[Bioc-devel] could not install S4Vectors in Mac OS 10.8.5
Ou, Jianhong
Jianhong.Ou at umassmed.edu
Mon May 2 21:34:47 CEST 2016
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]]
>>
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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