Hi Kenneth, Thank for the prompt response. Please see comment inline below.
Cheers, Loris Kenneth Hoste <[email protected]> writes: > Hi Loris, > > On 16/04/2020 13:08, Loris Bennett wrote: >> Hi, >> >> Using EB 4.2.0, I just ran >> >> eb V8-2.2-foss-2018b-R-3.5.1.eb --robot >> >> and got the following error: >> >> == FAILED: Installation ended unsuccessfully (build directory: >> /trinity/shared/easybuild/build/V8/2.2/foss-2018b-R-3.5.1): build failed >> (first 300 chars): Module command 'module load R/3.5.1-foss-2018b' failed >> with >> exit code 1; stderr: Lmod has detected the following error: The following >> module(s) are unknown: "Java/1.8" >> >> I can however load the individual modules 'Java/1.8' and >> 'R/3.5.1-foss-2018b' directly. >> >> Any ideas what the problem might be? > > Does the problem also occur when you're loading R/3.5.1-foss-2018b yourself > in a > clean environment (without loading Java first)? No. > We'll need some more information on this, preferably including (debug) log > that > gives us some more context. > > In addition: > > * Which version of Lmod are you using? 8.2.7 > * What's your EasyBuild configuration (output of "eb --show-config" should be > enough)? [build@admin eco]$ eb --show-config # # Current EasyBuild configuration # (C: command line argument, D: default value, E: environment variable, F: configuration file) # buildpath (F) = /trinity/shared/easybuild/build containerpath (F) = /trinity/shared/easybuild/containers git-working-dirs-path (F) = /trinity/home/build/git/easybuild-easyconfigs hooks (F) = /trinity/home/build/hooks/hpc_hooks.py installpath (E) = /trinity/shared/easybuild packagepath (F) = /trinity/shared/easybuild/packages prefix (E) = /trinity/shared/easybuild repositorypath (F) = /trinity/shared/easybuild/ebfiles_repo robot-paths (D) = /trinity/shared/easybuild/software/EasyBuild/4.2.0/easybuild/easyconfigs sourcepath (F) = /trinity/shared/easybuild/sources > * What output do you get from "module show Java/1.8" in a clean environment > (before loading that module)? [13:57:02] loris@login (999) ~ $ module show Java/1.8 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ /trinity/shared/easybuild/modules/all/Java/1.8.0_231.lua: ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ help([[ Description =========== Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. More information ================ - Homepage: https://java.com/ ]]) whatis("Description: Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.") whatis("Homepage: https://java.com/";) whatis("URL: