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

Hi Jianhong,

order() got a new argument in R 3.3 and the order() generic in
BiocGenerics was modified accordingly. Please try to re-install
BiocGenerics before you try to update S4Vectors. In fact, when
updating R, all your packages should be re-installed. Most people
don't do it because that takes a long time but there is no guarantee
that packages installed under a previous version of R will still work
properly with a new version of R.

H.

On 05/02/2016 12:00 PM, Ou, Jianhong wrote:

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/down
loaded_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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