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

This question should probably go on the support site as it is not about
package development.

You should update to Mavericks or higher. Earlier versions of Mac OS X
are no longer officially supported by R or Bioconductor (that's why a
binary is not available).


Dan


----- Original Message -----

From: "Jianhong Ou" <Jianhong.Ou at umassmed.edu>
To: "bioc-devel" <bioc-devel at r-project.org>
Sent: Monday, May 2, 2016 12:00:09 PM
Subject: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

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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