Message-ID: <5727A74A.4030003@fredhutch.org>
Date: 2016-05-02T19:15:22Z
From: Hervé Pagès
Subject: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5
In-Reply-To: <32331_1462215697_5727A410_32331_2121_2_D34D1D76.233FB%jianhong.ou@umassmed.edu>
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
>
> [[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