From ff1b9855a0563744bc6188d0588b230da6a57b0e Mon Sep 17 00:00:00 2001 From: Jim Hester Date: Thu, 20 Apr 2017 11:06:04 -0400 Subject: [PATCH] Update revdep results --- revdep/README.md | 291 ++++++++++++++++++++++++++++++ revdep/check.R | 6 +- revdep/checks.rds | Bin 0 -> 4933 bytes revdep/problems.md | 154 ++++++++++++++++ revdep/summary.md | 438 --------------------------------------------- revdep/timing.md | 27 +++ 6 files changed, 475 insertions(+), 441 deletions(-) create mode 100644 revdep/README.md create mode 100644 revdep/checks.rds create mode 100644 revdep/problems.md delete mode 100644 revdep/summary.md create mode 100644 revdep/timing.md diff --git a/revdep/README.md b/revdep/README.md new file mode 100644 index 0000000..e7203b1 --- /dev/null +++ b/revdep/README.md @@ -0,0 +1,291 @@ +# Setup + +## Platform + +|setting |value | +|:--------|:--------------------------------------| +|version |R version 3.3.2 RC (2016-10-26 r71594) | +|system |x86_64, darwin13.4.0 | +|ui |X11 | +|language |(EN) | +|collate |en_US.UTF-8 | +|tz |America/New_York | +|date |2017-04-20 | + +## Packages + +|package |* |version |date |source | +|:--------|:--|:----------|:----------|:--------------------------------| +|aws.s3 | |0.2.2 |2017-04-20 |Github (cloudyr/aws.s3@305e9da) | +|covr | |2.2.2 |2017-04-20 |Github (jimhester/covr@accef86) | +|digest | |0.6.12 |2017-01-27 |cran (@0.6.12) | +|httr | |1.2.1 |2016-07-03 |cran (@1.2.1) | +|memoise | |1.0.0 |2016-01-29 |cran (@1.0.0) | +|testthat | |1.0.2.9000 |2017-03-03 |Github (hadley/testthat@b72a228) | + +# Check results + +21 packages + +|package |version | errors| warnings| notes| +|:--------------|:-------|------:|--------:|-----:| +|biolink |0.1.2 | 1| 0| 0| +|BWStest |0.2.1 | 0| 0| 0| +|covr |2.2.2 | 0| 0| 0| +|devtools |1.12.0 | 0| 0| 0| +|functools |0.2.0 | 0| 0| 0| +|GSED |1.3 | 0| 0| 0| +|gWidgets2RGtk2 |1.0-5 | 1| 0| 0| +|gWidgets2tcltk |1.0-5 | 1| 0| 0| +|heemod |0.9.0 | 0| 0| 0| +|icd9 |1.3.1 | 0| 0| 1| +|opencage |0.1.0 | 0| 0| 0| +|OpenML |1.3 | 0| 0| 0| +|prcbench |0.7.3 | 0| 0| 1| +|regioneR |1.6.2 | 0| 1| 4| +|rgho |1.0.1 | 0| 0| 0| +|RSQLite |1.1-2 | 0| 0| 0| +|saeRobust |0.1.0 | 0| 0| 0| +|SamplingStrata |1.1 | 0| 0| 0| +|SIDES |1.10 | 0| 0| 0| +|surveillance |1.13.0 | 0| 0| 2| +|toaster |0.5.5 | 0| 0| 0| + +## biolink (0.1.2) +Maintainer: Aaron Wolen + +1 error | 0 warnings | 0 notes + +``` +checking tests ... ERROR +Running the tests in ‘tests/testthat.R’ failed. +Last 13 lines of output: + }) at /private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmpbeCFhk/devtools231b7fa9df2a/lintr/R/object_usage_linter.R:28 + 18: FUN(X[[i]], ...) + 19: codetools::findFuncLocals(formals(fun), body(fun)) at /private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmpbeCFhk/devtools231b7fa9df2a/lintr/R/object_usage_linter.R:53 + 20: findLocalsList(c(list(body), dropMissings(formals))) + 21: body(fun) + 22: get(fun, mode = "function", envir = parent.frame()) + + testthat results ================================================================ + OK: 138 SKIPPED: 0 FAILED: 1 + 1. Error: Package Style (@test-style.r#4) + + Error: testthat unit tests failed + Execution halted +``` + +## BWStest (0.2.1) +Maintainer: Steven E. Pav +Bug reports: https://github.com/shabbychef/BWStest/issues + +0 errors | 0 warnings | 0 notes + +## covr (2.2.2) +Maintainer: Jim Hester +Bug reports: https://github.com/jimhester/covr/issues + +0 errors | 0 warnings | 0 notes + +## devtools (1.12.0) +Maintainer: Hadley Wickham +Bug reports: https://github.com/hadley/devtools/issues + +0 errors | 0 warnings | 0 notes + +## functools (0.2.0) +Maintainer: Paul Hendricks +Bug reports: https://github.com/paulhendricks/functools/issues + +0 errors | 0 warnings | 0 notes + +## GSED (1.3) +Maintainer: Marie-Karelle Riviere + +0 errors | 0 warnings | 0 notes + +## gWidgets2RGtk2 (1.0-5) +Maintainer: John Verzani + +1 error | 0 warnings | 0 notes + +``` +checking package dependencies ... ERROR +Package required but not available: ‘RGtk2’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +``` + +## gWidgets2tcltk (1.0-5) +Maintainer: John Verzani + +1 error | 0 warnings | 0 notes + +``` +checking whether package ‘gWidgets2tcltk’ can be installed ... ERROR +Installation failed. +See ‘/Users/jhester/Dropbox/projects/memoise/revdep/checks/gWidgets2tcltk.Rcheck/00install.out’ for details. +``` + +## heemod (0.9.0) +Maintainer: Antoine Filipovic-Pierucci +Bug reports: https://github.com/pierucci/heemod/issues + +0 errors | 0 warnings | 0 notes + +## icd9 (1.3.1) +Maintainer: Jack O. Wasey +Bug reports: https://github.com/jackwasey/icd9/issues + +0 errors | 0 warnings | 1 note + +``` +checking dependencies in R code ... NOTE +Missing or unexported object: ‘devtools::load_data’ +``` + +## opencage (0.1.0) +Maintainer: Maëlle Salmon +Bug reports: http://github.com/ropenscilabs/opencage/issues + +0 errors | 0 warnings | 0 notes + +## OpenML (1.3) +Maintainer: Giuseppe Casalicchio +Bug reports: https://github.com/openml/openml-r/issues + +0 errors | 0 warnings | 0 notes + +## prcbench (0.7.3) +Maintainer: Takaya Saito +Bug reports: https://github.com/takayasaito/prcbench/issues + +0 errors | 0 warnings | 1 note + +``` +checking package dependencies ... NOTE +Package suggested but not available for checking: ‘PerfMeas’ +``` + +## regioneR (1.6.2) +Maintainer: Bernat Gel + +0 errors | 1 warning | 4 notes + +``` +checking whether package ‘regioneR’ can be installed ... WARNING +Found the following significant warnings: + Warning: package ‘S4Vectors’ was built under R version 3.3.3 + Warning: package ‘IRanges’ was built under R version 3.3.3 +See ‘/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00install.out’ for details. + +checking DESCRIPTION meta-information ... NOTE +Packages listed in more than one of Depends, Imports, Suggests, Enhances: + ‘memoise’ ‘GenomicRanges’ ‘BSgenome’ ‘rtracklayer’ ‘parallel’ +A package should be listed in only one of these fields. + +checking S3 generic/method consistency ... NOTE +Found the following apparent S3 methods exported but not registered: + print.permTestResults +See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ +manual. + +checking R code for possible problems ... NOTE +commonRegions: no visible global function definition for ‘hasArg’ + (/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/commonRegions.R:38) +commonRegions: no visible global function definition for ‘hasArg’ + (/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/commonRegions.R:39) +createFunctionsList: no visible global function definition for ‘hasArg’ + (/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/createFunctionsList.R:47) +createFunctionsList: no visible global function definition for ‘hasArg’ + (/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/createFunctionsList.R:48) +createFunctionsList: no visible global function definition for ‘hasArg’ +... 109 lines ... +uniqueRegions: no visible global function definition for ‘hasArg’ + (/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/uniqueRegions.R:37) +uniqueRegions: no visible global function definition for ‘hasArg’ + (/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/uniqueRegions.R:38) +Undefined global functions or variables: + hasArg is queryHits read.csv read.delim subjectHits +Consider adding + importFrom("methods", "hasArg", "is") + importFrom("utils", "read.csv", "read.delim") +to your NAMESPACE file (and ensure that your DESCRIPTION Imports field +contains 'methods'). + +checking Rd line widths ... NOTE +Rd file 'circularRandomizeRegions.Rd': + \usage lines wider than 90 characters: + circularRandomizeRegions(A, genome="hg19", mask=NULL, max.mask.overlap=NULL, max.retries=10, verbose=TRUE, ...) + +Rd file 'commonRegions.Rd': + \examples lines wider than 100 characters: + plotRegions(list(A, B, commons), chromosome="chr1", regions.labels=c("A", "B", "common"), regions.colors=3:1) + +Rd file 'createFunctionsList.Rd': +... 95 lines ... + plotRegions(list(A, B, splits), chromosome=1, regions.labels=c("A", "B", "splits"), regions.colors=3:1) + +Rd file 'subtractRegions.Rd': + \examples lines wider than 100 characters: + plotRegions(list(A, B, subtract), chromosome=1, regions.labels=c("A", "B", "subtract"), regions.colors=3:1) + +Rd file 'uniqueRegions.Rd': + \examples lines wider than 100 characters: + plotRegions(list(A, B, uniques), chromosome="chr1", regions.labels=c("A", "B", "uniques"), regions.colors=3:1) + +These lines will be truncated in the PDF manual. +``` + +## rgho (1.0.1) +Maintainer: Antoine Filipovic-Pierucci +Bug reports: https://github.com/pierucci/rgho/issues + +0 errors | 0 warnings | 0 notes + +## RSQLite (1.1-2) +Maintainer: Kirill Müller +Bug reports: https://github.com/rstats-db/RSQLite/issues + +0 errors | 0 warnings | 0 notes + +## saeRobust (0.1.0) +Maintainer: Sebastian Warnholz +Bug reports: https://github.com/wahani/saeRobust/issues + +0 errors | 0 warnings | 0 notes + +## SamplingStrata (1.1) +Maintainer: Giulio Barcaroli + +0 errors | 0 warnings | 0 notes + +## SIDES (1.10) +Maintainer: Marie-Karelle Riviere + +0 