Question: Trouble installing GOSemSim
0
gravatar for sergi.picart
3 months ago by
sergi.picart10
sergi.picart10 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 • 202 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by sergi.picart10

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 3 months ago by Lluís Revilla Sancho480

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

ADD REPLYlink written 3 months ago by sergi.picart10

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

ADD REPLYlink written 3 months ago by shepherl ♦♦ 1.4k
1

Hello, I've encountered the same issue and tried to follow your suggested solution. However, by running BiocManager::valid() I got an error:

loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning messages:
1: 3 packages out-of-date; 0 packages too new 
2: In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'urltools' is missing or broken
3: In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'ggforce' is missing or broken
4: In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'data.table' is missing or broken
5: In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'rlang' is missing or broken
6: In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'rJava' is missing or broken
7: In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'GOSemSim' is missing or broken

Do you have an idea how to fix it? Thank you!

ADD REPLYlink written 8 weeks ago by qiiiibeau10

What is your sessionInfo()?

ADD REPLYlink written 8 weeks ago by shepherl ♦♦ 1.4k

Yesterday when I restarted the R session there were no error anymore in the results of BiocManager::valid() and I was able to install GOSemSim. However, just now when I tried to ran sessionInfo() or BiocManager::valid() the same error appeared. Though my issue concerning to the subject is solved, I would like to understand what happened to my R. Appreciation in advance from a beginner in bioinfo :)

Below is the output of sessionInfo().

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] xlsx_0.6.1             igraph_1.2.4           org.Ce.eg.db_3.7.0     AnnotationDbi_1.44.0   IRanges_2.16.0        
 [6] S4Vectors_0.20.1       Biobase_2.42.0         BiocGenerics_0.28.0    clusterProfiler_3.10.1 GOSemSim_2.8.0        

loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning message:
In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'ggforce' is missing or broken
ADD REPLYlink written 8 weeks ago by qiiiibeau10

I believe the underlying problem is that some packages are installed with a previous or future version of R; BiocManager::valid() should report these, and it's not clear why this would clear up yesterday but re-appear today. Maybe you have two versions of R that are sharing the same .libPaths()?

ADD REPLYlink written 8 weeks ago by Martin Morgan ♦♦ 23k

I only have one version of R. But by .libPaths() I've realized that my packages were installed in two different directories.

> .libPaths()
[1] "C:/Users/qsun/Documents/R/win-library/3.5" "C:/Program Files/R/R-3.5.1/library"

I found this page where there's your answer as well, and consider remove packages from the 2nd directory with administrative rights and reinstall them into the first one to solve the packages update issue.

Still don't understand what happened to make that Error in x[["Version"]] : subscript out of bounds disappear and reappear though =_=

ADD REPLYlink written 8 weeks ago by qiiiibeau10

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 3 months ago by sergi.picart10
1

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

ADD REPLYlink written 3 months ago by shepherl ♦♦ 1.4k

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 3 months ago by sergi.picart10
Answer: Trouble installing GOSemSim
1
gravatar for sergi.picart
3 months ago by
sergi.picart10
sergi.picart10 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 3 months ago by sergi.picart10
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