From f42afd73619966862b089740fbfffd7905d1e6fe Mon Sep 17 00:00:00 2001 From: ranke Date: Mon, 28 Jul 2014 10:33:13 +0000 Subject: Address platform dependence of tests/pyrithione.R git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@102 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc --- ChangeLog | 10 +++++++ DESCRIPTION | 4 +-- GNUmakefile | 32 +++++----------------- tests/IM1xIPC81.Rout.save | 9 +++---- tests/IM1xVibrio.Rout.save | 9 +++---- tests/XY.Rout.save | 11 ++++---- tests/antifoul.Rout.save | 11 ++++---- tests/pyrithione.R | 2 +- tests/pyrithione.Rout.save | 67 ++++++++++++++++++++++------------------------ 9 files changed, 70 insertions(+), 85 deletions(-) diff --git a/ChangeLog b/ChangeLog index 35a8a35..c29f20a 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,13 @@ +2014-07-28 Johannes Ranke + + * DESCRIPTION: New verson 0.6.3 + + * inst/test: Reduced precision in pyrithione.R as results were + platform dependent. Updated all .Rout.save files + + * inst/doc/index.html: Make the index contain valid html. Thanks to + Kurt Hornik for checking HTML validity in CRAN packages. + 2014-03-18 Johannes Ranke * DESCRIPTION, NAMESPACE: New verson 0.6.1, with the drc package as diff --git a/DESCRIPTION b/DESCRIPTION index 4bf9df4..ba4f425 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: drfit -Version: 0.6.1 -Date: 2014-03-18 +Version: 0.6.3 +Date: 2014-07-28 Title: Dose-response data evaluation Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre"), email = "jranke@uni-bremen.de")) diff --git a/GNUmakefile b/GNUmakefile index dfc1b7b..64aa9d4 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -1,6 +1,7 @@ PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION) PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION) PKGSRC := $(shell basename $(PWD)) +TGZ := ../$(PKGNAME)_$(PKGVERS).tar.gz # Specify the directory holding R binaries. To use an alternate R build (say a # pre-prelease version) use `make RBIN=/path/to/other/R/` or `export RBIN=...` @@ -8,31 +9,6 @@ PKGSRC := $(shell basename $(PWD)) # containing the first instance of R on the PATH. RBIN ?= $(shell dirname "`which R`") -.PHONY: help - -help: - @echo "\nExecute development tasks for $(PKGNAME)\n" - @echo "Usage: \`make \` where is one of:" - @echo "" - @echo "Development Tasks" - @echo "-----------------" - @echo " build Create the package" - @echo " check Invoke build and then check the package" - @echo " install Invoke build and then install the result" - @echo "" - @echo "Packaging Tasks" - @echo "---------------" - @echo " release Give some reminders" - @echo "" - @echo "Using R in: $(RBIN)" - @echo "Set the RBIN environment variable to change this." - @echo "" - - -#------------------------------------------------------------------------------ -# Development Tasks -#------------------------------------------------------------------------------ - build: cd ..;\ "$(RBIN)/R" CMD build $(PKGSRC) @@ -44,3 +20,9 @@ install: build check: build cd ..;\ "$(RBIN)/R" CMD check --as-cran $(PKGNAME)_$(PKGVERS).tar.gz + +winbuilder: build + @echo "Uploading to R-release on win-builder" + curl -T $(TGZ) ftp://anonymous@win-builder.r-project.org/R-release/ + @echo "Uploading to R-devel on win-builder" + curl -T $(TGZ) ftp://anonymous@win-builder.r-project.org/R-devel/ diff --git a/tests/IM1xIPC81.Rout.save b/tests/IM1xIPC81.Rout.save