errors | 0 warnings | 0 notes + +## surveillance (1.13.0) +Maintainer: Sebastian Meyer +Bug reports: https://r-forge.r-project.org/tracker/?group_id=45 + +0 errors | 0 warnings | 2 notes + +``` +checking package dependencies ... NOTE +Package suggested but not available for checking: ‘INLA’ + +checking installed package size ... NOTE + installed size is 9.6Mb + sub-directories of 1Mb or more: + R 4.2Mb + doc 2.3Mb +``` + +## toaster (0.5.5) +Maintainer: Gregory Kanevsky +Bug reports: https://github.com/teradata-aster-field/toaster/issues + +0 errors | 0 warnings | 0 notes + diff --git a/revdep/check.R b/revdep/check.R index f62f397..bca914d 100644 --- a/revdep/check.R +++ b/revdep/check.R @@ -1,5 +1,5 @@ library("devtools") -res <- revdep_check(bioconductor = TRUE, threads = 4) -revdep_check_save_summary(res) -revdep_check_save_logs(res) +revdep_check_resume(bioconductor = TRUE) +revdep_check_save_summary() +revdep_check_print_problems() diff --git a/revdep/checks.rds b/revdep/checks.rds new file mode 100644 index 0000000000000000000000000000000000000000..da31d5dba2a3979495e9d003df8b5e01374accb2 GIT binary patch literal 4933 zcmV-L6T0jliwFP!000001MOYQa~sKd=Zbpl(pi^N&K^>(R66w9B6o=a2H+D#I-n$y z%N0q{fMl(+-q4Mi1~B40;O-evR4P@vB!5FT|3NCJRBkEXe9YsLQ%1qfnE#Ps|3b^rS7?`t%BzL=Ssnz}JHJ$+;9#xy?u5Psc+|G%G_n#Sil 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ze5|!-kh92?qeX@nT42>MjTcn+qLEXSw}wL3|9P8xLHEcqHx`#NHT;1Hc#na-gkE_j z4PTE}Nh~G1TJyGw79$g*9zaitnWARj4NLD8alFd>CG-`Wm$p{(=*_AS*z?fuYL+W zx!^*Z7}Cj{Nu?cdqdk5~9#WU}#PKOvZ-+73v5Kidhf?`|@f<&LIqxcRmA^o7EDG{4 zaMAZCd>B3~h+nv7r4p>nF%DyY=>f_xQ@cA8R~ zAQ_)_z$3}GNmJHH-oi34A+jBOvp-xo9x + +1 error | 0 warnings | 0 notes + +``` +checking tests ... ERROR +Running the tests in ‘tests/testthat.R’ failed. +Last 13 lines of output: + }) at /private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmpbeCFhk/devtools231b7fa9df2a/lintr/R/object_usage_linter.R:28 + 18: FUN(X[[i]], ...) + 19: codetools::findFuncLocals(formals(fun), body(fun)) at /private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmpbeCFhk/devtools231b7fa9df2a/lintr/R/object_usage_linter.R:53 + 20: findLocalsList(c(list(body), dropMissings(formals))) + 21: body(fun) + 22: get(fun, mode = "function", envir = parent.frame()) + + testthat results ================================================================ + OK: 138 SKIPPED: 0 FAILED: 1 + 1. Error: Package Style (@test-style.r#4) + + Error: testthat unit tests failed + Execution halted +``` + +## gWidgets2RGtk2 (1.0-5) +Maintainer: John Verzani + +1 error | 0 warnings | 0 notes + +``` +checking package dependencies ... ERROR +Package required but not available: ‘RGtk2’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +``` + +## gWidgets2tcltk (1.0-5) +Maintainer: John Verzani + +1 error | 0 warnings | 0 notes + +``` +checking whether package ‘gWidgets2tcltk’ can be installed ... ERROR +Installation failed. +See ‘/Users/jhester/Dropbox/projects/memoise/revdep/checks/gWidgets2tcltk.Rcheck/00install.out’ for details. +``` + +## regioneR (1.6.2) +Maintainer: Bernat Gel + +0 errors | 1 warning | 4 notes + +``` +checking whether package ‘regioneR’ can be installed ... WARNING +Found the following significant warnings: + Warning: package ‘S4Vectors’ was built under R version 3.3.3 + Warning: package ‘IRanges’ was built under R version 3.3.3 +See ‘/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00install.out’ for details. + +checking DESCRIPTION meta-information ... NOTE +Packages listed in more than one of Depends, Imports, Suggests, Enhances: + ‘memoise’ ‘GenomicRanges’ ‘BSgenome’ ‘rtracklayer’ ‘parallel’ +A package should be listed in only one of these fields. + +checking S3 generic/method consistency ... NOTE +Found the following apparent S3 methods exported but not registered: + print.permTestResults +See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ +manual. + +checking R code for possible problems ... NOTE +commonRegions: no visible global function definition for ‘hasArg’ + (/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/commonRegions.R:38) +commonRegions: no visible global function definition for ‘hasArg’ + (/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/commonRegions.R:39) +createFunctionsList: no visible global function definition for ‘hasArg’ + (/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/createFunctionsList.R:47) +createFunctionsList: no visible global function definition for ‘hasArg’ + (/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/createFunctionsList.R:48) +createFunctionsList: no visible global function definition for ‘hasArg’ +... 