Dan Tenenbaum | 4 Dec 08:20 2012

Re: IRanges install error with parallel/mcmapply

On Mon, Dec 3, 2012 at 2:34 PM, Dino Jolic <dino.jolic@...> wrote:
> 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

What command did you use to reinstall your packages? What command are
you using to install IRanges?

You should not be editing the NAMESPACE or other files in packages you
are trying to install.

The recommended way to update all your packages is:

source("http://bioconductor.org/biocLite.R")
biocLite(character())

Then install IRanges:
source("http://bioconductor.org/biocLite.R")
biocLite("IRanges")

If you are still having problems, please mail the output of the
sessionInfo() command along with the commands that caused the error
and all output.

Dan

>
> * 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
>
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