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Question: ‘IlluminaHumanMethylation450k.db’ had non-zero exit status
0
gravatar for ben.run974
3.1 years ago by
ben.run9740
United Kingdom
ben.run9740 wrote:

Hi,

I tried to install IlluminaHumanMethylation450k.db using biocLite but keep having some error messages. I have been able to install and use it in the past but I had to reinstall R in the meantime. I have checked that all dependancies are installed (methods, AnnotationDbi, org.Hs.eg.db).

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for help
> biocLite("IlluminaHumanMethylation450k.db")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version 3.1.1.
Installing package(s) 'IlluminaHumanMethylation450k.db'
trying URL 'http://bioconductor.org/packages/3.0/data/annotation/src/contrib/IlluminaHumanMethylation450k.db_2.0.7.tar.gz'
Content type 'application/x-gzip' length 63268195 bytes (60.3 Mb)
opened URL
=================================================
downloaded 60.3 Mb

* installing *source* package ‘IlluminaHumanMethylation450k.db’ ...
** R
** inst
** preparing package for lazy loading
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : 
  object 'createSimpleBimap' not found
Error : unable to load R code in package ‘IlluminaHumanMethylation450k.db’
ERROR: lazy loading failed for package ‘IlluminaHumanMethylation450k.db’
* removing ‘/home/benhur/R/x86_64-pc-linux-gnu-library/3.1/IlluminaHumanMethylation450k.db’

The downloaded source packages are in
	‘/tmp/RtmpSVWOdr/downloaded_packages’
Warning message:
In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘IlluminaHumanMethylation450k.db’ had non-zero exit status

 

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

other attached packages:
[1] BiocInstaller_1.16.0

loaded via a namespace (and not attached):
[1] tools_3.1.1

 

Hopefully someone would be able to help me :).

Cheers

Ben

ADD COMMENTlink modified 21 months ago by katwre0 • written 3.1 years ago by ben.run9740
0
gravatar for James W. MacDonald
3.1 years ago by
United States
James W. MacDonald45k wrote:

It's broken right now. See A: IlluminaHumanMethylation450k.db has undeclared dependency on AnnotationForge

You could hypothetically hack the source package to work, or just wait for Tim Triche to upload the new version.

ADD COMMENTlink written 3.1 years ago by James W. MacDonald45k
0
gravatar for James W. MacDonald
3.1 years ago by
United States
James W. MacDonald45k wrote:

Also note that you should really be using the FDb.InfiniumMethylation.hg19 package instead. Howeva:

mv /data/tmp/Rtmp4DWP9d/downloaded_packages/IlluminaHumanMethylation450k.db_2.0.7.tar.gz .

tar xvfz IlluminaHumanMethylation450k.db_2.0.7.tar.gz
<snip>
cd IlluminaHumanMethylation450k.db/R

sed -i 's/AnnotationForge:::createSimpleBimap/AnnotationDbi:::createSimpleBimap/g' zzz.R

cd ../../

R CMD INSTALL IlluminaHumanMethylation450k.db

* installing to library ‘/data/oldR/R-3.1.1/lib64/R/library’
* installing *source* package ‘IlluminaHumanMethylation450k.db’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning: 'IlluminaHumanMethylation450k.db' is deprecated.
Use 'FDb.InfiniumMethylation.hg19' instead.
Use 'FDb.InfiniumMethylation.hg18' instead.
Use 'mapToGenome() function in minfi or methylumi' instead.
See help("Deprecated")
* DONE (IlluminaHumanMethylation450k.db)

But like I said, use the FDb package instead...

ADD COMMENTlink written 3.1 years ago by James W. MacDonald45k

Hi, tried your way. But no luck. Here is the output:

* installing to library ‘/usr/local/lib/R/site-library’
* installing *source* package ‘IlluminaHumanMethylation450k.db’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error : .onLoad failed in loadNamespace() for 'IlluminaHumanMethylation450k.db', details:
  call: NULL
  error: 'fun' is defunct.
Use 'FDb.InfiniumMethylation.hg19' instead.
Use 'FDb.InfiniumMethylation.hg18' instead.
Use 'mapToGenome() function in minfi or methylumi' instead.
See help("Defunct")
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/IlluminaHumanMethylation450k.db’

What is that sed command doing? I can find no difference between the zzz.R files with and without using this command.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by ruhshan.ahmed0
1

You are getting a completely different error than Ben was getting. So why do you think that what I suggested to him would work for you? Is there a particular reason that the FDb.InfiniumMethylation.hg19 is not useful for you?

ADD REPLYlink written 2.4 years ago by James W. MacDonald45k

Thanks for quick response, actually i need to use UCSC CpG island name  "IlluminaHumanMethylation450kCPGINAME".