109 lines ... +uniqueRegions: no visible global function definition for ‘hasArg’ + (/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/uniqueRegions.R:37) +uniqueRegions: no visible global function definition for ‘hasArg’ + (/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/uniqueRegions.R:38) +Undefined global functions or variables: + hasArg is queryHits read.csv read.delim subjectHits +Consider adding + importFrom("methods", "hasArg", "is") + importFrom("utils", "read.csv", "read.delim") +to your NAMESPACE file (and ensure that your DESCRIPTION Imports field +contains 'methods'). + +checking Rd line widths ... NOTE +Rd file 'circularRandomizeRegions.Rd': + \usage lines wider than 90 characters: + circularRandomizeRegions(A, genome="hg19", mask=NULL, max.mask.overlap=NULL, max.retries=10, verbose=TRUE, ...) + +Rd file 'commonRegions.Rd': + \examples lines wider than 100 characters: + plotRegions(list(A, B, commons), chromosome="chr1", regions.labels=c("A", "B", "common"), regions.colors=3:1) + +Rd file 'createFunctionsList.Rd': +... 95 lines ... + plotRegions(list(A, B, splits), chromosome=1, regions.labels=c("A", "B", "splits"), regions.colors=3:1) + +Rd file 'subtractRegions.Rd': + \examples lines wider than 100 characters: + plotRegions(list(A, B, subtract), chromosome=1, regions.labels=c("A", "B", "subtract"), regions.colors=3:1) + +Rd file 'uniqueRegions.Rd': + \examples lines wider than 100 characters: + plotRegions(list(A, B, uniques), chromosome="chr1", regions.labels=c("A", "B", "uniques"), regions.colors=3:1) + +These lines will be truncated in the PDF manual. +``` + diff --git a/revdep/summary.md b/revdep/summary.md deleted file mode 100644 index fc0e229..0000000 --- a/revdep/summary.md +++ /dev/null @@ -1,438 +0,0 @@ -# Setup - -## Platform - -|setting |value | -|:--------|:----------------------------| -|version |R version 3.2.3 (2015-12-10) | -|system |x86_64, darwin15.2.0 | -|ui |unknown | -|language |(EN) | -|collate |en_US.UTF-8 | -|tz |America/New_York | -|date |2016-01-28 | - -## Packages - -|package | * |version |date |source | * | -|:-------|:--|:-------|:----|:------|:--| - -# Check results -11 checked out of 11 dependencies - -## crayon (1.3.1) -Maintainer: Gabor Csardi -Bug reports: https://github.com/gaborcsardi/crayon/issues - -__OK__ - -## devtools (1.10.0) -Maintainer: Hadley Wickham -Bug reports: https://github.com/hadley/devtools/issues - -``` -checking foreign function calls ... NOTE -Registration problem: - Evaluating ‘dll$foo’ during check gives error -‘object 'dll' not found’: - .C(dll$foo, 0L) -See chapter ‘System and foreign language interfaces’ in the ‘Writing R -Extensions’ manual. -``` -``` -checking R code for possible problems ... NOTE -Found the following calls to attach(): -File ‘devtools/R/package-env.r’: - attach(NULL, name = pkg_env_name(pkg)) -File ‘devtools/R/shims.r’: - attach(e, name = "devtools_shims", warn.conflicts = FALSE) -See section ‘Good practice’ in ‘?attach’. -``` -``` -DONE -Status: 2 NOTEs -``` - -## functools (0.2.0) -Maintainer: Paul Hendricks -Bug reports: https://github.com/paulhendricks/functools/issues - -__OK__ - -## gWidgets2RGtk2 (1.0-3) -Maintainer: John Verzani - -``` -checking tests ... ERROR -Running the tests in ‘tests/run-tests.R’ failed. -Last 13 lines of output: - 7: methods::new(def, ...) - 8: GSlider$new(toolkit, from, to, by, value, horizontal, handler, action, container, ...) - 9: .gslider.guiWidgetsToolkitRGtk2(toolkit, from, to, by, value, horizontal, handler, action, container = container, ...) - 10: .gslider(toolkit, from, to, by, value, horizontal, handler, action, container = container, ...) - 11: gslider(from = 0, to = 100, by = 1, cont = g) - 12: eval(expr, envir, enclos) - 13: eval(ei, envir) - 14: withVisible(eval(ei, envir)) - 15: source(i) - 16: FUN(X[[i]], ...) - 17: lapply(X = X, FUN = FUN, ...) - 18: sapply(f, function(i) { message("testing ", i) source(i)}) - aborting ... -``` -``` -DONE -Status: 1 ERROR -``` - -## gWidgets2tcltk (1.0-4) -Maintainer: John Verzani - -__OK__ - -## icd9 (1.3) -Maintainer: Jack O. Wasey -Bug reports: https://github.com/jackwasey/icd9/issues - -``` -checking data for non-ASCII characters ... NOTE - Note: found 14 marked Latin-1 strings - Note: found 39 marked UTF-8 strings -``` -``` -DONE -Status: 1 NOTE -``` - -## ltmle (0.9-6) -Maintainer: Joshua Schwab -Bug reports: https://github.com/joshuaschwab/ltmle/issues - -__OK__ - -## regioneR (1.2.0) -Maintainer: Bernat Gel - -``` -checking