[Bioc-devel] FW: Package build error

[Hervé Pagès]

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/veracruz1-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
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