Problem loading methylkit on Raven

[sr320]

Note working find before today. But today

library(methylKit)

Error: package or namespace load failed for ‘methylKit’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/home/sr320/R_libs/Matrix/libs/Matrix.so': libRlapack.so: cannot open shared object file: No such file or directory

For reference: #1237

[kubu4]

I'm still looking into this. I'm able to load methylKit on Raven without any issue.

Can you please post the output of the following command:

.libPaths()

[sr320]

[1] "/home/sr320/R_libs" "/opt/R/4.1.0/lib/R/library"

[kubu4]

Try to install the Matrix package and report back, please.

install.packages("Matrix")

[kubu4]

Interesting!

Give this a whirl.

Via Terminal:

Delete the offending package directory:
rm -rf /home/sr320/R_libs/Matrix/

Then, install it again.

Via RStudio:

install.packages("Matrix")

And, lastly, try to load methylKit again...

[sr320]

Did not work

> library(methylKit)
Error in library(methylKit) : there is no package called ‘methylKit’

[kubu4]

Weird! Try installing methylKit again? It's a BioConductor package (I'm on mobile ATM, so can't look it up).

[sr320]

no luck

[kubu4]

What happened this time? Also, might be worthwhile signing out and signing back in? Don't save any R session data when you close.

[sr320]

update

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.14")

The downloaded source packages are in
	‘/tmp/RtmpeXuY9E/downloaded_packages’
> BiocManager::install("methylKit")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Installing package(s) 'methylKit'
trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/methylKit_1.20.0.tar.gz'
Content type 'application/x-gzip' length 1327901 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

* installing *source* package ‘methylKit’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/sr320/R_libs/Rcpp/include' -I'/home/sr320/R_libs/Rhtslib/include' -I'/home/sr320/R_libs/zlibbioc/include' -I/usr/local/include   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/sr320/R_libs/Rcpp/include' -I'/home/sr320/R_libs/Rhtslib/include' -I'/home/sr320/R_libs/zlibbioc/include' -I/usr/local/include   -fpic  -g -O2  -c methCall.cpp -o methCall.o
g++ -std=gnu++11 -shared -L/opt/R/4.1.0/lib/R/lib -L/usr/local/lib -o methylKit.so RcppExports.o methCall.o /home/sr320/R_libs/Rhtslib/usrlib/libhts.a -lcurl -L/opt/R/4.1.0/lib/R/lib -lR
installing to /home/sr320/R_libs/00LOCK-methylKit/00new/methylKit/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/sr320/R_libs/mclust/libs/mclust.so':
  libRlapack.so: cannot open shared object file: No such file or directory
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘methylKit’
* removing ‘/home/sr320/R_libs/methylKit’
Warning in .inet_warning(msg) :
  installation of package ‘methylKit’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/RtmpeXuY9E/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /opt/R/4.1.0/lib/R/library
  packages:
    annotate, AnnotationDbi, backports, bbmle, Biobase, BiocGenerics, BiocIO, BiocParallel, BiocVersion,
    Biostrings, blob, broom, cachem, cli, colorspace, cpp11, crayon, curl, data.table, DelayedArray, DESeq2,
    digest, dplyr, fastseg, gargle, genefilter, geneplotter, generics, GenomeInfoDb, GenomeInfoDbData,
    GenomicAlignments, GenomicRanges, ggplot2, GO.db, googledrive, googlesheets4, haven, Hmisc, hms, htmlTable,
    htmltools, htmlwidgets, impute, IRanges, isoband, jpeg, KEGGREST, knitr, lattice, lifecycle, limma, lubridate,
    MatrixGenerics, matrixStats, methylKit, mgcv, mime, mvtnorm, nlme, openssl, pillar, preprocessCore, qvalue,
    R.utils, R6, Rcpp, RcppArmadillo, RCurl, readr, reprex, Rhtslib, rlang, rmarkdown, Rsamtools, RSQLite,
    rtracklayer, rvest, S4Vectors, snow, stringi, SummarizedExperiment, survival, tibble, tidyr, tinytex, utf8,
    uuid, viridis, xfun, XML, XVector, zlibbioc
> library(methylKit)
Error: package or namespace load failed for ‘methylKit’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/sr320/R_libs/mclust/libs/mclust.so':
  libRlapack.so: cannot open shared object file: No such file or directory

[kubu4]

FYI, I think your personal library path is set in this file:

/home/sr320/.Renviron

Interestingly, I have a similar line in my .Renviron file, but mine is commented out... I can't remember why I did this, nor how I've established a different install location for personal R packages. Grrrrrr! Ugh!

[sr320]

looked like

sr320@raven:~$ cat .Renviron 
# Set local library installation path
R_LIBS_USER=/home/sr320/R_libs

changed to

sr320@raven:~$ cat .Renviron 
# Set local library installation path
# R_LIBS_USER=/home/sr320/R_libs

closed terminal

Ran

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.14")
BiocManager::install("methylKit")

Upgrade 93 packages to Bioconductor version '3.14'? [y/n]: 
y
Error in packageVersion("BiocManager") : 
  there is no package called ‘BiocManager’

[sr320]

update

restarted R...

got past that error

doing something

[kubu4]

Can you please post the output of the following R command:

Sys.getenv()[ grep("LIB|PATH", names(Sys.getenv())) ]

For reference, here's what mine looks like (and, I see that the LD_LIBRAY_PATH is reading from the shared system libraries first, before my personal libraries):

LD_LIBRARY_PATH                              /opt/R/4.1.0/lib/R/lib::/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server
PATH                                         /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/usr/lib/rstudio-server/bin/postback:/usr/lib/rstudio-server/bin/postback:/usr/lib/rstudio-server/bin/postback
R_LIBS_SITE                                  
R_LIBS_USER                                  ~/R/x86_64-pc-linux-gnu-library/4.1
R_STRIP_SHARED_LIB                           strip --strip-unneeded
R_STRIP_STATIC_LIB                           strip --strip-debug
RMARKDOWN_MATHJAX_PATH                       /usr/lib/rstudio-server/resources/mathjax-27
RS_RPOSTBACK_PATH                            /usr/lib/rstudio-server/bin/rpostback

[sr320]

commenting out personal library worked!

> Sys.getenv()[ grep("LIB|PATH", names(Sys.getenv())) ]
LD_LIBRARY_PATH               /opt/R/4.1.0/lib/lib::/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server
PATH                          /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/usr/lib/rstudio-server/bin/postback
R_LIBS_SITE                   
R_LIBS_USER                   ~/R/x86_64-pc-linux-gnu-library/4.1
R_STRIP_SHARED_LIB            strip --strip-unneeded
R_STRIP_STATIC_LIB            strip --strip-debug
RMARKDOWN_MATHJAX_PATH        /usr/lib/rstudio-server/resources/mathjax-27
RS_RPOSTBACK_PATH             /usr/lib/rstudio-server/bin/rpostback

[sr320]

Update

this worked!

looked like

sr320@raven:~$ cat .Renviron 
# Set local library installation path
R_LIBS_USER=/home/sr320/R_libs

changed to

sr320@raven:~$ cat .Renviron 
# Set local library installation path
# R_LIBS_USER=/home/sr320/R_libs

closed terminal

Restarted R

Ran

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.14")
BiocManager::install("methylKit")

[kubu4]

Easy peasy!