DESCRIPTION meta-information ... NOTE -Packages listed in more than one of Depends, Imports, Suggests, Enhances: - ‘memoise’ ‘GenomicRanges’ ‘BSgenome’ ‘rtracklayer’ ‘parallel’ -A package should be listed in only one of these fields. -``` -``` -checking S3 generic/method consistency ... NOTE -Found the following apparent S3 methods exported but not registered: - print.permTestResults -See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ -manual. -``` -``` -checking R code for possible problems ... NOTE -copySeqLevels: no visible global function definition for ‘seqlevels<-’ - (/private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmprZ8p6a/check_cran12ff25dce9dcf/regioneR.Rcheck/00_pkg_src/regioneR/R/randomizeRegions.R:350) -copySeqLevels: no visible global function definition for ‘seqlevels’ - (/private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmprZ8p6a/check_cran12ff25dce9dcf/regioneR.Rcheck/00_pkg_src/regioneR/R/randomizeRegions.R:350) -copySeqLevels: no visible global function definition for ‘seqlevels’ - (/private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmprZ8p6a/check_cran12ff25dce9dcf/regioneR.Rcheck/00_pkg_src/regioneR/R/randomizeRegions.R:351) -createRandomRegions: no visible global function definition for - ‘seqlevels’ - (/private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmprZ8p6a/check_cran12ff25dce9dcf/regioneR.Rcheck/00_pkg_src/regioneR/R/createRandomRegions.R:50) -filterChromosomes: no visible global function definition for - ‘keepSeqlevels’ - (/private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmprZ8p6a/check_cran12ff25dce9dcf/regioneR.Rcheck/00_pkg_src/regioneR/R/filterChromosomes.R:53) -randomizeRegions: no visible global function definition for ‘seqlevels’ - (/private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmprZ8p6a/check_cran12ff25dce9dcf/regioneR.Rcheck/00_pkg_src/regioneR/R/randomizeRegions.R:75-83) -randomizeRegions: no visible global function definition for ‘IRanges’ - (/private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmprZ8p6a/check_cran12ff25dce9dcf/regioneR.Rcheck/00_pkg_src/regioneR/R/randomizeRegions.R:113) -resampleRegions: no visible global function definition for ‘seqlevels’ - (/private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmprZ8p6a/check_cran12ff25dce9dcf/regioneR.Rcheck/00_pkg_src/regioneR/R/resampleRegions.R:49) -toGRanges: no visible global function definition for ‘IRanges’ - (/private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmprZ8p6a/check_cran12ff25dce9dcf/regioneR.Rcheck/00_pkg_src/regioneR/R/toGRanges.R:128) -``` -``` -checking Rd line widths ... NOTE -Rd file 'circularRandomizeRegions.Rd': - \usage lines wider than 90 characters: - circularRandomizeRegions(A, genome="hg19", mask=NULL, max.mask.overlap=NULL, max.retries=10, verbose=TRUE, ...) - -Rd file 'commonRegions.Rd': - \examples lines wider than 100 characters: - plotRegions(list(A, B, commons), chromosome="chr1", regions.labels=c("A", "B", "common"), regions.colors=3:1) - -Rd file 'createFunctionsList.Rd': - \examples lines wider than 100 characters: - funcs <- createFunctionsList(FUN=f, param.name="b", values=c(1,2,3), func.names=c("plusone", "plustwo", "plusthree")) - -Rd file 'createRandomRegions.Rd': - \usage lines wider than 90 characters: - createRandomRegions(nregions=100, length.mean=250, length.sd=20, genome="hg19", mask=NULL, non.overlapping=TRUE) - -Rd file 'extendRegions.Rd': - \examples lines wider than 100 characters: - plotRegions(list(A, extend1, extend2, extend3), chromosome="chr1", regions.labels=c("A", "extend1", "extend2", "extend3"), regions.colo ... [TRUNCATED] - -Rd file 'joinRegions.Rd': - \examples lines wider than 100 characters: - plotRegions(list(A, join1, join2, join3), chromosome="chr1", regions.labels=c("A", "join1", "join2", "join3"), regions.colors=4:1) - -Rd file 'localZScore.Rd': - \examples lines wider than 100 characters: - A <- createRandomRegions(nregions=20, length.mean=10000, length.sd=20000, genome=genome, non.overlapping=FALSE) - B <- c(A, createRandomRegions(nregions=10, length.mean=10000, length.sd=20000, genome=genome, non.overlapping=FALSE)) - pt2 <- permTest(A=A, B=B, ntimes=10, randomize.function=randomizeRegions, evaluate.function=list(overlap=numOverlaps, distance=meanDist ... [TRUNCATED] - -Rd file 'mergeRegions.Rd': - \examples lines wider than 100 characters: - plotRegions(list(A, B, merges), chromosome="chr1", regions.labels=c("A", "B", "merges"), regions.colors=3:1) - -Rd file 'numOverlaps.Rd': - \examples lines wider than 100 characters: - A <- createRandomRegions(nregions=20, length.mean=10000000, length.sd=20000, genome=genome, non.overlapping=FALSE) - B <- c(A, createRandomRegions(nregions=10, length.mean=10000, length.sd=20000, genome=genome, non.overlapping=FALSE)) - -Rd file 'overlapGraphicalSummary.Rd': - \usage lines wider than 90 characters: - overlapGraphicalSummary(A, B, regions.labels=c("A","B"), regions.colors=c("black","forestgreen","darkred"), ...) - -Rd file 'overlapPermTest.Rd': - \examples lines wider than 100 characters: - A <- createRandomRegions(nregions=20, length.mean=10000000, length.sd=20000, genome=genome, non.overlapping=FALSE) - B <- c(A, createRandomRegions(nregions=10, length.mean=10000, length.sd=20000, genome=genome, non.overlapping=FALSE)) - -Rd file 'overlapRegions.Rd': - \usage lines wider than 90 characters: - overlapRegions(A, B, colA=NULL, colB=NULL, type="any", min.bases=1, min.pctA=NULL, min.pctB=NULL, get.pctA=FALSE, get.pctB=FALSE, get.b ... [TRUNCATED] - -Rd file 'permTest.Rd': - \usage lines wider than 90 characters: - permTest(A, ntimes=100, randomize.function, evaluate.function, alternative="auto", min.parallel=1000, force.parallel=NULL, randomize.fu ... [TRUNCATED] - \examples lines wider than 100 characters: - A <- createRandomRegions(nregions=20, length.mean=10000000, length.sd=20000, genome=genome, non.overlapping=FALSE) - B <- c(A, createRandomRegions(nregions=10, length.mean=10000, length.sd=20000, genome=genome, non.overlapping=FALSE)) - pt2 <- permTest(A=A, B=B, ntimes=10, alternative="auto", verbose=TRUE, genome=genome, evaluate.function=meanDistance, randomize.functio ... [TRUNCATED] - -Rd file 'plot.localZScoreResults.Rd': - \examples lines wider than 100 characters: - A <- createRandomRegions(nregions=20, length.mean=10000000, length.sd=20000, genome=genome, non.overlapping=FALSE) - B <- c(A, createRandomRegions(nregions=10, length.mean=100000, length.sd=20000, genome=genome, non.overlapping=FALSE)) - -Rd file 'plot.localZScoreResultsList.Rd': - \examples lines wider than 100 characters: - A <- createRandomRegions(nregions=20, length.mean=10000000, length.sd=20000, genome=genome, non.overlapping=FALSE) - B <- c(A, createRandomRegions(nregions=10, length.mean=100000, length.sd=20000, genome=genome, non.overlapping=FALSE)) - pt2 <- permTest(A=A, B=B, ntimes=10, randomize.function=randomizeRegions, evaluate.function=list(overlap=numOverlaps, distance=meanDist ... [TRUNCATED] - -Rd file 'plot.permTestResults.Rd': - \examples lines wider than 100 characters: - A <- createRandomRegions(nregions=20, length.mean=10000000, length.sd=20000, genome=genome, non.overlapping=FALSE) - B <- c(A, createRandomRegions(nregions=10, length.mean=10000, length.sd=20000, genome=genome, non.overlapping=FALSE)) - pt2 <- permTest(A=A, B=B, ntimes=10, alternative="auto", genome=genome, evaluate.function=meanDistance, randomize.function=randomizeReg ... [TRUNCATED] - -Rd file 'plot.permTestResultsList.Rd': - \examples lines wider than 100 characters: - A <- createRandomRegions(nregions=20, length.mean=10000000, length.sd=20000, genome=genome, non.overlapping=FALSE) - B <- c(A, createRandomRegions(nregions=10, length.mean=10000, length.sd=20000, genome=genome, non.overlapping=FALSE)) - pt2 <- permTest(A=A, B=B, ntimes=10, alternative="auto", genome=genome, evaluate.function=list(distance=meanDistance, numberOfOverlaps= ... [TRUNCATED] - -Rd file 'plotRegions.Rd': - \usage lines wider than 90 characters: - plotRegions(x, chromosome, start=NULL, end=NULL, regions.labels=NULL, regions.colors=NULL, ...) - -Rd file 'print.permTestResults.Rd': - \examples lines wider than 100 characters: - A <- createRandomRegions(nregions=20, length.mean=10000000, length.sd=20000, genome=genome, non.overlapping=FALSE) - B <- c(A, createRandomRegions(nregions=10, length.mean=10000, length.sd=20000, genome=genome, non.overlapping=FALSE)) - pt <- permTest(A=A, B=B, ntimes=10, alternative="auto", verbose=TRUE, genome=genome, evaluate.function=meanDistance, randomize.function ... [TRUNCATED] - -Rd file 'randomizeRegions.Rd': - \usage lines wider than 90 characters: - randomizeRegions(A, genome="hg19", mask=NULL, allow.overlaps=TRUE, per.chromosome=FALSE, ...) - -Rd file 'recomputePermTest.Rd': - \examples lines wider than 100 characters: - resPerm <- permTest(A=A, B=B, ntimes=5, alternative="less", genome="hg19", evaluate.function=meanDistance, randomize.function=randomize ... [TRUNCATED] - -Rd file 'splitRegions.Rd': - \examples lines wider than 100 characters: - plotRegions(list(A, B, splits), chromosome=1, regions.labels=c("A", "B", "splits"), regions.colors=3:1) - -Rd file 'subtractRegions.Rd': - \examples lines wider than 100 characters: - plotRegions(list(A, B, subtract), chromosome=1, regions.labels=c("A", "B", "subtract"), regions.colors=3:1) - -Rd file 'uniqueRegions.Rd': - \examples lines wider than 100 characters: - plotRegions(list(A, B, uniques), chromosome="chr1", regions.labels=c("A", "B", "uniques"), regions.colors=3:1) - -These lines will be truncated in the PDF manual. -``` -``` -DONE -Status: 4 NOTEs -``` - -## SamplingStrata (1.1) -Maintainer: Giulio Barcaroli - -__OK__ - -## surveillance (1.10-0) -Maintainer: Sebastian Meyer -Bug reports: https://r-forge.r-project.org/tracker/?group_id=45 - -``` -checking package dependencies ... NOTE -Package suggested but not available for checking: ‘INLA’ -``` -``` -checking installed package size ... NOTE - installed size is 7.8Mb - sub-directories of 1Mb or more: - R 4.3Mb -``` -``` -checking Rd cross-references ... NOTE -Packages unavailable to check Rd xrefs: ‘coin’, ‘VGAM’ -``` -``` -checking examples ... ERROR -Running examples in ‘surveillance-Ex.R’ failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: twinstim_epitest -> ### Title: Permutation Test for Space-Time Interaction in '"twinstim"' -> ### Aliases: epitest coef.epitest plot.epitest -> ### Keywords: htest -> -> ### ** Examples -> -> data("imdepi") -> data("imdepifit") -> -> ## test for space-time interaction of the B-cases -> ## assuming spatial interaction to be constant within 50 km -> imdepiB50 <- update(subset(imdepi, type == "B"), eps.s = 50) -Note: dropped type(s) "C" -> imdfitB50 <- update(imdepifit, data = imdepiB50, -+ epidemic = ~1, epilink = "identity", -+ siaf = NULL, control.siaf = NULL, -+ start = c("e.(Intercept)" = 1e-6)) -updating list of potential sources ... -assuming constant spatial interaction 'siaf.constant()' -assuming constant temporal interaction 'tiaf.constant()' - -minimizing the negative log-likelihood using 'nlminb()' ... -initial parameters: - h.(Intercept) h.I(start/365 - 3.5) h.sin(2 * pi * start/365) - -20.53057516 -0.04567343 0.21693842 -h.cos(2 * pi * start/365) e.(Intercept) - 0.31764884 0.00000100 -negative log-likelihood and parameters in each iteration: - 0: 4927.5404: -20.5306 -0.0456734 0.216938 0.317649 1.00000e-06 - 1: 4926.2928: -20.5603 -0.0230546 0.157162 0.404814 1.12303e-06 - 2: 4926.2858: -20.5566 -0.0221811 0.165123 0.402575 1.13028e-06 - 3: 4926.2858: -20.5567 -0.0222681 0.164822 0.403248 1.13028e-06 - -MLE: - h.(Intercept) h.I(start/365 - 3.5) h.sin(2 * pi * start/365) - -2.055673e+01 -2.226812e-02 1.648220e-01 -h.cos(2 * pi * start/365) e.(Intercept) - 4.032484e-01 1.130280e-06 -loglik(MLE) = -4926.286 - -Done. -> -> ## simple likelihood ratio test -> epitest(imdfitB50, imdepiB50, method = "LRT") - - Likelihood Ratio Test for Space-Time Interaction - -data: imdepiB50 -twinstim: imdfitB50 -D = 105.76, df = 1, p-value < 2.2e-16 - -> -> ## permutation test (only few permutations for speed, in parallel) -> et <- epitest(imdfitB50, imdepiB50, B = 4 + 25*surveillance.options("allExamples"), -+ verbose = 2 * (.Platform$OS.type == "unix"), -+ .seed = 1, .parallel = 2) -Endemic/Epidemic log-likelihoods, LRT statistic, and simple R0: -l0 = -4979 | l1 = -4926 | D = 105.8 | simpleR0 = 0.27 - -Results from B=4 permutations of time: - - *** caught segfault *** -address 0x110, cause 'memory not mapped' - -Traceback: - 1: drop(mmhGrid %*% beta) - 2: .hIntTW(beta, uppert = uppert) - 3: heIntTWK(beta0, beta, gammapred, siafpars, tiafpars) - 4: objective(.par, ...) - 5: nlminb(start = optimArgs$par, objective = negll, gradient = negsc, hessian = if (doHessian) neghess else NULL, control = nlminbControl, lower = optimArgs$lower, upper = optimArgs$upper) - 6: twinstim(endemic = ~offset(log(popdensity)) + I(start/365 - 3.5) + sin(2 * pi * start/365) + cos(2 * pi * start/365), epidemic = ~1, data = .permdata, subset = !is.na(agegrp), start = c(-20.55672518676, -0.0222681194425509, 0.164822014646932, 0.403248413226967, 1.13028012099544e-06), epilink = "identity", optim.args = list( control = list(trace = FALSE)), model = FALSE, cumCIF = FALSE, control.siaf = list(siafInt = NULL), cores = 1, verbose = FALSE) - 7: eval(expr, envir, enclos) - 8: eval(call, parent.frame()) - 9: update.twinstim(model, data = .permdata, control.siaf = list(siafInt = .siafInt), model = FALSE, cumCIF = FALSE, cores = 1, verbose = FALSE, optim.args = list(fixed = fixed, control = list(trace = is.numeric(verbose) && verbose >= 3))) -10: FUN(X[[i]], ...) -11: