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.