Last updated on 2022-01-06 15:51:13 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.99.14 | 628.05 | 402.92 | 1030.97 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 0.99.14 | 459.89 | 306.79 | 766.68 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.99.14 | 1541.04 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 0.99.14 | 1373.96 | NOTE | |||
| r-devel-windows-x86_64-new-UL | 0.99.14 | 657.00 | 562.00 | 1219.00 | NOTE | |
| r-devel-windows-x86_64-new-TK | 0.99.14 | NOTE | ||||
| r-patched-linux-x86_64 | 0.99.14 | 539.00 | 192.39 | 731.39 | ERROR | |
| r-release-linux-x86_64 | 0.99.14 | 528.50 | 192.65 | 721.15 | ERROR | |
| r-release-macos-arm64 | 0.99.14 | ERROR | ||||
| r-release-macos-x86_64 | 0.99.14 | ERROR | ||||
| r-release-windows-ix86+x86_64 | 0.99.14 | 665.00 | 39.00 | 704.00 | ERROR | |
| r-oldrel-macos-x86_64 | 0.99.14 | ERROR | ||||
| r-oldrel-windows-ix86+x86_64 | 0.99.14 | 867.00 | 40.00 | 907.00 | ERROR |
gcc-ASAN gcc-UBSAN M1mac M1mac noOMP noOMP
Version: 0.99.14
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-new-UL, r-devel-windows-x86_64-new-TK, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.99.14
Check: installed package size
Result: NOTE
installed size is 65.0Mb
sub-directories of 1Mb or more:
doc 2.6Mb
libs 62.0Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64-new-UL
Version: 0.99.14
Check: examples
Result: ERROR
Running examples in ‘BigDataStatMeth-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bdCrossprod
> ### Title: Crossproduct of DelayedArray
> ### Aliases: bdCrossprod
>
> ### ** Examples
>
>
> library(DelayedArray)
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: ‘MatrixGenerics’
The following objects are masked from ‘package:matrixStats’:
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:Matrix’:
expand, unname
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Attaching package: ‘DelayedArray’
The following objects are masked from ‘package:base’:
aperm, apply, rowsum, scale, sweep
>
> n <- 100
> p <- 60
>
> X <- matrix(rnorm(n*p), nrow=n, ncol=p)
>
> # without DelayedArray
> bdCrossprod(X)
[,1] [,2] [,3] [,4] [,5]
[1,] 81.0550927 -0.49637465 2.01369284 -3.8857354 14.86778280
[2,] -0.4963746 90.97864395 -4.97067333 -5.6891795 15.14248536
[3,] 2.0136928 -4.97067333 105.98885926 11.4017437 3.44053581
[4,] -3.8857354 -5.68917953 11.40174373 97.6248135 2.54128247
[5,] 14.8677828 15.14248536 3.44053581 2.5412825 135.58443168
[6,] -9.9308029 -1.67862986 -4.27357031 -9.4305103 -9.97619997
[7,] 6.1193988 -8.41344754 -4.44296865 -14.6254464 8.80802449
[8,] 3.5003399 6.99323931 -16.14234131 2.2905400 12.80999664
[9,] 6.6733596 -0.07540405 0.09717535 23.3515608 10.29227400
[10,] 8.2828486 -1.73918478 -19.85067297 12.3644248 -11.39701974
[11,] -12.6899584 -10.55007247 -3.58096248 0.1756843 0.34051618
[12,] -8.2304039 -1.70465616 -3.71431805 -0.2999867 -6.38310283
[13,] 1.4496223 12.99341581 4.43733418 -14.9974984 5.30490324
[14,] -8.4957559 -1.97108062 -5.98270438 -13.9543771 5.99821064
[15,] 0.3951284 -11.84869423 -17.88749642 9.8725465 9.37189613
[16,] -4.2885569 2.42618160 -16.25187198 27.0340707 -1.14375626
