CRAN Package Check Results for Package grpreg

Last updated on 2020-02-21 00:49:42 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 3.2-1 18.20 70.48 88.68 ERROR
r-devel-linux-x86_64-debian-gcc 3.2.2 11.44 57.81 69.25 NOTE
r-devel-linux-x86_64-fedora-clang 3.2.2 111.89 NOTE
r-devel-linux-x86_64-fedora-gcc 3.2.2 107.19 NOTE
r-devel-windows-ix86+x86_64 3.2-1 33.00 113.00 146.00 OK
r-devel-windows-ix86+x86_64-gcc8 3.2.2 44.00 146.00 190.00 OK
r-patched-linux-x86_64 3.2-1 11.82 66.45 78.27 OK
r-patched-solaris-x86 3.2.2 145.40 NOTE
r-release-linux-x86_64 3.2.2 11.28 66.33 77.61 NOTE
r-release-windows-ix86+x86_64 3.2-1 28.00 123.00 151.00 OK
r-release-osx-x86_64 3.2.2 OK
r-oldrel-windows-ix86+x86_64 3.2.2 27.00 135.00 162.00 OK
r-oldrel-osx-x86_64 3.2.2 OK

Check Details

Version: 3.2-1
Check: examples
Result: ERROR
    Running examples in 'grpreg-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: AUC.cv.grpsurv
    > ### Title: Calculates AUC for cv.grpsurv objects
    > ### Aliases: AUC AUC.cv.grpsurv
    >
    > ### ** Examples
    >
    > ## Don't show:
    > set.seed(1)
    > ## End(Don't show)
    > data(Lung)
    > X <- Lung$X
    > y <- Lung$y
    > group <- Lung$group
    >
    > cvfit <- cv.grpsurv(X, y, group, returnY=TRUE)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    grpreg
     --- call from context ---
    newXG(X[Y$ind, ], group, group.multiplier, 1, bilevel)
     --- call from argument ---
    if (class(X) != "matrix") {
     tmp <- try(X <- model.matrix(~0 + ., data = X), silent = TRUE)
     if (class(tmp)[1] == "try-error")
     stop("X must be a matrix or able to be coerced to a matrix")
    }
     --- R stacktrace ---
    where 1: newXG(X[Y$ind, ], group, group.multiplier, 1, bilevel)
    where 2: grpsurv(X = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
    1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
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    1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
    2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
    2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
    2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0.0061217724767008,
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    0.00426514631382178, 0.0450435971069386, -0.0203042994335781,
    0.0748454190836945, -0.00828119537134596, 0.0450435971069386,
    -0.128990028555456, 0.0450435971069386, 0.0596828892838488, 0.00426514631382178,
    -0.144516738264222, -0.0725712554007047, 0.0596828892838488,
    -0.150886479861744, -0.00828119537134596, -0.0532341858826609,
    -0.0725712554007047, 0.0596828892838488, -0.0725712554007047,
    0.0596828892838488, -0.13368780589659, 0.0309275425529641, 0.0596828892838488,
    0.0596828892838488, -0.144516738264222, -0.0318041658728746,
    -0.0532341858826609, -0.0203042994335781, 0.0450435971069386,
    0.0596828892838488, 0.0309275425529641, 0.0596828892838488, 0.0596828892838488,
    0.0748454190836945, -0.104966542961565, 0.683301368126593, -0.0203042994335781,
    0.0596828892838488, 0.0173347256219251, 0.0450435971069386, 0.0450435971069386,
    0.0173347256219251, -0.13368780589659, 0.0450435971069386, 0.0450435971069386,
    0.0173347256219251, -0.0203042994335781, 0.0309275425529641,
    0.0309275425529641, 0.0450435971069386, 0.0450435971069386, 0.0309275425529641,
    -0.0427807946892355, 0.0450435971069386, 0.0309275425529641,
    0.0309275425529641, -0.0898153744270061, 0.0309275425529641,
    -0.0631643394531506, 0.0173347256219251, -0.0532341858826609,
    -0.0427807946892355, 0.0748454190836945, 0.0173347256219251,
