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urgency=medium + + * Disable reprotest + * New upstream version + + -- Andreas Tille Thu, 14 Oct 2021 23:12:17 +0200 + +r-cran-qtl (1.48-1-1) unstable; urgency=medium + + * New upstream version + * Standards-Version: 4.6.0 (routine-update) + + -- Andreas Tille Sun, 29 Aug 2021 18:18:11 +0200 + r-cran-qtl (1.47-9-1) unstable; urgency=medium * New upstream version diff -Nru r-cran-qtl-1.47-9/debian/control r-cran-qtl-1.50/debian/control --- r-cran-qtl-1.47-9/debian/control 2021-01-16 13:55:46.000000000 +0000 +++ r-cran-qtl-1.50/debian/control 2021-10-14 21:12:17.000000000 +0000 @@ -8,7 +8,7 @@ Build-Depends: debhelper-compat (= 13), dh-r, r-base-dev -Standards-Version: 4.5.1 +Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-cran-qtl Vcs-Git: https://salsa.debian.org/r-pkg-team/r-cran-qtl.git Homepage: https://cran.r-project.org/package=qtl diff -Nru r-cran-qtl-1.47-9/debian/salsa-ci.yml r-cran-qtl-1.50/debian/salsa-ci.yml --- r-cran-qtl-1.47-9/debian/salsa-ci.yml 2021-01-16 13:55:46.000000000 +0000 +++ r-cran-qtl-1.50/debian/salsa-ci.yml 2021-10-14 21:12:17.000000000 +0000 @@ -2,3 +2,8 @@ include: - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml +# R creates .rdb files and .rds with some randomness. +# https://tests.reproducible-builds.org/debian/issues/unstable/randomness_in_r_rdb_rds_databases_issue.html +# Thus reprotest is disabled here +variables: + SALSA_CI_DISABLE_REPROTEST: 1 diff -Nru r-cran-qtl-1.47-9/DESCRIPTION r-cran-qtl-1.50/DESCRIPTION --- r-cran-qtl-1.47-9/DESCRIPTION 2021-01-07 21:30:03.000000000 +0000 +++ r-cran-qtl-1.50/DESCRIPTION 2021-10-06 16:00:02.000000000 +0000 @@ -1,6 +1,6 @@ Package: qtl -Version: 1.47-9 -Date: 2021-01-07 +Version: 1.50 +Date: 2021-10-06 Title: Tools for Analyzing QTL Experiments Author: Karl W Broman and Hao Wu, with ideas from Gary Churchill and Saunak Sen and contributions from @@ -24,6 +24,6 @@ Encoding: UTF-8 ByteCompile: true NeedsCompilation: yes -Packaged: 2021-01-07 18:59:36 UTC; kbroman +Packaged: 2021-10-06 14:40:11 UTC; kbroman Repository: CRAN -Date/Publication: 2021-01-07 21:30:03 UTC +Date/Publication: 2021-10-06 16:00:02 UTC Binary files /tmp/tmpzttm7lm1/BvVKY1Lr24/r-cran-qtl-1.47-9/inst/doc/bcsft.pdf and /tmp/tmpzttm7lm1/HmzXymX7f6/r-cran-qtl-1.50/inst/doc/bcsft.pdf differ Binary files /tmp/tmpzttm7lm1/BvVKY1Lr24/r-cran-qtl-1.47-9/inst/doc/rqtltour2.pdf and /tmp/tmpzttm7lm1/HmzXymX7f6/r-cran-qtl-1.50/inst/doc/rqtltour2.pdf differ Binary files /tmp/tmpzttm7lm1/BvVKY1Lr24/r-cran-qtl-1.47-9/inst/doc/rqtltour.pdf and /tmp/tmpzttm7lm1/HmzXymX7f6/r-cran-qtl-1.50/inst/doc/rqtltour.pdf differ diff -Nru r-cran-qtl-1.47-9/inst/INSTALL_ME.txt r-cran-qtl-1.50/inst/INSTALL_ME.txt --- r-cran-qtl-1.47-9/inst/INSTALL_ME.txt 2021-01-07 18:58:40.000000000 +0000 +++ r-cran-qtl-1.50/inst/INSTALL_ME.txt 2021-10-06 14:39:00.000000000 +0000 @@ -28,7 +28,7 @@ INSTALLATION OF R AND R/QTL (Windows) 1. The Windows version of R is distributed as a single file, with a - name something like R-4.0.3-win.exe. Install R by executing + name something like R-4.1.1-win.exe. Install R by executing this file. We recommend installing R in "c:\R" rather than "c:\Program Files\R". Why didn't Microsoft use "Programs" rather than "Program files"? @@ -39,16 +39,16 @@ This will download the binary from CRAN and install it. - Alternatively, you can download the "qtl_1.47-9.zip" (or the + Alternatively, you can download the "qtl_1.50.zip" (or the equivalent). Then start R and select (on the menu bar) "Packages" and then "Install package from local zip file...". - Find the file "qtl_1.47-9.zip" on your hard drive, and click + Find the file "qtl_1.50.zip" on your hard drive, and click "Open". -INSTALLATION OF R AND R/QTL (MacOS version 10.5 and above) +INSTALLATION OF R AND R/QTL (MacOS version 10.13 and above) - 1. Download the file R-4.0.3.pkg, double-click it, and follow the + 1. Download the file R-4.1.1.pkg, double-click it, and follow the instructions. 