
again soon and see what I get.


Thanks,
-- 
Ioannis Vardaxis

Stipendiat IMF
NTNU




On 27/10/2017, 19:03, "Hervé Pagès" <hpages at fredhutch.org> wrote:

>Adding 'SystemRequirements: C++11' works for me (I'm on Linux):
>
>hpages at latitude:~/MACPET$ git diff
>diff --git a/DESCRIPTION b/DESCRIPTION
>index d8238b6..061d692 100644
>--- a/DESCRIPTION
>+++ b/DESCRIPTION
>@@ -7,6 +7,7 @@ Author: Ioannis Vardaxis
>  Maintainer: Ioannis Vardaxis <ioannis.vardaxis at ntnu.no>
>  Description: The MACPET package can be used for binding site analysis
>for ChIA-PET data. MACPET reads ChIA-PET data in BAM or SAM for
>  License: GPL-3
>+SystemRequirements: C++11
>  Encoding: UTF-8
>  LazyData: true
>  ByteCompile: true
>
>
>hpages at latitude:~$ Rbiocdev CMD INSTALL MACPET
>* installing to library '/home/hpages/R/R-3.4.2-bioc36/library'
>* installing *source* package 'MACPET' ...
>** libs
>g++ -std=gnu++11 -I/home/hpages/R/R-3.4.2-bioc36/include -DNDEBUG
>-I"/home/hpages/R/R-3.4.2-bioc36/library/Rcpp/include"
>-I/usr/local/include   -fpic  -g -O2 -c
>PeakFinderSubFunctions_SGT_Rcpp.cpp -o PeakFinderSubFunctions_SGT_Rcpp.o
>g++ -std=gnu++11 -I/home/hpages/R/R-3.4.2-bioc36/include -DNDEBUG
>-I"/home/hpages/R/R-3.4.2-bioc36/library/Rcpp/include"
>-I/usr/local/include   -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
>g++ -std=gnu++11 -shared -L/home/hpages/R/R-3.4.2-bioc36/lib
>-L/usr/local/lib64 -o MACPET.so PeakFinderSubFunctions_SGT_Rcpp.o
>RcppExports.o -L/home/hpages/R/R-3.4.2-bioc36/lib -lR
>installing to /home/hpages/R/R-3.4.2-bioc36/library/MACPET/libs
>** R
>** inst
>** byte-compile and prepare package for lazy loading
>** help
>...
>
>Works for other BioC packages too e.g. InteractionSet
>(showing compilation output on Mac):
>
> 
>https://bioconductor.org/checkResults/3.6/bioc-LATEST/InteractionSet/verac
>ruz1-install.html
>
>It would be more useful if you showed us the full output of
>'R CMD INSTALL'.
>
>But you should not hesitate to add 'SystemRequirements: C++11', bump
>the version, and see what the single package builder says (provide the
>link if you want to discuss it).
>
>Thanks,
>H.
>
>
>On 10/27/2017 09:50 AM, Ioannis Vardaxis wrote:
>> Hey again,
>>
>>
>> I think I have fixed the \insertRef macro problem now. However I still
>> need help with the c++11 problems I mentioned in the previous email.
>>
>> My package builds and R-checks (and BiocChecks) with no errors and
>>warning
>> though. I get some notes from BiocCheck but I don¹t think they are of
>> immediate importance.
>>
>> Best,
>>
>
>-- 
>Hervé Pagès
>
>Program in Computational Biology
>Division of Public Health Sciences
>Fred Hutchinson Cancer Research Center
>1100 Fairview Ave. N, M1-B514
>P.O. Box 19024
>Seattle, WA 98109-1024
>
>E-mail: hpages at fredhutch.org
>Phone:  (206) 667-5791
>Fax:    (206) 667-1319