    -0.111757270794441, 0.0309275425529641, 0.0450435971069386, 0.0869841118454277,
    0.0463123598903983, -0.165180750275754, 0.0381780094993925, 0.0544467102814043,
    -0.0757028959746897, 0.0869841118454277, 0.0788497614544219,
    -0.124508998320725, 0.0951184622364336, 0.184596316537498, 0.0381780094993925,
    0.0381780094993925, -0.0512998448016721, -0.0838372463656955,
    0.0219093087173808, -0.132643348711731, -0.189583801448772, 0.0381780094993925,
    -0.0187624432376486, -0.0268967936286545, 0.070715411063416,
    0.0381780094993925, 0.0544467102814043, -0.100105947147707, -0.0431654944106662,
    0.0869841118454277, 0.0788497614544219, -0.124508998320725, -0.0268967936286545,
    -0.132643348711731, 0.0463123598903984, 0.0544467102814043, 0.0544467102814043,
    -0.0268967936286545, 0.0625810606724101, 0.0137749583263749,
    0.070715411063416, -0.0431654944106662, 0.0300436591083866, 0.070715411063416,
    0.111387163018445, -0.0838372463656955, 0.0788497614544219, 0.070715411063416,
    0.0219093087173808, 0.0137749583263749, 0.0300436591083866, -0.165180750275754,
    -0.0675685455836838, 0.0381780094993925, 0.0463123598903984,
    -0.124508998320725, -0.197718151839778, 0.0625810606724101, 0.0300436591083866,
    -0.0512998448016721, -0.0919715967567014, 0.0381780094993925,
    0.0788497614544219, -0.108240297538713, -0.140777699102737, 0.0625810606724101,
    0.0300436591083866, 0.0137749583263749, 0.0625810606724101, -0.165180750275754,
    -0.0431654944106662, -0.17331510066676, -0.0350311440196603,
    0.0137749583263749, -0.0838372463656955, -0.0512998448016721,
    0.0951184622364336, -0.0675685455836838, 0.0300436591083866,
    0.0544467102814043, -0.00249374245563684, 0.0300436591083866,
    0.0463123598903984, 0.0381780094993925, -0.00249374245563684,
    0.0463123598903984, -0.0512998448016721, -0.189583801448772,
    0.0381780094993925, 0.0951184622364336, -0.0594341951926779,
    -0.148912049493743, 0.0869841118454277, -0.181449451057766, 0.103252812627439,
    0.0300436591083866, 0.0137749583263749, -0.116374647929719, -0.0350311440196603,
    0.0625810606724101, -0.0757028959746897, 0.111387163018445, 0.0788497614544219,
    0.0300436591083866, 0.103252812627439, 0.0951184622364336, 0.0219093087173808,
    0.103252812627439, 0.00564060793536903, 0.070715411063416, 0.0137749583263749,
    0.0869841118454277, -0.0106280928466427, -0.157046399884748,
    0.0300436591083866, -0.0675685455836838, -0.124508998320725,
    0.0951184622364336, 0.0625810606724101, 0.0219093087173808, 0.184596316537498,
    -0.00249374245563684, 0.0381780094993925, 0.0137749583263749,
    0.0300436591083866, -0.132643348711731, 0.0869841118454277, 0.0381780094993925,
    -0.108240297538713, 0.0788497614544219, -0.157046399884748, 0.0625810606724101,
    0.0381780094993925, -0.0757028959746897, 0.0463123598903984,
    0.0544467102814043, 0.0463123598903984, 0.070715411063416, 0.0544467102814043,
    -0.17331510066676, 0.0548020981629596, -0.0289333798093117, 0.120763893224915,
    -0.0413247303033442, -0.0150901142818055, -0.0623525587050209,
    0.0548020981629603, 0.0351511725015578, 0.0157504168455607, 0.0759049388578369,
    0.403862578710767, -0.0413247303033442, -0.0413247303033442,
    -0.081803193528412, -0.0529651836969424, -0.0617516861909866,
    0.0338492820544835, 0.201194959454216, -0.0413247303033442, -0.0874105628242968,
    -0.0881865930505367, 0.0169521618736293, -0.0413247303033442,
    -0.0150901142818055, -0.0298346885803633, -0.0853829084025943,