2. To install R/qtl, the simplest approach is to start R and type @@ -58,7 +58,7 @@ This will download the binary from CRAN and install it. Alternatively, download the compiled version of R/qtl for - Mac OS X, a file like "qtl_1.47-9.tgz". Then start R and + Mac OS X, a file like "qtl_1.50.tgz". Then start R and select (on the menu bar) "Packages & Data" -> "Package Installer". Select "Local Binary Package" from the drop-down menu at the top of the window that comes up. Click "Install" @@ -78,19 +78,19 @@ This will download the binary from CRAN and install it. Alternatively, download the R/qtl source code (a file like - "qtl_1.47-9.tar.gz"). Go into the directory containing the + "qtl_1.50.tar.gz"). Go into the directory containing the file and do one of the following: a. To install R/qtl in the standard location (/usr/local/lib/R/library), type - R CMD INSTALL qtl_1.47-9.tar.gz + R CMD INSTALL qtl_1.50.tar.gz You'll probably need to be superuser. b. To install the package locally, type - R CMD INSTALL --library=/home/auser/Rlibs qtl_1.47-9.tar.gz + R CMD INSTALL --library=/home/auser/Rlibs qtl_1.50.tar.gz (where "/home/auser/Rlibs" should be replaced with the appropriate directory). diff -Nru r-cran-qtl-1.47-9/man/cim.Rd r-cran-qtl-1.50/man/cim.Rd --- r-cran-qtl-1.47-9/man/cim.Rd 2018-10-03 11:55:17.000000000 +0000 +++ r-cran-qtl-1.50/man/cim.Rd 2021-06-30 11:45:10.000000000 +0000 @@ -16,7 +16,7 @@ method=c("em", "imp", "hk", "ehk"), imp.method=c("imp", "argmax"), error.prob=0.0001, map.function=c("haldane", "kosambi", "c-v", "morgan"), - n.perm) + addcovar=NULL, n.perm) } \arguments{ \item{cross}{An object of class \code{cross}. See @@ -39,6 +39,7 @@ the missing marker genotype data.} \item{map.function}{Map function used when imputing the missing marker genotype data.} + \item{addcovar}{Optional numeric matrix of additional covariates to include.} \item{n.perm}{If specified, a permutation test is performed rather than an analysis of the observed data. This argument defines the number of permutation replicates.} diff -Nru r-cran-qtl-1.47-9/man/effectscan.Rd r-cran-qtl-1.50/man/effectscan.Rd --- r-cran-qtl-1.47-9/man/effectscan.Rd 2020-06-16 20:31:18.000000000 +0000 +++ r-cran-qtl-1.50/man/effectscan.Rd 2021-01-26 22:22:20.000000000 +0000 @@ -35,7 +35,7 @@ \item{alternate.chrid}{If TRUE and more than one chromosome is plotted, alternate the placement of chromosome axis labels, so that they may be more easily distinguished.} - \item{\dots}{Passed to the function \code{\link[base]{plot}} when it + \item{\dots}{Passed to the function \code{plot} when it is called.} } \value{ diff -Nru r-cran-qtl-1.47-9/man/mqmplotmultitrait.Rd r-cran-qtl-1.50/man/mqmplotmultitrait.Rd --- r-cran-qtl-1.47-9/man/mqmplotmultitrait.Rd 2020-06-16 20:31:45.000000000 +0000 +++ r-cran-qtl-1.50/man/mqmplotmultitrait.Rd 2021-01-26 22:22:33.000000000 +0000 @@ -23,7 +23,7 @@ \item{meanprofile}{ Plot a mean/median profile from the group selected } \item{theta}{ Horizontal axis rotation in a 3D plot } \item{phi}{ Vertical axis rotation in a 3D plot } - \item{\dots}{Additional arguments passed to \code{\link[base]{plot}}.} + \item{\dots}{Additional arguments passed to \code{plot}.