Ошибка при установке пакетов в R

Question

Мне нужно установить 2 пакета в R, чтобы запустить другую библиотеку.

При установке limma и IRanges от Bioconductor, я получаю следующее сообщение об ошибке:

> install.packages("IRanges_1.18.4.tar.gz") 
Installing package into ‘C:/Users/Zambidis Lab/Documents/R/win-library/3.0’ 
(as ‘lib’ is unspecified) 
inferring 'repos = NULL' from 'pkgs' 
* installing *source* package 'IRanges' ... 
** libs 

*** arch - i386 
Warning: running command 'make -f "C:/PROGRA~1/R/R-32~1.0/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-32~1.0/share/make/winshlib.mk" SHLIB="IRanges.dll" OBJECTS="AEbufs.o CompressedIRangesList_class.o CompressedList_class.o DataFrame_class.o GappedRanges_class.o Grouping_class.o Hits_class.o IRanges_class.o IRanges_constructor.o IntervalTree.o Ocopy_byteblocks.o R_init_IRanges.o RangedData_class.o Ranges_comparison.o RleViews_utils.o Rle_class.o Rle_utils.o SEXP_utils.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o SimpleList_class.o SimpleRangesList_class.o Vector_class.o XDoubleViews_utils.o XIntegerViews_utils.o XRawList_comparison.o XVectorList_class.o XVector_class.o anyMissing.o common.o compact_bitvector.o coverage_methods.o dlist.o encodeOverlaps_methods.o errabort.o hash_utils.o int_utils.o inter_range_methods.o localmem.o memalloc.o rbTree.o safe_arithm.o sort_utils.o str_utils.o ucsc_handlers.o vector_copy.o"' had status 127 
ERROR: compilation failed for package 'IRanges' 
* removing 'C:/Users/Zambidis Lab/Documents/R/win-library/3.0/IRanges' 
* restoring previous 'C:/Users/Zambidis Lab/Documents/R/win-library/3.0/IRanges' 
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) : 
    problem copying C:\Users\Zambidis Lab\Documents\R\win-library\3.0\00LOCK-IRanges\IRanges\libs\x64\IRanges.dll to C:\Users\Zambidis Lab\Documents\R\win-library\3.0\IRanges\libs\x64\IRanges.dll: Permission denied 
Warning messages: 
1: running command '"C:/PROGRA~1/R/R-32~1.0/bin/x64/R" CMD INSTALL -l "C:\Users\Zambidis Lab\Documents\R\win-library\3.0" "IRanges_1.18.4.tar.gz"' had status 1 
2: In install.packages("IRanges_1.18.4.tar.gz") : 
    installation of package ‘IRanges_1.18.4.tar.gz’ had non-zero exit status 

Я попытался установить GO.db хотя ошибка такая же:

> source("http://bioconductor.org/biocLite.R") 
    Bioconductor version 2.12 (BiocInstaller 1.10.4), ?biocLite for help 
    A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help 
    > biocLite("GO.db") 
    BioC_mirror: http://bioconductor.org 
    Using Bioconductor version 2.12 (BiocInstaller 1.10.4), R version 3.2.0. 
    Temporarily using Bioconductor version 2.12 
    Installing package(s) 'GO.db' 
    Warning: unable to access index for repository http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.2 
    Warning: unable to access index for repository http://bioconductor.org/packages/2.12/data/annotation/bin/windows/contrib/3.2 
    Warning: unable to access index for repository http://bioconductor.org/packages/2.12/data/experiment/bin/windows/contrib/3.2 
    Warning: unable to access index for repository http://bioconductor.org/packages/2.12/extra/bin/windows/contrib/3.2 
    installing the source package ‘GO.db’ 

trying URL 'http://bioconductor.org/packages/2.12/data/annotation/src/contrib/GO.db_2.9.0.tar.gz' 
Content type 'application/x-gzip' length 25473946 bytes (24.3 MB) 
downloaded 24.3 MB 

* installing *source* package 'GO.db' ... 
** R 
** inst 
** preparing package for lazy loading 
** help 
*** installing help indices 
** building package indices 
** testing if installed package can be loaded 
*** arch - i386 
Error : .onLoad failed in loadNamespace() for 'GO.db', details: 
    call: match.arg(synchronous, c("off", "normal", "full")) 
    error: 'arg' must be NULL or a character vector 
Error: loading failed 
Execution halted 
*** arch - x64 
Error : .onLoad failed in loadNamespace() for 'GO.db', details: 
    call: match.arg(synchronous, c("off", "normal", "full")) 
    error: 'arg' must be NULL or a character vector 
Error: loading failed 
Execution halted 
ERROR: loading failed for 'i386', 'x64' 
* removing 'C:/Users/Zambidis Lab/Documents/R/win-library/3.0/GO.db' 
* restoring previous 'C:/Users/Zambidis Lab/Documents/R/win-library/3.0/GO.db' 

The downloaded source packages are in 
     ‘C:\Users\Zambidis Lab\AppData\Local\Temp\RtmpU3gtWD\downloaded_packages’ 
Old packages: 'IRanges', 'limma' 
Update all/some/none? [a/s/n]: a 
Warning: unable to access index for repository http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.2 
Warning: unable to access index for repository http://bioconductor.org/packages/2.12/data/annotation/bin/windows/contrib/3.2 
Warning: unable to access index for repository http://bioconductor.org/packages/2.12/data/experiment/bin/windows/contrib/3.2 
Warning: unable to access index for repository http://bioconductor.org/packages/2.12/extra/bin/windows/contrib/3.2 
Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘IRanges’ ‘limma’ 
    These will not be installed 
Warning messages: 
1: running command '"C:/PROGRA~1/R/R-32~1.0/bin/x64/R" CMD INSTALL -l "C:\Users\Zambidis Lab\Documents\R\win-library\3.0" C:\Users\ZAMBID~1\AppData\Local\Temp\RtmpU3gtWD/downloaded_packages/GO.db_2.9.0.tar.gz' had status 1 
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : 
    installation of package ‘GO.db’ had non-zero exit status 

Answer 1

Для IRanges, вы «Попробуйте установить пакет, который требует компиляторов« R tools », которых у вас нет.

Для GO.db на вас, к сожалению, влияет изменение пакета RSQLite; ваши варианты - либо обновить R до текущей версии, либо установить предыдущую версию RSQLite. Вы можете попытаться установить version 0.11.4 RSQLite, но это будет проблемой по той же причине, что и при установке IRanges.

Ваш лучший выбор в основном начать с текущей версией R, и ВСЕГДА source("http://bioconductor.org/biocLite.R") и biocLite()