    0.0548020981629603, 0.0351511725015578, 0.0157504168455607, -0.0881865930505367,
    0.0338492820544835, -0.0289333798093119, -0.0150901142818055,
    -0.0150901142818055, -0.0881865930505367, 0.000205066279174847,
    -0.0697872915845967, 0.0169521618736293, -0.0853829084025943,
    -0.0522641657639024, 0.0169521618736293, 0.122466365348012, -0.0529651836969424,
    0.0351511725015578, 0.0169521618736293, -0.0617516861909866,
    -0.0697872915845967, -0.0522641657639024, 0.120763893224915,
    -0.0702880186796253, -0.0413247303033442, -0.0289333798093119,
    0.0157504168455607, 0.230909144930932, 0.000205066279174847,
    -0.0522641657639024, -0.081803193528412, -0.0421258936553899,
    -0.0413247303033442, 0.0351511725015578, -0.0160915684718627,
    0.0534000622968803, 0.000205066279174847, -0.0522641657639024,
    -0.0697872915845967, 0.000205066279174847, 0.120763893224915,
    -0.0853829084025943, 0.146122333601208, -0.0875107082433025,
    -0.0697872915845967, -0.0529651836969424, -0.081803193528412,
    0.0759049388578369, -0.0702880186796253, -0.0522641657639024,
    -0.0150901142818055, -0.0815027572713949, -0.0522641657639024,
    -0.0289333798093119, -0.0413247303033442, -0.0815027572713949,
    -0.0289333798093119, -0.081803193528412, 0.201194959454216, -0.0413247303033442,
    0.0759049388578369, -0.0767715636207557, 0.0744027575727512,
    0.0548020981629603, 0.172932689010975, 0.0984596945861876, -0.0522641657639024,
    -0.0697872915845967, -0.000896533329888041, -0.0875107082433025,
    0.000205066279174847, -0.0623525587050209, 0.122466365348012,
    0.0351511725015578, -0.0522641657639024, 0.0984596945861876,
    0.0759049388578369, -0.0617516861909866, 0.0984596945861876,
    -0.0763709819447328, 0.0169521618736293, -0.0697872915845967,
    0.0548020981629603, -0.0851826175645829, 0.0968573678820961,
    -0.0522641657639024, -0.0702880186796253, 0.0157504168455607,
    0.0759049388578369, 0.000205066279174847, -0.0617516861909866,
    0.403862578710767, -0.0815027572713949, -0.0413247303033442,
    -0.0697872915845967, -0.0522641657639024, 0.0338492820544835,
    0.0548020981629603, -0.0413247303033442, -0.0160915684718627,
    0.0351511725015578, 0.0968573678820961, 0.000205066279174847,
    -0.0413247303033442, -0.0623525587050209, -0.0289333798093119,
    -0.0150901142818055, -0.0289333798093119, 0.0169521618736293,
    -0.0150901142818055, 0.146122333601208, -0.0353120652880378,
    -0.0440072858687125, -0.0598441258918498, -0.0378521995613759,
    -0.047940351813509, 0.109701439789258, -0.0353120652880377, -0.0433372541330285,
    0.0790671084170324, -0.0235297694106945, 0.441851506888557, -0.0378521995613759,
    -0.0378521995613759, 0.0887001362338182, 0.112344751459234, -0.0201040351949282,
    0.0609636181924395, -0.209859891651225, -0.0378521995613759,
    0.0416605186882972, 0.0545391438733193, -0.047912353279629, -0.0378521995613759,
    -0.047940351813509, 0.109253586522657, 0.0783659699800421, -0.0353120652880377,
    -0.0433372541330285, 0.0790671084170324, 0.0545391438733193,
    0.0609636181924395, -0.0440072858687129, -0.047940351813509,
    -0.047940351813509, 0.0545391438733193, -0.0493443800618018,
    -0.00912499180374213, -0.047912353279629, 0.0783659699800421,
    -0.0297821102254603, -0.047912353279629, 0.0125342127768982,
    0.112344751459234, -0.0433372541330285, -0.047912353279629, -0.0201040351949282,
    -0.00912499180374213, -0.0297821102254603, -0.0598441258918499,
    0.104674888472388, -0.0378521995613759, -0.0440072858687129,
    0.0790671084170324, -0.272818755103798, -0.0493443800618018,
