[Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

Mon May 2 21:00:09 CEST 2016

Hi,

I got error when I update S4Vectors in R 3.3 RC r70564 today. I also tried r70549, same error like this

> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.21.6), R 3.3.0 RC (2016-04-28 r70564).
Old packages: 'S4Vectors'
Update all/some/none? [a/s/n]:
a
trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/S4Vectors_0.9.52.tar.gz'
Content type 'application/x-gzip' length 225431 bytes (220 KB)
==================================================
downloaded 220 KB

* installing *source* package ‘S4Vectors’ ...
** libs
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c AEbufs.c -o AEbufs.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c DataFrame_class.c -o DataFrame_class.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c Hits_class.c -o Hits_class.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c List_class.c -o List_class.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c Rle_class.c -o Rle_class.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c Rle_utils.c -o Rle_utils.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c SEXP_utils.c -o SEXP_utils.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c SimpleList_class.c -o SimpleList_class.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c anyMissing.c -o anyMissing.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c eval_utils.c -o eval_utils.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c hash_utils.c -o hash_utils.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c int_utils.c -o int_utils.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c logical_utils.c -o logical_utils.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c safe_arithm.c -o safe_arithm.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c sort_utils.c -o sort_utils.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c str_utils.c -o str_utils.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c vector_utils.c -o vector_utils.o
gcc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o eval_utils.o hash_utils.o int_utils.o logical_utils.o safe_arithm.o sort_utils.o str_utils.o vector_utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘head’ from package ‘utils’ in package ‘S4Vectors’
Creating a generic function for ‘tail’ from package ‘utils’ in package ‘S4Vectors’
Creating a generic function for ‘na.omit’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘na.exclude’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘transform’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘merge’ from package ‘base’ in package ‘S4Vectors’
Creating a new generic function for ‘rowSums’ in package ‘S4Vectors’
Creating a new generic function for ‘colSums’ in package ‘S4Vectors’
Creating a new generic function for ‘rowMeans’ in package ‘S4Vectors’
Creating a new generic function for ‘colMeans’ in package ‘S4Vectors’
Creating a generic function for ‘as.matrix’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘window’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘with’ from package ‘base’ in package ‘S4Vectors’
Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’
Creating a generic function for ‘by’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘%in%’ from package ‘base’ in package ‘S4Vectors’
Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’
Creating a generic function for ‘as.table’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘t’ from package ‘base’ in package ‘S4Vectors’
Error in rematchDefinition(definition, fdef, mnames, fnames, signature) :
  arguments (na.last, decreasing) after '...' in the generic must appear in the method, in the same place at the end of the argument list
Error : unable to load R code in package ‘S4Vectors’
ERROR: lazy loading failed for package ‘S4Vectors’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors’

The downloaded source packages are in
‘/private/var/folders/n4/11sc2xz13k56hl85z_h2rgq00000gn/T/RtmpjkynR7/downloaded_packages’
Warning message:
In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘S4Vectors’ had non-zero exit status
> sessionInfo()
R version 3.3.0 RC (2016-04-28 r70564)
Platform: x86_64-apple-darwin12.5.0 (64-bit)
Running under: OS X 10.8.5 (Mountain Lion)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    methods   stats     graphics  grDevices datasets  utils     base

other attached packages:
[1] S4Vectors_0.9.41     BiocGenerics_0.17.5  BiocInstaller_1.21.6

loaded via a namespace (and not attached):
[1] tools_3.3.0

Yours Sincerely,

Jianhong Ou

TEL: 508-856-5379
LRB 608
Bioinformatician of Bioinformatics core at
Department of Molecular, Cell and Cancer Biology
364 Plantation Street Worcester,
MA 01605

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