[17,] 15.1748202 7.01298176 8.42226926 10.1849476 4.55937206
[18,] -4.2366820 -17.43834945 0.63102984 -8.1880753 -3.00472336
[19,] -8.2669963 -9.80927338 17.39196801 13.6905870 -6.46861183
[20,] 13.2812089 -2.46404728 -21.26770104 -11.5316647 13.18801312
[21,] 7.0059986 14.55441470 14.85358722 6.7322927 2.35729077
[22,] -9.5864098 -1.17419382 13.12187592 21.9667601 -0.54474061
[23,] -12.2468856 10.40840781 0.75234045 -9.3812652 -7.19742001
[24,] 7.7366750 -0.77942174 -4.92268477 3.6095945 -0.27578344
[25,] 6.1591597 -17.24162009 24.24584213 -10.3936819 9.77829058
[26,] -2.9364207 -1.17613356 -3.37556371 0.9497670 -10.73390060
[27,] -5.8093689 -10.19317056 -12.91751960 4.9441268 -2.17886264
[28,] -2.1418544 -7.64386166 -10.25710418 -17.9238494 -5.46093653
[29,] -3.3616555 6.23083925 -0.72688249 6.4304600 -3.32930573
[30,] 0.9787916 -0.96722537 3.65942173 -5.2595178 -11.80750921
[31,] 13.4880815 13.73124163 7.86566537 5.4145375 16.47559432
[32,] -8.5350709 4.97935331 -18.94437263 -7.1166255 -3.94259710
[33,] 8.6730844 -6.04526479 -6.90749229 -6.7426107 11.38690364
[34,] 18.8718720 -18.30891756 -4.78415378 -2.6120459 4.78721117
[35,] 10.4461472 -19.80551900 13.83424085 8.6692713 -5.96260527
[36,] -4.2049190 -15.42814473 6.74612837 20.7092792 -6.50488204
[37,] -1.3401418 11.22477166 2.56160838 -7.1410463 20.69698981
[38,] 1.0872075 -6.48636459 -5.59717144 -9.3490896 -17.64891354
[39,] 2.8236842 -5.91075329 10.97163831 -12.0023946 -31.87371620
[40,] -1.1263198 -0.10850037 12.44409357 1.2722152 -2.79631946
[41,] -7.6923612 -0.34393030 -8.94232685 1.9809870 -1.41626686
[42,] -15.2538768 -3.80199010 -9.18411509 -5.4950602 4.27020408
[43,] -0.5163611 -15.56276982 -12.03516701 4.0218935 -22.48306241
[44,] -3.2395209 -11.32164419 3.39333143 8.9402307 -6.27990242
[45,] 2.6191508 -13.10669813 5.80668782 9.6692926 -4.22786269
[46,] 0.8170621 -1.57639204 6.40120072 0.4099638 -6.05037164
[47,] -14.8956315 -2.92252067 9.33883411 3.3272261 -13.85545621
[48,] -3.6624587 -5.73661087 -0.70677131 7.6796933 -6.48912327
[49,] -7.0335163 13.27188528 -0.86023319 -8.2995555 -15.48670692
[50,] 13.8075667 0.63952484 -12.89370498 15.5889760 -8.01972453
[51,] -9.0796899 7.43332364 -2.85530142 8.0414439 -2.91730319
[52,] -4.3287340 10.75826464 25.93216089 -11.6266628 -11.28899035
[53,] -9.9072607 15.25026707 -0.28763368 13.3006904 11.07500569
[54,] -6.1718831 15.31611874 2.37079745 -6.9428280 -5.82737308
[55,] 4.9958579 5.65285935 -6.02141613 -10.9951182 0.04120373
[56,] -4.7129858 -0.10618025 14.72548202 16.2683339 14.49898434
[57,] 3.6224919 1.78069113 -10.55279524 14.3426088 6.64585422
[58,] -1.3240313 11.39368507 -11.30608184 0.4766264 -6.58139490
[59,] -6.7569798 9.16489117 -3.40349318 -1.7722203 8.27607243
[60,] -1.1860511 -7.23422450 -7.49157959 -10.3121088 21.24078823
[,6] [,7] [,8] [,9] [,10] [,11]
[1,] -9.9308029 6.1193988 3.5003399 6.67335956 8.2828486 -12.6899584
[2,] -1.6786299 -8.4134475 6.9932393 -0.07540405 -1.7391848 -10.5500725
[3,] -4.2735703 -4.4429687 -16.1423413 0.09717535 -19.8506730 -3.5809625
[4,] -9.4305103 -14.6254464 2.2905400 23.35156081 12.3644248 0.1756843
