[BioC] IRanges install error with parallel/mcmapply

[Dino Jolic]

Hi,

I had IRanges Version: 1.14.4 installed before and recently I had to reinstall all of my R packages. Now, I've got an error while installing the newer 1.16.4

* installing *source* package ‘IRanges’ ...
** libs
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c AEbufs.c -o AEbufs.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c CompressedList_class.c -o CompressedList_class.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c DataFrame_class.c -o DataFrame_class.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c GappedRanges_class.c -o GappedRanges_class.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c Grouping_class.c -o Grouping_class.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c Hits_class.c -o Hits_class.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c IRanges_class.c -o IRanges_class.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c IRanges_constructor.c -o IRanges_constructor.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c IRanges_utils.c -o IRanges_utils.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c IntervalTree.c -o IntervalTree.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c R_init_IRanges.c -o R_init_IRanges.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c RangedData_class.c -o RangedData_class.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c Ranges_comparison.c -o Ranges_comparison.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c RleViews_utils.c -o RleViews_utils.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c Rle_class.c -o Rle_class.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c Rle_utils.c -o Rle_utils.o
Rle_utils.c: In function ‘Rle_integer_runq’:
Rle_utils.c:735:6: warning: implicit declaration of function ‘roundingScale’ [-Wimplicit-function-declaration]
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c SEXP_utils.c -o SEXP_utils.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c SharedDouble_utils.c -o SharedDouble_utils.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c SharedInteger_utils.c -o SharedInteger_utils.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c SharedRaw_utils.c -o SharedRaw_utils.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c SharedVector_class.c -o SharedVector_class.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c SimpleList_class.c -o SimpleList_class.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c Vector_class.c -o Vector_class.o
Vector_class.c: In function ‘vector_seqselect’:
Vector_class.c:95:4: warning: implicit declaration of function ‘UNIMPLEMENTED_TYPE’ [-Wimplicit-function-declaration]
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c XDoubleViews_utils.c -o XDoubleViews_utils.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c XIntegerViews_utils.c -o XIntegerViews_utils.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c XRawList_comparison.c -o XRawList_comparison.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c XVectorList_class.c -o XVectorList_class.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c XVector_class.c -o XVector_class.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c common.c -o common.o
common.c: In function ‘firstWordInFile’:
common.c:1787:6: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c compact_bitvector.c -o compact_bitvector.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c coverage.c -o coverage.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c dlist.c -o dlist.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c encode_overlaps.c -o encode_overlaps.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c errabort.c -o errabort.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c hash_utils.c -o hash_utils.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c int_utils.c -o int_utils.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c localmem.c -o localmem.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c memalloc.c -o memalloc.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c rbTree.c -o rbTree.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c safe_arithm.c -o safe_arithm.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c sort_utils.c -o sort_utils.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c str_utils.c -o str_utils.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c ucsc_handlers.c -o ucsc_handlers.o
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -O3 -pipe  -g -c vector_copy.c -o vector_copy.o
gcc -std=gnu99 -shared -o IRanges.so AEbufs.o CompressedIRangesList_class.o CompressedList_class.o DataFrame_class.o GappedRanges_class.o Grouping_class.o Hits_class.o IRanges_class.o IRanges_constructor.o IRanges_utils.o IntervalTree.o Ocopy_byteblocks.o R_init_IRanges.o RangedData_class.o Ranges_comparison.o RleViews_utils.o Rle_class.o Rle_utils.o SEXP_utils.o SharedDouble_utils.o SharedInteger_utils.o SharedRaw_utils.o SharedVector_class.o SimpleList_class.o SimpleRangesList_class.o Vector_class.o XDoubleViews_utils.o XIntegerViews_utils.o XRawList_comparison.o XVectorList_class.o XVector_class.o anyMissing.o common.o compact_bitvector.o coverage.o dlist.o encode_overlaps.o errabort.o hash_utils.o int_utils.o localmem.o memalloc.o rbTree.o safe_arithm.o sort_utils.o str_utils.o ucsc_handlers.o vector_copy.o -L/usr/lib/R/lib -lR
installing to /ebio/abt6/djolic/Rdir/IRanges/libs
** R
** inst
** preparing package for lazy loading
Error : object ‘mcmapply’ is not exported by 'namespace:parallel'
ERROR: lazy loading failed for package ‘IRanges’

I looked into the NAMESPACE file and there is a change from the previous version, such as:
importFrom(parallel, mclapply, mcmapply)

Could this just be the cause?
Naively, I just tried removing the line and the install goes on, but crashes at a latter point.

Thanks,
Dino