index 203ac66..3ed2681 100644 --- a/tests/IM1xIPC81.Rout.save +++ b/tests/IM1xIPC81.Rout.save @@ -1,7 +1,6 @@ -R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" -Copyright (C) 2012 The R Foundation for Statistical Computing -ISBN 3-900051-07-0 +R version 3.1.1 (2014-07-10) -- "Sock it to Me" +Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. @@ -17,8 +16,6 @@ Type 'demo()' for some demos, 'help()' for on-line help, or Type 'q()' to quit R. > library(drfit) -Loading required package: MASS -Loading required package: RODBC > data(IM1xIPC81) > rIM1xIPC81 <- drfit(IM1xIPC81,linlogit=TRUE) @@ -89,4 +86,4 @@ Waiting for profiling to be done... > > proc.time() user system elapsed - 0.852 0.024 0.869 + 1.111 0.808 0.789 diff --git a/tests/IM1xVibrio.Rout.save b/tests/IM1xVibrio.Rout.save index e54ba59..4878972 100644 --- a/tests/IM1xVibrio.Rout.save +++ b/tests/IM1xVibrio.Rout.save @@ -1,7 +1,6 @@ -R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" -Copyright (C) 2012 The R Foundation for Statistical Computing -ISBN 3-900051-07-0 +R version 3.1.1 (2014-07-10) -- "Sock it to Me" +Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. @@ -17,8 +16,6 @@ Type 'demo()' for some demos, 'help()' for on-line help, or Type 'q()' to quit R. > library(drfit) -Loading required package: MASS -Loading required package: RODBC > data(IM1xVibrio) > rIM1xVibrio <- drfit(IM1xVibrio) @@ -75,4 +72,4 @@ Waiting for profiling to be done... > > proc.time() user system elapsed - 0.864 0.024 0.879 + 1.261 0.995 0.953 diff --git a/tests/XY.Rout.save b/tests/XY.Rout.save index fc5b0cd..a3f84c0 100644 --- a/tests/XY.Rout.save +++ b/tests/XY.Rout.save @@ -1,7 +1,7 @@ -R version 2.9.2 (2009-08-24) -Copyright (C) 2009 The R Foundation for Statistical Computing -ISBN 3-900051-07-0 +R version 3.1.1 (2014-07-10) -- "Sock it to Me" +Copyright (C) 2014 The R Foundation for Statistical Computing +Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. @@ -16,8 +16,6 @@ Type 'demo()' for some demos, 'help()' for on-line help, or Type 'q()' to quit R. > library(drfit) -Loading required package: MASS -Loading required package: RODBC > data(XY) > rXY <- drfit(XY,logit=TRUE,weibull=TRUE,chooseone=FALSE) @@ -45,3 +43,6 @@ Substance Y: Fitting data... 4 3.0096 2.03624 5 NA NA > +> proc.time() + user system elapsed + 0.609 0.379 0.491 diff --git a/tests/antifoul.Rout.save b/tests/antifoul.Rout.save index 6846b1e..ff69334 100644 --- a/tests/antifoul.Rout.save +++ b/tests/antifoul.Rout.save @@ -1,7 +1,7 @@ -R version 2.9.2 (2009-08-24) -Copyright (C) 2009 The R Foundation for Statistical Computing -ISBN 3-900051-07-0 +R version 3.1.1 (2014-07-10) -- "Sock it to Me" +Copyright (C) 2014 The R Foundation for Statistical Computing +Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. @@ -16,8 +16,6 @@ Type 'demo()' for some demos, 'help()' for on-line help, or Type 'q()' to quit R. > library(drfit) -Loading required package: MASS -Loading required package: RODBC > data(antifoul) > rantifoul <- drfit(antifoul) @@ -36,3 +34,6 @@ Waiting for profiling to be done... 1 0.19286 -0.16436 0.67637 2 0.22866 -0.39792 0.41696 > +> proc.time() + user system elapsed + 0.743 0.555 0.612 diff --git a/tests/pyrithione.R b/tests/pyrithione.R index 3a3ff23..87552aa 100644 --- a/tests/pyrithione.R +++ b/tests/pyrithione.R @@ -1,4 +1,4 @@ library(drfit) data(pyrithione) rpyr <- drfit(pyrithione,linlogit=TRUE,linlogitWrong=c("MSPT","MSPHI","PyS")) -print(rpyr,digits=4) +print(rpyr,digits=2) diff --git a/tests/pyrithione.Rout.save b/tests/pyrithione.Rout.save index eb92b80..f796a40 100644 --- a/tests/pyrithione.Rout.save +++ b/tests/pyrithione.Rout.save @@ -1,7 +1,6 @@ -R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" -Copyright (C) 2012 The R Foundation for Statistical Computing -ISBN 3-900051-07-0 +R version 3.1.1 (2014-07-10) -- "Sock it to Me" +Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. @@ -17,8 +16,6 @@ Type 'demo()' for some demos, 'help()' for on-line help, or Type 'q()' to quit R. > library(drfit) -Loading required package: MASS -Loading required package: RODBC > data(pyrithione) > rpyr <- drfit(pyrithione,linlogit=TRUE,linlogitWrong=c("MSPT","MSPHI","PyS")) @@ -75,36 +72,36 @@ Waiting for profiling to be done... NaJ: Fitting data... -> print(rpyr,digits=4) - Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit -1 Na Pyrithion 20 108 -2.1072 2.000 linlogit -0.3461 -0.4276 -0.26479 microM -2 Pyridin 19 161 0.5918 3.699 inactive NA NA NA microM -3 PyNO 19 81 0.5918 3.699 no fit NA NA NA microM -4 (PT)2 19 81 -2.4082 2.000 linlogit -0.4197 -0.5326 NA microM -5 MSO2P 28 108 -1.7093 3.699 inactive NA NA NA microM -6 MSPHI 19 81 0.5918 3.699 probit 3.6625 3.5546 3.88019 microM -7 PyS 18 80 -0.4082 3.000 probit 2.6818 NA NA microM -8 Zn Pyrithion 27 81 -2.1072 2.000 linlogit -0.4133 -0.5293 -0.29980 microM -9 Cu Pyrithion 19 79 -2.4082 2.000 linlogit -0.3075 -0.4753 -0.15444 microM -10 Fe Pyrithion 19 81 -2.4082 2.000 linlogit -0.3535 -0.5004 -0.21460 microM -11 MSPT 18 108 -0.4082 3.000 probit 2.1385 2.0709 2.20511 microM -12 TBT 38 135 -2.7093 2.398 linlogit -0.1581 -0.2602 -0.05047 microM -13 NaJ 10 108 0.5918 3.301 inactive NA NA NA microM - sigma a b c -1 0.2086 -0.3461 2.1188 -0.26700 -2 NA NA NA NA -3 0.1073 NA NA NA -4 0.2051 -0.4197 1.8467 -0.51507 -5 NA NA NA NA -6 0.1294 3.6625 0.4387 NA -7 0.1340 2.6818 0.1250 NA -8 0.2288 -0.4133 1.7425 0.61081 -9 0.2449 -0.3075 1.0151 -0.04897 -10 0.2338 -0.3535 1.1823 0.02508 -11 0.2288 2.1385 0.2113 NA -12 0.1926 -0.1581 1.0407 -0.02416 -13 NA NA NA NA +> print(rpyr,digits=2) + Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma +1 Na Pyrithion 20 108 -2.11 2.0 linlogit -0.35 -0.43 -0.26 microM 0.21 +2 Pyridin 19 161 0.59 3.7 inactive NA NA NA microM NA +3 PyNO 19 81 0.59 3.7 no fit NA NA NA microM 0.11 +4 (PT)2 19 81 -2.41 2.0 linlogit -0.42 -0.53 NA microM 0.21 +5 MSO2P 28 108 -1.71 3.7 inactive NA NA NA microM NA +6 MSPHI 19 81 0.59 3.7 probit 3.66 3.55 3.88 microM 0.13 +7 PyS 18 80 -0.41 3.0 probit 2.68 NA NA microM 0.13 +8 Zn Pyrithion 27 81 -2.11 2.0 linlogit -0.41 -0.53 -0.30 microM 0.23 +9 Cu Pyrithion 19 79 -2.41 2.0 linlogit -0.31 -0.48 -0.15 microM 0.24 +10 Fe Pyrithion 19 81 -2.41 2.0 linlogit -0.35 -0.50 -0.21 microM 0.23 +11 MSPT 18 108 -0.41 3.0 probit 2.14 2.07 2.21 microM 0.23 +12 TBT 38 135 -2.71 2.4 linlogit -0.16 -0.26 -0.05 microM 0.19 +13 NaJ 10 108 0.59 3.3 inactive NA NA NA microM NA + a b c +1 -0.35 2.12 -0.267 +2 NA NA NA +3 NA NA NA +4 -0.42 1.85 -0.515 +5 NA NA NA +6 3.66 0.44 NA +7 2.68 0.13 NA +8 -0.41 1.74 0.611 +9 -0.31 1.02 -0.049 +10 -0.35 1.18 0.025 +11 2.14 0.21 NA +12 -0.16 1.04 -0.024 +13 NA NA NA > > proc.time() user system elapsed - 1.556 0.044 1.595 + 2.302 1.804 1.550 -- cgit v1.2.1