[5,] -9.9762000 8.8080245 12.8099966 10.29227400 -11.3970197 0.3405162
[6,] 92.6151553 1.6824797 -16.1627513 15.87237738 -6.4415196 -5.0996671
[7,] 1.6824797 119.6356049 11.6144904 0.11941823 -9.4522555 2.5440995
[8,] -16.1627513 11.6144904 119.2029246 -4.05189872 8.5882169 7.8610494
[9,] 15.8723774 0.1194182 -4.0518987 117.27864397 22.6663154 -14.0915232
[10,] -6.4415196 -9.4522555 8.5882169 22.66631536 110.1512540 3.3203161
[11,] -5.0996671 2.5440995 7.8610494 -14.09152322 3.3203161 104.9804330
[12,] -1.8453425 0.6877980 -2.4614510 -16.59976863 -1.0763712 12.0760430
[13,] 8.2014806 9.9893558 -1.4408390 -1.67816543 20.3418426 6.1942670
[14,] 3.3580841 -3.7386492 4.1805392 -16.31583950 -1.2456966 9.0118068
[15,] -6.9700306 10.9840256 27.8575541 10.40659562 -18.7870573 8.9206000
[16,] -6.3081705 -16.9543882 23.3717097 -2.80003547 23.9726241 7.2713315
[17,] 0.6803194 18.7831707 -20.3449411 6.29491288 15.7004316 -6.6514306
[18,] 11.3677988 -1.2199254 -18.8399141 -10.85707531 -9.8132425 -16.6435175
[19,] -0.1276837 -2.1616072 -6.9254815 29.94729273 -14.7677297 4.8861188
[20,] -20.1841288 14.6906494 27.6148127 1.39049635 -1.9705054 4.8560776
[21,] -1.5498570 -5.3407762 -21.5770083 5.32174958 4.7675964 1.9687727
[22,] -12.6944969 -7.1119379 -1.1671080 25.23981082 15.2182413 3.1359897
[23,] 7.6833451 14.3016682 -1.6372096 -10.09821896 6.6159484 11.1043217
[24,] 8.1890417 -9.4794336 -8.5880521 -1.10520514 -17.4224920 5.2493575
[25,] -3.1550401 -11.3552345 -10.0994053 -0.63600962 1.6201849 11.8080087
[26,] 11.3794056 9.6759770 -20.9505389 -4.21151930 0.2571942 5.1374407
[27,] -8.3360623 7.9102357 -9.5290162 1.26859205 11.4465606 17.2226333
[28,] 13.1359311 4.2280627 5.3034441 6.44903849 13.2959147 -7.3031668
[29,] -5.9681800 6.7815310 6.2854904 3.80969559 4.5802715 6.6750778
[30,] -6.4608860 13.7115207 13.2301872 0.51246914 4.0796638 24.3345206
[31,] -19.8791498 -8.4822482 5.9745112 6.77775333 -2.0729250 1.9248054
[32,] -1.5056574 -16.9305186 -10.7897586 -9.53881281 -3.2293712 15.7449157
[33,] 1.0963879 13.5435890 11.9088236 -10.43685377 -8.3985770 27.2198772
[34,] -0.1504193 5.8814935 -1.0552062 43.32424265 17.4151022 -18.3426481
[35,] 11.8937863 -6.0708949 -10.0586370 12.73896910 1.5692205 -6.9742599
[36,] 15.1913562 3.9524892 -5.1856369 0.18945220 -9.0505385 -0.2662558
[37,] 19.5178730 31.1676150 3.3916654 -7.96846286 -11.8794845 1.7917374
[38,] 23.2267867 -2.3904429 2.2681612 7.49588115 25.1116050 8.7577301
[39,] 5.8299620 2.4156617 -16.4873916 1.21704035 -4.7642068 -4.5065091
[40,] -5.3580017 10.2012898 -6.3998916 -15.65898054 -27.8194649 -12.2135449
[41,] -0.3101817 3.7769307 25.0405066 11.31657934 0.7026392 -4.3161288
[42,] 13.8669035 -11.7519580 -13.6101125 3.89312041 -20.8653554 6.9924565
[43,] -4.9965045 -5.4890376 -8.4805666 -0.59350526 3.2821421 -3.0506808
[44,] -1.5279292 -4.0431082 7.3010128 -6.72091102 -0.2797331 10.1565913
[45,] -2.2088535 -2.3399517 0.6408552 6.39036929 13.6958087 -3.7860378
[46,] 1.3843284 8.0931070 4.7304363 -14.28856076 -11.7223243 3.5735950
[47,] -5.2130365 -19.1021005 4.8152711 -17.96558836 -4.4474162 1.8337328
