[Bioc-devel] could not install S4Vectors in Mac OS 10.8.5
Martin Morgan
martin.morgan at roswellpark.org
Tue Jul 5 12:09:08 CEST 2016
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" <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
>>>>
>>> --
>>> 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: hpages at fredhutch.org
>>> Phone: (206) 667-5791
>>> Fax: (206) 667-1319
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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