* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/MBNMAtime.Rcheck’ * using R Under development (unstable) (2023-10-16 r85339) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-13 (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘MBNMAtime/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MBNMAtime’ version ‘0.2.4’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘MBNMAtime’ can be installed ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [18s/19s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘MBNMAtime-Ex.R’ failed The error most likely occurred in: > ### Name: genspline > ### Title: Generates spline basis matrices for fitting to time-course > ### function > ### Aliases: genspline > > ### ** Examples > > x <- 0:100 > > genspline(x) 1 2 0 0.00 0.00 1 0.02 0.00 2 0.04 0.00 3 0.06 0.00 4 0.08 0.00 5 0.10 0.00 6 0.12 0.00 7 0.14 0.00 8 0.16 0.00 9 0.18 0.00 10 0.20 0.00 11 0.22 0.00 12 0.24 0.00 13 0.26 0.00 14 0.28 0.00 15 0.30 0.00 16 0.32 0.00 17 0.34 0.00 18 0.36 0.00 19 0.38 0.00 20 0.40 0.00 21 0.42 0.00 22 0.44 0.00 23 0.46 0.00 24 0.48 0.00 25 0.50 0.00 26 0.52 0.00 27 0.54 0.00 28 0.56 0.00 29 0.58 0.00 30 0.60 0.00 31 0.62 0.00 32 0.64 0.00 33 0.66 0.00 34 0.68 0.00 35 0.70 0.00 36 0.72 0.00 37 0.74 0.00 38 0.76 0.00 39 0.78 0.00 40 0.80 0.00 41 0.82 0.00 42 0.84 0.00 43 0.86 0.00 44 0.88 0.00 45 0.90 0.00 46 0.92 0.00 47 0.94 0.00 48 0.96 0.00 49 0.98 0.00 50 1.00 0.00 51 0.98 0.02 52 0.96 0.04 53 0.94 0.06 54 0.92 0.08 55 0.90 0.10 56 0.88 0.12 57 0.86 0.14 58 0.84 0.16 59 0.82 0.18 60 0.80 0.20 61 0.78 0.22 62 0.76 0.24 63 0.74 0.26 64 0.72 0.28 65 0.70 0.30 66 0.68 0.32 67 0.66 0.34 68 0.64 0.36 69 0.62 0.38 70 0.60 0.40 71 0.58 0.42 72 0.56 0.44 73 0.54 0.46 74 0.52 0.48 75 0.50 0.50 76 0.48 0.52 77 0.46 0.54 78 0.44 0.56 79 0.42 0.58 80 0.40 0.60 81 0.38 0.62 82 0.36 0.64 83 0.34 0.66 84 0.32 0.68 85 0.30 0.70 86 0.28 0.72 87 0.26 0.74 88 0.24 0.76 89 0.22 0.78 90 0.20 0.80 91 0.18 0.82 92 0.16 0.84 93 0.14 0.86 94 0.12 0.88 95 0.10 0.90 96 0.08 0.92 97 0.06 0.94 98 0.04 0.96 99 0.02 0.98 100 0.00 1.00 > > # Generate a quadratic B-spline with 1 equally spaced internal knot > genspline(x, spline="bs", knots=2, degree=2) 1 2 3 4 0 0.00000 0.00000 0.00000 0.0000 1 0.05865 0.00045 0.00000 0.0000 2 0.11460 0.00180 0.00000 0.0000 3 0.16785 0.00405 0.00000 0.0000 4 0.21840 0.00720 0.00000 0.0000 5 0.26625 0.01125 0.00000 0.0000 6 0.31140 0.01620 0.00000 0.0000 7 0.35385 0.02205 0.00000 0.0000 8 0.39360 0.02880 0.00000 0.0000 9 0.43065 0.03645 0.00000 0.0000 10 0.46500 0.04500 0.00000 0.0000 11 0.49665 0.05445 0.00000 0.0000 12 0.52560 0.06480 0.00000 0.0000 13 0.55185 0.07605 0.00000 0.0000 14 0.57540 0.08820 0.00000 0.0000 15 0.59625 0.10125 0.00000 0.0000 16 0.61440 0.11520 0.00000 0.0000 17 0.62985 0.13005 0.00000 0.0000 18 0.64260 0.14580 0.00000 0.0000 19 0.65265 0.16245 0.00000 0.0000 20 0.66000 0.18000 0.00000 0.0000 21 0.66465 0.19845 0.00000 0.0000 22 0.66660 0.21780 0.00000 0.0000 23 0.66585 