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Question: Dada2 and GenomeInfoDbData installation
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gravatar for navlern
16 months ago by
navlern0
navlern0 wrote:

Hi all,

I cannot install the Dada2 package. Every time I try to load it it gives me an error message:

This is the output from R

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.6 (BiocInstaller 1.27.2), ?biocLite for help
> biocLite("dada2")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.27.2), R 3.4.0 (2017-04-21).
Installing package(s) ‘dada2’
trying URL 'https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/dada2_1.5.0.zip'
Content type 'application/zip' length 4437866 bytes (4.2 MB)
downloaded 4.2 MB

package ‘dada2’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\zqd803\AppData\Local\Temp\RtmpEdlefH\downloaded_packages
> library(dada2)

Error: package or namespace load failed for ‘dada2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 der er ingen pakke med navn ‘GenomeInfoDbData’

 

It says no package called "GenomeInfoDbData"

I also tried

> devtools::install_github("benjjneb/dada2")
Downloading GitHub repo benjjneb/dada2@master
from URL https://api.github.com/repos/benjjneb/dada2/zipball/master
trying URL 'https://cran.rstudio.com/bin/windows/Rtools/Rtools34.exe'
Content type 'application/x-msdos-program' length 108085090 bytes (103.1 MB)
downloaded 103.1 MB

Error: running command '"C:/Program Files/R/R-3.4.0/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD config CC' had status 2

Then I tried to install the package GenomeInfoDbData but I get another error message

> biocLite("GenomeInfoDbData", dep=T)
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.27.2), R 3.4.0 (2017-04-21).
Installing package(s) ‘GenomeInfoDbData’
Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  : 
  missing value where TRUE/FALSE needed

 

Tried to enter

 .libPaths()
[1] "C:/Program Files/R/R-3.4.0/library" 

And in that folder I can find GenomeInfoDbData (I can also find the zip  here: C:\Users\zqd803\AppData\Local\Temp\RtmpEdlefH\downloaded_packages as would be expected from the output from running biocLite("dada2")​)

I looked at other Q and A and often you ask for 

> R.version
               _                           
platform       x86_64-w64-mingw32          
arch           x86_64                      
os             mingw32                     
system         x86_64, mingw32             
status                                     
major          3                           
minor          4.0                         
year           2017                        
month          04                          
day            21                          
svn rev        72570                       
language       R                           
version.string R version 3.4.0 (2017-04-21)
nickname       You Stupid Darkness         
> packageVersion("BiocInstaller")
[1] ‘1.27.2’
> packageVersion("ShortRead")
[1] ‘1.35.1’

 

Can you help solving this? 

ADD COMMENTlink modified 15 months ago by jiangjing_ing0 • written 16 months ago by navlern0

BTW, i noticed you are using the development version of Bioconductor (i.e. v3.6), whereas below I use the release version (v3.5)... Maybe for BioC-development the procedure is different?

ADD REPLYlink written 16 months ago by Guido Hooiveld2.3k
1
gravatar for Guido Hooiveld
16 months ago by
Guido Hooiveld2.3k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.3k wrote:

Works fine for me: I started a fresh R-session, then 1st installed the library GenomeInfoDbData, followed by installation of dada2.

Please notice that i did not provide the argument dep=T with biocLite().
While being on Windows, I also had Rtools installed before starting R (because GenomeInfoDbData is only available as source).
"Rtools: Tools to build R and R packages (managed by Duncan Murdoch). This is what you want to build your own packages on Windows, or to build R itself."

 

> biocLite("GenomeInfoDbData")  #note that I did not use the argument dep=T like you did.
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 Patched (2017-05-10
  r72670).
Installing package(s) ‘GenomeInfoDbData’
installing the source package ‘GenomeInfoDbData’

trying URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/GenomeInfoDbData_0.99.0.tar.gz'
Content type 'application/x-gzip' length 16238792 bytes (15.5 MB)
downloaded 15.5 MB

* installing *source* package 'GenomeInfoDbData' ...
** data
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (GenomeInfoDbData)

The downloaded source packages are in
        ‘D:\TMP\RtmpiqM0Rd\downloaded_packages’

