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/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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