R 4.3.0: Test installing on C4

[HenrikBengtsson]

There are 250 CRAN and Bioconductor 3.17 packages that does not install in R 4.3.0 on CentOS 7.9 when installing in batch mode:

Packages that failed to install: [n=250] AFM, AlphaHull3D, biplotbootGUI, Boov, bpca, brainKCCA, brainR, BRugs, cgalMeshes, cgalPolygons, ChaosGame, cheem, ch
emmodlab, circularEV, ClaimsProblems, ClusROC, cmcR, cncaGUI, Compositional, concom, ConsRankClass, controlfunctionIV, corregp, CovTools, cubing, curvHDR, D3m
irt, dbcsp, delaunay, Directional, diveR, DiversityOccupancy, doolkit, dti, dymo, eegkit, ER, espadon, evolqg, Evomorph, export, fabisearch, factset.protobuf.
stach.v2, fdaPDE, fingerPro, fitbitViz, frontiles, fsbrain, gellipsoid, GENEAsphere, gensphere, geoelectrics, gMOIP, GoodFibes, GPareto, GPGame, Greymodels, g
yro, HDiR, hillshader, HiveR, HUM, HybridMicrobiomes, hyper.fit, icosa, image.textlinedetector, interpolation, IOLS, ivdoctr, jack, jacobi, JFM, kernhaz, Kern
SmoothIRT, kml, kml3d, landsepi, lazyNumbers, lba, lmviz, longitudinalData, loon, loon.ggplot, loon.shiny, loon.tourr, LOST, LSAfun, LSDinterface, LSDsensitiv
ity, Maeswrap, maotai, MapeBay, mathml, mcauchyd, mcca, MDSMap, mdsOpt, MeshesTools, metadynminer3d, mggd, MinkowskiSum, mlmts, moko, molaR, morph, morphomap,
 MSQC, mully, MultBiplotR, multibiplotGUI, multiblock, multibridge, MultiscaleDTM, mvmesh, nat, nat.nblast, nat.templatebrains, neuroim, NNS, nnspat, NPCirc, 
OceanView, OCNet, OpenCL, OpenRepGrid, optBiomarker, optiSel, optiSolve, ora, orthoDr, particle.swarm.optimisation, patternize, pcaL1, pcds, PCRedux, plsVarSe
l, PolygonSoup, polymapR, PortfolioOptim, practicalSigni, predict3d, predictoR, prWarp, QFASA, qspray, qtlc, Rarefy, RationalMatrix, rayshader, RCDT, RcmdrPlu
gin.EZR, Rcplex, RcppMeCab, Rdimtools, refreg, regressoR, rfviz, rgl2gltf, rglplus, rglwidget, Riemann, rivnet, rLiDAR, RmecabKo, rminer, RockFab, ROCS, ROI.p
lugin.cplex, ROI.plugin.symphony, rolog, ROracle, Rpolyhedra, Rpoppler, RQuantLib, rswipl, Rsymphony, rTLsDeep, SEERaBomb, SenTinMixt, shinyRGL, SLBDD, smooth
APC, snpReady, SpatialfdaR, spherepc, sphereplot, sphereTessellation, SphericalCubature, spinifex, SRTsim, StatDA, stopp, stops, stpp, surveyvoi, switchboard,
 symbolicDA, T4cluster, TDAkit, tessellation, TestGardener, tfevents, traineR, transforEmotion, traveltimeR, treespace, treetop, trinROC, TSclust, TSCS, TSdis
t, TukeyRegion, UBayFS, ucie, valse, vegan3d, vennplot, VIRF, x3ptools, zenplots, BGmix, BiGGR, ChemmineOB, ChIC, clippda, DaMiRseq, DeepBlueR, fCI, FLAMES, G
ARS, gpuMagic, iCheck, m6Aboost, MoonlightR, MsBackendRawFileReader, NanoMethViz, NormqPCR, omada, OmicsLonDA, OMICsPCA, optimalFlow, Rarr, rawrr, RDRToolbox,
 RMassBank, rsbml, TrajectoryGeometry, traviz, tscR, TTMap

[HenrikBengtsson]

1. Some of the above packages should have been excluded, because they were known not to install on Wynton/C4, because we lack some system libraries.

