CRAN Package Check Results for Package ctsemOMX

Last updated on 2021-01-08 11:48:50 CET.

Check Details

Version: 1.0.2
Check: Rd cross-references
Result: WARN
    Missing link or links in documentation object 'ctModelFromFit.Rd':
     'Kalman'
    
    See section 'Cross-references' in the 'Writing R Extensions' manual.
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-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64

Version: 1.0.2
Flags: --no-vignettes
Check: Rd cross-references
Result: WARN
    Missing link or links in documentation object 'ctModelFromFit.Rd':
     'Kalman'
    
    See section 'Cross-references' in the 'Writing R Extensions' manual.
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0.2
Check: examples
Result: ERROR
    Running examples in ‘ctsemOMX-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: ctGenerateFromFit
    > ### Title: Generates data according to the model estimated in a ctsemFit
    > ### object.
    > ### Aliases: ctGenerateFromFit
    >
    > ### ** Examples
    >
    >
    > data(AnomAuth)
    > AnomAuthmodel <- ctModel(LAMBDA = matrix(c(1, 0, 0, 1), nrow = 2, ncol = 2),
    + Tpoints = 5, n.latent = 2, n.manifest = 2, MANIFESTVAR=diag(0, 2))
    Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
    > AnomAuthfit <- ctFit(AnomAuth, AnomAuthmodel)
    wide format data detected
    Running ctsemCarefulFit with 14 parameters
    Running ctsem with 14 parameters
    
    Beginning initial fit attempt
    Running ctsem with 14 parameters
    
     *** caught segfault ***
    address 10000c, cause 'memory not mapped'
    
     *** caught segfault ***
    address 16453000, cause 'memory not mapped'
Flavor: r-patched-solaris-x86

Version: 1.0.2
Check: tests
Result: ERROR
     Running ‘testthat.R’ [24s/64s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(ctsemOMX)
     Loading required package: ctsem
     Loading required package: Rcpp
     ctsem also changes in time, for manual run ctDocs(), for blog see https://cdriver.netlify.app/, for citation info run citation('ctsem'), for original OpenMx functionality install.packages('ctsemOMX')
     Loading required package: OpenMx
     To take full advantage of multiple cores, use:
     mxOption(key='Number of Threads', value=parallel::detectCores()) #now
     Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx)
    
     Attaching package: 'ctsemOMX'
    
     The following objects are masked from 'package:ctsem':
    
     ctFit, ctIndplot
    
     > pdf(NULL)
     > test_check("ctsemOMX")
    
