* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/nCal.Rcheck’ * using R Under development (unstable) (2021-09-11 r80888) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘nCal/DESCRIPTION’ ... OK * this is package ‘nCal’ version ‘2021.9-12’ * 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 ‘nCal’ can be installed ... [22s/23s] 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 ... [37s/37s] 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 R/sysdata.rda ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘doRUnit.R’ [17s/17s] [17s/17s] ERROR Running the tests in ‘tests/doRUnit.R’ failed. Complete output: > ## unit tests will not be done if RUnit is not available > if(require("RUnit", quietly=TRUE)) { + + ## --- Setup --- + + pkg <- "nCal" # <-- Change to package name! + if(Sys.getenv("RCMDCHECK") == "FALSE") { + ## Path to unit tests for standalone running under Makefile (not R CMD check) + ## PKG/tests/../inst/unitTests + path <- file.path(getwd(), "unitTests") + } else { + ## Path to unit tests for R CMD check + ## PKG.Rcheck/tests/../PKG/unitTests + path <- system.file("unitTests", package=pkg) + } + cat("\nRunning unit tests\n") + print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path)) + + library(package=pkg, character.only=TRUE) + + ## If desired, load the name space to allow testing of private functions + ## if (is.element(pkg, loadedNamespaces())) + ## attach(loadNamespace(pkg), name=paste("namespace", pkg, sep=":"), pos=3) + ## + ## or simply call PKG:::myPrivateFunction() in tests + + ## --- Testing --- + + ## Define tests + testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), + dirs=path) + ## Run + tests <- runTestSuite(testSuite) + + ## Default report name + pathReport <- tempdir() + + ## Report to stdout and text files + cat("------------------- UNIT TEST SUMMARY ---------------------\n\n") + printTextProtocol(tests, showDetails=FALSE) + # printTextProtocol(tests, showDetails=FALSE, + # fileName=paste(pathReport, "Summary.txt", sep="")) + # printTextProtocol(tests, showDetails=TRUE, + # fileName=paste(pathReport, ".txt", sep="")) + # + # ## Report to HTML file + # printHTMLProtocol(tests, fileName=paste(pathReport, ".html", sep="")) + + ## Return stop() to cause R CMD check stop in case of + ## - failures i.e. FALSE to unit tests or + ## - errors i.e. R errors + tmp <- getErrors(tests) + if(tmp$nFail > 0 | tmp$nErr > 0) { + stop(paste("\n\nunit testing failed (#test failures: ", tmp$nFail, + ", #R errors: ", tmp$nErr, ")\n\n", sep="")) + } + } else { + warning("cannot run unit tests -- package RUnit is not available") + } Running unit tests $pkg [1] "nCal" $getwd [1] "/data/gannet/ripley/R/packages/tests-Suggests/nCal.Rcheck/tests" $pathToUnitTests [1] "/tmp/Rtmp8Oz7dK/RLIBS_2d55b3b92b7da/nCal/unitTests" Loading required package: drc Loading required package: MASS 'drc' has been loaded. Please cite R and 'drc' if used for a publication, for references type 'citation()' and 'citation('drc')'. Attaching package: 'drc' The following objects are masked from 'package:stats': gaussian, getInitial Loading required package: gdata gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED. gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED. Attaching package: 'gdata' The following object is masked from 'package:stats': nobs The following object is masked from 'package:utils': object.size The following object is masked from 'package:base': startsWith Loading required package: kyotil Attaching package: 'kyotil' The following objects are masked from 'package:gdata': last, trim Loading required package: gWidgets2 Loading required package: digest Executing test function test.5PL ... Error in FivePL.t.inv(y, param) : y and param not match in length In addition: Warning messages: 1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry Error in FivePL.t(log(x), param) : t or x and param not match in length Error in FivePL.t(log(x), param) : t or x and param not match in length Error in integrate(function(y) { : non-finite function value done successfully. Executing test function test.bcrm ... parameterization = gh ; error.model = norm ; mean.model = 5PL ; prior = cytokine ; prior.sensitivity = none check parameter Timing stopped at: 0.044 0 0.045 Error in loadNamespace(name) : there is