[48,] 14.9257246 -5.7951027 -3.8626724 3.42334644 14.6406401 24.2886754
[49,] -4.7677712 -2.2772196 1.3598465 -8.40049324 0.1755423 -12.3997213
[50,] 4.5105080 3.9269453 -10.2666957 16.69198046 9.8470730 -11.8276204
[51,] 10.7244905 6.0416465 -0.1173996 -9.18569693 -5.1426092 -2.8320362
[52,] 9.5395965 -2.4425359 -10.6175613 4.10263909 -11.6769866 0.6262070
[53,] 10.6462704 -8.3477934 -8.9650647 0.61694190 3.9948279 -11.9174158
[54,] -0.1257433 -5.3322415 13.9216417 11.13969211 10.8394214 -4.3559417
[55,] -1.0180750 9.4554997 12.8719201 -23.82440733 -16.3503189 4.9521552
[56,] -7.6631353 -14.0906684 4.2367528 -2.08159278 7.4076149 -4.0545920
[57,] 8.7154727 0.7216291 9.8478937 -11.93926571 12.7197734 -16.7897377
[58,] -3.0770475 5.4841867 -0.5374688 1.35377657 2.1415518 -6.9942871
[59,] 1.4715710 3.6168567 -13.5260934 -7.99679840 7.7892446 14.2236878
[60,] 0.5854433 -24.7466810 3.8821314 -3.41211305 2.0977651 -2.2016587
[,12] [,13] [,14] [,15] [,16]
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[9,] -16.59976863 -1.6781654 -16.31583950 10.4065956 -2.80003547
[10,] -1.07637119 20.3418426 -1.24569660 -18.7870573 23.97262408
[11,] 12.07604300 6.1942670 9.01180676 8.9206000 7.27133155
[12,] 98.60388865 -7.6166663 10.89566109 -7.8020127 7.58517814
[13,] -7.61666634 121.0017341 11.52244153 -9.2727555 -7.00399484
[14,] 10.89566109 11.5224415 76.72945495 -8.9665810 -3.67961616
[15,] -7.80201266 -9.2727555 -8.96658102 107.3580700 0.43275375
[16,] 7.58517814 -7.0039948 -3.67961616 0.4327538 110.97490736
[17,] 9.38464195 -5.8545270 4.36282152 -11.1446383 -10.38680267
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[19,] -1.17750565 5.3416462 -1.34514168 14.7193671 -6.82665444
[20,] -8.39160439 -8.8354351 1.77566438 18.7733665 -3.63619859
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[22,] 1.99300459 -22.7459413 -1.04203213 -14.8758425 18.49511303
[23,] -10.79084056 3.4495101 -4.64765984 8.6389633 0.05980191
[24,] -12.99284637 8.4991441 6.17684247 -4.6719039 -11.14666363
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[44,] -14.54560472 -14.9931989 5.11155467 8.3111972 1.40973309
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[49,] 15.81894545 -7.6173063 0.60540483 -8.2200601 -3.68754395
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[,56] [,57] [,58] [,59] [,60]
[1,] -4.71298584 3.6224919 -1.3240313 -6.7569798 -1.1860511
[2,] -0.10618025 1.7806911 11.3936851 9.1648912 -7.2342245
[3,] 14.72548202 -10.5527952 -11.3060818 -3.4034932 -7.4915796
[4,] 16.26833386 14.3426088 0.4766264 -1.7722203 -10.3121088
[5,] 14.49898434 6.6458542 -6.5813949 8.2760724 21.2407882
[6,] -7.66313532 8.7154727 -3.0770475 1.4715710 0.5854433
[7,] -14.09066844 0.7216291 5.4841867 3.6168567 -24.7466810
[8,] 4.23675280 9.8478937 -0.5374688 -13.5260934 3.8821314
[9,] -2.08159278 -11.9392657 1.3537766 -7.9967984 -3.4121131
[10,] 7.40761485 12.7197734 2.1415518 7.7892446 2.0977651
[11,] -4.05459196 -16.7897377 -6.9942871 14.2236878 -2.2016587
[12,] 4.60086065 -9.7337955 -1.0482847 -0.9959113 -0.8283364
[13,] -23.00393501 -1.2158018 9.3010339 -1.3826220 -2.1744033
[14,] 1.08157002 -3.2335439 -8.2860585 -5.8602007 2.5441734