> biocLite("dada2")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 Patched (2017-05-10
  r72670).
Installing package(s) ‘dada2’
also installing the dependencies ‘ShortRead’, ‘RcppParallel’

trying URL 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/ShortRead_1.34.0.zip'
Content type 'application/zip' length 10513693 bytes (10.0 MB)
downloaded 10.0 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/RcppParallel_4.3.20.zip'
Content type 'application/zip' length 3378549 bytes (3.2 MB)
downloaded 3.2 MB

trying URL 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/dada2_1.4.0.zip'
Content type 'application/zip' length 4442346 bytes (4.2 MB)
downloaded 4.2 MB

package ‘ShortRead’ successfully unpacked and MD5 sums checked
package ‘RcppParallel’ successfully unpacked and MD5 sums checked
package ‘dada2’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        D:\TMP\RtmpiqM0Rd\downloaded_packages
> library(dada2)
Loading required package: Rcpp
> sessionInfo()
R version 3.4.0 Patched (2017-05-10 r72670)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] 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] dada2_1.4.0          Rcpp_0.12.11         BiocInstaller_1.26.0

loaded via a namespace (and not attached):
 [1] compiler_3.4.0             RColorBrewer_1.1-2        
 [3] GenomeInfoDb_1.12.1        plyr_1.8.4                
 [5] XVector_0.16.0             bitops_1.0-6              
 [7] tools_3.4.0                zlibbioc_1.22.0           
 [9] tibble_1.3.3               gtable_0.2.0              
[11] lattice_0.20-35            rlang_0.1.1               
[13] Matrix_1.2-10              DelayedArray_0.2.5        
[15] parallel_3.4.0             GenomeInfoDbData_0.99.0   
[17] hwriter_1.3.2              stringr_1.2.0             
[19] Biostrings_2.44.1          S4Vectors_0.14.2          
[21] IRanges_2.10.2             stats4_3.4.0              
[23] grid_3.4.0                 Biobase_2.36.2            
[25] data.table_1.10.4          BiocParallel_1.10.1       
[27] latticeExtra_0.6-28        magrittr_1.5              
[29] ggplot2_2.2.1              reshape2_1.4.2            
[31] scales_0.4.1               Rsamtools_1.28.0          
[33] matrixStats_0.52.2         BiocGenerics_0.22.0       
[35] GenomicRanges_1.28.3       GenomicAlignments_1.12.1  
[37] ShortRead_1.34.0           SummarizedExperiment_1.6.3
[39] colorspace_1.3-2           stringi_1.1.5             
[41] RCurl_1.95-4.8             RcppParallel_4.3.20       
[43] lazyeval_0.2.0             munsell_0.4.3             
>


 

 

 

ADD COMMENTlink modified 16 months ago • written 16 months ago by Guido Hooiveld2.3k

Thanks a lot for your reply, However, it doesn't work for me. Tried to do as you write and started a fresh r session and this is what I got:

 

> biocLite("GenomeInfoDbData")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.27.2), R 3.4.0 (2017-04-21).
Installing package(s) ‘GenomeInfoDbData’
installing the source package ‘GenomeInfoDbData’

trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/GenomeInfoDbData_0.99.0.tar.gz'
Content type 'application/x-gzip' length 16238792 bytes (15.5 MB)
downloaded 15.5 MB

'C:\Program' blev ikke genkendt som en intern eller ekstern kommando,
et program eller en batchfil.

The downloaded source packages are in
    ‘C:\Users\zqd803\AppData\Local\Temp\RtmpGyDXVo\downloaded_packages’
Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  : 
  missing value where TRUE/FALSE needed
In addition: Warning messages:
1: running command '"C:/Program Files/R/R-3.4.0/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.4.0\library" C:\Users\zqd803\AppData\Local\Temp\RtmpGyDXVo/downloaded_packages/GenomeInfoDbData_0.99.0.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomeInfoDbData’ had non-zero exit status

 

 

What is written in Danish can be translated to something like

'C: \ Program' was not recognized as an internal or external command,
A program or a batch file.

ADD REPLYlink written 16 months ago by navlern0

Could it be Rtools is not (properly) installed? See my updated answer above. Otherwise I don't know...

ADD REPLYlink written 16 months ago by Guido Hooiveld2.3k
Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  : 
  missing value where TRUE/FALSE needed

is a known issue with R and is most easily fixed by installing the 'patched' version of R. The 'C:\Program' is likely because of the space in the file path; you'd like to arrange for R to use a path without spaces; I am not exactly sure how to do that.

ADD REPLYlink written 16 months ago by Martin Morgan ♦♦ 22k
0
gravatar for jiangjing_ing
15 months ago by
jiangjing_ing0 wrote:

Hi~

I meet the same problem with you. Did you solve that?

Hope to know the solution :)

ADD COMMENTlink written 15 months ago by jiangjing_ing0

Are you using the most recent version of R, 3.4.1?

ADD REPLYlink written 15 months ago by Martin Morgan ♦♦ 22k
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