ADD REPLYlink written 2.4 years ago by ruhshan.ahmed0

In that case, you need to make a new post asking why the current version of that package won't install. When I try to install it, I get the same error as you.

ADD REPLYlink written 2.4 years ago by James W. MacDonald45k
0
gravatar for ben.run974
3.1 years ago by
ben.run9740
United Kingdom
ben.run9740 wrote:

Thank you!!

Unfortunately I'm using another package that depends on IlluminaHumanMethylation450k.db so I have to install it :)

Cheers,

Ben

ADD COMMENTlink written 3.1 years ago by ben.run9740
0
gravatar for katwre
21 months ago by
katwre0
Germany
katwre0 wrote:

Installation of IlluminaHumanMethylation450k.db using biocLite (still) doesn't work :(

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS release 6.7 (Final)

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

attached base packages:
 [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] rtracklayer_1.30.1   genomation_1.3.4     limma_3.26.3         colorfulVennPlot_2.4 ChIPpeakAnno_3.4.5   RSQLite_1.0.0       
 [7] DBI_0.3.1            VennDiagram_1.6.16   futile.logger_1.4.1  Biostrings_2.38.3    XVector_0.10.0       BiocInstaller_1.20.1
[13] Vennerable_3.0       xtable_1.8-2         gtools_3.5.0         reshape_0.8.5        RColorBrewer_1.1-2   lattice_0.20-33     
[19] RBGL_1.46.0          graph_1.48.0         GenomicRanges_1.22.2 GenomeInfoDb_1.6.1   IRanges_2.4.6        S4Vectors_0.8.5     
[25] BiocGenerics_0.16.1 

loaded via a namespace (and not attached):
 [1] Biobase_2.30.0               httr_1.1.0                   regioneR_1.2.3               AnnotationHub_2.2.3          splines_3.2.3               
 [6] shiny_0.13.0                 interactiveDisplayBase_1.8.0 BSgenome_1.38.0              Rsamtools_1.22.0             impute_1.44.0               
[11] chron_2.3-47                 digest_0.6.9                 colorspace_1.2-6             htmltools_0.3                httpuv_1.3.3                
[16] plyr_1.8.3                   XML_3.98-1.3                 biomaRt_2.26.1               zlibbioc_1.16.0              GO.db_3.2.2                 
[21] scales_0.3.0                 BiocParallel_1.4.3           ggplot2_2.0.0                seqPattern_1.2.0             SummarizedExperiment_1.0.2  
[26] GenomicFeatures_1.22.7       survival_2.38-3              magrittr_1.5                 mime_0.4                     memoise_1.0.0               
[31] MASS_7.3-45                  tools_3.2.3                  data.table_1.9.6             matrixStats_0.50.1           gridBase_0.4-7              
[36] stringr_1.0.0                munsell_0.4.2                plotrix_3.6-1                AnnotationDbi_1.32.3         ensembldb_1.2.2             
[41] lambda.r_1.1.7               RCurl_1.95-4.7               bitops_1.0-6                 gtable_0.1.2                 multtest_2.26.0             
[46] reshape2_1.4.1               R6_2.1.2                     GenomicAlignments_1.6.1      futile.options_1.0.0         KernSmooth_2.23-15          
[51] readr_0.2.2                  stringi_1.0-1                Rcpp_0.12.3 

 

 

ADD COMMENTlink modified 21 months ago • written 21 months ago by katwre0
1

Right. And this is because the package is now defunct, which means it is no longer supported, and will be removed soon, probably in the next release. As I mentioned multiple times in this thread, you should be using the FDb.InfiniumMethylation.hg19 package instead, which is intended to replace the IlluminaHumanMethylation450k.db package.

If you are using a package that depends on the IlluminaHumanMethylation450k.db package (which seems not to be possible since it won't build, but whatever), you have two choices. Either take it upon yourself to fix the IlluminaHumanMethylation450k.db package so it will build, or contact the maintainer of the package that depends on it and have them switch to using the Fdb.InfiniumMethylation.hg19 package. The latter seems to be the easier way to go, but ymmv.

ADD REPLYlink written 21 months ago by James W. MacDonald45k

Thank you for your reply! Fdb.InfiniumMethylation.hg19 package works for me!

ADD REPLYlink written 21 months ago by katwre0

But in my case, I need this package because I'm trying to do a practise of my Master, and I had a problem with our website Rstudio app, and now I can't install the package.....

You would be able to install it from an old repository or something like that if you want to use it...

I need to use the package anyway, so if someone can help me, it would be great.

Thank you
 

ADD REPLYlink modified 21 months ago • written 21 months ago by alvaropc630

Did you manage to use your library? I have similar problem - I have to use Aclust library, which needs IlluminaHumanMethylation450k.db. I'd be really grateful for any information how you solved this problem, if you did.

Kind regards,

Agata

ADD REPLYlink written 15 months ago by aagata.szymanek0
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