https://java.com/";) conflict("Java") prepend_path("CPATH","/trinity/shared/easybuild/software/Java/1.8.0_231/include") prepend_path("LD_LIBRARY_PATH","/trinity/shared/easybuild/software/Java/1.8.0_231/lib") prepend_path("LIBRARY_PATH","/trinity/shared/easybuild/software/Java/1.8.0_231/lib") prepend_path("MANPATH","/trinity/shared/easybuild/software/Java/1.8.0_231/man") prepend_path("PATH","/trinity/shared/easybuild/software/Java/1.8.0_231/bin") setenv("EBROOTJAVA","/trinity/shared/easybuild/software/Java/1.8.0_231") setenv("EBVERSIONJAVA","1.8.0_231") setenv("EBDEVELJAVA","/trinity/shared/easybuild/software/Java/1.8.0_231/easybuild/Java-1.8.0_231-easybuild-devel") prepend_path("PATH","/trinity/shared/easybuild/software/Java/1.8.0_231") setenv("JAVA_HOME","/trinity/shared/easybuild/software/Java/1.8.0_231") > Same request for "R/3.5.1-foss-2018b". $ module show R/3.5.1-foss-2018b ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ /trinity/shared/easybuild/modules/all/R/3.5.1-foss-2018b.lua: ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ help([[ Description =========== R is a free software environment for statistical computing and graphics. More information ================ - Homepage: http://www.r-project.org/ Included extensions =================== abc-2.1, abc.data-1.0, abind-1.4-5, acepack-1.4.1, adabag-4.2, ade4-1.7-11, adegenet-2.1.1, adephylo-1.1-11, ADGofTest-0.3, aggregation-1.0.1, akima-0.6-2, AlgDesign-1.1-7.3, animation-2.5, aod-1.3, ape-5.1, arm-1.10-1, asnipe-1.1.11, assertthat-0.2.0, AUC-0.3.0, audio-0.1-5.1, b-a, backports-1.1.2, bartMachine-1.2.4.2, bartMachineJARs-1.1, base64-2.0, base64enc-0.1-3, BatchJobs-1.7, BayesianTools-0.1.5, bayesm-3.1-0.1, BB-2014.10-1, BBmisc-1.11, BDgraph-2.51, beanplot-1.2, beeswarm-0.2.3, BH-1.66.0-1, BiasedUrn-1.07, bibtex-0.4.2, bibtex-0.4.2, bigmemory-4.5.33, bigmemory.sri-0.1.3, bindr-0.1.1, bindrcpp-0.2.2, bio3d-2.3-4, biom-0.3.12, bit-1.1-14, bit64-0.9-7, bitops-1.0-6, blob-1.1.1, bmp-0.3, bnlearn-4.3, bold-0.5.0, boot-1.3-20, bootstrap-2017.2, brew-1.0-6, brglm-0.6.1, bridgedist-0.1.0, bridgesampling-0.4-0, Brobdingnag-1.2-6, broom-0.5.0, bst-0.3-15, Cairo-1.5-9, 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load("LibTIFF/4.0.9-GCCcore-7.3.0") load("Java/1.8") load("Tk/8.6.8-GCCcore-7.3.0") load("cURL/7.60.0-GCCcore-7.3.0") load("libxml2/2.9.8-GCCcore-7.3.0") load("GDAL/2.2.3-foss-2018b-Python-3.6.6") load("PROJ/5.0.0-foss-2018b") load("GMP/6.1.2-GCCcore-7.3.0") load("NLopt/2.4.2-GCCcore-7.3.0") load("FFTW/3.3.8-gompi-2018b") load("libsndfile/1.0.28-GCCcore-7.3.0") load("ICU/61.1-GCCcore-7.3.0") load("HDF5/1.10.2-foss-2018b") load("UDUNITS/2.2.26-foss-2018b") load("GSL/2.5-GCC-7.3.0-2.30") prepend_path("LD_LIBRARY_PATH","/trinity/shared/easybuild/software/R/3.5.1-foss-2018b/lib64") prepend_path("LD_LIBRARY_PATH","/trinity/shared/easybuild/software/R/3.5.1-foss-2018b/lib64/R/lib") prepend_path("LIBRARY_PATH","/trinity/shared/easybuild/software/R/3.5.1-foss-2018b/lib64") prepend_path("LIBRARY_PATH","/trinity/shared/easybuild/software/R/3.5.1-foss-2018b/lib64/R