Error in { : task 1 failed - "dimension of 'A' must be at least 3"

Hi, I'm getting a weird error and I'm not sure what could be causing it since I've run the same code on the same object previously with no errors. Do you know what could be causing this?

> re_ln = nebula(nebuladata$count, nebuladata$sid, pred=df, offset=nebuladata$offset, method='LN')
Remove  15323  genes having low expression.
Analyzing  16198  genes with  49  subjects and  108553  cells.
Error in { : task 1 failed - "dimension of 'A' must be at least 3"

> traceback()
6: stop(simpleError(msg, call = expr))
5: e$fun(obj, substitute(ex), parent.frame(), e$data)
4: (function (obj, ex) 
   {
       e <- getDoPar()
       e$fun(obj, substitute(ex), parent.frame(), e$data)
   })(structure(list(args = gid(.doRNG.stream = list(c(10407L, 220730650L, 
   -1488635949L, -1374262536L, -161857383L, 472285062L, -19665841L
   ), c(10407L, 560444745L, -1449673117L, 329269002L, -1373225926L, 
   -191104363L, -956007088L), c(10407L, -261277466L, -2118084130L, 
   1649378238L, 67990833L, -1279070037L, 188772905L), c(10407L, 
   -223684078L, -1818867022L, 1615198839L, -272343810L, 1794737318L, 
   1058720021L), c(10407L, 492047571L, -1596484842L, -760964706L, 
   1456602701L, 43415024L, -2070155503L), c(10407L, 1092576449L, 
   1743234594L, -2017218414L, 761191585L, -1459191673L, -2007975220L
   ), c(10407L, -1057075553L, 2059021047L, 1768162781L, -1590191593L, 
   -1834679500L, -1430620074L), c(10407L, 709041855L, -642880334L, 
   1543041301L, -1215006062L, 1983836141L, 1623775403L), c(10407L, 
   80649392L, -1899410628L, -380477119L, -1833639677L, 946607684L, 
   -1490667455L), c(10407L, -856805405L, -212980410L, -911654134L, 
   598016867L, 1602113084L, 953134033L), c(10407L, -961928782L, 
   -891978046L, -1209218494L, 427359974L, 873300585L, -1639542444L
    ...
3: do.call(`%dopar%`, list(obj, ex), envir = parent.frame())
2: foreach(i = gid, .combine = "cbind") %dorng% {
       posv = call_posindy(count, i - 1, nind)
       if ((posv$mct * mfs) < 3) {
           ord = 3
       }
       else {
           ord = 1
       }
       para = c(log(posv$mct) - moffset, rep(0, nb - 1))
       re_t = tryCatch({
           ref = switch(opt, lbfgs = lbfgs(c(para, 1, cell_init), 
               ptmg_ll_der, posindy = posv$posindy, X = pred, offset = offset, 
               Y = posv$Y, n_one = posv$n_onetwo, ytwo = posv$ytwo, 
               fid = fid, cumsumy = cumsumy[i, ], posind = posind[[i]], 
               nb = nb, k = k, nind = nind, lower = lower, upper = upper, 
               control = list(ftol_abs = eps)), trust = trust(objfun = ptmg_ll_der_hes3, 
               c(para, 0, 0), 2, 100, posindy = posv$posindy, X = pred, 
               offset = offset, Y = posv$Y, n_one = posv$n_onetwo, 
               ytwo = posv$ytwo, fid = fid, cumsumy = cumsumy[i, 
                   ], posind = posind[[i]], nb = nb, k = k, nind = nind), 
    ...
1: nebula(nebuladata$count, nebuladata$sid, pred = df, offset = nebuladata$offset, 
       method = "LN")

Hi Meaksu,

This error has been reported in Getting error - "dimension of 'A' must be at least 3" · Issue #33 · lhe17/nebula · GitHub https://github.com/lhe17/nebula/issues/33

This bug was introduced in v1.4.2. You could upgrade your version to v1.5.1.

Best regards, Liang

On Wed, Jan 10, 2024 at 8:16 PM meaksu @.***> wrote:

Hi, I'm getting a weird error and I'm not sure what could be causing it since I've run the same code on the same object previously with no errors. Do you know what could be causing this?

re_ln = nebula(nebuladata$count, nebuladata$sid, pred=df, offset=nebuladata$offset, method='LN') Remove 15323 genes having low expression. Analyzing 16198 genes with 49 subjects and 108553 cells. Error in { : task 1 failed - "dimension of 'A' must be at least 3"

traceback() 6: stop(simpleError(msg, call = expr)) 5: e$fun(obj, substitute(ex), parent.frame(), e$data) 4: (function (obj, ex) { e <- getDoPar() e$fun(obj, substitute(ex), parent.frame(), e$data) })(structure(list(args = gid(.doRNG.stream = list(c(10407L, 220730650L, -1488635949L, -1374262536L, -161857383L, 472285062L, -19665841L ), c(10407L, 560444745L, -1449673117L, 329269002L, -1373225926L, -191104363L, -956007088L), c(10407L, -261277466L, -2118084130L, 1649378238L, 67990833L, -1279070037L, 188772905L), c(10407L, -223684078L, -1818867022L, 1615198839L, -272343810L, 1794737318L, 1058720021L), c(10407L, 492047571L, -1596484842L, -760964706L, 1456602701L, 43415024L, -2070155503L), c(10407L, 1092576449L, 1743234594L, -2017218414L, 761191585L, -1459191673L, -2007975220L ), c(10407L, -1057075553L, 2059021047L, 1768162781L, -1590191593L, -1834679500L, -1430620074L), c(10407L, 709041855L, -642880334L, 1543041301L, -1215006062L, 1983836141L, 1623775403L), c(10407L, 80649392L, -1899410628L, -380477119L, -1833639677L, 946607684L, -1490667455L), c(10407L, -856805405L, -212980410L, -911654134L, 598016867L, 1602113084L, 953134033L), c(10407L, -961928782L, -891978046L, -1209218494L, 427359974L, 873300585L, -1639542444L ... 3: do.call(%dopar%, list(obj, ex), envir = parent.frame()) 2: foreach(i = gid, .combine = "cbind") %dorng% { posv = call_posindy(count, i - 1, nind) if ((posv$mct * mfs) < 3) { ord = 3 } else { ord = 1 } para = c(log(posv$mct) - moffset, rep(0, nb - 1)) re_t = tryCatch({ ref = switch(opt, lbfgs = lbfgs(c(para, 1, cell_init), ptmg_ll_der, posindy = posv$posindy, X = pred, offset = offset, Y = posv$Y, n_one = posv$n_onetwo, ytwo = posv$ytwo, fid = fid, cumsumy = cumsumy[i, ], posind = posind[[i]], nb = nb, k = k, nind = nind, lower = lower, upper = upper, control = list(ftol_abs = eps)), trust = trust(objfun = ptmg_ll_der_hes3, c(para, 0, 0), 2, 100, posindy = posv$posindy, X = pred, offset = offset, Y = posv$Y, n_one = posv$n_onetwo, ytwo = posv$ytwo, fid = fid, cumsumy = cumsumy[i, ], posind = posind[[i]], nb = nb, k = k, nind = nind), ... 1: nebula(nebuladata$count, nebuladata$sid, pred = df, offset = nebuladata$offset, method = "LN")

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lhe17 / nebula

Error in { : task 1 failed - "dimension of 'A' must be at least 3" #40