Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:44:23 -0400 (Wed, 16 Oct 2019).
Package 683/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
GladiaTOX 1.0.0 PMP S.A. R Support
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: GladiaTOX |
Version: 1.0.0 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GladiaTOX.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GladiaTOX_1.0.0.tar.gz |
StartedAt: 2019-10-16 04:05:49 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 04:11:10 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 321.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GladiaTOX.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GladiaTOX.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GladiaTOX_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GladiaTOX.Rcheck' * using R version 3.6.1 (2019-07-05) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'GladiaTOX/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'GladiaTOX' version '1.0.0' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'GladiaTOX' can be installed ... OK * checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: sql 3.8Mb * 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 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 ... OK * checking Rd files ... OK * checking Rd metadata ... 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed gtoxRun 29.43 2.50 30.16 assignDefaultMthds 27.44 2.67 38.89 glPlotPie 5.03 1.70 4.57 glPlotStat 4.55 1.96 3.67 glPlotToxInd 4.62 1.85 3.37 glComputeToxInd 3.81 2.41 3.07 exportResultForToxpiGUI 3.76 1.88 2.83 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed assignDefaultMthds 29.81 2.52 30.75 gtoxRun 29.59 2.00 30.25 glPlotToxInd 4.88 2.85 3.91 glPlotStat 3.86 2.77 3.76 glPlotPie 4.14 1.83 4.02 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GladiaTOX.Rcheck/00check.log' for details.
GladiaTOX.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GladiaTOX_1.0.0.tar.gz && rm -rf GladiaTOX.buildbin-libdir && mkdir GladiaTOX.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GladiaTOX.buildbin-libdir GladiaTOX_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GladiaTOX_1.0.0.zip && rm GladiaTOX_1.0.0.tar.gz GladiaTOX_1.0.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 2076k 100 2076k 0 0 20.9M 0 --:--:-- --:--:-- --:--:-- 22.5M install for i386 * installing *source* package 'GladiaTOX' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'GladiaTOX' finding HTML links ... done MC2_Methods html MC3_Methods html MC5_Methods html MC6_Methods html Models html SC1_Methods html SC2_Methods html assay_funcs html assignDefaultMthds html blineShift html buildAssayTab html config_funcs html deleteStudy html exportResultForToxpiGUI html exportResultTable html flareFunc html glComputeToxInd html glPlotPie html glPlotPieLogo html glPlotPosCtrl html glPlotStat html glPlotToxInd html gtoxAICProb html gtoxAddModel html gtoxAppend html gtoxCalcVmad html gtoxCascade html gtoxCode2CASN html gtoxDelete html gtoxFit html gtoxImportThermoDB html gtoxListFlds html gtoxLoadApid html gtoxLoadChem html gtoxLoadClib html gtoxLoadData html finding level-2 HTML links ... done gtoxLoadUnit html gtoxLoadVehicle html gtoxLoadVmad html gtoxLoadWaid html gtoxMakeAeidPlts html gtoxPlotErrBar html gtoxPlotFitc html gtoxPlotFits html gtoxPlotM4ID html gtoxPlotPie html gtoxPlotPieLgnd html gtoxPlotPlate html gtoxPlotWin html gtoxPrepOtpt html gtoxReport html gtoxRun html gtoxSetWllq html gtoxSubsetChid html gtoxWriteData html hill_utils html interlaceFunc html is.odd html loadAnnot html lu html lw html mc1 html mc2 html mc3 html mc4 html mc5 html mc6 html mthd_funcs html prepareDatForDB html query_funcs html registerMthd html rgstr_funcs html sc1 html sc2 html sink_reset html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'GladiaTOX' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'GladiaTOX' as GladiaTOX_1.0.0.zip * DONE (GladiaTOX) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'GladiaTOX' successfully unpacked and MD5 sums checked