[15,] -7.04055442 5.4539729 15.5843463 3.6948226 13.4415306
[16,] 21.14264095 -0.6667444 7.3777070 6.9436033 8.4299586
[17,] 18.00385508 -3.0611771 12.8822657 -5.2126315 -7.6266346
[18,] 23.67670321 -3.8731502 -1.5444936 -7.1368378 -1.2321708
[19,] 0.01004236 -20.6930307 7.9497370 -4.3895570 -11.9105280
[20,] -2.05085589 -5.9006744 2.5484288 -11.2424956 0.9621778
[21,] 3.50299402 3.2310017 1.9145303 6.4796176 -12.2080998
[22,] 8.49823348 8.3228603 -4.8995776 0.2535846 -10.8380162
[23,] 12.39584307 13.4945784 1.8282309 10.4381601 -8.5024373
[24,] -8.99185267 -3.9386709 -1.4503746 -2.9725994 1.1283349
[25,] -12.31949576 4.5939683 -6.8245065 11.2740162 6.6321765
[26,] 8.18526867 14.2777336 4.6659709 2.1953090 7.1480537
[27,] -8.99777322 -3.2521830 -5.6483284 20.6223209 10.6897076
[28,] 10.00328739 17.9415572 -9.2245041 13.5272761 8.8896631
[29,] -10.55750188 -1.3254102 -18.1968041 3.8107774 1.7539299
[30,] -11.97758436 -0.7656068 7.2561074 12.1862253 18.4999670
[31,] 9.45820320 -9.5999281 -16.8810396 4.2149474 13.8116213
[32,] -6.93731660 4.3033465 5.4264932 -9.4325657 -7.3435927
[33,] 12.15203878 16.8515243 -0.8225964 1.7264171 -17.3271244
[34,] -5.46646561 -8.6660153 -4.2171503 -8.8747289 14.6399957
[35,] 10.00231976 15.2366496 -8.9196750 -17.1878200 -6.6416784
[36,] 3.94143339 6.0984521 -19.4438805 -8.0322873 5.5495903
[37,] -14.29422063 12.1804150 -6.2130939 2.5603477 0.9587113
[38,] 15.27701208 5.4085763 -12.5925448 6.6252472 5.4066275
[39,] 9.21915835 4.9693770 22.4600508 -5.1867490 -9.0697539
[40,] -1.42560100 2.3052799 -16.3833700 9.1868939 -5.2450258
[41,] -13.82596647 24.3886792 3.9125686 5.5718468 -0.2469396
[42,] 6.23723227 -12.5282648 -24.0929888 -2.4739482 8.0168266
[43,] -5.58961594 12.3551152 -12.1994911 -8.5348544 15.1319430
[44,] -2.52686186 -9.8673276 -14.2186196 -7.4898626 -2.3941793
[45,] 12.60903947 13.4526519 -8.9567406 -1.9899344 1.6452868
[46,] 8.25669148 0.2029400 -0.3306192 -14.0683451 0.4058286
[47,] -10.99689487 -14.5076536 -9.0840154 -12.8423954 -1.0265339
[48,] 2.94110993 -5.0877622 -24.3603334 9.4219976 -6.3596564
[49,] -13.40882806 -6.8968165 5.7007932 1.8203081 3.6751551
[50,] -1.83141703 0.7427221 -18.0851862 -3.9183913 -0.6155979
[51,] -8.52602534 -5.9829167 3.3300019 -9.6947232 1.5522016
[52,] 4.21871621 -15.7950772 -2.3661493 -4.8195598 8.8020402
[53,] 5.84503907 -6.1421693 -13.3198026 5.5666639 4.5136853
[54,] -11.44669914 -3.3185304 20.9619685 -0.4478787 10.8076043
[55,] -8.25330350 8.1183942 5.0386341 -1.8611837 9.9237273
[56,] 114.10139591 13.1259608 0.6456431 -19.1281867 -3.7022355
[57,] 13.12596085 109.5229051 -1.8059321 -5.8334050 0.4987011
[58,] 0.64564305 -1.8059321 90.4925031 6.6639200 6.1532960
[59,] -19.12818670 -5.8334050 6.6639200 99.0036297 7.5371517
[60,] -3.70223547 0.4987011 6.1532960 7.5371517 93.3635495
>
> # with DelayedArray
> XD <- DelayedArray(X)
> bdCrossprod(XD)
Error in bdCrossprod(XD) : No such namespace: beachmat.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.99.14
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘BigDataStatMeth_hdf5.Rmd’ using rmarkdown
--- finished re-building ‘BigDataStatMeth_hdf5.Rmd’