/lib") prepend_path("MANPATH","/trinity/shared/easybuild/software/R/3.5.1-foss-2018b/share/man") prepend_path("PATH","/trinity/shared/easybuild/software/R/3.5.1-foss-2018b/bin") prepend_path("PKG_CONFIG_PATH","/trinity/shared/easybuild/software/R/3.5.1-foss-2018b/lib64/pkgconfig") setenv("EBROOTR","/trinity/shared/easybuild/software/R/3.5.1-foss-2018b") setenv("EBVERSIONR","3.5.1") setenv("EBDEVELR","/trinity/shared/easybuild/software/R/3.5.1-foss-2018b/easybuild/R-3.5.1-foss-2018b-easybuild-devel") setenv("EBEXTSLISTR","b-a,d-a,g-r,g-r,g-r,m-e,s-p,s-t,s-t,t-o,u-t,Rmpi-0.6-7,abind-1.4-5,magic-1.5-8,geometry-0.3-6,bit-1.1-14,filehash-2.4-1,ff-2.2-14,bnlearn-4.3,bootstrap-2017.2,combinat-0.0-8,deal-1.2-37,fdrtool-1.2.15,formatR-1.5,gtools-3.8.1,gdata-2.18.0,GSA-1.03,highr-0.7,infotheo-1.2.0,lars-1.2,lazy-1.2-16,kernlab-0.9-27,mime-0.5,markdown-0.8,mlbench-2.1-1,NLP-0.1-11,mclust-5.4.1,RANN-2.6,rmeta-3.0,segmented-0.5-3.0,som-0.3-5.1,SuppDists-1.1-9.4,stabledist-0.7-1,survivalROC-1.0.3,pspline-1.0-18,timeDate-3043.102,longmemo-1.0-0,ADGofTest-0.3,MASS-7.3-50,ade4-1.7-11,AlgDesign-1.1-7.3,base64enc-0.1-3,BH-1.66.0-1,brew-1.0-6,Brobdingnag-1.2-6,corpcor-1.6.9,longitudinal-1.1.12,backports-1.1.2,checkmate-1.8.5,Rcpp-0.12.18,cubature-1.4,DEoptimR-1.0-8,digest-0.6.15,fastmatch-1.1-0,ffbase-0.12.3,iterators-1.0.10,maps-3.3.0,nnls-1.4,sendmailR-1.2-1,dotCall64-1.0-0,spam-2.2-0,subplex-1.5-4,stringi-1.2.4,magrittr-1.5,glue-1.3.0,stringr-1.3.1,evaluate-0.11,logspline-2.1.11,ncbit-2013.03.29,permute-0.9-4,plotrix-3.7-2,randomForest-4.6-14,scatterplot3d-0.3-41,SparseM-1.77,tripack-1.3-8,irace-3.1,rJava-0.9-10,lattice-0.20-35,RColorBrewer-1.1-2,latticeExtra-0.6-28,Matrix-1.2-14,png-0.1-7,RcppArmadillo-0.9.100.5.0,plyr-1.8.4,gtable-0.2.0,reshape2-1.4.3,dichromat-2.0-0,colorspace-1.3-2,munsell-0.5.0,labeling-0.3,R6-2.2.2,viridisLite-0.3.0,scales-1.0.0,rlang-0.2.2,assertthat-0.2.0,crayon-1.3.4,cli-1.0.0,utf8-1.1.4,fansi-0.3.0,pillar-1.3.0,tibble-1.4.2,lazyeval-0.2.1,withr-2.1.2,nlme-3.1-137,mgcv-1.8-24,ggplot2-3.0.0,pROC-1.12.1,quadprog-1.5-5,BB-2014.10-1,BBmisc-1.11,fail-1.3,rlecuyer-0.3-4,snow-0.4-2,tree-1.0-39,pls-2.6-0,class-7.3-14,e1071-1.7-0,nnet-7.3-12,minqa-1.2.4,RcppEigen-0.3.3.4.0,MatrixModels-0.4-1,quantreg-5.36,robustbase-0.93-2,sp-1.3-1,zoo-1.8-3,lmtest-0.9-36,vcd-1.4-4,snowfall-1.84-6.1,rpart-4.1-13,survival-2.42-6,pkgconfig-2.0.2,bindr-0.1.1,plogr-0.2.0,bindrcpp-0.2.2,purrr-0.2.5,tidyselect-0.2.4,dplyr-0.7.6,tidyr-0.8.1,mnormt-1.5-5,foreign-0.8-71,psych-1.8.4,broom-0.5.0,nloptr-1.0.4,lme4-1.1-18-1,jomo-2.6-3,hms-0.4.2,readr-1.1.1,forcats-0.3.0,haven-1.1.2,pan-1.6,mitml-0.3-6,mice-3.3.0,urca-1.3-0,fracdiff-1.4-2,logistf-1.23,akima-0.6-2,bitops-1.0-6,boot-1.3-20,mixtools-1.1.0,cluster-2.0.7-1,gclus-1.3.1,coda-0.19-1,codetools-0.2-15,foreach-1.4.4,doMC-1.3.5,DBI-1.0.0,gam-1.16