    -0.0297821102254603, 0.0887001362338182, 0.112297806148354, -0.0378521995613759,
    -0.0433372541330285, 0.102905075248179, 0.0383277669832172, -0.0493443800618018,
    -0.0297821102254603, -0.00912499180374213, -0.0493443800618018,
    -0.0598441258918499, 0.0783659699800421, -0.103679594379213,
    0.0668766334152217, -0.00912499180374213, 0.112344751459234,
    0.0887001362338182, -0.0235297694106945, 0.104674888472388, -0.0297821102254603,
    -0.047940351813509, 0.0155079307247432, -0.0297821102254603,
    -0.0440072858687129, -0.0378521995613759, 0.0155079307247432,
    -0.0440072858687129, 0.0887001362338182, -0.209859891651225,
    -0.0378521995613759, -0.0235297694106945, 0.0975721148425878,
    0.0108525374554031, -0.0353120652880377, -0.153582510521018,
    -0.00768334916703667, -0.0297821102254603, -0.00912499180374213,
    0.0929452549909579, 0.0668766334152217, -0.0493443800618018,
    0.109701439789258, 0.0125342127768982, -0.0433372541330285, -0.0297821102254603,
    -0.00768334916703667, -0.0235297694106945, -0.0201040351949282,
    -0.00768334916703667, 0.00284800261413577, -0.047912353279629,
    -0.00912499180374213, -0.0353120652880377, 0.0285477751941177,
    -0.0217690877249652, -0.0297821102254603, 0.104674888472388,
    0.0790671084170324, -0.0235297694106945, -0.0493443800618018,
    -0.0201040351949282, 0.441851506888557, 0.0155079307247432, -0.0378521995613759,
    -0.00912499180374213, -0.0297821102254603, 0.0609636181924395,
    -0.0353120652880377, -0.0378521995613759, 0.102905075248179,
    -0.0433372541330285, -0.0217690877249652, -0.0493443800618018,
    -0.0378521995613759, 0.109701439789258, -0.0440072858687129,
    -0.047940351813509, -0.0440072858687129, -0.047912353279629,
    -0.047940351813509, -0.103679594379213, 0, 1, 0, 1, 1, 0, 1,
    0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0,
    1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0,
    0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 1, 1, 1,
    0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 1,
    0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0,
    1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0,
    0, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
    1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
    1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
    1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
    1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
    1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1,
    1, 1, 1, 1, 1, 1), y = c(72, 411, 228, 126, 118, 10, 82, 110,
    314, 100, 42, 8, 144, 25, 11, 30, 384, 4, 54, 13, 123, 97, 153,
    59, 117, 16, 151, 22, 56, 21, 18, 139, 20, 31, 52, 287, 18, 51,
    122, 27, 54, 7, 63, 392, 10, 8, 92, 35, 117, 132, 12, 162, 3,
    95, 177, 162, 216, 553, 278, 12, 260, 200, 156, 182, 143, 105,
    103, 250, 100, 999, 112, 87, 231, 242, 991, 111, 1, 587, 389,
    33, 25, 357, 467, 201, 1, 30, 44, 283, 15, 25, 103, 21, 13, 87,
    2, 20, 7, 24, 99, 8, 99, 61, 25, 95, 80, 51, 29, 24, 18, 83,
    31, 51, 90, 52, 73, 8, 36, 48, 7, 140, 186, 84, 19, 45, 80, 52,
    164, 19, 53, 15, 43, 340, 133, 111, 231, 378, 49, 1, 1, 1, 1,
    1, 1, 1, 1, 1, 0, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1,
    1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
    1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1,
    1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
    1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
    0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