--- re-building ‘BigDataStatMeth_memory.Rmd’ using rmarkdown
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:Matrix':
expand, unname
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
aperm, apply, rowsum, scale, sweep
Quitting from lines 155-160 (BigDataStatMeth_memory.Rmd)
Error: processing vignette 'BigDataStatMeth_memory.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘BigDataStatMeth_memory.Rmd’
SUMMARY: processing the following file failed:
‘BigDataStatMeth_memory.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.99.14
Check: examples
Result: ERROR
Running examples in ‘BigDataStatMeth-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bdCrossprod
> ### Title: Crossproduct of DelayedArray
> ### Aliases: bdCrossprod
>
> ### ** Examples
>
>
> library(DelayedArray)
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: ‘MatrixGenerics’
The following objects are masked from ‘package:matrixStats’:
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:Matrix’:
expand, unname
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Attaching package: ‘DelayedArray’
The following objects are masked from ‘package:base’:
aperm, apply, rowsum, scale, sweep
>
> n <- 100
> p <- 60
>
> X <- matrix(rnorm(n*p), nrow=n, ncol=p)
>
> # without DelayedArray
> bdCrossprod(X)
[,1] [,2] [,3] [,4] [,5]
[1,] 81.0550927 -0.49637465 2.01369284 -3.8857354 14.86778280
[2,] -0.4963746 90.97864395 -4.97067333 -5.6891795 15.14248536
[3,] 2.0136928 -4.97067333 105.98885926 11.4017437 3.44053581
[4,] -3.8857354 -5.68917953 11.40174373 97.6248135 2.54128247
[5,] 14.8677828 15.14248536 3.44053581 2.5412825 135.58443168
[6,] -9.9308029 -1.67862986 -4.27357031 -9.4305103 -9.97619997
[7,] 6.1193988 -8.41344754 -4.44296865 -14.6254464 8.80802449
[8,] 3.5003399 6.99323931 -16.14234131 2.2905400 12.80999664
[9,] 6.6733596 -0.07540405 0.09717535 23.3515608 10.29227400
[10,] 8.2828486 -1.73918478 -19.85067297 12.3644248 -11.39701974
[11,] -12.6899584 -10.55007247 -3.58096248 0.1756843 0.34051618
[12,] -8.2304039 -1.70465616 -3.71431805 -0.2999867 -6.38310283
[13,] 1.4496223 12.99341581 4.43733418 -14.9974984 5.30490324
[14,] -8.4957559 -1.97108062 -5.98270438 -13.9543771 5.99821064
[15,] 0.3951284 -11.84869423 -17.88749642 9.8725465 9.37189613
[16,] -4.2885569 2.42618160 -16.25187198 27.0340707 -1.14375626
[17,] 15.1748202 7.01298176 8.42226926 10.1849476 4.55937206
[18,] -4.2366820 -17.43834945 0.63102984 -8.1880753 -3.00472336
[19,] -8.2669963 -9.80927338 17.39196801 13.6905870 -6.46861183
[20,] 13.2812089 -2.46404728 -21.26770104 -11.5316647 13.18801312
[21,] 7.0059986 14.55441470 14.85358722 6.7322927 2.35729077
[22,] -9.5864098 -1.17419382 13.12187592 21.9667601 -0.54474061
[23,] -12.2468856 10.40840781 0.75234045 -9.3812652 -7.19742001
[24,] 7.7366750 -0.77942174 -4.92268477 3.6095945 -0.27578344
[25,] 6.1591597 -17.24162009 24.24584213 -10.3936819 9.77829058
[26,] -2.9364207 -1.17613356 -3.37556371 0.9497670 -10.73390060
[27,] -5.8093689 -10.19317056 -12.91751960 4.9441268 -2.17886264
[28,] -2.1418544 -7.64386166 -10.25710418 -17.9238494 -5.46093653