no package called 'coda' In addition: Warning messages: 1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry done successfully. Executing test function test.ncal ... Error in ncal.formula(log(fi) ~ expected_conc, dat.std, return.fits = TRUE) : assay_id missing from data In addition: Warning messages: 1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry Error in ncal.formula(log(fi) ~ expected_conc, dat, return.fits = TRUE) : well_role missing from data a = Test p = Run 1 gofs = 0.747 NA NA s = 1 dil. = 1 [1] 3.938894078 0.162769075 51.361767779 37.090316619 71.124526018 [6] 0.020554418 0.005939354 8.360107437 s = 2 dil. = 1 [1] 9.21034 Inf 10000.00000 NaN NaN NaN [7] NaN Inf s = 3 dil. = 1 [1] -1.3703174 Inf 0.2540263 NaN NaN NaN NaN [8] Inf s = 4 dil. = 1 [1] -5.674972e-01 1.173724e+01 5.669426e-01 3.619967e-11 8.879194e+09 [6] 1.041892e+02 3.357354e+01 6.654340e+00 s = 5 dil. = 1 [1] 1.211634e+01 1.544867e+01 1.828354e+05 6.974593e-09 4.792936e+18 [6] 1.294197e+02 1.092416e+02 2.824563e+06 [1] "nCal 600" [1] "nCal 620" [1] "nCal 640" a = Test p = Run 1 devs.tmp = 244 263 338 NaN Iter 0. theta: 72.94029 31155.58 6.780068 9583.041 1.148624 g.hat: 2 deviance: 243.7845 Iter 1. theta: 78.17042 31632.68 6.698783 9916.431 1.135714 g.hat: 1.90303 deviance: 241.7502 Iter 2. theta: 76.64438 31192.07 6.666484 9782.873 1.148918 g.hat: 1.909631 deviance: 240.5888 max iter reached s = 1 dil. = 1 [1] 3.925904e+00 7.693240e-02 5.069889e+01 4.346861e+01 5.913179e+01 [6] 7.240135e-08 5.918522e-03 3.900387e+00 s = 2 dil. = 1 [1] 9.21034 Inf 10000.00000 NaN NaN NaN [7] NaN Inf s = 3 dil. = 1 [1] -1.3703174 Inf 0.2540263 NaN NaN NaN NaN [8] Inf s = 4 dil. = 1 [1] 0.225826082 1.278165386 1.253357664 0.097246655 16.153824829 [6] 0.001746149 1.631960605 1.601998383 s = 5 dil. = 1 [1] 9.21034 Inf 10000.00000 NaN NaN NaN [7] NaN Inf [1] "nCal 600" [1] "nCal 620" [1] "nCal 640" a = Test p = Run 1 gofs = 0.75 NA NA s = 1 dil. = 1 [1] 3.982961971 0.162938619 53.675785146 38.748216695 74.354129216 [6] 0.021924957 0.004624036 8.745858291 s = 2 dil. = 1 [1] 9.21034 Inf 10000.00000 NaN NaN NaN [7] NaN Inf s = 3 dil. = 1 [1] -1.3703174 Inf 0.2540263 NaN NaN NaN NaN [8] Inf s = 4 dil. = 1 [1] 0.13669414 1.67569493 1.14647744 0.04016755 32.72318995 2.36374821 [7] 0.44420528 1.92114643 s = 5 dil. = 1 [1] 9.21034 Inf 10000.00000 NaN NaN NaN [7] NaN Inf [1] "nCal 600" [1] "nCal 620" [1] "nCal 640" gofs = 0.99 0.961 0.738 gofs = 0.414 NA NA gofs = 0.391 NA NA gofs = 0.948 0.938 0.948 devs.tmp = 257 252 284 315 Iter 0. theta: 1119.571 23733.11 6.995483 3731.555 1.97059 g.hat: 1 deviance: 252.0762 gofs = 0.464 NA NA Iter 1. theta: 1138.656 23111.59 6.916057 3733.939 1.876568 g.hat: 1.311761 deviance: 251.3024 gofs = 0.479 NA NA Iter 2. theta: 1136.4 22946.91 6.908332 3747.649 1.808419 g.hat: 1.342599 deviance: 251.3181 dev increasing, stop and revert to previous fit gofs = 0.99 0.961 0.738 c d g h f 1075.846140 21520.444847 6.993643 4111.915451 1.017377 gofs = 0.99 0.961 0.738 gofs = 0.414 NA NA gofs = 0.391 NA NA gofs = 0.948 0.938 0.948 devs.tmp = 257 252 284 315 Iter 0. theta: 1119.571 23733.11 6.995483 3731.555 1.97059 g.hat: 1 deviance: 252.0762 gofs = 0.464 NA NA Iter 1. theta: 1138.656 23111.59 6.916057 3733.939 1.876568 g.hat: 1.311761 deviance: 251.3024 max iter reached Iter 1. theta: 1153.994 23114.08 6.84794 3704.095 2.180626 g.hat: 1.343335 deviance: 250.2805 Iter 2. theta: 1160.456 23115.67 6.839619 3693.42 2.226138 g.hat: 1.34563 deviance: 250.2472 Iter 3. theta: 1160.456 23115.67 6.839569 3693.42 2.226122 g.hat: 1.345633 deviance: 250.2472 converged done successfully. ------------------- UNIT TEST SUMMARY --------------------- RUNIT TEST PROTOCOL -- Mon Sep 13 17:13:35 2021 *********************************************** Number of test functions: 3 Number of errors: 1 Number of failures: 0 1 Test Suite : nCal unit testing - 3 test functions, 1 error, 0 failures ERROR in test.bcrm: Error in loadNamespace(name) : there is no package called 'coda' Error: unit testing failed (#test failures: 0, #R errors: 1) In addition: There were 26 warnings (use warnings() to see them) Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/data/gannet/ripley/R/packages/tests-Suggests/nCal.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 3:01.50, 166.74 + 12.64