    1, 1, 1, 1, 1, 1, 1), group = c(1L, 2L, 2L, 2L, 3L, 3L, 4L, 4L,
    4L, 5L, 6L, 6L, 6L, 6L), returnX = TRUE)
    where 3: do.call("grpsurv", fit.args)
    where 4: cv.grpsurv(X, y, group, returnY = TRUE)
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (X, g, m, ncolY, bilevel)
    {
     if (class(X) != "matrix") {
     tmp <- try(X <- model.matrix(~0 + ., data = X), silent = TRUE)
     if (class(tmp)[1] == "try-error")
     stop("X must be a matrix or able to be coerced to a matrix")
     }
     if (storage.mode(X) == "integer")
     storage.mode(X) <- "double"
     if (any(is.na(X)))
     stop("Missing data (NA's) detected in X. You must eliminate missing data (e.g., by removing cases, removing features, or imputation) before passing X to grpreg")
     if (length(g) != ncol(X))
     stop("Dimensions of group is not compatible with X")
     xnames <- if (is.null(colnames(X)))
     paste("V", 1:ncol(X), sep = "")
     else colnames(X)
     G <- setupG(g, m, bilevel)
     if (ncolY > 1) {
     X <- multiX(X, ncolY)
     G <- multiG(G, ncolY)
     }
     std <- .Call("standardize", X)
     XX <- std[[1]]
     center <- std[[2]]
     scale <- std[[3]]
     nz <- which(scale > 1e-06)
     if (length(nz) != ncol(X)) {
     XX <- XX[, nz, drop = FALSE]
     G <- subsetG(G, nz)
     }
     G <- reorderG(G, attr(G, "m"), bilevel)
     if (attr(G, "reorder"))
     XX <- XX[, attr(G, "ord")]
     if (!bilevel) {
     XX <- orthogonalize(XX, G)
     g <- attr(XX, "group")
     }
     else {
     g <- as.integer(G)
     }
     m <- attr(G, "m")
     if (all(is.na(m))) {
     m <- if (bilevel)
     rep(1, max(g))
     else sqrt(table(g[g != 0]))
     }
     return(list(X = XX, g = g, m = m, reorder = attr(G, "reorder"),
     ord.inv = attr(G, "ord.inv"), names = xnames, center = center,
     scale = scale, nz = nz))
    }
    <bytecode: 0xc19c460>
    <environment: namespace:grpreg>
     --- function search by body ---
    Function newXG in namespace grpreg has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(X) != "matrix") { : the condition has length > 1
    Calls: cv.grpsurv -> do.call -> grpsurv -> newXG
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 3.2-1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'getting-started.rmd' using rmarkdown
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    grpreg
     --- call from context ---
    newXG(X, group, group.multiplier, attr(yy, "m"), bilevel)
     --- call from argument ---
    if (class(X) != "matrix") {
     tmp <- try(X <- model.matrix(~0 + ., data = X), silent = TRUE)
     if (class(tmp)[1] == "try-error")
     stop("X must be a matrix or able to be coerced to a matrix")
    }
     --- R stacktrace ---
    where 1: newXG(X, group, group.multiplier, attr(yy, "m"), bilevel)
    where 2: grpreg(X, y, group, penalty = "grLasso")
    where 3: eval(expr, envir, enclos)
    where 4: eval(expr, envir, enclos)
    where 5: withVisible(eval(expr, envir, enclos))
    where 6: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
     error = eHandler, message = mHandler)
    where 7: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
     enclos)), warning = wHandler, error = eHandler, message = mHandler))
    where 8: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    where 9: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
     debug = debug, last = i == length(out), use_try = stop_on_error !=
     2L, keep_warning = keep_warning, keep_message = keep_message,
     output_handler = output_handler, include_timing = include_timing)
    where 10: evaluate::evaluate(...)