GladiaTOX.Rcheck/tests_i386/testthat.Rout R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(GladiaTOX) Loading required package: data.table GladiaTOX (v1.0.0) loaded with the following settings: TCPL_DB: C:/Users/biocbuild/bbs-3.9-bioc/R/library/GladiaTOX/sql/gladiatoxdb.sqlite TCPL_USER: NA TCPL_HOST: NA TCPL_DRVR: SQLite Default settings stored in gtox config file. See ?gtoxConf for more information. > > options(testthat.junit.output_file="tests-out.xml") > test_dir("testthat") v | OK F W S | Context / | 0 | test_assignDefaultMthds - | 1 | test_assignDefaultMthds v | 1 | test_assignDefaultMthds [0.5 s] / | 0 | test_exportResultTable \ | 2 | test_exportResultTable v | 2 | test_exportResultTable [2.8 s] / | 0 | getsplit x | 0 1 | getsplit -------------------------------------------------------------------------------- test_getsplit.R:4: error: getsplit:split word correctly could not find function "getsplit" 1: expect_equal(getsplit("toto_tata", "_", 1), "toto") at testthat/test_getsplit.R:4 2: quasi_label(enquo(object), label, arg = "object") 3: eval_bare(get_expr(quo), get_env(quo)) -------------------------------------------------------------------------------- / | 0 | test_glComputeToxInd - | 0 1 | test_glComputeToxInd v | 1 3 | test_glComputeToxInd [3.1 s] -------------------------------------------------------------------------------- test_glComputeToxInd.R:3: warning: glComputeToxInd:returns correct values no non-missing arguments to min; returning Inf test_glComputeToxInd.R:3: warning: glComputeToxInd:returns correct values no non-missing arguments to min; returning Inf test_glComputeToxInd.R:3: warning: glComputeToxInd:returns correct values no non-missing arguments to max; returning -Inf -------------------------------------------------------------------------------- / | 0 | test_gtoxAICProb v | 1 | test_gtoxAICProb / | 0 | Calculate Vmad v | 1 | Calculate Vmad / | 0 | Check assay component table \ | 2 | Check assay component table v | 2 | Check assay component table [0.1 s] / | 0 | Check assay endpoint table \ | 2 | Check assay endpoint table v | 2 | Check assay endpoint table [0.1 s] / | 0 | test_gtoxLoadAid v | 1 | test_gtoxLoadAid / | 0 | Check assay plate table v | 2 | Check assay plate table / | 0 | test_gtoxLoadAsid v | 3 | test_gtoxLoadAsid / | 0 | Check assay chemical table v | 3 | Check assay chemical table / | 0 | Check assay well table v | 2 | Check assay well table / | 0 | test_is.odd x | 0 1 | test_is.odd -------------------------------------------------------------------------------- test_is.odd.R:2: error: is.odd:has the expected behavior could not find function "is.odd" 1: .handleSimpleError(function (e) { handled <<- TRUE test_error <<- e options(expressions = expressions_opt_new) on.exit(options(expressions = expressions_opt), add = TRUE) e$expectation_calls <- frame_calls(11, 2) test_error <<- e register_expectation(e) e$handled <- TRUE test_error <<- e }, "could not find function \"is.odd\"", base::quote(is.odd(2))) at testthat/test_is.odd.R:2 2: eval(code, test_env) -------------------------------------------------------------------------------- / | 0 | test_lu v | 1 | test_lu / | 0 | test_lw v | 1 | test_lw / | 0 | test_mc2 x | 0 1 | test_mc2 -------------------------------------------------------------------------------- test_mc2.R:2: error: mc2_mthds:returns log10 among the list of mc2 functions could not find function "mc2_mthds" 1: .handleSimpleError(function (e) { handled <<- TRUE test_error <<- e options(expressions = expressions_opt_new) on.exit(options(expressions = expressions_opt), add = TRUE) e$expectation_calls <- frame_calls(11, 2) test_error <<- e register_expectation(e) e$handled <- TRUE test_error <<- e }, "could not find function \"mc2_mthds\"", base::quote(mc2_mthds())) at testthat/test_mc2.R:2 2: eval(code, test_env) -------------------------------------------------------------------------------- / | 0 | test_mc3 x | 0 1 | test_mc3 -------------------------------------------------------------------------------- test_mc3.R:2: error: mc3:returns resp.log2 among the list of mc2 functions could not find function "mc3_mthds" 1: expect_true("resp.log2" %in% names(mc3_mthds())) at testthat/test_mc3.R:2 2: quasi_label(enquo(object), label, arg = "object") 3: eval_bare(get_expr(quo), get_env(quo)) 4: "resp.log2" %in% names(mc3_mthds()) -------------------------------------------------------------------------------- / | 0 | test_mc5 x | 0 1 | test_mc5 -------------------------------------------------------------------------------- test_mc5.R:2: error: mc5:returns bmad5 among the list of mc2 functions could not find function "mc5_mthds" 1: expect_true("bmad5" %in% names(mc5_mthds())) at testthat/test_mc5.R:2 2: quasi_label(enquo(object), label, arg = "object") 3: eval_bare(get_expr(quo), get_env(quo)) 4: "bmad5" %in% names(mc5_mthds()) -------------------------------------------------------------------------------- / | 