2. It looks like rgl and dependent packages need to be installed in an interactive session. . After running source("cran.R") on the remaining packages, we get:

Number of installed packages: 23190
Number of packages installed this round: 174
Packages that failed to install: [n=35] AlphaHull3D, Boov, cgalMeshes, cgalPolygons, delaunay, factset.protobuf.stach.v2, image.textlinedetector, interpolation, jack, landsepi, lazyNumbers, mathml, MeshesTools, MinkowskiSum, multibiplotGUI, multibridge, PolygonSoup, qspray, RationalMatrix, rolog, rswipl, sphereTessellation, surveyvoi, tfevents, traveltimeR, valse, BGmix, ChIC, DeepBlueR, FLAMES, NanoMethViz, omada, OmicsLonDA, Rarr, tscR

[HenrikBengtsson]

> source("cran.R")
Start time: 2023-06-16 03:44:01.092758
Current time: 2023-06-16 03:44:01.096001
Number of parallel installs: 1
R package repositories: [n=6] CRAN='https://cloud.r-project.org', BioCsoft='https://bioconductor.org/packages/3.17/bioc', BioCann='https://bioconductor.org/packages/3.17/data/annotation', BioCexp='https://bioconductor.org/packages/3.17/data/experiment', BioCworkflows='https://bioconductor.org/packages/3.17/workflows', henrikbengtsson='https://henrikbengtsson.github.io/drat/'
Number of available packages: 23241
Number of installed packages: 23196
Packages excluded: [n=112] agRee, AlphaHull3D, bcrm, Bergm, BGmix, biplotbootGUI, bizdays, Boov, BRugs, cgalMeshes, cgalPolygons, ChemmineOB, ChIC, cncaGUI, ConcordanceTest, cosso, CVXR, dclone, dcmle, DeepBlueR, delaunay, designmatch, diveR, eatATA, factset.protobuf.stach.v2, ffsimulator, FLAMES, fPortfolio, FRAPO, gemtc, gpuMagic, hdme, HyRiM, image.textlinedetector, interpolation, ITRSelect, jack, kantorovich, landsepi, lazyNumbers, loon, loon.ggplot, loon.shiny, loon.tourr, lpda, LPmerge, mathml, MCDA, MeshesTools, MinkowskiSum, miscF, MsBackendRawFileReader, MSCMT, MultAlloc, multibiplotGUI, multibridge, multinomineq, NanoMethViz, natstrat, npbr, omada, OmicsLonDA, OpenCL, optrefine, ora, ordinalbayes, otinference, parma, PolygonSoup, PortfolioOptim, PottsUtils, prioriactions, PVAClone, qspray, R2WinBUGS, Rarr, RationalMatrix, rawrr, Rcplex, RcppMeCab, relations, rfviz, Rglpk, RMassBank, RmecabKo, ROI.models.miplib, ROI.plugin.cplex, ROI.plugin.glpk, ROI.plugin.symphony, rolog, ROracle, Rpoppler, RQuantLib, rswipl, Rsymphony, rtsdata, sbw, sdcTable, sharx, sphereTessellation, strand, stratbr, StratifiedSampling, surveyvoi, switchboard, tfevents, traveltimeR, tscR, TukeyRegion, valse, visaOTR, zenplots
Number of packages to install: 0
Number of install chunks: 0 (50 packages per chunk)
Number of installed packages: 23196
Number of packages installed this round: 0
Packages that failed to install: [n=0] 
Total processing time: 54.75162 secs
Finish time: 2023-06-16 03:44:55.848178