lapply(X = S, FUN = FUN, ...) -12: doTryCatch(return(expr), name, parentenv, handler) -13: tryCatchOne(expr, names, parentenv, handlers[[1L]]) -14: tryCatchList(expr, classes, parentenv, handlers) -15: 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 msg <- conditionMessage(e) sm <- strsplit(msg, "\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 && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) - *** caught segfault *** - -address 0x110, cause 'memory not mapped' -16: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) -17: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) -18: FUN(X[[i]], ...) -19: lapply(seq_len(cores), inner.do) -20: parallel::mclapply(X = X, FUN = .FUN, ..., mc.preschedule = TRUE, mc.set.seed = TRUE, mc.silent = FALSE, mc.cores = .parallel) -21: plapply(X = integer(B), FUN = permfits1, .verbose = .verbose, ...) -22: epitest(imdfitB50, imdepiB50, B = 4 + 25 * surveillance.options("allExamples"), verbose = 2 * (.Platform$OS.type == "unix"), .seed = 1, .parallel = 2) -aborting ... - -Traceback: - 1: drop(mmhGrid %*% beta) - 2: .hIntTW(beta, uppert = uppert) - 3: heIntTWK(beta0, beta, gammapred, siafpars, tiafpars) - 4: objective(.par, ...) - 5: nlminb(start = optimArgs$par, objective = negll, gradient = negsc, hessian = if (doHessian) neghess else NULL, control = nlminbControl, lower = optimArgs$lower, upper = optimArgs$upper) - 6: twinstim(endemic = ~offset(log(popdensity)) + I(start/365 - 3.5) + sin(2 * pi * start/365) + cos(2 * pi * start/365), epidemic = ~1, data = .permdata, subset = !is.na(agegrp), start = c(-20.55672518676, -0.0222681194425509, 0.164822014646932, 0.403248413226967, 1.13028012099544e-06), epilink = "identity", optim.args = list( control = list(trace = FALSE)), model = FALSE, cumCIF = FALSE, control.siaf = list(siafInt = NULL), cores = 1, verbose = FALSE) - 7: eval(expr, envir, enclos) - 8: eval(call, parent.frame()) - 9: update.twinstim(model, data = .permdata, control.siaf = list(siafInt = .siafInt), model = FALSE, cumCIF = FALSE, cores = 1, verbose = FALSE, optim.args = list(fixed = fixed, control = list(trace = is.numeric(verbose) && verbose >= 3))) -10: FUN(X[[i]], ...) -11: lapply(X = S, FUN = FUN, ...) -12: doTryCatch(return(expr), name, parentenv, handler) -13: tryCatchOne(expr, names, parentenv, handlers[[1L]]) -14: tryCatchList(expr, classes, parentenv, handlers) -15: 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 msg <- conditionMessage(e) sm <- strsplit(msg, "\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 && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) -16: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) -17: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) -18: FUN(X[[i]], ...) -19: lapply(seq_len(cores), inner.do) -20: parallel::mclapply(X = X, FUN = .FUN, ..., mc.preschedule = TRUE, mc.set.seed = TRUE, mc.silent = FALSE, mc.cores = .parallel) -21: plapply(X = integer(B), FUN = permfits1, .verbose = .verbose, ...) -22: epitest(imdfitB50, imdepiB50, B = 4 + 25 * surveillance.options("allExamples"), verbose = 2 * (.Platform$OS.type == "unix"), .seed = 1, .parallel = 2) -aborting ... -Error in as.data.frame(t(vapply(X = permfits, FUN = "[[", "stats", FUN.VALUE = numeric(5L), : - error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': Error in vapply(X = permfits, FUN = "[[", "stats", FUN.VALUE = numeric(5L), : - values must be length 5, - but FUN(X[[1]]) result is length 0 -Calls: t -> vapply -Calls: epitest -> as.data.frame -Execution halted -``` -``` -DONE -Status: 1 ERROR, 3 NOTEs -``` - -## toaster (0.4.2) -Maintainer: Gregory Kanevsky -Bug reports: https://github.com/teradata-aster-field/toaster/issues - -__OK__ - diff --git a/revdep/timing.md b/revdep/timing.md new file mode 100644 index 0000000..441787b --- /dev/null +++ b/revdep/timing.md @@ -0,0 +1,27 @@ +# Check times + +| |package |version | check_time| +|:--|:--------------|:-------|----------:| +|14 |regioneR |1.6.2 | 734.7| +|1 |biolink |0.1.2 | 443.1| +|20 |surveillance |1.13.0 | 385.1| +|18 |SamplingStrata |1.1 | 306.7| +|9 |heemod |0.9.0 | 268.7| +|17 |saeRobust |0.1.0 | 251| +|10 |icd9 |1.3.1 | 143.4| +|13 |prcbench |0.7.3 | 122| +|4 |devtools |1.12.0 | 103.4| +|12 |OpenML |1.3 | 87.3| +|15 |rgho |1.0.1 | 62.6| +|3 |covr |2.2.2 | 58.5| +|21 |toaster |0.5.5 | 58.3| +|16 |RSQLite |1.1-2 | 50.8| +|6 |GSED |1.3 | 48.9| +|19 |SIDES |1.10 | 47.7| +|2 |BWStest |0.2.1 | 28.4| +|11 |opencage |0.1.0 | 19.7| +|5 |functools |0.2.0 | 14.5| +|8 |gWidgets2tcltk |1.0-5 | 10.4| +|7 |gWidgets2RGtk2 |1.0-5 | 5.3| + +