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Question: Unable to install any bioconductor packages
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gravatar for sebastien200109
11 months ago by
sebastien2001090 wrote:

Hi,

I've been using Bioconductor and packages Limma and Oligo for quite a time to analyze affymetrix data. But my Oligo package is suddently missing.

I tried to re-install it using the bioclite() installer but this is what I got:

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
Warning message:
Bioconductor version 3.4 is too old for R version 3.4.1; see https://bioconductor.org/install/#troubleshoot-biocinstaller 
> biocLite("oligo")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.4.1 (2017-06-30).
Installing package(s) ‘oligo’
also installing the dependencies ‘GenomicRanges’, ‘SummarizedExperiment’, ‘oligoClasses’

Warning: unable to access index for repository https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.4:
  cannot open URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.4/data/experiment/bin/windows/contrib/3.4:
  cannot open URL 'https://bioconductor.org/packages/3.4/data/experiment/bin/windows/contrib/3.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.4/extra/bin/windows/contrib/3.4:
  cannot open URL 'https://bioconductor.org/packages/3.4/extra/bin/windows/contrib/3.4/PACKAGES'
Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘GenomicRanges’ ‘oligo’
Do you want to attempt to install these from sources?
y/n: y
installing the source packages ‘GenomicRanges’, ‘SummarizedExperiment’, ‘oligoClasses’, ‘oligo’

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/GenomicRanges_1.26.4.tar.gz'
Content type 'application/x-gzip' length 1042629 bytes (1018 KB)
downloaded 1018 KB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/SummarizedExperiment_1.4.0.tar.gz'
Content type 'application/x-gzip' length 978079 bytes (955 KB)
downloaded 955 KB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/oligoClasses_1.36.0.tar.gz'
Content type 'application/x-gzip' length 372029 bytes (363 KB)
downloaded 363 KB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/oligo_1.38.0.tar.gz'
Content type 'application/x-gzip' length 28420483 bytes (27.1 MB)
downloaded 27.1 MB

* installing *source* package 'GenomicRanges' ...
** libs

*** arch - i386
c:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-34~1.1/include" -DNDEBUG  -I"C:/Program Files/R/R-3.4.1/library/S4Vectors/include" -I"C:/Program Files/R/R-3.4.1/library/IRanges/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
c:/Rtools/mingw_32/bin/gcc: not found
make: *** [IRanges_stubs.o] Error 127
Warning: l'exécution de la commande 'make -f "C:/PROGRA~1/R/R-34~1.1/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-34~1.1/share/make/winshlib.mk" SHLIB="GenomicRanges.dll" OBJECTS="IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o"' renvoie un statut 2
ERROR: compilation failed for package 'GenomicRanges'
* removing 'C:/Program Files/R/R-3.4.1/library/GenomicRanges'
ERROR: dependency 'GenomicRanges' is not available for package 'SummarizedExperiment'
* removing 'C:/Program Files/R/R-3.4.1/library/SummarizedExperiment'
ERROR: dependencies 'GenomicRanges', 'SummarizedExperiment' are not available for package 'oligoClasses'
* removing 'C:/Program Files/R/R-3.4.1/library/oligoClasses'
ERROR: dependency 'oligoClasses' is not available for package 'oligo'
* removing 'C:/Program Files/R/R-3.4.1/library/oligo'

The downloaded source packages are in
	‘C:\Users\Seb\AppData\Local\Temp\RtmpWy74Gx\downloaded_packages’
Old packages: 'IRanges', 'S4Vectors', 'XVector'
Update all/some/none? [a/s/n]: 
a
Warning: unable to access index for repository https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.4:
  cannot open URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.4/data/experiment/bin/windows/contrib/3.4:
  cannot open URL 'https://bioconductor.org/packages/3.4/data/experiment/bin/windows/contrib/3.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.4/extra/bin/windows/contrib/3.4:
  cannot open URL 'https://bioconductor.org/packages/3.4/extra/bin/windows/contrib/3.4/PACKAGES'
Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘IRanges’ ‘S4Vectors’ ‘XVector’
Do you want to attempt to install these from sources?
y/n: y
installing the source packages ‘IRanges’, ‘S4Vectors’, ‘XVector’

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/IRanges_2.8.2.tar.gz'
Content type 'application/x-gzip' length 476385 bytes (465 KB)
downloaded 465 KB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/S4Vectors_0.12.2.tar.gz'
Content type 'application/x-gzip' length 414697 bytes (404 KB)
downloaded 404 KB

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/XVector_0.14.1.tar.gz'
Content type 'application/x-gzip' length 58510 bytes (57 KB)
downloaded 57 KB

* installing *source* package 'S4Vectors' ...
** libs

*** arch - i386
c:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-34~1.1/include" -DNDEBUG     -I"d:/Compiler/gcc-4.9.3/local330/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c AEbufs.c -o AEbufs.o
c:/Rtools/mingw_32/bin/gcc: not found
make: *** [AEbufs.o] Error 127
Warning: l'exécution de la commande 'make -f "C:/PROGRA~1/R/R-34~1.1/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-34~1.1/share/make/winshlib.mk" SHLIB="S4Vectors.dll" OBJECTS="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"' renvoie un statut 2
ERROR: compilation failed for package 'S4Vectors'
* removing 'C:/Program Files/R/R-3.4.1/library/S4Vectors'
* restoring previous 'C:/Program Files/R/R-3.4.1/library/S4Vectors'
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
  problème lors de la copie de C:\Program Files\R\R-3.4.1\library\00LOCK-S4Vectors\S4Vectors\libs\x64\S4Vectors.dll vers C:\Program Files\R\R-3.4.1\library\S4Vectors\libs\x64\S4Vectors.dll: Permission denied
* installing *source* package 'IRanges' ...
** libs

