Question: Trouble installing GOSemSim
0
gravatar for sergi.picart
4 weeks ago by
sergi.picart0 wrote:

When I try to install GOSemSim I get the following error with S4Vectors

> BiocManager::install("GOSemSim")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.2 (2018-12-20)
Installing package(s) 'GOSemSim'
trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/GOSemSim_2.8.0.tar.gz'
Content type 'application/x-gzip' length 604232 bytes (590 KB)
==================================================
downloaded 590 KB

* installing *source* package ‘GOSemSim’ ...
** libs
g++  -I"/usr/share/R/include" -DNDEBUG  -I"/home/sergi/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-i39faS/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ICmethod.cpp -o ICmethod.o
g++  -I"/usr/share/R/include" -DNDEBUG  -I"/home/sergi/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include"    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-i39faS/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o GOSemSim.so ICmethod.o RcppExports.o -L/usr/lib/R/lib -lR
installing to /home/sergi/R/x86_64-pc-linux-gnu-library/3.5/GOSemSim/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error : object ‘elementLengths’ is not exported by 'namespace:S4Vectors'
ERROR: lazy loading failed for package ‘GOSemSim’
* removing ‘/home/sergi/R/x86_64-pc-linux-gnu-library/3.5/GOSemSim’

What am I doing wrong? Thank you

Session info (after loading S4Vectors):

> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

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

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

other attached packages:
[1] S4Vectors_0.20.1    BiocGenerics_0.28.0

loaded via a namespace (and not attached):
[1] BiocManager_1.30.4 compiler_3.5.2     tools_3.5.2
gosemsim s4vectors • 91 views
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by sergi.picart0

did you try updating S4Vectors package? The problem seems to be a change on that package that it is needed by GOSemSim

ADD REPLYlink written 4 weeks ago by Lluís Revilla Sancho460

Yes, it is already in its latest version 0.20.1 (https://bioconductor.org/packages/release/bioc/html/S4Vectors.html)

ADD REPLYlink written 4 weeks ago by sergi.picart0

What is the result of BiocManager::valid() ?

ADD REPLYlink written 4 weeks ago by shepherl ♦♦ 1.3k

This is the output. I will try to update the out-of-date packages

> BiocManager::valid()

* sessionInfo()

R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

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

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.4 compiler_3.5.2     tools_3.5.2       

Bioconductor version '3.8'

  * 85 packages out-of-date
  * 0 packages too new

create a valid installation with

  BiocManager::install(c(
    "AER", "affy", "affyio", "AnnotationDbi", "BH", "BiocGenerics",
    "BiocInstaller", "bit", "bootstrap", "couchDB", "curl", "data.table",
    "devtools", "diptest", "DO.db", "doParallel", "doSNOW", "DT",
    "dynamicTreeCut", "fastcluster", "fastmatch", "ff", "flexmix", "foreach",
    "fpc", "GenomeInfoDb", "GenomeInfoDbData", "git2r", "GO.db", "GOSemSim",
    "gridBase", "gss", "hgu133plus2.db", "htmlwidgets", "httr", "igraph",
    "irlba", "iterators", "jsonlite", "KEGG.db", "littler", "magrittr",
    "Matching", "mclust", "modeltools", "mzR", "NLP", "NMF", "openssl",
    "org.Hs.eg.db", "pcaMethods", "permute", "pkgconfig", "pkgmaker", "plogr",
    "prabclus", "preprocessCore", "PubMedWordcloud", "qvalue", "R6",
    "RcppArmadillo", "registry", "Rgraphviz", "rhandsontable", "rjson",
    "rlang", "rngtools", "rstudioapi", "rvcheck", "S4Vectors", "scales",
    "stringr", "tibble", "tidyr", "tm", "trimcluster", "viridis", "whisker",
    "withr", "wordcloud", "XML", "xtable", "zlibbioc"
  ), update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message:
85 packages out-of-date; 0 packages too new
ADD REPLYlink written 4 weeks ago by sergi.picart0
1

Please let us know if you continue to have issues after correcting to a valid install.

ADD REPLYlink written 4 weeks ago by shepherl ♦♦ 1.3k

It's working now - thank you very much for a prompt and precise help! I ran the following chunk:

  BiocManager::install(c(
    "AER", "affy", "affyio", "AnnotationDbi", "BH", "BiocGenerics",
    "BiocInstaller", "bit", "bootstrap", "couchDB", "curl", "data.table",
    "devtools", "diptest", "DO.db", "doParallel", "doSNOW", "DT",
    "dynamicTreeCut", "fastcluster", "fastmatch", "ff", "flexmix", "foreach",
    "fpc", "GenomeInfoDb", "GenomeInfoDbData", "git2r", "GO.db", "GOSemSim",
    "gridBase", "gss", "hgu133plus2.db", "htmlwidgets", "httr", "igraph",
    "irlba", "iterators", "jsonlite", "KEGG.db", "littler", "magrittr",
    "Matching", "mclust", "modeltools", "mzR", "NLP", "NMF", "openssl",
    "org.Hs.eg.db", "pcaMethods", "permute", "pkgconfig", "pkgmaker", "plogr",
    "prabclus", "preprocessCore", "PubMedWordcloud", "qvalue", "R6",
    "RcppArmadillo", "registry", "Rgraphviz", "rhandsontable", "rjson",
    "rlang", "rngtools", "rstudioapi", "rvcheck", "S4Vectors", "scales",
    "stringr", "tibble", "tidyr", "tm", "trimcluster", "viridis", "whisker",
    "withr", "wordcloud", "XML", "xtable", "zlibbioc"
  ), update = TRUE, ask = FALSE)
ADD REPLYlink written 4 weeks ago by sergi.picart0
Answer: Trouble installing GOSemSim
0
gravatar for sergi.picart
4 weeks ago by
sergi.picart0 wrote:

The solution was to run BiocManager::valid() to spot outdated packages, thanks to Lluís and shepherl. The same command also suggests a call to BiocManager::install with the names of such packages (see comments). Afterwards, BiocManager::install("GOSemSim") did the trick.

ADD COMMENTlink written 4 weeks ago by sergi.picart0
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