     *** caught segfault ***
     address 0, cause 'memory not mapped'
    
     Traceback:
     1: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer, beginMessage)
     2: mxRun(model = model, suppressWarnings = T, unsafe = T, silent = T, intervals = intervals, beginMessage = T)
     3: runWithCounter(model, numdone, silent, intervals = F)
     4: doTryCatch(return(expr), name, parentenv, handler)
     5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     6: tryCatchList(expr, classes, parentenv, handlers)
     7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
     8: try(runWithCounter(model, numdone, silent, intervals = F))
     9: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
     10: suppressWarnings(try(runWithCounter(model, numdone, silent, intervals = F)))
     11: mxTryHard(fit$mxobj, initialTolerance = 1e-14, initialGradientIterations = 1, showInits = FALSE, checkHess = TRUE, greenOK = FALSE, iterationSummary = FALSE, bestInitsOutput = FALSE, verbose = fit$ctfitargs$verbose, extraTries = fit$ctfitargs$retryattempts, loc = 1, scale = 0.1, paste = FALSE)
     12: ctRefineTo(dat = gd, m, retryattempts = 3, objective = "Kalman", stationary = c("T0MEANS", "T0VAR"), carefulFit = TRUE)
     13: eval(code, test_env)
     14: eval(code, test_env)
     15: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
     16: doTryCatch(return(expr), name, parentenv, handler)
     17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     18: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     19: doTryCatch(return(expr), name, parentenv, handler)
     20: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     21: tryCatchList(expr, classes, parentenv, handlers)
     22: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
     23: test_code(desc, code, env = parent.frame(), reporter = reporter)
     24: test_that("time calc", { set.seed(4) nsubjects = 20 TDPREDEFFECT = matrix(c(-20, 1, -1, 20), 2, 2) gm = ctModel(Tpoints = 10, n.latent = 2, n.manifest = 3, LAMBDA = matrix(c(1, 0, 0, 0, 1, 0.5), ncol = 2), DRIFT = matrix(c(-0.3, 0, 0, -0.05), 2, 2), DIFFUSION = diag(2, 2), CINT = matrix(c(5, 3), ncol = 1), TDPREDEFFECT = TDPREDEFFECT, TDPREDVAR = diag(0.002, 10 * 2), MANIFESTVAR = diag(0.3, 3), T0VAR = diag(2), n.TDpred = 2, TDPREDMEANS = matrix(rep(c(1, rep(0, 4), 0, rep(0, 4)), 2), ncol = 1)) gd = ctGenerate(gm, nsubjects, burnin = 50) m = ctModel(Tpoints = 10, n.latent = 2, n.manifest = 3, LAMBDA = matrix(c(1, 0, 0, 0, 1, 0.5), ncol = 2), DRIFT = matrix(c(-0.3, 0, 0, -0.05), 2, 2), TDPREDEFFECT = matrix(c("td1", 1, -1, 20), 2, 2), CINT = matrix(c(5, 3), ncol = 1), MANIFESTMEANS = matrix(c(0, 0, 0), ncol = 1), n.TDpred = 2) f1 = ctRefineTo(dat = gd, m, retryattempts = 3, objective = "Kalman", stationary = c("T0MEANS", "T0VAR"), carefulFit = TRUE) f2 = ctRefineTo(dat = gd, m, retryattempts = 3, objective = "mxRAM", stationary = c("T0MEANS", "T0VAR"), carefulFit = TRUE) expect_equal(f1$mxobj$output$estimate[-1], f2$mxobj$output$estimate[-1], tolerance = 0.001)})
     25: eval(code, test_env)
     26: eval(code, test_env)
     27: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
     28: doTryCatch(return(expr), name, parentenv, handler)
     29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     30: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     31: doTryCatch(return(expr), name, parentenv, handler)
     32: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     33: tryCatchList(expr, classes, parentenv, handlers)
     34: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
     35: test_code(NULL, exprs, env)
     36: source_file(path, child_env(env), wrap = wrap)
     37: FUN(X[[i]], ...)
     38: lapply(test_paths, test_one_file, env = env, wrap = wrap)
     39: force(code)
     40: doWithOneRestart(return(expr), restart)
     41: withOneRestart(expr, restarts[[1L]])
     42: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     43: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap))
     44: test_files(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package)
     45: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package, parallel = parallel)
     46: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
     47: test_check("ctsemOMX")
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 1.0.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘ctsem.rnw’ using knitr
    Observations with missing time information found - removing 1 rows
    Discrete time points created: 4
    Extracting first non-missing value for time independent predictors
    imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
    Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
    Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
    wide format data detected
    Running ctsemCarefulFit with 16 parameters
    Running ctsem with 16 parameters
    
    Beginning initial fit attempt
    Running ctsem with 16 parameters
    
     *** caught segfault ***
    address 5c, cause 'memory not mapped'
    
     *** caught segfault ***
    address 61264eb0, cause 'memory not mapped'
    Warning: stack imbalance in 'lazyLoadDBfetch', 63 then 56
    Quitting from lines 410-415 (ctsem.rnw)
    Error: processing vignette 'ctsem.rnw' failed with diagnostics:
    R_Reprotect: only 64 protected items, can't reprotect index 64
    --- failed re-building ‘ctsem.rnw’
    
    SUMMARY: processing the following file failed:
     ‘ctsem.rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.0.2
Check: for non-standard things in the check directory
Result: NOTE
    Found the following files/directories:
     ‘core’
Flavor: r-patched-solaris-x86

Version: 1.0.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘ctsem.rnw’ using knitr
    Observations with missing time information found - removing 1 rows
    Discrete time points created: 4
    Extracting first non-missing value for time independent predictors
    imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
    Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
    Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
    wide format data detected
    Running ctsemCarefulFit with 16 parameters
    Running ctsem with 16 parameters
    
    Beginning initial fit attempt
    Running ctsem with 16 parameters
    
     Lowest minimum so far: 4345.85436626721
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
     Not all eigenvalues of the Hessian are positive: 2265877167.45618, 858622.535865752, 174432.374425837, 106332.534634008, 2404.14338576438, 1515.26892105873, 753.957929903672, 422.941617599806, 337.304847207439, 81.3529720557753, 71.7746562810274, 0.270877616891719, 0.000990003447345578, 0.0000778436209684442, -0.000035198219867717, -141.434381947167
    
    Beginning fit attempt 1 of at maximum 5 extra tries
    Running ctsem with 16 parameters
    
     Lowest minimum so far: 4345.60004760687
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
     Not all eigenvalues of the Hessian are positive: 3354490876.29145, 1093934.98802932, 187673.884971439, 126959.941626984, 2424.15607707378, 1121.16759261386, 889.86154421705, 338.802563830431, 327.364644085503, 131.251443572662, 80.354787688875, 0.177615554581881, 0.000850405277234094, 0.0000352862941430477, -0.000234931837912, -60.4440819646513
    
