BioC 2.14: CHECK report for externalVector on zin2

Package: externalVector

Version: 1.27.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings externalVector_1.27.0.tar.gz

StartedAt: 2013-10-08 00:07:57 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 00:08:04 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 6.9 seconds

RetCode: 1

Status:  ERROR

CheckDir: externalVector.Rcheck

Warnings: NA

* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/externalVector.Rcheck’
* using R Under development (unstable) (2013-10-02 r64018)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘externalVector/DESCRIPTION’ ... OK
* this is package ‘externalVector’ version ‘1.27.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘externalVector’ can be installed ... [4s/6s] ERROR
Installation failed.
See ‘/home/biocbuild/bbs-2.14-bioc/meat/externalVector.Rcheck/00install.out’ for details.

* installing *source* package ‘externalVector’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c allocator.c -o allocator.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c arraySummary.c -o arraySummary.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c coerce.c -o coerce.o
coerce.c: In function ‘ComplexFromString’:
coerce.c:213:18: warning: initialization from incompatible pointer type [enabled by default]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c externalVector.c -o externalVector.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c groups.c -o groups.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c math.c -o math.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c slice.c -o slice.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c storage.c -o storage.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c subscript.c -o subscript.o
subscript.c: In function ‘SubscriptList’:
subscript.c:422:20: warning: assignment from incompatible pointer type [enabled by default]
subscript.c:464:16: warning: assignment from incompatible pointer type [enabled by default]
subscript.c:478:28: warning: assignment from incompatible pointer type [enabled by default]
gcc -std=gnu99 -shared -L/usr/local/lib -o externalVector.so allocator.o arraySummary.o coerce.o externalVector.o groups.o math.o slice.o storage.o subscript.o -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-bioc/meat/externalVector.Rcheck/externalVector/libs
** R
** preparing package for lazy loading
Error in setGeneric("anyNA", function(x) standardGeneric("anyNA")) : 
  ‘anyNA’ is a primitive function;  methods can be defined, but the generic function is implicit, and cannot be changed.
Error : unable to load R code in package ‘externalVector’
ERROR: lazy loading failed for package ‘externalVector’
* removing ‘/home/biocbuild/bbs-2.14-bioc/meat/externalVector.Rcheck/externalVector’