Dear Bioconductor Support,

Am I the only one having trouble updating Bioconductor?

/Daniil

R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

... some output removed ...

[Previously saved workspace restored]

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.4), ?biocLite for help
A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install
> biocLite("BiocUpgrade")
Error: Bioconductor version 3.0 cannot be upgraded with R version 3.1.0

Upgrade also dies with the dialog box "The program can't start because Rzlib.dll is missing from your computer..." Reinstalling R 3.2.0 does not help.

> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.4), R version 3.2.0.
Old packages: 'BayesPeak', 'Biostrings', 'biovizBase', 'casper', 'CGEN', 'ChemmineR', 'chimera', 'ChIPpeakAnno', 'chopsticks', 'cisPath', 'CNORode', 'ddgraph', 'DESeq2',
  'DiffBind', 'easyRNASeq', 'EBImage', 'edgeR', 'flowClust', 'flowCore', 'flowWorkspace', 'gdsfmt', 'GenomicAlignments', 'GenomicFeatures', 'GenomicRanges', 'graph',
  'GWASTools', 'IRanges', 'limma', 'manipulate', 'mosaics', 'pdInfoBuilder', 'pRoloc', 'qpgraph', 'Rsamtools', 'rsbml', 'rTANDEM', 'rtracklayer', 'SeqArray', 'VanillaICE',
  'VariantAnnotation'
Update all/some/none? [a/s/n]: a
Warning: unable to access index for repository http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.2
Warning: unable to access index for repository http://bioconductor.org/packages/3.0/data/annotation/bin/windows/contrib/3.2
Warning: unable to access index for repository http://bioconductor.org/packages/3.0/data/experiment/bin/windows/contrib/3.2
Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘BayesPeak’ ‘Biostrings’ ‘biovizBase’ ‘casper’ ‘CGEN’
  ‘ChemmineR’ ‘chimera’ ‘chopsticks’ ‘cisPath’ ‘CNORode’ ‘ddgraph’ ‘DESeq2’ ‘DiffBind’ ‘EBImage’ ‘edgeR’ ‘flowClust’ ‘flowCore’ ‘flowWorkspace’ ‘gdsfmt’
  ‘GenomicAlignments’ ‘GenomicRanges’ ‘graph’ ‘IRanges’ ‘limma’ ‘mosaics’ ‘pdInfoBuilder’ ‘pRoloc’ ‘qpgraph’ ‘Rsamtools’ ‘rsbml’ ‘rTANDEM’ ‘rtracklayer’
  ‘SeqArray’ ‘VanillaICE’ ‘VariantAnnotation’
  These will not be installed
trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.2/manipulate_1.0.1.zip'
Content type 'application/zip' length 35696 bytes (34 KB)
downloaded 34 KB

package ‘manipulate’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\Danill Sarkisyan\AppData\Local\Temp\RtmpuoJO2E\downloaded_packages
installing the source packages ‘ChIPpeakAnno’, ‘easyRNASeq’, ‘GenomicFeatures’, ‘GWASTools’

trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/ChIPpeakAnno_2.16.4.tar.gz'
Content type 'application/x-gzip' length 11006883 bytes (10.5 MB)
downloaded 10.5 MB

trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/easyRNASeq_2.2.1.tar.gz'
Content type 'application/x-gzip' length 593747 bytes (579 KB)
downloaded 579 KB

trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/GenomicFeatures_1.18.7.tar.gz'
Content type 'application/x-gzip' length 801238 bytes (782 KB)
downloaded 782 KB

trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/GWASTools_1.12.2.tar.gz'
Content type 'application/x-gzip' length 1366528 bytes (1.3 MB)
downloaded 1.3 MB

* installing *source* package 'easyRNASeq' ...
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
  namespace 'Biostrings' 2.34.0 is being loaded, but >= 2.34.1 is required
ERROR: lazy loading failed for package 'easyRNASeq'
* removing 'C:/R/library/easyRNASeq'
* restoring previous 'C:/R/library/easyRNASeq'
* installing *source* package 'GenomicFeatures' ...
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
  namespace 'rtracklayer' 1.26.2 is being loaded, but >= 1.26.3 is required
ERROR: lazy loading failed for package 'GenomicFeatures'
* removing 'C:/R/library/GenomicFeatures'
* restoring previous 'C:/R/library/GenomicFeatures'
* installing *source* package 'GWASTools' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error in inDL(x, as.logical(local), as.logical(now), ...) :
  unable to load shared object 'C:/R/library/gdsfmt/libs/x64/gdsfmt.dll':
  LoadLibrary failure:  The specified module could not be found.

Error : package 'gdsfmt' could not be loaded
ERROR: lazy loading failed for package 'GWASTools'
* removing 'C:/R/library/GWASTools'
* restoring previous 'C:/R/library/GWASTools'
* installing *source* package 'ChIPpeakAnno' ...
** R
** data
** inst
** preparing package for lazy loading
Error : .onLoad failed in loadNamespace() for 'GO.db', details:
  call: ls(envir, all.names = TRUE)
  error: 2 arguments passed to .Internal(ls) which requires 3
ERROR: lazy loading failed for package 'ChIPpeakAnno'
* removing 'C:/R/library/ChIPpeakAnno'
* restoring previous 'C:/R/library/ChIPpeakAnno'

The downloaded source packages are in
        ‘C:\Users\Danill Sarkisyan\AppData\Local\Temp\RtmpuoJO2E\downloaded_packages’
Warning messages:
1: running command '"C:/R/R-3.2.0/bin/x64/R" CMD INSTALL -l "C:\R\library" C:\Users\DANILL~1\AppData\Local\Temp\RtmpuoJO2E/downloaded_packages/easyRNASeq_2.2.1.tar.gz' had status 1
2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘easyRNASeq’ had non-zero exit status
3: running command '"C:/R/R-3.2.0/bin/x64/R" CMD INSTALL -l "C:\R\library" C:\Users\DANILL~1\AppData\Local\Temp\RtmpuoJO2E/downloaded_packages/GenomicFeatures_1.18.7.tar.gz' had status 1
4: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘GenomicFeatures’ had non-zero exit status
5: running command '"C:/R/R-3.2.0/bin/x64/R" CMD INSTALL -l "C:\R\library" C:\Users\DANILL~1\AppData\Local\Temp\RtmpuoJO2E/downloaded_packages/GWASTools_1.12.2.tar.gz' had status 1
6: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘GWASTools’ had non-zero exit status
7: running command '"C:/R/R-3.2.0/bin/x64/R" CMD INSTALL -l "C:\R\library" C:\Users\DANILL~1\AppData\Local\Temp\RtmpuoJO2E/downloaded_packages/ChIPpeakAnno_2.16.4.tar.gz' had status 1
8: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘ChIPpeakAnno’ had non-zero exit status

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.16.4

loaded via a namespace (and not attached):
[1] tools_3.2.0
>

Hi Daniil,

I believe your problem is that you are trying to upgrade packages that you haven't installed yet. Since R 3.2.0 is a brand-new release, you have to install all the Bioconductor packages from the companion 3.1 version like this:

source("http://bioconductor.org/biocLite.R")
biocLite()

Hope this helps,

Jenny