    Beginning fit attempt 2 of at maximum 5 extra tries
    Running ctsem with 16 parameters
    
     Lowest minimum so far: 4344.92817213696
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
     Not all eigenvalues of the Hessian are positive: 12821437818.2582, 3997399.34344556, 490457.836528037, 325096.253015783, 2396.76518858563, 1522.09886943861, 670.107546833218, 384.188877072761, 336.76799528395, 81.3333621935671, 40.8078275639537, 25.4096092022785, 0.0335353726097448, 0.00230352964943181, -0.000927314217301221, -0.00225563653992078
    
    Beginning fit attempt 3 of at maximum 5 extra tries
    Running ctsem with 16 parameters
    
     Fit attempt worse than current best: 4599.21145593635 vs 4344.92817213696
    
    Beginning fit attempt 4 of at maximum 5 extra tries
    Running ctsem with 16 parameters
    
     Fit attempt worse than current best: 4364.34553579234 vs 4344.92817213696
    
    Beginning fit attempt 5 of at maximum 5 extra tries
    Running ctsem with 16 parameters
    
     Lowest minimum so far: 4190.79777582726
    
    Retry limit reached
    
    Solution found
    
    
     Solution found! Final fit=4190.7978 (started at 4727.4692) (6 attempt(s): 6 valid, 0 errors)
    
    wide format data detected
    Running ctsemCarefulFit with 15 parameters
    Running ctsem with 15 parameters
    
    Beginning initial fit attempt
    Running ctsem with 15 parameters
    
     Lowest minimum so far: 4196.73541494076
    
    Solution found
    
    
     Solution found! Final fit=4196.7354 (started at 4882.1499) (1 attempt(s): 1 valid, 0 errors)
    
    NPSOL optimizer not available - switching to CSOLNP - consider installing OpenMx using command: source('http://openmx.psyc.virginia.edu/getOpenMx.R')
    Running ctsem with 16 parameters
    Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
    wide format data detected
    Running ctsemCarefulFit with 19 parameters
    Running ctsem with 19 parameters
    
    Beginning initial fit attempt
    Running ctsem with 19 parameters
    
     Lowest minimum so far: 4151.13132113271
    
    Solution found
    
    
     Solution found! Final fit=4151.1313 (started at 4301.6568) (1 attempt(s): 1 valid, 0 errors)
    
    Plotting fit
    Plotting fit
    Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
    wide format data detected
    Running ctsemCarefulFit with 23 parameters
    Running ctsem with 23 parameters
    
    Beginning initial fit attempt
    Running ctsem with 23 parameters
    
     Lowest minimum so far: 4245.25700751421
    
    Solution found
    
    
     Solution found! Final fit=4245.257 (started at 4370.0907) (1 attempt(s): 1 valid, 0 errors)
    
    Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
    Some free parameters in matrices set to zero!
    Discrete time points created: 19
    imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
    Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
    Some free parameters in matrices set to zero!
    Discrete time points created: 19
    imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
    Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
    Some free parameters in matrices set to zero!
    Discrete time points created: 19
    imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
    Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
    Some free parameters in matrices set to zero!
    Discrete time points created: 19
    imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
    Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
    wide format data detected
    No missing time dependent predictors - TDPREDVAR and TDPREDMEANS fixed to observed moments for speed
    Running ctsemCarefulFit with 18 parameters
    Running ctsem with 18 parameters
    
    Beginning initial fit attempt
    Running ctsem with 18 parameters
    
     Lowest minimum so far: -461.763330928791
    
    Solution found
    
    
     Solution found! Final fit=-461.76333 (started at -404.21165) (1 attempt(s): 1 valid, 0 errors)
    
    Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
    wide format data detected
    No missing time dependent predictors - TDPREDVAR and TDPREDMEANS fixed to observed moments for speed
    transformedParams=TRUE and non positive DIFFUSION diagonal specified, setting to .00001.
    Running ctsemCarefulFit with 18 parameters
    Running ctsem with 18 parameters
    
    Beginning initial fit attempt
    Running ctsem with 18 parameters
    
     Lowest minimum so far: -456.192135641282
    
    Solution found
    
    
     Solution found! Final fit=-456.19214 (started at 91.449557) (1 attempt(s): 1 valid, 0 errors)
    
    Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
    wide format data detected
    Single subject dataset or Kalman objective specified - ignoring any specified between subject
     variance matrices (TRAITVAR, T0TRAITEFFECT,MANIFESTTRAITVAR, TIPREDEFFECT, TIPREDVAR, TDTIPREDCOV, T0TIPREDEFFECT)
    Running ctsemCarefulFit with 11 parameters
    Running ctsem with 11 parameters
    
    Beginning initial fit attempt
    Running ctsem with 11 parameters
    
     Lowest minimum so far: -138.198676577172
    
    Solution found
    
    
     Solution found! Final fit=-138.19868 (started at 670.38458) (1 attempt(s): 1 valid, 0 errors)
    
    Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
    Begin carefulFit start value estimation for group g1
    Begin carefulFit start value estimation for group g2
    Running ctsem multigroup with 13 parameters
    
    Beginning initial fit attempt
    Running ctsem multigroup with 13 parameters
    
     Lowest minimum so far: -109.136426537257
    
    Solution found
    
    
     Solution found! Final fit=-109.13643 (started at 6182.4813) (1 attempt(s): 1 valid, 0 errors)
    
    Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
    Some free parameters in matrices set to zero!
    Discrete time points created: 200
    imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
    Plotting rows 1,
    Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
    wide format data detected
    Single subject dataset or Kalman objective specified - ignoring any specified between subject
     variance matrices (TRAITVAR, T0TRAITEFFECT,MANIFESTTRAITVAR, TIPREDEFFECT, TIPREDVAR, TDTIPREDCOV, T0TIPREDEFFECT)
    transformedParams=TRUE and non positive DIFFUSION diagonal specified, setting to .00001.
    Running ctsemCarefulFit with 7 parameters
    Running ctsem with 7 parameters
    
    Beginning initial fit attempt
    Running ctsem with 7 parameters
    
     Lowest minimum so far: 750.518796542596
    
    Solution found
    
    
     Solution found! Final fit=750.5188 (started at 1246.0943) (1 attempt(s): 1 valid, 0 errors)
    
    Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
    wide format data detected
    transformedParams=TRUE and non positive DIFFUSION diagonal specified, setting to .00001.
    Running ctsem with 9 parameters
    
    Beginning initial fit attempt
    Running ctsem with 9 parameters
    
     Lowest minimum so far: -3462.15389492831
    
    Solution found
    
    
     Solution found! Final fit=-3462.1539 (started at -3145.5663) (1 attempt(s): 1 valid, 0 errors)
    
    wide format data detected
    Running ctsem with 16 parameters
    
    Beginning initial fit attempt
    Running ctsem with 16 parameters
    
    Solution found
    
    
     Solution found! Final fit=4190.7978 (started at 4190.7978) (1 attempt(s): 1 valid, 0 errors)
    
    Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
    wide format data detected
    Running ctsemCarefulFit with 19 parameters
    Running ctsem with 19 parameters
    
    Beginning initial fit attempt
    Running ctsem with 19 parameters
    
     Lowest minimum so far: 4151.13132113271
    
    Solution found
    
    
     Solution found! Final fit=4151.1313 (started at 4301.6569) (1 attempt(s): 1 valid, 0 errors)
    
    NPSOL optimizer not available - switching to CSOLNP - consider installing OpenMx using command: source('http://openmx.psyc.virginia.edu/getOpenMx.R')
    Running ctsem with 19 parameters
    wide format data detected
    Running ctsemCarefulFit with 19 parameters
    Running ctsem with 19 parameters
    
    Beginning initial fit attempt
    Running ctsem with 19 parameters
    
     Lowest minimum so far: 4203.31303537745
    
    Solution found
    
    
     Solution found! Final fit=4203.313 (started at 4349.5531) (1 attempt(s): 1 valid, 0 errors)
    
    NPSOL optimizer not available - switching to CSOLNP - consider installing OpenMx using command: source('http://openmx.psyc.virginia.edu/getOpenMx.R')
    Running ctsem with 19 parameters
    Error: processing vignette 'ctsem.rnw' failed with diagnostics:
    Running ‘texi2dvi’ on ‘ctsem.tex’ failed.
    LaTeX errors:
    ! Undefined control sequence.
    \hyper@linkurl ...tionraw >>}\relax \Hy@colorlink
     \@urlcolor #1\Hy@xspace@en...
    l.130 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.130 \begin{document}
    
    ! Undefined control sequence.
    \hyper@linkurl ...tionraw >>}\relax \Hy@colorlink
     \@urlcolor #1\Hy@xspace@en...
    l.130 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.130 \begin{document}
    
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.130 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.130 \begin{document}
    
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.130 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.130 \begin{document}
    
    --- failed re-building ‘ctsem.rnw’
    
    SUMMARY: processing the following file failed:
     ‘ctsem.rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-linux-x86_64