On 07/05/2016 05:01 AM, Christian Arnold wrote:
Hi,
I am receiving the same error message, but under different conditions,
and I don't know how to fix it. If anyone has an idea, much appreciated!
Here is my setup:
1) R Under development (unstable) (2016-01-06 r69881) (3.3.0)
This is from before R 3.3.0 was released, on 3 May 06. It should be updated.
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.1 LTS
2) Bioconductor version 3.4 (devel)
3) I updated BiocGenerics to the latest version, which worked fine
(other attached packages:
[1] BiocGenerics_0.19.1 BiocInstaller_1.23.5)
4) If I try to install S4Vectors either via biocLite("S4Vectors") or
manually via R CMD INSTALL, I get the message:
/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’/
Any ideas, what am I overseeing? The only weird thing I noticed is the
following:
> biocLite("BiocUpgrade")
Error: Bioconductor version 3.4 cannot be upgraded with R version 3.3.0
I think this is basically a red herring, but you're using the devel
version of Bioconductor (the odd-numbered 'y' version in x.y.z of
BiocInstaller. The devel version will become the release, and use R
version 3.3.x in October. At that point, to use the next 'devel' version
(which is what you'd be upgrading to) you'd need to use the current
devel (3.4) version of R. So no, you cannot upgrade Biocondcutor with
the 3.3.* series of R.
See BiocInstaller:::.biocUpgrade for possible outcomes -- you can not
upgrade with the current version of R; you can upgrade but only to
devel, so you should useDevel(); the upgrade proceeds
I thought R >=3.3.0 is sufficient for Bioconductor 3.4, shouldn't I
receive a "already the latest version" message instead?
Thanks!
On 02.05.2016 21:32, Ou, Jianhong wrote:
Dear Herve,
After reinstalling BiocGenerics, there is no errors any more. Thank you
very much.
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
On 5/2/16 3:15 PM, "Hervé Pagès" <hpa...@fredhutch.org> wrote:
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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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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