0.23805 0.00000 0.0000 24 0.66240 0.25920 0.00000 0.0000 25 0.65625 0.28125 0.00000 0.0000 26 0.64740 0.30420 0.00000 0.0000 27 0.63585 0.32805 0.00000 0.0000 28 0.62160 0.35280 0.00000 0.0000 29 0.60465 0.37845 0.00000 0.0000 30 0.58500 0.40500 0.00000 0.0000 31 0.56265 0.43245 0.00000 0.0000 32 0.53760 0.46080 0.00000 0.0000 33 0.50985 0.49005 0.00000 0.0000 34 0.48020 0.51960 0.00020 0.0000 35 0.45125 0.54750 0.00125 0.0000 36 0.42320 0.57360 0.00320 0.0000 37 0.39605 0.59790 0.00605 0.0000 38 0.36980 0.62040 0.00980 0.0000 39 0.34445 0.64110 0.01445 0.0000 40 0.32000 0.66000 0.02000 0.0000 41 0.29645 0.67710 0.02645 0.0000 42 0.27380 0.69240 0.03380 0.0000 43 0.25205 0.70590 0.04205 0.0000 44 0.23120 0.71760 0.05120 0.0000 45 0.21125 0.72750 0.06125 0.0000 46 0.19220 0.73560 0.07220 0.0000 47 0.17405 0.74190 0.08405 0.0000 48 0.15680 0.74640 0.09680 0.0000 49 0.14045 0.74910 0.11045 0.0000 50 0.12500 0.75000 0.12500 0.0000 51 0.11045 0.74910 0.14045 0.0000 52 0.09680 0.74640 0.15680 0.0000 53 0.08405 0.74190 0.17405 0.0000 54 0.07220 0.73560 0.19220 0.0000 55 0.06125 0.72750 0.21125 0.0000 56 0.05120 0.71760 0.23120 0.0000 57 0.04205 0.70590 0.25205 0.0000 58 0.03380 0.69240 0.27380 0.0000 59 0.02645 0.67710 0.29645 0.0000 60 0.02000 0.66000 0.32000 0.0000 61 0.01445 0.64110 0.34445 0.0000 62 0.00980 0.62040 0.36980 0.0000 63 0.00605 0.59790 0.39605 0.0000 64 0.00320 0.57360 0.42320 0.0000 65 0.00125 0.54750 0.45125 0.0000 66 0.00020 0.51960 0.48020 0.0000 67 0.00000 0.49005 0.50985 0.0001 68 0.00000 0.46080 0.53760 0.0016 69 0.00000 0.43245 0.56265 0.0049 70 0.00000 0.40500 0.58500 0.0100 71 0.00000 0.37845 0.60465 0.0169 72 0.00000 0.35280 0.62160 0.0256 73 0.00000 0.32805 0.63585 0.0361 74 0.00000 0.30420 0.64740 0.0484 75 0.00000 0.28125 0.65625 0.0625 76 0.00000 0.25920 0.66240 0.0784 77 0.00000 0.23805 0.66585 0.0961 78 0.00000 0.21780 0.66660 0.1156 79 0.00000 0.19845 0.66465 0.1369 80 0.00000 0.18000 0.66000 0.1600 81 0.00000 0.16245 0.65265 0.1849 82 0.00000 0.14580 0.64260 0.2116 83 0.00000 0.13005 0.62985 0.2401 84 0.00000 0.11520 0.61440 0.2704 85 0.00000 0.10125 0.59625 0.3025 86 0.00000 0.08820 0.57540 0.3364 87 0.00000 0.07605 0.55185 0.3721 88 0.00000 0.06480 0.52560 0.4096 89 0.00000 0.05445 0.49665 0.4489 90 0.00000 0.04500 0.46500 0.4900 91 0.00000 0.03645 0.43065 0.5329 92 0.00000 0.02880 0.39360 0.5776 93 0.00000 0.02205 0.35385 0.6241 94 0.00000 0.01620 0.31140 0.6724 95 0.00000 0.01125 0.26625 0.7225 96 0.00000 0.00720 0.21840 0.7744 97 0.00000 0.00405 0.16785 0.8281 98 0.00000 0.00180 0.11460 0.8836 99 0.00000 0.00045 0.05865 0.9409 100 0.00000 0.00000 0.00000 1.0000 > > # Generate a natural spline with 2 knots at selected quantiles > genspline(x, spline="ns", knots=c(0.1, 0.5)) 1 2 3 0 0.000000000 0.00000000 0.00000000 1 -0.014156667 0.03969467 -0.02551800 2 -0.028112452 0.07916287 -0.05089041 3 -0.041666470 0.11817812 -0.07597165 4 -0.054617838 0.15651395 -0.10061611 5 -0.066765674 0.19394389 -0.12467821 6 -0.077909094 0.23024146 -0.14801237 7 -0.087847215 0.26518020 -0.17047299 8 -0.096379153 0.29853363 -0.19191448 9 -0.103304027 0.33007527 -0.21219125 10 -0.108420951 0.35957866 -0.23115771 11 -0.111576347 0.38686644 -0.24869787 12 -0.112805841 0.41195769 -0.26481407 13 -0.112192366 0.43492063 -0.27953826 14 -0.109818852 0.45582345 -0.29290238 15 -0.105768230 0.47473438 -0.30493837 16 -0.100123432 0.49172161 -0.31567818 17 -0.092967387 0.50685335 -0.32515374 18 -0.084383028 0.52019781 -0.33339701 19 -0.074453285 0.53182320 -0.34043991 20 -0.063261088 0.54179771 -0.34631440 21 -0.050889370 0.55018957 -0.35105242 22 -0.037421061 0.55706697 -0.35468591 23 -0.022939091 0.56249812 -0.35724681 24 -0.007526393 0.56655123 -0.35876706 25 0.008734103 0.56929451 -0.35927861 26 0.025759467 0.57079616 -0.35881340 27 0.043466767 0.57112439 -0.35740338 28 0.061773071 0.57034740 -0.35508047 29 0.080595450 0.56853341 -0.35187663 30 0.099850972 0.56575061 -0.34782381 31 0.119456707 0.56206722 -0.34295393 32 0.139329723 0.55755144 -0.33729894 33 0.159387088 0.55227149 -0.33089080 34 0.179545874 0.54629555 -0.32376143 35 0.199723147 0.53969185 -0.31594278 36 0.219835978 0.53252859 -0.30746679 37 0.239801435 0.52487398 -0.29836542 38 0.259536588 0.51679622 -0.28867059 39 0.278958505 0.50836352 -0.27841425 40 0.297984256 0.49964408 -0.26762834 41 0.316530909 0.49070612 -0.25634481 42 0.334515533 0.48161784 -0.24459560 43 0.351855199 0.47244744 -0.23241264 44 0.368466973 0.46326314 -0.21982789 45 0.384267926 0.45413314 -0.20687329 46 0.399175127 0.44512564 -0.19358077 47 0.413105645 0.43630886 -0.17998228 48 0.425976548 0.42775100 -0.16610977 49 0.437704905 0.41952026 -0.15199517 50 0.448207787 0.41168486 -0.13767043 51 0.457420444 0.40430009 -0.12316276 52 0.465350863 0.39736958 -0.10848045 53 0.472025210 0.39088408 -0.09362707 54 0.477469654 0.38483430 -0.07860618 55 0.481710364 0.37921098 -0.06342134 56 0.484773507 0.37400485 -0.04807613 57 0.486685252 0.36920663 -0.03257410 58 0.487471767 0.36480705 -0.01691882 59 0.487159219 0.36079685 -0.00111385 60 0.485773778 0.35716676 0.01483724 61 0.483341610 0.35390749 0.03093090 62 0.479888885 0.35100979 0.04716355 63 0.475441771 0.34846438 0.06353163 64 0.470026435 0.34626198 0.08003158 65 0.463669046 0.34439334 0.09665984 66 0.456395772 0.34284917 0.11341283 67 0.448232780 0.34162021 0.13028700 68 0.439206240 0.34069719 0.14727879 69 0.429342320 0.34007084 0.16438462 70 0.418667187 0.33973188 0.18160094 71 0.407207009 0.33967104 0.19892417 72 0.394987955 0.33987906 0.21635076 73 0.382036194 0.34034666 0.23387715 74 0.368377892 0.34106457 0.25149976 75 0.354039218 0.34202352 0.26921504 76 0.339046341 0.34321424 0.28701941 77 0.323425429 0.34462747 0.30490933 78 0.307202649 0.34625392 0.32288121 79 0.290404170 0.34808433 0.34093151 80 0.273056159 0.35010942 0.35905664 81 0.255184786 0.35231993 0.37725306 82 0.236816218 0.35470659 0.39551719 83 0.217976624 0.35726012 0.41384548 84 0.198692171 0.35997126 0.43223435 85 