*** arch - i386
c:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-34~1.1/include" -DNDEBUG  -I"C:/Program Files/R/R-3.4.1/library/S4Vectors/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
c:/Rtools/mingw_32/bin/gcc: not found
make: *** [CompressedAtomicList_utils.o] Error 127
Warning: l'exécution de la commande 'make -f "C:/PROGRA~1/R/R-34~1.1/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-34~1.1/share/make/winshlib.mk" SHLIB="IRanges.dll" OBJECTS="CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o Ranges_comparison.o RleViews_utils.o S4Vectors_stubs.o SimpleRangesList_class.o coverage_methods.o inter_range_methods.o"' renvoie un statut 2
ERROR: compilation failed for package 'IRanges'
* removing 'C:/Program Files/R/R-3.4.1/library/IRanges'
* restoring previous 'C:/Program Files/R/R-3.4.1/library/IRanges'
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
  problème lors de la copie de C:\Program Files\R\R-3.4.1\library\00LOCK-IRanges\IRanges\libs\x64\IRanges.dll vers C:\Program Files\R\R-3.4.1\library\IRanges\libs\x64\IRanges.dll: Permission denied
* installing *source* package 'XVector' ...
** libs

*** arch - i386
c:/Rtools/mingw_32/bin/gcc  -I"C:/Program Files/R/R-3.4.1/library/zlibbioc/include" -I"C:/PROGRA~1/R/R-34~1.1/include" -DNDEBUG  -I"C:/Program Files/R/R-3.4.1/library/S4Vectors/include" -I"C:/Program Files/R/R-3.4.1/library/IRanges/include"   -I"d:/Compiler/gcc-4.9.3/local330/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
c:/Rtools/mingw_32/bin/gcc: not found
make: *** [IRanges_stubs.o] Error 127
Warning: l'exécution de la commande 'make -f "Makevars.win" -f "C:/PROGRA~1/R/R-34~1.1/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-34~1.1/share/make/winshlib.mk" SHLIB="XVector.dll" OBJECTS="IRanges_stubs.o Ocopy_byteblocks.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XRawList_comparison.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o"' renvoie un statut 2
ERROR: compilation failed for package 'XVector'
* removing 'C:/Program Files/R/R-3.4.1/library/XVector'
* restoring previous 'C:/Program Files/R/R-3.4.1/library/XVector'
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
  problème lors de la copie de C:\Program Files\R\R-3.4.1\library\00LOCK-XVector\XVector\libs\x64\XVector.dll vers C:\Program Files\R\R-3.4.1\library\XVector\libs\x64\XVector.dll: Permission denied

The downloaded source packages are in
	‘C:\Users\Seb\AppData\Local\Temp\RtmpWy74Gx\downloaded_packages’
There were 14 warnings (use warnings() to see them)

If this may help:

> warnings()
Messages d'avis :
1: running command '"C:/PROGRA~1/R/R-34~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.4.1\library" C:\Users\Seb\AppData\Local\Temp\RtmpWy74Gx/downloaded_packages/GenomicRanges_1.26.4.tar.gz' had status 1
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicRanges’ had non-zero exit status
3: running command '"C:/PROGRA~1/R/R-34~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.4.1\library" C:\Users\Seb\AppData\Local\Temp\RtmpWy74Gx/downloaded_packages/SummarizedExperiment_1.4.0.tar.gz' had status 1
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘SummarizedExperiment’ had non-zero exit status
5: running command '"C:/PROGRA~1/R/R-34~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.4.1\library" C:\Users\Seb\AppData\Local\Temp\RtmpWy74Gx/downloaded_packages/oligoClasses_1.36.0.tar.gz' had status 1
6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘oligoClasses’ had non-zero exit status
7: running command '"C:/PROGRA~1/R/R-34~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.4.1\library" C:\Users\Seb\AppData\Local\Temp\RtmpWy74Gx/downloaded_packages/oligo_1.38.0.tar.gz' had status 1
8: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘oligo’ had non-zero exit status
9: running command '"C:/PROGRA~1/R/R-34~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.4.1\library" C:\Users\Seb\AppData\Local\Temp\RtmpWy74Gx/downloaded_packages/S4Vectors_0.12.2.tar.gz' had status 1
10: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘S4Vectors’ had non-zero exit status
11: running command '"C:/PROGRA~1/R/R-34~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.4.1\library" C:\Users\Seb\AppData\Local\Temp\RtmpWy74Gx/downloaded_packages/IRanges_2.8.2.tar.gz' had status 1
12: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘IRanges’ had non-zero exit status
13: running command '"C:/PROGRA~1/R/R-34~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.4.1\library" C:\Users\Seb\AppData\Local\Temp\RtmpWy74Gx/downloaded_packages/XVector_0.14.1.tar.gz' had status 1
14: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘XVector’ had non-zero exit status

 

I have the same problem with all the packages I tried to install. Never had this issue before.

Any help will be appreciated,

Thanks!

S.

See the warning when you source biocLite:

Warning message:
Bioconductor version 3.4 is too old for R version 3.4.1; see https://bioconductor.org/install/#troubleshoot-biocinstaller 

 

You have probably updated the R version without updating the Bioconductor packages.

 

ADD REPLYlink written 11 months ago by Lluís R370

Follow the steps in Troubleshoot BiocInstaller to remove your bad version of BiocInstaller.

ADD REPLYlink written 11 months ago by Martin Morgan ♦♦ 22k
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