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### Running command:
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### /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('HilbertVisGUI_1.71.0.tar.gz','quit-with-status'=TRUE)"
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── Installing HilbertVisGUI ────────────────────────────────────────────────────
✔ Package installed successfully
── HilbertVisGUI session metadata ──────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp1mozCt/fileb09912aca5aa2/HilbertVisGUI
→ BiocVersion: 3.24
→ Package: HilbertVisGUI
→ PackageVersion: 1.71.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/HilbertVisGUI.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp1mozCt/fileb09912aca5aa2/HilbertVisGUI
→ installDir: /tmp/Rtmp1mozCt/fileb09912018a311
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on HilbertVisGUI ──────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 2.6.0 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (100%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
Rnw vignette(s) found:
• HilbertVisGUI.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/HilbertVisGUI.Rnw
* Checking package installation calls in R code...
* Checking for library/require of HilbertVisGUI...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
Found in files:
• R/HilbertCurveDisplay.R (line 47, column 16)
• R/HilbertCurveDisplay.R (line 58, column 22)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/loadLib.R (line 28, column 7)
• ...
• cat() in R/loadLib.R (line 78, column 4)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
Found in files:
• loadLib.R (line 10, column 19)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 4 times)
• <<- in R/loadLib.R (line 9, column 8)
• ...
• <<- in R/loadLib.R (line 15, column 33)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 2
functions greater than 50 lines.
The longest 5 functions are:
• failedToLoadDLL() (R/loadLib.R): 63 lines
• hilbertDisplay() (R/HilbertCurveDisplay.R): 57 lines
* Checking man page documentation...
| Cannot connect to an X display. Most functionality of
| HilbertVisGUI will be unavailable. Make sure that the DISPLAY
| environment variable is set properly.
Warning in dyn.load(file, DLLpath = DLLpath, ...) :
Cannot connect to X display.
*** caught segfault ***
address 0x10, cause 'memory not mapped'
Traceback:
1: dyn.unload(file)
2: library.dynam.unload(dll[["name"]], libpath)
3: fun(...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(fun(...), error = identity)
8: runHook(".onUnload", ns, nspath)
9: unloadNamespace(pkg_ns)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: 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, nlines = 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))})
14: try(unloadNamespace(pkg_ns), silent = TRUE)
15: checkExportsAreDocumented(.BiocPackage, lib.loc = libloc)
16: checkManDocumentation(.BiocPackage, libloc)
17: BiocCheckRun(package = package, checkDir = checkDir, debug = debug, ...)
18: BiocCheck::BiocCheck("HilbertVisGUI_1.71.0.tar.gz", `quit-with-status` = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