[29,] -3.3616555 6.23083925 -0.72688249 6.4304600 -3.32930573
[30,] 0.9787916 -0.96722537 3.65942173 -5.2595178 -11.80750921
[31,] 13.4880815 13.73124163 7.86566537 5.4145375 16.47559432
[32,] -8.5350709 4.97935331 -18.94437263 -7.1166255 -3.94259710
[33,] 8.6730844 -6.04526479 -6.90749229 -6.7426107 11.38690364
[34,] 18.8718720 -18.30891756 -4.78415378 -2.6120459 4.78721117
[35,] 10.4461472 -19.80551900 13.83424085 8.6692713 -5.96260527
[36,] -4.2049190 -15.42814473 6.74612837 20.7092792 -6.50488204
[37,] -1.3401418 11.22477166 2.56160838 -7.1410463 20.69698981
[38,] 1.0872075 -6.48636459 -5.59717144 -9.3490896 -17.64891354
[39,] 2.8236842 -5.91075329 10.97163831 -12.0023946 -31.87371620
[40,] -1.1263198 -0.10850037 12.44409357 1.2722152 -2.79631946
[41,] -7.6923612 -0.34393030 -8.94232685 1.9809870 -1.41626686
[42,] -15.2538768 -3.80199010 -9.18411509 -5.4950602 4.27020408
[43,] -0.5163611 -15.56276982 -12.03516701 4.0218935 -22.48306241
[44,] -3.2395209 -11.32164419 3.39333143 8.9402307 -6.27990242
[45,] 2.6191508 -13.10669813 5.80668782 9.6692926 -4.22786269
[46,] 0.8170621 -1.57639204 6.40120072 0.4099638 -6.05037164
[47,] -14.8956315 -2.92252067 9.33883411 3.3272261 -13.85545621
[48,] -3.6624587 -5.73661087 -0.70677131 7.6796933 -6.48912327
[49,] -7.0335163 13.27188528 -0.86023319 -8.2995555 -15.48670692
[50,] 13.8075667 0.63952484 -12.89370498 15.5889760 -8.01972453
[51,] -9.0796899 7.43332364 -2.85530142 8.0414439 -2.91730319
[52,] -4.3287340 10.75826464 25.93216089 -11.6266628 -11.28899035
[53,] -9.9072607 15.25026707 -0.28763368 13.3006904 11.07500569
[54,] -6.1718831 15.31611874 2.37079745 -6.9428280 -5.82737308
[55,] 4.9958579 5.65285935 -6.02141613 -10.9951182 0.04120373
[56,] -4.7129858 -0.10618025 14.72548202 16.2683339 14.49898434
[57,] 3.6224919 1.78069113 -10.55279524 14.3426088 6.64585422
[58,] -1.3240313 11.39368507 -11.30608184 0.4766264 -6.58139490
[59,] -6.7569798 9.16489117 -3.40349318 -1.7722203 8.27607243
[60,] -1.1860511 -7.23422450 -7.49157959 -10.3121088 21.24078823
[,6] [,7] [,8] [,9] [,10] [,11]
[1,] -9.9308029 6.1193988 3.5003399 6.67335956 8.2828486 -12.6899584
[2,] -1.6786299 -8.4134475 6.9932393 -0.07540405 -1.7391848 -10.5500725
[3,] -4.2735703 -4.4429687 -16.1423413 0.09717535 -19.8506730 -3.5809625
[4,] -9.4305103 -14.6254464 2.2905400 23.35156081 12.3644248 0.1756843
[5,] -9.9762000 8.8080245 12.8099966 10.29227400 -11.3970197 0.3405162
[6,] 92.6151553 1.6824797 -16.1627513 15.87237738 -6.4415196 -5.0996671
[7,] 1.6824797 119.6356049 11.6144904 0.11941823 -9.4522555 2.5440995
[8,] -16.1627513 11.6144904 119.2029246 -4.05189872 8.5882169 7.8610494
[9,] 15.8723774 0.1194182 -4.0518987 117.27864397 22.6663154 -14.0915232
[10,] -6.4415196 -9.4522555 8.5882169 22.66631536 110.1512540 3.3203161
[11,] -5.0996671 2.5440995 7.8610494 -14.09152322 3.3203161 104.9804330
[12,] -1.8453425 0.6877980 -2.4614510 -16.59976863 -1.0763712 12.0760430
[13,] 8.2014806 9.9893558 -1.4408390 -1.67816543 20.3418426 6.1942670
[14,] 3.3580841 -3.7386492 4.1805392 -16.31583950 -1.2456966 9.0118068
[15,] -6.9700306 10.9840256 27.8575541 10.40659562 -18.7870573 8.9206000
