Message-ID: <577B7766.4030204@embl.de>
Date: 2016-07-05T09:01:26Z
From: Christian Arnold
Subject: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5
In-Reply-To: <D34D24A6.23401%jianhong.ou@umassmed.edu>
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/
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