[Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

Dan Tenenbaum dtenenba at fredhutch.org
Mon May 2 21:39:03 CEST 2016 

Well, you can tell your helpdesk that this is going to impact people's work as the OS you are using will no longer be supported by R/Bioconductor starting with the release this week.

Mavericks was released 3 years ago. It seems reasonable to support it now.

Dan


----- Original Message -----
> From: "Jianhong Ou" <Jianhong.Ou at umassmed.edu>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Monday, May 2, 2016 12:34:47 PM
> Subject: Re: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

> Hi Dan,
> 
> Thank you for your answer. I hope I can update to Mavericks but our help
> desk just ask me to hold on current OS.
> 
> 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 3:04 PM, "Dan Tenenbaum" <dtenenba at fredhutch.org> wrote:
> 
>>This question should probably go on the support site as it is not about
>>package development.
>>
>>You should update to Mavericks or higher. Earlier versions of Mac OS X
>>are no longer officially supported by R or Bioconductor (that's why a
>>binary is not available).
>>
>>
>>Dan
>>
>>
>>----- Original Message -----
>>> From: "Jianhong Ou" <Jianhong.Ou at umassmed.edu>
>>> To: "bioc-devel" <bioc-devel at r-project.org>
>>> Sent: Monday, May 2, 2016 12:00:09 PM
>>> Subject: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5
>>
>>> 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

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