    where 11: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
     options$include) 0L else 2L, output_handler = knit_handlers(options$render,
     options))
    where 12: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
     stop_on_error = if (options$error && options$include) 0L else 2L,
     output_handler = knit_handlers(options$render, options)))
    where 13: block_exec(params)
    where 14: call_block(x)
    where 15: process_group.block(group)
    where 16: process_group(group)
    where 17: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
     error = function(e) {
     setwd(wd)
     cat(res, sep = "\n", file = output %n% "")
     message("Quitting from lines ", paste(current_lines(i),
     collapse = "-"), " (", knit_concord$get("infile"),
     ") ")
     })
    where 18: process_file(text, output)
    where 19: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
    where 20: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
     output_dir = getwd(), ...)
    where 21: vweave_rmarkdown(...)
    where 22: engine$weave(file, quiet = quiet, encoding = enc)
    where 23: doTryCatch(return(expr), name, parentenv, handler)
    where 24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 25: tryCatchList(expr, classes, parentenv, handlers)
    where 26: tryCatch({
     engine$weave(file, quiet = quiet, encoding = enc)
     setwd(startdir)
     output <- find_vignette_product(name, by = "weave", engine = engine)
     if (!have.makefile && vignette_is_tex(output)) {
     texi2pdf(file = output, clean = FALSE, quiet = quiet)
     output <- find_vignette_product(name, by = "texi2pdf",
     engine = engine)
     }
     outputs <- c(outputs, output)
    }, error = function(e) {
     thisOK <<- FALSE
     fails <<- c(fails, file)
     message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
     file, conditionMessage(e)))
    })
    where 27: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/grpreg.Rcheck/vign_test/grpreg",
     ser_elibs = "/tmp/RtmpPESR46/file27962225dbac.rds")
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (X, g, m, ncolY, bilevel)
    {
     if (class(X) != "matrix") {
     tmp <- try(X <- model.matrix(~0 + ., data = X), silent = TRUE)
     if (class(tmp)[1] == "try-error")
     stop("X must be a matrix or able to be coerced to a matrix")
     }
     if (storage.mode(X) == "integer")
     storage.mode(X) <- "double"
     if (any(is.na(X)))
     stop("Missing data (NA's) detected in X. You must eliminate missing data (e.g., by removing cases, removing features, or imputation) before passing X to grpreg")
     if (length(g) != ncol(X))
     stop("Dimensions of group is not compatible with X")
     xnames <- if (is.null(colnames(X)))
     paste("V", 1:ncol(X), sep = "")
     else colnames(X)
     G <- setupG(g, m, bilevel)
     if (ncolY > 1) {
     X <- multiX(X, ncolY)
     G <- multiG(G, ncolY)
     }
     std <- .Call("standardize", X)
     XX <- std[[1]]
     center <- std[[2]]
     scale <- std[[3]]
     nz <- which(scale > 1e-06)
     if (length(nz) != ncol(X)) {
     XX <- XX[, nz, drop = FALSE]
     G <- subsetG(G, nz)
     }
     G <- reorderG(G, attr(G, "m"), bilevel)
     if (attr(G, "reorder"))
     XX <- XX[, attr(G, "ord")]
     if (!bilevel) {
     XX <- orthogonalize(XX, G)
     g <- attr(XX, "group")
     }
     else {
     g <- as.integer(G)
     }
     m <- attr(G, "m")
     if (all(is.na(m))) {
     m <- if (bilevel)
     rep(1, max(g))
     else sqrt(table(g[g != 0]))
     }
     return(list(X = XX, g = g, m = m, reorder = attr(G, "reorder"),
     ord.inv = attr(G, "ord.inv"), names = xnames, center = center,
     scale = scale, nz = nz))
    }
    <bytecode: 0x61b3108>
    <environment: namespace:grpreg>
     --- function search by body ---
    Function newXG in namespace grpreg has this body.
     ----------- END OF FAILURE REPORT --------------
    Quitting from lines 51-52 (getting-started.rmd)
    Error: processing vignette 'getting-started.rmd' failed with diagnostics:
    the condition has length > 1
    --- failed re-building 'getting-started.rmd'
    
    SUMMARY: processing the following file failed:
     'getting-started.rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 3.2.2
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘grpregOverlap’
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-linux-x86_64