Hi Lucas, thanks for your QA effort.
On Wed, May 02, 2018 at 10:53:42PM +0200, Lucas Nussbaum wrote: > > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE > > -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE > > -I"/usr/lib/R/site-library/S4Vectors/include" > > -I"/usr/lib/R/site-library/IRanges/include" > > -I"/usr/lib/R/site-library/XVector/include" > > -I"/usr/lib/R/site-library/Biostrings/include" > > -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 > > -fdebug-prefix-map=/build/r-base-3.4.4=. -fstack-protector-strong -Wformat > > -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c writevcf.c > > -o writevcf.o > > Error: Functions found when exporting methods from the namespace 'IRanges' > > which are not S4 generic: 'endoapply', 'mendoapply' > > Execution halted > > Error: Functions found when exporting methods from the namespace 'IRanges' > > which are not S4 generic: 'endoapply', 'mendoapply' > > Execution halted > > Error: Functions found when exporting methods from the namespace 'IRanges' > > which are not S4 generic: 'endoapply', 'mendoapply' > > Execution halted > > g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o VariantAnnotation.so > > Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o > > XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o > > writevcf.o /libbam.a /libbcf.a /libtabix.a -lz -pthread -L/usr/lib/R/lib -lR > > Error: Functions found when exporting methods from the namespace 'IRanges' > > which are not S4 generic: 'endoapply', 'mendoapply' > > Execution halted > > Error: Functions found when exporting methods from the namespace 'IRanges' > > which are not S4 generic: 'endoapply', 'mendoapply' > > Execution halted > > Error: Functions found when exporting methods from the namespace 'IRanges' > > which are not S4 generic: 'endoapply', 'mendoapply' > > Execution halted > > g++: error: /libbam.a: No such file or directory > > g++: error: /libbcf.a: No such file or directory > > g++: error: /libtabix.a: No such file or directory > > make[1]: *** [/usr/share/R/share/make/shlib.mk:6: VariantAnnotation.so] > > Error 1 while this issue seems totally unrelated to the new upstream version of BioConductor packages I will upload all preconditions for the new version first and check the issue in the new version. Kind regards Andreas. -- http://fam-tille.de