,gamlss.data-5.0-1,gamlss.dist-5.0-6,gamlss-5.1-2,gamlss.tr-5.1-0,hwriter-1.3.2,KernSmooth-2.23-15,xts-0.11-0,curl-3.2,TTR-0.23-3,quantmod-0.4-13,mvtnorm-1.0-8,pcaPP-1.9-73,numDeriv-2016.8-1,SQUAREM-2017.10-1,lava-1.6.3,prodlim-2018.04.18,pscl-1.5.2,memoise-1.1.0,bit64-0.9-7,prettyunits-1.0.2,blob-1.1.1,RSQLite-2.1.1,data.table-1.11.4,BatchJobs-1.7,sandwich-2.5-0,sfsmisc-1.1-2,spatial-7.3-11,VGAM-1.0-5,waveslim-1.7.5,xtable-1.8-2,profileModel-0.5-9,brglm-0.6.1,deSolve-1.21,tseriesChaos-0.1-13,tseries-0.10-45,fastICA-1.2-1,R.methodsS3-1.7.1,R.oo-1.22.0,cgdsr-1.2.10,R.utils-2.6.0,R.matlab-3.6.1,gbm-2.1.3,Formula-1.2-3,acepack-1.4.1,proto-1.0.0,gridExtra-2.3,chron-2.3-52,viridis-0.5.1,yaml-2.2.0,jsonlite-1.5,htmltools-0.3.6,htmlwidgets-1.2,knitr-1.20,rstudioapi-0.7,htmlTable-1.12,Hmisc-4.1-1,fastcluster-1.1.25,registry-0.5,bibtex-0.4.2,pkgmaker-0.27,rngtools-1.3.1,doParallel-1.0.11,gridBase-0.4-7,NMF-0.21.0,irlba-2.3.2,igraph-1.2.2,GeneNet-1.2.13,ape-5.1,RJSONIO-1.3-0,caTools-1.17.1.1,gplots-3.0.1,ROCR-1.0-7,later-0.7.3,promises-1.0.1,httpuv-1.4.5,rjson-0.2.20,sourcetools-0.1.7,shiny-1.1.0,seqinr-3.4-5,LearnBayes-2.15.1,deldir-0.1-15,gmodels-2.18.1,expm-0.999-2,spData-0.2.9.3,spdep-0.7-8,vegan-2.5-2,adegenet-2.1.1,progress-1.2.0,rncl-0.8.3,XML-3.98-1.15,praise-1.0.0,testthat-2.0.0,rprojroot-1.3-2,xfun-0.3,tinytex-0.6,rmarkdown-1.10,openssl-1.0.2,httr-1.3.1,reshape-0.8.7,xml2-1.2.0,triebeard-0.3.0,urltools-1.7.1,httpcode-0.2.0,crul-0.6.0,bold-0.5.0,rredlist-0.5.0,rentrez-1.2.1,rotl-3.0.4,solrium-1.0.0,ritis-0.7.2,worrms-0.2.8,natserv-0.1.4,WikipediR-1.5.0,WikidataR-1.4.0,wikitaxa-0.2.0,taxize-0.9.4,uuid-0.1-2,RNeXML-2.1.2,phylobase-0.8.4,adephylo-1.1-11,animation-2.5,bigmemory.sri-0.1.3,bigmemory-4.5.33,calibrate-1.7.2,clusterGeneration-1.3.4,raster-2.6-7,dismo-1.1-4,extrafontdb-1.0,Rttf2pt1-1.3.7,extrafont-0.17,fields-9.6,shapefiles-0.7,fossil-0.3.7,geiger-2.0.6,glmnet-2.0-16,crosstalk-1.0.0,miniUI-0.1.1.1,ps-1.1.0,processx-3.2.0,webshot-0.5.0,manipulateWidget-0.10.0,rgl-0.99.16,labdsv-1.8-0,stabs-0.6-3,modeltools-0.2-22,strucchange-1.5-1,TH.data-1.0-9,multcomp-1.4-8,coin-1.2-2,party-1.3-1,libcoin-1.0-1,inum-1.0-0,partykit-1.2-2,mboost-2.9-0,msm-1.6.6,nor1mix-1.2-3,np-0.60-8,polynom-1.3-9,polspline-1.1.13,rms-5.1-2,RWekajars-3.9.2-1,RWeka-0.4-38,slam-0.1-43,tm-0.7-5,TraMineR-2.0-8,chemometrics-1.4.2,FNN-1.1.2.1,ipred-0.9-7,statmod-1.4.30,miscTools-0.6-22,maxLik-1.3-4,mlogit-0.3-0,getopt-1.20.2,gsalib-2.1,optparse-1.6.0,labelled-1.1.0,classInt-0.2-3,questionr-0.6.3,klaR-0.6-14,neuRosim-0.2-12,locfit-1.5-9.1,GGally-1.4.0,beanplot-1.2,clValid-0.6-6,matrixStats-0.54.0,DiscriMiner-0.1-29,ellipse-0.4.1,leaps-3.0,pbkrtest-0.4-7,carData-3.0-1,mapt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-- Dr. Loris Bennett (Mr.) ZEDAT, Freie Universität Berlin Email [email protected]