} } \author{ diff -Nru r-cran-qtl-1.47-9/man/plotLodProfile.Rd r-cran-qtl-1.50/man/plotLodProfile.Rd --- r-cran-qtl-1.47-9/man/plotLodProfile.Rd 2020-06-16 20:31:51.000000000 +0000 +++ r-cran-qtl-1.50/man/plotLodProfile.Rd 2021-01-26 22:23:08.000000000 +0000 @@ -40,7 +40,7 @@ \item{showallchr}{If FALSE (the default), only show the chr with a QTL} \item{labelsep}{If \code{qtl.labels=TRUE}, separation between peak LOD and QTL label, as percent of the height of the plot.} - \item{\dots}{Passed to the function \code{\link[base]{plot}} when it + \item{\dots}{Passed to the function \code{plot} when it is called.} } \value{None.} diff -Nru r-cran-qtl-1.47-9/man/plot.map.Rd r-cran-qtl-1.50/man/plot.map.Rd --- r-cran-qtl-1.47-9/man/plot.map.Rd 2020-06-16 20:32:33.000000000 +0000 +++ r-cran-qtl-1.50/man/plot.map.Rd 2021-01-26 22:22:49.000000000 +0000 @@ -36,7 +36,7 @@ \item{alternate.chrid}{If TRUE and more than one chromosome is plotted, alternate the placement of chromosome axis labels, so that they may be more easily distinguished.} - \item{\dots}{Passed to \code{\link[base]{plot}}.} + \item{\dots}{Passed to \code{plot}.} } \value{None.} diff -Nru r-cran-qtl-1.47-9/man/plotModel.Rd r-cran-qtl-1.50/man/plotModel.Rd --- r-cran-qtl-1.47-9/man/plotModel.Rd 2020-06-16 20:32:37.000000000 +0000 +++ r-cran-qtl-1.50/man/plotModel.Rd 2021-01-26 22:23:11.000000000 +0000 @@ -34,7 +34,7 @@ \item{order}{Optional vector indicating a permutation of the QTL to define where they are to appear in the plot. QTL are placed around a circle, starting at the top and going clockwise.} - \item{\dots}{Passed to the function \code{\link[base]{plot}}.} + \item{\dots}{Passed to the function \code{plot}.} } %\details{ diff -Nru r-cran-qtl-1.47-9/man/plot.pxg.Rd r-cran-qtl-1.50/man/plot.pxg.Rd --- r-cran-qtl-1.47-9/man/plot.pxg.Rd 2020-06-16 20:32:41.000000000 +0000 +++ r-cran-qtl-1.50/man/plot.pxg.Rd 2021-01-26 22:22:53.000000000 +0000 @@ -34,7 +34,7 @@ markers are used.} \item{col}{A vector of colors to use for the confidence intervals (optional).} - \item{\dots}{Passed to \code{\link[base]{plot}}.} + \item{\dots}{Passed to \code{plot}.} } \details{ diff -Nru r-cran-qtl-1.47-9/man/plot.scanone.Rd r-cran-qtl-1.50/man/plot.scanone.Rd --- r-cran-qtl-1.47-9/man/plot.scanone.Rd 2020-06-16 20:32:48.000000000 +0000 +++ r-cran-qtl-1.50/man/plot.scanone.Rd 2021-01-26 22:23:02.000000000 +0000 @@ -47,7 +47,7 @@ \item{bandcol}{Optional color for alternating bands to indicate chromosomes. If NULL (the default), no bands are plotted. A good choice might be \code{bandcol="gray70"}.} - \item{type}{Type of plot (see \code{\link[base]{plot}}): for + \item{type}{Type of plot (see \code{plot}): for example, \code{type="l"} for lines or \code{type="p"} for points only, may be of length 1 or 3.} \item{cex}{Point size expansion, for example if \code{type="p"} is used. @@ -58,7 +58,7 @@ and \code{pch=21} are used. See \code{\link[graphics]{points}}. May be of length 1 or 3.} \item{bgrect}{Optional background color for the rectangular plotting region.} - \item{\dots}{Passed to the function \code{\link[base]{plot}} when it + \item{\dots}{Passed to the function \code{plot} when it is called.} } \value{None.