"minfi" loading problem because of couldn't "bumphunter" load
4
1
Entering edit mode
@juan-pablocerapio-arroyo-10842
Last seen 5.1 years ago
France/Paris/Institut Pasteur

Dear all,

i couldn't load "minfi", i installed it using:

source("https://bioconductor.org/biocLite.R")
biocLite("minfi")

Apparently no errors:

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘minfi’
essai de l'URL 'https://bioconductor.org/packages/3.5/bioc/bin/macosx/el-capitan/contrib/3.4/minfi_1.22.1.tgz'
Content type 'application/x-gzip' length 825920 bytes (806 KB)
==================================================
downloaded 806 KB


The downloaded binary packages are in
    /var/folders/mf/_xyr2hm93rx845kbc_8hcwwc0000gn/T//RtmpNwrMaY/downloaded_packages
 

Them when i tried to load it:

library(minfi)

I'm getting:

Le chargement a nécessité le package : bumphunter
Error: package or namespace load failed for ‘bumphunter’ in dyn.load(file, DLLpath = DLLpath, ...):
 impossible de charger l'objet partagé '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so, 6): Library not loaded: /usr/local/opt/openssl/lib/libssl.1.0.0.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so
  Reason: image not found
Erreur : le package ‘bumphunter’ ne peut être chargé

So i tried reinstalling "bumphunter"

remove.packages("bumphunter")

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

biocLite("bumphunter")

library(bumphunter)

Erreur : package or namespace load failed for ‘bumphunter’ in dyn.load(file, DLLpath = DLLpath, ...):
 impossible de charger l'objet partagé '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so, 6): Library not loaded: /usr/local/opt/openssl/lib/libssl.1.0.0.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so
  Reason: image not found

So i tried reinstalling "rtracklayer"

remove.packages("rtracklayer")

source("https://bioconductor.org/biocLite.R")
biocLite("rtracklayer")

library(rtracklayer)

Erreur : package or namespace load failed for ‘rtracklayer’ in dyn.load(file, DLLpath = DLLpath, ...):
 impossible de charger l'objet partagé '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so, 6): Library not loaded: /usr/local/opt/openssl/lib/libssl.1.0.0.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rtracklayer/libs/rtracklayer.so
  Reason: image not found

So i checked too for maybe old package using biocValid():

[1] TRUE

So i have no clue how is going on, if some on could help me please.

Thanks.

Jp

R session info sessionInfo()

R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8

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

other attached packages:
 [1] devtools_1.12.0            tidyr_0.6.2               
 [3] locfit_1.5-9.1             iterators_1.0.8           
 [5] foreach_1.4.3              Biostrings_2.44.0         
 [7] XVector_0.16.0             SummarizedExperiment_1.6.1
 [9] DelayedArray_0.2.1         matrixStats_0.52.2        
[11] Biobase_2.36.2             GenomicRanges_1.28.1      
[13] GenomeInfoDb_1.12.0        IRanges_2.10.0            
[15] S4Vectors_0.14.0           BiocGenerics_0.22.0       
[17] BiocInstaller_1.26.0      

loaded via a namespace (and not attached):
 [1] doRNG_1.6.6              GenomeInfoDbData_0.99.0  Rsamtools_1.28.0        
 [4] RSQLite_1.1-2            lattice_0.20-35          digest_0.6.12           
 [7] Matrix_1.2-10            XML_3.98-1.7             biomaRt_2.32.0          
[10] zlibbioc_1.22.0          xtable_1.8-2             BiocParallel_1.10.1     
[13] tibble_1.3.0             pkgmaker_0.22            withr_1.0.2             
[16] magrittr_1.5             memoise_1.1.0            tools_3.4.0             
[19] registry_0.3             stringr_1.2.0            rngtools_1.2.4          
[22] AnnotationDbi_1.38.0     compiler_3.4.0           grid_3.4.0            

[25] RCurl_1.95-4.8           rstudioapi_0.6           bitops_1.0-6            

[28] codetools_0.2-15         DBI_0.6-1                GenomicAlignments_1.12.0
[31] stringi_1.1.5            Rcpp_0.12.10  

bumphunter minfi loading error rtracklayer • 2.6k views
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1
Entering edit mode
@herve-pages-1542
Last seen 1 day ago
Seattle, WA, United States

Hi,

As Kasper said, this is a problem with the rtracklayer Mac binary.  While we figure out a way to fix it, you should be able to work around this problem by installing the openssl library with:

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew install openssl

Then try to install and load rtracklayer again with:

biocLite("rtracklayer")
library(rtracklayer)

Sorry for the inconvenience,

H.

Edit (May 25, 2017): The rtracklayer Mac binary has been updated and does not require installing the openssl library on the user machine anymore. Please update with biocLite() (this should install rtracklayer >= 1.36.3).

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0
Entering edit mode

Thanks so much for the help and the clarification! I downloaded homebrew and installed openssl, reloaded my packages, and everything worked just fine.

Thanks again!

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0
Entering edit mode

There is a new rtracklayer Mac binary that addresses this issue. See edit to my answer above.

H.

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0
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AEGentry • 0
@aegentry-12981
Last seen 5.1 years ago
USA/Richmond/VCU

I am having the identical problem. And I am running the same R version, platform, and macOS.

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0
Entering edit mode
This is an rtracklayer issue. It appears to me that the shipped binaries (for rtracklayer) for OS X requires that libssl is installed. You should either install libssl, or (perhaps better) see if someone can fix the binaries. Best, Kasper On Sun, May 7, 2017 at 9:15 PM, gentryae [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User gentryae <https: support.bioconductor.org="" u="" 12981=""/> wrote Answer: > "minfi" loading problem because of couldn't "bumphunter" load > <https: support.bioconductor.org="" p="" 95659="" #95676="">: > > I am having the identical problem. And I am running the same R version, > platform, and macOS. > > ------------------------------ > > Post tags: bumphunter, minfi, loading error, rtracklayer > > You may reply via email or visit https://support.bioconductor. > org/p/95659/#95676 >
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0
Entering edit mode
AEGentry • 0
@aegentry-12981
Last seen 5.1 years ago
USA/Richmond/VCU

Thank you so much for your response.

So sorry, but what is libssl?

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nilan666 • 0
@nilan666-13122
Last seen 5.0 years ago

This had been bugging me for over a week..!

Issue was I had macports installed instead of homebrew so could not follow the instructions above. What I did ultimately find was that the 'openssl' library needed to be upgraded. However, the 'selfupdate' command of macports was breaking for some reason.

Ultimately what I did was run the following command

sudo port -v upgrade outdated

Then I went to RStudio and typed the following commands : 

source('https://bioconductor.org/biocLite.R') #worked today after upgrading openSSL
biocLite()

biocLite('minfi')

Over the course of the installation, it asked for the upgradation of the outdated package 'rtracklater' which it successfully managed and now I can finally use the package.

So, being able to upgrade openssl in macports was essential.

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0
Entering edit mode

Hi,

Please note that the latest rtracklayer Mac binary (1.36.3) doesn't require that you install openssl anymore.

Cheers,

H.

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