Question: "minfi" loading problem because of couldn't "bumphunter" load
1
gravatar for juan-pablo.cerapio-arroyo
2.3 years ago by
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  

ADD COMMENTlink modified 2.2 years ago by nilan6660 • written 2.3 years ago by juan-pablo.cerapio-arroyo10
Answer: "minfi" loading problem because of couldn't "bumphunter" load
1
gravatar for Hervé Pagès
2.3 years ago by
Hervé Pagès ♦♦ 14k
United States
Hervé Pagès ♦♦ 14k wrote:

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).

ADD COMMENTlink modified 2.2 years ago • written 2.3 years ago by Hervé Pagès ♦♦ 14k

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!

ADD REPLYlink written 2.3 years ago by AEGentry0

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

H.

ADD REPLYlink written 2.2 years ago by Hervé Pagès ♦♦ 14k
Answer: "minfi" loading problem because of couldn't "bumphunter" load
0
gravatar for AEGentry
2.3 years ago by
AEGentry0
USA/Richmond/VCU
AEGentry0 wrote:

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

ADD COMMENTlink written 2.3 years ago by AEGentry0
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 >
ADD REPLYlink written 2.3 years ago by Kasper Daniel Hansen6.4k
Answer: "minfi" loading problem because of couldn't "bumphunter" load
0
gravatar for AEGentry
2.3 years ago by
AEGentry0
USA/Richmond/VCU
AEGentry0 wrote:

Thank you so much for your response.

So sorry, but what is libssl?

ADD COMMENTlink written 2.3 years ago by AEGentry0
Answer: "minfi" loading problem because of couldn't "bumphunter" load
0
gravatar for nilan666
2.2 years ago by
nilan6660
nilan6660 wrote:

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.

ADD COMMENTlink written 2.2 years ago by nilan6660

Hi,

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

Cheers,

H.

ADD REPLYlink written 2.2 years ago by Hervé Pagès ♦♦ 14k
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