0 | test_mc6 x | 0 1 | test_mc6 -------------------------------------------------------------------------------- test_mc6.R:2: error: mc6:returns pintool among the list of mc2 functions could not find function "mc6_mthds" 1: expect_true("pintool" %in% names(mc6_mthds())) at testthat/test_mc6.R:2 2: quasi_label(enquo(object), label, arg = "object") 3: eval_bare(get_expr(quo), get_env(quo)) 4: "pintool" %in% names(mc6_mthds()) -------------------------------------------------------------------------------- / | 0 | test_sc1 x | 0 1 | test_sc1 -------------------------------------------------------------------------------- test_sc1.R:2: error: sc1:returns pval.zero among the list of sc1 functions could not find function "sc1_mthds" 1: expect_true("pval.zero" %in% names(sc1_mthds())) at testthat/test_sc1.R:2 2: quasi_label(enquo(object), label, arg = "object") 3: eval_bare(get_expr(quo), get_env(quo)) 4: "pval.zero" %in% names(sc1_mthds()) -------------------------------------------------------------------------------- / | 0 | test_sc2 x | 0 1 | test_sc2 -------------------------------------------------------------------------------- test_sc2.R:2: error: sc2:returns pval.zero among the list of sc2 functions could not find function "sc2_mthds" 1: expect_true("bmad6" %in% names(sc2_mthds())) at testthat/test_sc2.R:2 2: quasi_label(enquo(object), label, arg = "object") 3: eval_bare(get_expr(quo), get_env(quo)) 4: "bmad6" %in% names(sc2_mthds()) -------------------------------------------------------------------------------- == Results ===================================================================== Duration: 7.2 s OK: 23 Failed: 8 Warnings: 3 Skipped: 0 > test_check("GladiaTOX") == testthat results =========================================================== [ OK: 32 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ] > > proc.time() user system elapsed 17.54 9.70 16.51 |
GladiaTOX.Rcheck/tests_x64/testthat.Rout R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(GladiaTOX) Loading required package: data.table GladiaTOX (v1.0.0) loaded with the following settings: TCPL_DB: C:/Users/biocbuild/bbs-3.9-bioc/R/library/GladiaTOX/sql/gladiatoxdb.sqlite TCPL_USER: NA TCPL_HOST: NA TCPL_DRVR: SQLite Default settings stored in gtox config file. See ?gtoxConf for more information. > > options(testthat.junit.output_file="tests-out.xml") > test_dir("testthat") v | OK F W S | Context / | 0 | test_assignDefaultMthds - | 1 | test_assignDefaultMthds v | 1 | test_assignDefaultMthds [0.7 s] / | 0 | test_exportResultTable \ | 2 | test_exportResultTable v | 2 | test_exportResultTable [1.9 s] / | 0 | getsplit x | 0 1 | getsplit -------------------------------------------------------------------------------- test_getsplit.R:4: error: getsplit:split word correctly could not find function "getsplit" 1: expect_equal(getsplit("toto_tata", "_", 1), "toto") at testthat/test_getsplit.R:4 2: quasi_label(enquo(object), label, arg = "object") 3: eval_bare(get_expr(quo), get_env(quo)) -------------------------------------------------------------------------------- / | 0 | test_glComputeToxInd - | 0 1 | test_glComputeToxInd v | 1 3 | test_glComputeToxInd [2.6 s] -------------------------------------------------------------------------------- test_glComputeToxInd.R:3: warning: glComputeToxInd:returns correct values no non-missing arguments to min; returning Inf test_glComputeToxInd.R:3: warning: glComputeToxInd:returns correct values no non-missing arguments to min; returning Inf test_glComputeToxInd.R:3: warning: glComputeToxInd:returns correct values no non-missing arguments to max; returning -Inf -------------------------------------------------------------------------------- / | 0 | test_gtoxAICProb v | 1 | test_gtoxAICProb / | 0 | Calculate Vmad v | 1 | Calculate Vmad / | 0 | Check assay component table \ | 2 | Check assay component table v | 2 | Check assay component table [0.1 s] / | 0 | Check assay endpoint table \ | 2 | Check assay endpoint table v | 2 | Check assay endpoint table [0.2 s] / | 0 | test_gtoxLoadAid v | 1 | test_gtoxLoadAid / | 0 | Check assay plate table v | 2 | Check assay plate table / | 0 | test_gtoxLoadAsid v | 3 | test_gtoxLoadAsid / | 0 | Check assay chemical table v | 3 | Check assay chemical table / | 0 | Check assay well table v | 2 | Check assay well table / | 0 | test_is.odd x | 0 1 | test_is.odd -------------------------------------------------------------------------------- test_is.odd.R:2: error: is.odd:has the expected behavior could not find function "is.odd" 1: .handleSimpleError(function (e) { handled <<- TRUE test_error <<- e options(expressions = expressions_opt_new) on.exit(options(expressions = expressions_opt), add = TRUE) e$expectation_calls <- frame_calls(11, 2) test_error <<- e register_expectation(e) e$handled <- TRUE test_error <<- e }, "could not find function \"is.odd\"", base::quote(is.odd(2))) at testthat/test_is.odd.R:2 2: eval(code, test_env) -------------------------------------------------------------------------------- / | 0 | test_lu v | 1 | test_lu / | 0 | test_lw v | 1 | test_lw / | 0 | test_mc2 x | 0 1 | test_mc2 -------------------------------------------------------------------------------- test_mc2.R:2: error: mc2_mthds:returns log10 among the list of mc2 functions could not find function "mc2_mthds" 1: .handleSimpleError(function (e) { handled <<- TRUE test_error <<- e options(expressions = expressions_opt_new) on.exit(options(expressions = expressions_opt), add = TRUE) e$expectation_calls <- frame_calls(11, 2) test_error <<- e register_expectation(e) e$handled <- TRUE test_error <<- e }, "could not find function \"mc2_mthds\"", base::quote(mc2_mthds())) at testthat/test_mc2.R:2 2: eval(code, test_env) -------------------------------------------------------------------------------- / | 0 | test_mc3 x | 0 1 | test_mc3 -------------------------------------------------------------------------------- test_mc3.R:2: error: mc3:returns resp.log2 among the list of mc2 functions could not find function "mc3_mthds" 1: expect_true("resp.log2" %in% names(mc3_mthds())) at testthat/test_mc3.R:2 2: quasi_label(enquo(object), label, arg = "object") 3: eval_bare(get_expr(quo), get_env(quo)) 4: "resp.log2" %in% names(mc3_mthds()) -------------------------------------------------------------------------------- / | 0 | test_mc5 x | 0 1 | test_mc5 -------------------------------------------------------------------------------- test_mc5.R:2: error: mc5:returns bmad5 among the list of mc2 functions could not find function "mc5_mthds" 1: expect_true("bmad5" %in% names(mc5_mthds())) at testthat/test_mc5.R:2 2: quasi_label(enquo(object), label, arg = "object") 3: eval_bare(get_expr(quo), get_env(quo)) 4: "bmad5" %in% names(mc5_mthds()) -------------------------------------------------------------------------------- / | 0 | test_mc6 x | 0 1 | test_mc6 -------------------------------------------------------------------------------- test_mc6.R:2: error: mc6:returns pintool among the list of mc2 functions could not find function "mc6_mthds" 1: expect_true("pintool" %in% names(mc6_mthds())) at testthat/test_mc6.R:2 2: quasi_label(enquo(object), label, arg = "object") 3: eval_bare(get_expr(quo), get_env(quo)) 4: "pintool" %in% names(mc6_mthds()) -------------------------------------------------------------------------------- / | 0 | test_sc1 x | 0 1 | test_sc1 -------------------------------------------------------------------------------- test_sc1.R:2: error: sc1:returns pval.zero among the list of sc1 functions could not find function "sc1_mthds" 1: expect_true("pval.zero" %in% names(sc1_mthds())) at testthat/test_sc1.R:2 2: quasi_label(enquo(object), label, arg = "object") 3: eval_bare(get_expr(quo), get_env(quo)) 4: "pval.zero" %in% names(sc1_mthds()) -------------------------------------------------------------------------------- / | 0 | test_sc2 x | 0 1 | test_sc2 -------------------------------------------------------------------------------- test_sc2.R:2: error: sc2:returns pval.zero among the list of sc2 functions could not find function "sc2_mthds" 1: expect_true("bmad6" %in% names(sc2_mthds())) at testthat/test_sc2.R:2 2: quasi_label(enquo(object), label, arg = "object") 3: eval_bare(get_expr(quo), get_env(quo)) 4: "bmad6" %in% names(sc2_mthds()) -------------------------------------------------------------------------------- == Results ===================================================================== Duration: 6.0 s OK: 23 Failed: 8 Warnings: 3 Skipped: 0 > test_check("GladiaTOX") == testthat results =========================================================== [ OK: 32 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ] > > proc.time() user system elapsed 15.67 7.75 14.43 |
GladiaTOX.Rcheck/examples_i386/GladiaTOX-Ex.timings
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GladiaTOX.Rcheck/examples_x64/GladiaTOX-Ex.timings
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