0.178989027 0.36283072 0.45068025 86 0.158893362 0.36582925 0.46917961 87 0.138431342 0.36895757 0.48772886 88 0.117629137 0.37220642 0.50632445 89 0.096512914 0.37556651 0.52496280 90 0.075108841 0.37902858 0.54364036 91 0.053443087 0.38258336 0.56235356 92 0.031541819 0.38622157 0.58109883 93 0.009431207 0.38993395 0.59987262 94 -0.012862583 0.39371123 0.61867135 95 -0.035313382 0.39754414 0.63749147 96 -0.057895021 0.40142339 0.65632941 97 -0.080581333 0.40533973 0.67518160 98 -0.103346149 0.40928388 0.69404449 99 -0.126163302 0.41324658 0.71291450 100 -0.149006623 0.41721854 0.73178808 > > # Generate a piecewise linear spline with 3 equally spaced knots > genspline(x, spline="ls", knots=3) Error in loadNamespace(x) : there is no package called ‘lspline’ Calls: genspline ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(checkmate) > library(testthat) > library(MBNMAtime) Attaching package: 'MBNMAtime' The following object is masked from 'package:base': rank > library(igraph) Error in library(igraph) : there is no package called 'igraph' Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [36s/37s] ERROR Error(s) in re-building vignettes: --- re-building ‘consistencychecking-3.Rmd’ using rmarkdown Quitting from lines 41-45 [unnamed-chunk-1] (consistencychecking-3.Rmd) Error: processing vignette 'consistencychecking-3.Rmd' failed with diagnostics: there is no package called 'igraph' --- failed re-building ‘consistencychecking-3.Rmd’ --- re-building ‘dataexploration-1.Rmd’ using rmarkdown Quitting from lines 72-77 [unnamed-chunk-1] (dataexploration-1.Rmd) Error: processing vignette 'dataexploration-1.Rmd' failed with diagnostics: there is no package called 'igraph' --- failed re-building ‘dataexploration-1.Rmd’ --- re-building ‘mbnmatime-overview.Rmd’ using rmarkdown --- finished re-building ‘mbnmatime-overview.Rmd’ --- re-building ‘outputs-4.Rmd’ using rmarkdown Quitting from lines 48-52 [unnamed-chunk-2] (outputs-4.Rmd) Error: processing vignette 'outputs-4.Rmd' failed with diagnostics: there is no package called 'crayon' --- failed re-building ‘outputs-4.Rmd’ --- re-building ‘predictions-5.Rmd’ using rmarkdown Quitting from lines 66-77 [unnamed-chunk-3] (predictions-5.Rmd) Error: processing vignette 'predictions-5.Rmd' failed with diagnostics: there is no package called 'crayon' --- failed re-building ‘predictions-5.Rmd’ --- re-building ‘runmbnmatime-2.Rmd’ using rmarkdown Quitting from lines 122-123 [unnamed-chunk-3] (runmbnmatime-2.Rmd) Error: processing vignette 'runmbnmatime-2.Rmd' failed with diagnostics: there is no package called 'crayon' --- failed re-building ‘runmbnmatime-2.Rmd’ SUMMARY: processing the following files failed: ‘consistencychecking-3.Rmd’ ‘dataexploration-1.Rmd’ ‘outputs-4.Rmd’ ‘predictions-5.Rmd’ ‘runmbnmatime-2.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 3 ERRORs See ‘/data/gannet/ripley/R/packages/tests-Suggests/MBNMAtime.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 1:39.15, 91.57 + 6.63