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Question: Problems updating Bioconductor with R 3.2.0
1
gravatar for daniil.sarkisyan
2.6 years ago by
Sweden
daniil.sarkisyan10 wrote:

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
>

ADD COMMENTlink modified 2.6 years ago by Dan Tenenbaum ♦♦ 8.2k • written 2.6 years ago by daniil.sarkisyan10
1

No. There was a post on bio-devel. Try remove.packages("BiocInstaller"). Then start over.

ADD REPLYlink written 2.6 years ago by Charles Berry290
1
gravatar for Jenny Drnevich
2.6 years ago by
Jenny Drnevich1.9k
United States
Jenny Drnevich1.9k wrote:

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

ADD COMMENTlink written 2.6 years ago by Jenny Drnevich1.9k

Hi all,

following Jenny's suggestions, I got 14 warnings

> warnings()
Warnmeldungen:
1: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘evaluate’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘np’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘sem’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘reshape2’ had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘Ecfun’ had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘BayesX’ had non-zero exit status
7: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘maxLik’ had non-zero exit status
8: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘Ecdat’ had non-zero exit status
9: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘ggplot2’ had non-zero exit status
10: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘mlogit’ had non-zero exit status
11: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘sampleSelection’ had non-zero exit status
12: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘truncreg’ had non-zero exit status
13: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘Hmisc’ had non-zero exit status
14: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘rms’ had non-zero exit status

 

Then I tried to install EBImage:

> biocLite("EBImage")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.1), R version 3.2.0.
Installing package(s) ‘EBImage’
also installing the dependency ‘fftwtools’

versuche URL 'http://cran.rstudio.com/src/contrib/fftwtools_0.9-7.tar.gz'
Content type 'application/x-gzip' length 145998 bytes (142 KB)
==================================================
downloaded 142 KB

versuche URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/EBImage_4.10.0.tar.gz'
Content type 'application/x-gzip' length 4114806 bytes (3.9 MB)
==================================================
downloaded 3.9 MB

* installing *source* package ‘fftwtools’ ...
** Paket ‘fftwtools’ erfolgreich entpackt und MD5 Summen überprüft
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c fftwtools.c -o fftwtools.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o fftwtools.so fftwtools.o -lfftw3 -lm -L/usr/lib/R/lib -lR
/usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/local/lib/libfftw3.a: could not read symbols: Bad value
collect2: ld gab 1 als Ende-Status zurück
make: *** [fftwtools.so] Fehler 1
ERROR: compilation failed for package ‘fftwtools’
* removing ‘/home/nik/R/x86_64-pc-linux-gnu-library/3.2/fftwtools’
ERROR: dependency ‘fftwtools’ is not available for package ‘EBImage’
* removing ‘/home/nik/R/x86_64-pc-linux-gnu-library/3.2/EBImage’

The downloaded source packages are in
    ‘/tmp/Rtmp7tiueA/downloaded_packages’
Old packages: 'abind', 'acepack', 'AER', 'akima',

... some output deleted ...

'xtable', 'xts', 'Zelig', 'zoo', 'spatial'
Update all/some/none? [a/s/n]:
n
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘fftwtools’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘EBImage’ had non-zero exit status
 

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C               LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8     LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8   
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] BiocInstaller_1.18.1

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

Any help is appreciated.

Michl

 

ADD REPLYlink written 2.6 years ago by mondmichl0

It seems like you have other problems, based on your warnings. You need to post the entire output of the biocLite() command. Somewhere in there is a an error which indicates the problem. It's probably a missing system dependency. To narrow things down a bit you could rty installing one package at a time (for each package mentioned in the warnings: evaluate, np, sem, etc) and see what the error is.

ADD REPLYlink written 2.6 years ago by Dan Tenenbaum ♦♦ 8.2k

Thank you Dan,

I  have reinstalled all packages, removed the causes of the errors and followed Steves and Hervés suggestions, now EBImage is working again.

Cheers

Michl

ADD REPLYlink written 2.6 years ago by mondmichl0
0
gravatar for Dan Tenenbaum
2.6 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:
You need to install fftw3: sudo apt-get install fftw3
ADD COMMENTlink written 2.6 years ago by Dan Tenenbaum ♦♦ 8.2k

Thank you, Dan. Ubuntu says, I allready have the newest version of libfftw3-3.

ADD REPLYlink written 2.6 years ago by mondmichl0

Is there something like a "libfftw3-devel" package? Try that.

ADD REPLYlink written 2.6 years ago by Steve Lianoglou12k

All I can find about a libfftw3 devel package seems to be a bit old.

On the other hand, EBImage worked very well on my Computer until the update R 3.2.0 / Bioconductor 3.1.

ADD REPLYlink written 2.6 years ago by mondmichl0

I confirm. You need libfftw3-dev:

  sudo apt-get install libfftw3-dev

EBImage has changed in BioC 3.1: now it depends on CRAN package fftwtools which requires libfftw3-dev to compile.

More generally speaking, not because something "worked" (whatever that means) with a previous version of R/BioC doesn't mean it will work with a new version of R/BioC. Software evolve, that's why we have new versions.

Cheers,

H.

ADD REPLYlink written 2.6 years ago by Hervé Pagès ♦♦ 13k

Thank you, Steve and Hervé. I got it now.

Cheers

Michl
 

ADD REPLYlink written 2.6 years ago by mondmichl0
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