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)
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 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, "Herv? Pag?s" <hpages at 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 [[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Herv? Pag?s 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: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
????????????????????????? Christian Arnold, PhD Staff Bioinformatician SCB Unit - Computational Biology Joint appointment Genome Biology Joint appointment European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory (EMBL) Meyerhofstrasse 1; 69117, Heidelberg, Germany Email: christian.arnold at embl.de Phone: +49(0)6221-387-8472 Web: http://www.zaugg.embl.de/ [[alternative HTML version deleted]]