[16,] -6.3081705 -16.9543882 23.3717097 -2.80003547 23.9726241 7.2713315
[17,] 0.6803194 18.7831707 -20.3449411 6.29491288 15.7004316 -6.6514306
[18,] 11.3677988 -1.2199254 -18.8399141 -10.85707531 -9.8132425 -16.6435175
[19,] -0.1276837 -2.1616072 -6.9254815 29.94729273 -14.7677297 4.8861188
[20,] -20.1841288 14.6906494 27.6148127 1.39049635 -1.9705054 4.8560776
[21,] -1.5498570 -5.3407762 -21.5770083 5.32174958 4.7675964 1.9687727
[22,] -12.6944969 -7.1119379 -1.1671080 25.23981082 15.2182413 3.1359897
[23,] 7.6833451 14.3016682 -1.6372096 -10.09821896 6.6159484 11.1043217
[24,] 8.1890417 -9.4794336 -8.5880521 -1.10520514 -17.4224920 5.2493575
[25,] -3.1550401 -11.3552345 -10.0994053 -0.63600962 1.6201849 11.8080087
[26,] 11.3794056 9.6759770 -20.9505389 -4.21151930 0.2571942 5.1374407
[27,] -8.3360623 7.9102357 -9.5290162 1.26859205 11.4465606 17.2226333
[28,] 13.1359311 4.2280627 5.3034441 6.44903849 13.2959147 -7.3031668
[29,] -5.9681800 6.7815310 6.2854904 3.80969559 4.5802715 6.6750778
[30,] -6.4608860 13.7115207 13.2301872 0.51246914 4.0796638 24.3345206
[31,] -19.8791498 -8.4822482 5.9745112 6.77775333 -2.0729250 1.9248054
[32,] -1.5056574 -16.9305186 -10.7897586 -9.53881281 -3.2293712 15.7449157
[33,] 1.0963879 13.5435890 11.9088236 -10.43685377 -8.3985770 27.2198772
[34,] -0.1504193 5.8814935 -1.0552062 43.32424265 17.4151022 -18.3426481
[35,] 11.8937863 -6.0708949 -10.0586370 12.73896910 1.5692205 -6.9742599
[36,] 15.1913562 3.9524892 -5.1856369 0.18945220 -9.0505385 -0.2662558
[37,] 19.5178730 31.1676150 3.3916654 -7.96846286 -11.8794845 1.7917374
[38,] 23.2267867 -2.3904429 2.2681612 7.49588115 25.1116050 8.7577301
[39,] 5.8299620 2.4156617 -16.4873916 1.21704035 -4.7642068 -4.5065091
[40,] -5.3580017 10.2012898 -6.3998916 -15.65898054 -27.8194649 -12.2135449
[41,] -0.3101817 3.7769307 25.0405066 11.31657934 0.7026392 -4.3161288
[42,] 13.8669035 -11.7519580 -13.6101125 3.89312041 -20.8653554 6.9924565
[43,] -4.9965045 -5.4890376 -8.4805666 -0.59350526 3.2821421 -3.0506808
[44,] -1.5279292 -4.0431082 7.3010128 -6.72091102 -0.2797331 10.1565913
[45,] -2.2088535 -2.3399517 0.6408552 6.39036929 13.6958087 -3.7860378
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>
> # with DelayedArray
> XD <- DelayedArray(X)
> bdCrossprod(XD)
Error in bdCrossprod(XD) : No such namespace: beachmat.
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.99.14
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘BigDataStatMeth_hdf5.Rmd’ using rmarkdown
--- finished re-building ‘BigDataStatMeth_hdf5.Rmd’
--- re-building ‘BigDataStatMeth_memory.Rmd’ using rmarkdown
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:Matrix':
expand, unname
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
aperm, apply, rowsum, scale, sweep
Quitting from lines 155-160 (BigDataStatMeth_memory.Rmd)
Error: processing vignette 'BigDataStatMeth_memory.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘BigDataStatMeth_memory.Rmd’
SUMMARY: processing the following file failed:
‘BigDataStatMeth_memory.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.99.14
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64