Problems updating Bioconductor with R 3.2.0
2
1
Entering edit mode
@daniilsarkisyan-7626
Last seen 3.8 years ago
Sweden

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
>

upgrade r update • 14k views
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1
Entering edit mode

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

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1
Entering edit mode
Jenny Drnevich ★ 2.0k
@jenny-drnevich-2812
Last seen 1 day ago
United States

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

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0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

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0
Entering edit mode
Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 3.1 years ago
United States
You need to install fftw3: sudo apt-get install fftw3
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

Cheers

Michl
 

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