[Bioc-devel] could not install S4Vectors in Mac OS 10.8.5
Ou, Jianhong
Jianhong.Ou at umassmed.edu
Mon May 2 21:32:21 CEST 2016
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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