} diff -Nru r-cran-qtl-1.47-9/MD5 r-cran-qtl-1.50/MD5 --- r-cran-qtl-1.47-9/MD5 2021-01-07 21:30:03.000000000 +0000 +++ r-cran-qtl-1.50/MD5 2021-10-06 16:00:02.000000000 +0000 @@ -1,16 +1,16 @@ -c87ed00afad777f82c3aa868beb287a6 *DESCRIPTION +6db914321492bea36ffd495b14fc8b04 *DESCRIPTION 62828318221a847e7f41b6d51f00b703 *NAMESPACE -6f24e6e92f1351eebdf20b52089a61d6 *NEWS.md +1f601c194b3947444d53907841e1de5b *NEWS.md be09adead3e7ef2c4a141178391fde75 *R/add.cim.covar.R b28895ea5226f6e156ef723ad8e4e731 *R/add_threshold.R e96452b91bdba02c6ab9af6ee9f7c4f6 *R/addmarker.R -c9e592ed73fc354dfc11533111b295c4 *R/addqtl.R +b1d8c2315fdfd2debb84895fc539576e *R/addqtl.R ced11f727f3d1eb662ad0517f029671f *R/argmax.geno.R 2340f2602a8b6258e48e8b167368ed3e *R/arithscan.R 97af0f1804dd15031ede03e3daf6b42c *R/bcsft.R 9a14a20468f7ab3183aee675bfd97eb4 *R/calc.genoprob.R a40a1704d82bfd8130bd8b88017d4c6e *R/calc.pairprob.R -8bd04ba13c3d6f57e0b8943172f18c01 *R/cim.R +9aab668013c4fe2cfd10f0c180846861 *R/cim.R d6c7261007d45b195229986396803847 *R/comparegeno.R ed3f6b1e8c227f2d9d9642baf4fb7f44 *R/compareorder.R 1aee46951f22a531b7b01234f74f6965 *R/countXO.R @@ -75,15 +75,15 @@ c564f5e24b346138464cf16491c52a7e *R/sim.geno.R 6980a20ffc5d0321117edc2e4afe5f06 *R/sim_ril.R 5294ad76b17a60a7386033d1c1c561df *R/simulate.R -0f9e2ad94965354a49c83e6fbf6725ab *R/stepwiseqtl.R -d88a7995b71e357df7b5282cf464b271 *R/stepwiseqtlX.R +13556e3d4959cc0e4013bb7629a7511c *R/stepwiseqtl.R +24a640234a26f07e9cca87cd3a8ebb23 *R/stepwiseqtlX.R d63a57f1d4d586a30656d925021625d2 *R/summary.cross.R bfeff37af8d7e5e5ae3f2ab83a0d7cad *R/summary.scanone.R e5dc28ba49a85c734a503c1b0e2ce47c *R/summary.scantwo.R 46359713b056180eae672649e7b3813a *R/summary.scantwo.old.R c6cd187dda5782475986d51d763ded86 *R/transformPheno.R 091d00be07f8abf6c5745010691b908e *R/tryallpositions.R -380b3d4914a63d84104f89d4b37b5df0 *R/util.R +6e9fed691a90d241f5af71b234c431da *R/util.R 1ce029f5927df7e1f08001129b67e9e4 *R/vbscan.R 7a088a393e967649514591691eb020b4 *R/viridis.R a77efd38e7c69e08c2f71a80ca2056c2 *R/write.cross.R @@ -91,22 +91,22 @@ 715d9d5eb3a8e9b2ddfeee7cd06c58bd *R/write.cross.qtab.R f404008174661ddf0883f62ef3ea5f2b *R/xchr.R bd88f15cd17c31b5eb589c28244f5e9a *README.md -25ceaf9d5e9b8bfc1f22dd95516cd1ad *build/vignette.rds -745c9e943ab09e66463c5b66af69db3a *data/badorder.RData -90ec3963670f3a39d060844b4619a0b8 *data/bristle3.RData -50b4daf10945bce3c9a6711e29d717d4 *data/bristleX.RData -b6f39cfab137e7a05523db40b9cc2c75 *data/fake.4way.RData -8d5b63d0f811c9cea12837e5cf427680 *data/fake.bc.RData -eb4cb0110d59fd171c7e1c35f7ff6e60 *data/fake.f2.RData -1813e06be7e138ac6e55769003ee9839 *data/hyper.RData -88495d8b2c2efe8c951876a6a739670b *data/listeria.RData -9c690e46847e751d54312c8283826eb4 *data/locations.RData -25a93083130819844fc6bc1a0041fbc7 *data/map10.RData -bac2490ecdc2e5783b0d087acfec10c9 *data/mapthis.RData -5df94254dc6ed37e4fc289c4b125c903 *data/multitrait.RData +194fc83bac21916540e8a0a7321c6247 *build/vignette.rds +b1524e632a59aaaca7a37521e9ac7a42 *data/badorder.RData +70b5d99dbf5a96b276ce89a139c2643b *data/bristle3.RData +4889e6035f2b1184983c370a61622d49 *data/bristleX.RData +be49d1012b531435ef876e62215d433a *data/fake.4way.RData +b6457d28af1b502b5604cbd5d5ab42f6 *data/fake.bc.RData +39d8e1e83853cb4a8a631d23b6212df8 *data/fake.f2.RData +93d05ec26232d40072b549a13de56250 *data/hyper.RData +61f4e3cddaa20acfcd0cba5e536ca708 *data/listeria.RData +901db2d6a2b59d6bcb1d4ab5f62ed8ff *data/locations.RData +d3aa73fd4191ee23ce931b76e73a8d33 *data/map10.RData +ed616c102f83800a2101eb50beb589ce *data/mapthis.RData +99668998516a2076872651dc01dd909d *data/multitrait.RData bc02b0de935ba3c5aa8e7cc4a9c23a14 *inst/BUGS.txt 986cd348f290739701e237a15516bb1d *inst/CITATION -59900c111f01cfbdf0648ddcf983a586 *inst/INSTALL_ME.txt +d88f2f435c73190e9a7076c20f63d940 *inst/INSTALL_ME.txt c8b990e307ecee343beb5a217265ffcf *inst/MQM-TODO.txt 1723dec70d7b0ed3c1c99e7b7581e948 *inst/contrib/bin/CMakeLists.txt 1e10167bc08e8c501be1ac201247af7d *inst/contrib/bin/FindRLibs.cmake @@ -208,7 +208,7 @@ b8f91bbddb0c0dcee45085b0fe945c6f *inst/doc/Sources/rqtltour2.tex f61f48adc17761dab61e5035a6037632 *inst/doc/bcsft.R 504a78535def937ee020d9e8f1de9b55 *inst/doc/bcsft.Rnw -5cdcc0087c4be727eb2a35d2dae2464f *inst/doc/bcsft.pdf +1e134db0d8acf2acf57853d5e1b46458 *inst/doc/bcsft.pdf ccbd21a4f84d3800e3330b0171883b26 *inst/doc/geneticmaps.R f326aab03d4745094152713cca6cbe25 *inst/doc/geneticmaps.pdf 40eb8179441ce7496f6c5e252c8b2b56 *inst/doc/new_multiqtl.R @@ -218,9 +218,9 @@ a808a0dcf90e74a422bf3ea84f4bd55b *inst/doc/new_summary_scantwo.R 83dbe80c9f5b641b0b269be341c80df2 *inst/doc/new_summary_scantwo.pdf 20f1ad8aeb8fd6c722ed5a3de0885cc8 *inst/doc/rqtltour.R -2dda2eaa9b291963a146f90a7ef8719f *inst/doc/rqtltour.pdf +90baacfd462b5d4f1c52769928d69b94 *inst/doc/rqtltour.pdf ea48cfd7fee328162b3fb49a827f3606 *inst/doc/rqtltour2.R -79011fab6f3e7dee79f9196083f2dc14 *inst/doc/rqtltour2.pdf +a8b3c5d26b901d8d3d4e66629bd4b0ca *inst/doc/rqtltour2.pdf 1b42a662f601adaa9660800eefa4e42f *inst/sampledata/README.txt f6a9eebc3f37d26e0a5b8ed672354712 *inst/sampledata/gen.txt 9198bd35e7a221556c5e2008d00cf84c *inst/sampledata/listeria.csv @@ -269,7 +269,7 @@ 46d5d8d2dfc2f065759e40033cea4182 *man/checkAlleles.Rd b9af71345d58afd2c17534e0a5d6eeef *man/chrlen.Rd 428cccc523bb4c1d0652a5b9bc4a0324 *man/chrnames.Rd -a51921c980e6573eccdbfca80638577a *man/cim.Rd +8e4800de61407c628121e608e1da1816 *man/cim.Rd 0ae5cc5df4a84c8e6baae5743f9b0204 *man/clean.cross.Rd 70163f97553c9222e8d7543759e63e1e *man/clean.scantwo.Rd ee627a0a2ba4ce60e121b7f30aaa94f1 *man/cleanGeno.Rd @@ -290,7 +290,7 @@ 03ee72ec78dd8f17196c064955aa7bb8 *man/dropfromqtl.Rd 50c0383bc2a1d703f337308beea715f7 *man/droponemarker.Rd 20a1ba2a468712aa6e2cce39906dfc39 *man/effectplot.Rd -ef705df86b5bfba2831a92420d75ead1 *man/effectscan.Rd +efe76948b0045fbb3b2a1ec127e0f0cd *man/effectscan.Rd ba754810996dd8a30f86ac801971b80e *man/est.map.Rd 79efffb2eb8b8eb3f6c55758334cad76 *man/est.rf.Rd 4577babbe8a9c70d29866599d8586883 *man/fake.4way.Rd @@ -346,7 +346,7 @@ 473ba8d3015e59d28311c978c7f8ceee *man/mqmplotcofactors.Rd f46fdd26452138dcb77b17871de28356 *man/mqmplotdirectedqtl.Rd 5f2afbf606154abe44b0e3224c0334f0 *man/mqmplotheatmap.Rd -4d28e1cd5860f183f68ca2ed57e01e2e *man/mqmplotmultitrait.Rd +b78d0d41723e19052938716cd5cb2091 *man/mqmplotmultitrait.Rd 419cd927868afa5273de640ddd8e10de *man/mqmplotpermutations.Rd 361780d3a75584838be03ec97504b20a *man/mqmplotsingletrait.Rd c4ef7276e92570328925b96df8d53bcd *man/mqmprocesspermutation.Rd @@ -373,21 +373,21 @@ cf52d169fbe659014b98205455a66cb3 *man/plot.errorlod.Rd 56e38e40ee921ed4f17a3331f70f6c0e *man/plot.geno.Rd b1b532da805f90da6302084ee7080281 *man/plot.info.Rd -85daef7895b97dd3b54da9a41dd648c8 *man/plot.map.Rd +14e264d9f7a854e539df059980bce1e8 *man/plot.map.Rd afcbe156c50fc7ff07768e39b7699fcb *man/plot.missing.Rd 3b91f822260d90298216e71c9db7e78c *man/plot.pheno.Rd -845bb12fe54d8db2536a6dac65e3399a *man/plot.pxg.Rd +4e0d4e4593cb0c5b985f21d81729b3ca *man/plot.pxg.Rd fa1341c1ee50a187e2cfedf9f0e469d3 *man/plot.qtl.Rd 60eb653f330f2de81f36faa0dff3e8a8 *man/plot.rf.Rd 4f6d4d35ac0443e4e96f30627a903cd5 *man/plot.rfmatrix.Rd 1f944b4c13638a9624593e5bb4418abc *man/plot.scanPhyloQTL.Rd -1b59197c83db01be76f7b0f4688dd867 *man/plot.scanone.Rd +0c08ce497212258d5efc8cb4827df61b *man/plot.scanone.Rd da9bc9c310625a01053c67bba28b85fd *man/plot.scanoneboot.Rd 14c3631c3e3dc859b2a72b58123c5c6b *man/plot.scanoneperm.Rd db0d226dac51acbef28f62ee54ea8e8a *man/plot.scantwo.Rd 3d08b8ed50d0e354a692380e873f7dae *man/plot.scantwoperm.Rd -2afe6e9061673182fd0fd6b34cb37913 *man/plotLodProfile.Rd -efab39df43df0c10955985bfb9a30c17 *man/plotModel.Rd +7865a9f4e52fae8e6dce6d9fca702ce3 *man/plotLodProfile.Rd +2038d82010b3d2e1cc4ce13439c93f99 *man/plotModel.Rd d57d5963d614a7c8e4edbdc336b996b6 *man/pull.argmaxgeno.Rd d6831e4937aa81bb8a0e433e2d14cd60 *man/pull.draws.Rd d0ffa1979385a65020f3689470f45650 *man/pull.geno.Rd @@ -465,7 +465,7 @@ cc1b8f0530ac6a6a2de49e5d25c47a70 *src/discan.h 64d3c7c88d2e84d8b28cc7bb7f9cb4b1 *src/discan_covar.c e32c99d76c228876c47c043289b9df59 *src/discan_covar.h -aca6bdc300f2b2bf8198c0a2ae5e2dca *src/effectscan.c +288dd85cac5595f09b9c02c3e622a801 *src/effectscan.c cec64a0383167ff081d6e5701fea37b9 *src/effectscan.h 91d0c646d29cfcdab1a35348ae688992 *src/fill_geno_nodblXO.c 5625aff805e480b0e7e5f12d7e8e35ff *src/fill_geno_nodblXO.h @@ -513,8 +513,8 @@ c8febdc02d9cf116c7df6dac19943c88 *src/inferFounderHap.h dcc492e6edf2d1029027605ddfd942e7 *src/info.c 9bf82156882dcb0303db6607335a9a17 *src/info.h -89ae76ebd36bdda1b9df5ccc17602c23 *src/lapackutil.c -37a9ebf0cdd07c045cbaeaa11f5cd428 *src/lapackutil.h +b0dead9922c5a7db6f304b6e5771dc50 *src/lapackutil.c +77940ed0df05e1c3d0bd8c6336fc05c3 *src/lapackutil.h 1f42b2427d1613ddbce94cf7a656b9ec *src/markerlrt.c 5f0df67e4b39c52fe4aadd5802df643a *src/markerlrt.h 507d03c39679c9be3dbab2cb097f813b *src/mqm.h @@ -580,7 +580,7 @@ 009203746e8805eb38f82fee79cd0518 *src/summary_scantwo.c 645229bb47522e6c198dd10c603c25d1 *src/summary_scantwo.h 845c5433a9eb7bbc01a92ba395fc6c32 *src/test_bcsft.c -56f3ab65e40110d6393e5c261e1cbed9 *src/util.c +d998a178319a9cd5b1f4904bd1ed5202 *src/util.c d00e596a6b5ded548cd672c357b0d7c8 *src/util.h a752e137e6514c25709667e8dc3d1af5 *src/vbscan.c 5fb15aa5b6d413aa8d80d1fdefbc86d5 *src/vbscan.h diff -Nru r-cran-qtl-1.47-9/NEWS.md r-cran-qtl-1.50/NEWS.md --- r-cran-qtl-1.47-9/NEWS.md 2021-01-07 18:46:12.000000000 +0000 +++ r-cran-qtl-1.50/NEWS.md 2021-10-06 14:37:43.000000000 +0000 @@ -16,6 +16,32 @@ at https://www.r-project.org/Licenses/GPL-3 ---------------------------------------------------------------------- +## Verison 1.50, 2021-10-06 + +## New features + +- `cim()` now includes an `addcovar` argument for including additional + covariates in the model. + +### Minor changes + +- Revised qtlversion() to handle a case like "1.50". + +- Added `#define USE_FC_LEN_T` in C code that calls Fortran, because + of a change in R 3.6.5 that's going to be required in R 4.2.0. + + +## Version 1.48, 2021-03-24 + +### Bug fixes + +- Fixed bug in `addqtl()` and `addpair()` in which the argument + `forceXcovar` wasn't getting passed to `scanqtl()`. + +- Fixed bug in `stepwiseqtl()` regarding the way the null LOD score is + calculated. + + ## Version 1.47, 2021-01-07 ### Minor changes diff -Nru r-cran-qtl-1.47-9/R/addqtl.R r-cran-qtl-1.50/R/addqtl.R --- r-cran-qtl-1.47-9/R/addqtl.R 2020-02-28 18:56:12.000000000 +0000 +++ r-cran-qtl-1.50/R/addqtl.R 2021-03-24 15:02:04.000000000 +0000 @@ -2,8 +2,8 @@ # # addqtl.R # -# copyright (c) 2007-2020, Karl W. Broman -# last modified Feb, 2020 +# copyright (c) 2007-2021, Karl W. Broman +# last modified Mar, 2021 # first written Nov, 2007 # # This program is free software; you can redistribute it and/or @@ -540,7 +540,7 @@ sqout <- scanqtl(cross, pheno.col=pheno.col, chr=thechr, pos=thepos, covar=covar, formula=newformula, method=method, model=model, incl.markers=incl.markers, verbose=verbose.scanqtl, - tol=tol, maxit=maxit) + tol=tol, maxit=maxit, forceXcovar=forceXcovar) matrix1.rank <- c(matrix1.rank, attr(sqout, "matrix.rank")) matrix1.ncol <- c(matrix1.ncol, attr(sqout, "matrix.ncol")) @@ -991,7 +991,7 @@ temp1 <- scanqtl(cross, pheno.col=pheno.col, chr=thechr, pos=thepos, covar=covar, formula=newformula1, method=method, model=model, incl.markers=incl.markers, verbose=verbose.scanqtl, - tol=tol, maxit=maxit) - lod0 + tol=tol, maxit=maxit, forceXcovar=forceXcovar) - lod0 if(!is.null(newformula2)) { if(verbose) @@ -1000,7 +1000,7 @@ temp2 <- scanqtl(cross, pheno.col=pheno.col, chr=thechr, pos=thepos, covar=covar, formula=newformula2, method=method, model=model, incl.markers=incl.markers, verbose=verbose.scanqtl, - tol=tol, maxit=maxit) - lod0 + tol=tol, maxit=maxit, forceXcovar=forceXcovar) - lod0 } else { if(i != j && scanbothways) { @@ -1009,7 +1009,7 @@ temp1r <- scanqtl(cross, pheno.col=pheno.col, chr=thechr, pos=thepos, covar=covar, formula=newformula1, method=method, model=model, incl.markers=incl.markers, verbose=verbose.scanqtl, - tol=tol, maxit=maxit) - lod0 + tol=tol, maxit=maxit, forceXcovar=forceXcovar) - lod0 } } @@ -1045,11 +1045,11 @@ lod.m1[whi] <- scanqtl(cross, pheno.col=pheno.col, chr=thechr, pos=thepos, covar=covar, formula=newformula1.minus1, method=method, model=model, incl.markers=incl.markers, - verbose=verbose.scanqtl, tol=tol, maxit=maxit) - lod0 + verbose=verbose.scanqtl, tol=tol, maxit=maxit, forceXcovar=forceXcovar) - lod0 lod.m2[whi] <- scanqtl(cross, pheno.col=pheno.col, chr=thechr, pos=thepos, covar=covar, formula=newformula1.minus2, method=method, model=model, incl.markers=incl.markers, - verbose=verbose.scanqtl, tol=tol, maxit=maxit) - lod0 + verbose=verbose.scanqtl, tol=tol, maxit=maxit, forceXcovar=forceXcovar) - lod0 } diff -Nru r-cran-qtl-1.47-9/R/cim.R r-cran-qtl-1.50/R/cim.R --- r-cran-qtl-1.47-9/R/cim.R 2019-12-17 21:02:56.000000000 +0000 +++ r-cran-qtl-1.50/R/cim.R 2021-06-30 11:47:28.000000000 +0000 @@ -2,8 +2,8 @@ # # cim.R # -# copyright (c) 2007-2019, Karl W Broman -# last modified Dec, 2019 +# copyright (c) 2007-2021, Karl W Broman +# last modified Jun, 2021 # first written Jan, 2007 # # This program is free software; you can redistribute it and/or @@ -34,12 +34,19 @@ method=c("em", "imp", "hk", "ehk"), imp.method=c("imp", "argmax"), error.prob=0.0001, map.function=c("haldane", "kosambi", "c-v", "morgan"), - n.perm) + addcovar=NULL, n.perm) { method <- match.arg(method) imp.method <- match.arg(imp.method) map.function <- match.arg(map.function) + if(!is.null(addcovar)) { + if(!is.matrix(addcovar)) addcovar <- as.matrix(addcovar) + if(nrow(addcovar) != nind(cross)) { + stop("nrow(addcovar) != no. individuals in cross") + } + } + type <- crosstype(cross) if(type=="4way") stop("cim() has not been implemented for 4-way crosses") @@ -78,7 +85,8 @@ cross$pheno[,pheno.col] <- y temp <- cim(cross, pheno.col=pheno.col, n.marcovar=n.marcovar, window=window, method=method, imp.method=imp.method, - error.prob=error.prob, map.function=map.function) + error.prob=error.prob, map.function=map.function, + addcovar=addcovar) results[i,1] <- max(temp[,3], na.rm=TRUE) } class(results) <- c("scanoneperm", "matrix") @@ -104,7 +112,7 @@ if(type=="f2") useac <- expandf2covar(ac) else useac <- ac - firstscan <- scanone(cross, pheno.col=pheno.col, addcovar=useac, + firstscan <- scanone(cross, pheno.col=pheno.col, addcovar=cbind(useac,addcovar), method=method) # scan again, dropping one marker covariate at a time @@ -112,7 +120,7 @@ if(type=="f2") useac <- expandf2covar(ac[,-i]) else useac <- ac[,-i] - temp <- scanone(cross, pheno.col=pheno.col, addcovar=useac, + temp <- scanone(cross, pheno.col=pheno.col, addcovar=cbind(useac,addcovar), method=method, chr=chrpos[i,1]) wh1 <- (firstscan[,1]==chrpos[i,1] & firstscan[,2] >= chrpos[i,2]-window & firstscan[,2] <= chrpos[i,2]+window) @@ -149,7 +157,7 @@ if(type=="f2") useac <- expandf2covar(tempac) else useac <- tempac - temp <- scanone(cross, pheno.col=pheno.col, addcovar=useac, + temp <- scanone(cross, pheno.col=pheno.col, addcovar=cbind(useac,addcovar), method=method, chr=j) firstscan[whpos2,3] <- temp[whpos,3] diff -Nru r-cran-qtl-1.47-9/R/stepwiseqtl.R r-cran-qtl-1.50/R/stepwiseqtl.R --- r-cran-qtl-1.47-9/R/stepwiseqtl.R 2019-12-17 21:02:56.000000000 +0000 +++ r-cran-qtl-1.50/R/stepwiseqtl.R 2021-07-29 20:12:26.000000000 +0000 @@ -1,8 +1,8 @@ ###################################################################### # stepwiseqtl.R # -# copyright (c) 2007-2019, Karl W Broman -# last modified Dec, 2019 +# copyright (c) 2007-2021, Karl W Broman +# last modified Mar, 2021 # first written Nov, 2007 # # This program is free software; you can redistribute it and/or @@ -245,7 +245,12 @@ else firstformula <- formula } else { - lod0 <- length(pheno)/2 * log10(sum((pheno-mean(pheno))^2) / sum(lm(pheno ~ as.matrix(covar))$resid^2)) + nullformula <- as.formula(paste("y~", paste(names(covar), collapse="+"))) + tempqtl <- makeqtl(cross, chrnames(cross)[1], 0, what=ifelse(method=="imp", "draws", "prob")) + fit <- fitqtl(cross, pheno.col, tempqtl, covar=covar, formula=nullformula, + method=method, model=model, dropone=FALSE, get.ests=FALSE, + run.checks=FALSE, tol=tol, maxit=maxit, forceXcovar=forceXcovar) + lod0 <- fit$result.full[1,4] if(startatnull) firstformula <- as.formula(paste("y~", paste(names(covar), collapse="+"), "+", "Q1")) else firstformula <- formula diff -Nru r-cran-qtl-1.47-9/R/stepwiseqtlX.R r-cran-qtl-1.50/R/stepwiseqtlX.R --- r-cran-qtl-1.47-9/R/stepwiseqtlX.R 2019-12-17 21:02:56.000000000 +0000 +++ r-cran-qtl-1.50/R/stepwiseqtlX.R 2021-03-24 16:03:09.000000000 +0000 @@ -1,7 +1,7 @@ ###################################################################### # stepwiseqtlX.R # -# copyright (c) 2013-2014, Karl W Broman and Quoc Tran +# copyright (c) 2013-2021, Karl W Broman and Quoc Tran # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License, @@ -363,7 +363,12 @@ else firstformula <- formula } else { - lod0 <- length(pheno)/2 * log10(sum((pheno-mean(pheno))^2) / sum(lm(pheno ~ as.matrix(covar))$resid^2)) + nullformula <- as.formula(paste("y~", paste(names(covar), collapse="+"))) + tempqtl <- makeqtl(cross, chrnames(cross)[1], 0, what=ifelse(method=="imp", "draws", "prob")) + fit <- fitqtl(cross, pheno.col, tempqtl, covar=covar, formula=nullformula, + method=method, model=model, dropone=FALSE, get.ests=FALSE, + run.checks=FALSE, tol=tol, maxit=maxit, forceXcovar=forceXcovar) + lod0 <- fit$result.full[1,4] if(startatnull) firstformula <- as.formula(paste("y~", paste(names(covar), collapse="+"), "+", "Q1")) else firstformula <- formula diff -Nru r-cran-qtl-1.47-9/R/util.R r-cran-qtl-1.50/R/util.R --- r-cran-qtl-1.47-9/R/util.R 2020-10-26 16:26:59.000000000 +0000 +++ r-cran-qtl-1.50/R/util.R 2021-08-05 20:47:19.000000000 +0000 @@ -3161,8 +3161,12 @@ { version <- unlist(packageVersion("qtl")) - # make it like #.#-# - paste(c(version,".","-")[c(1,4,2,5,3)], collapse="") + if(length(version) == 3) { + # make it like #.#-# + return( paste(c(version, ".", "-")[c(1,4,2,5,3)], collapse="") ) + } + + paste(version, collapse=".") } diff -Nru r-cran-qtl-1.47-9/src/effectscan.c r-cran-qtl-1.50/src/effectscan.c --- r-cran-qtl-1.47-9/src/effectscan.c 2016-09-19 17:12:54.000000000 +0000 +++ r-cran-qtl-1.50/src/effectscan.c 2021-09-25 21:11:15.000000000 +0000 @@ -2,9 +2,9 @@ * * effectscan.c * - * copyright (c) 2007-8, Karl W Broman + * copyright (c) 2007-2021, Karl W Broman * - * last modified Jan, 2008 + * last modified Sep, 2021 * first written Sep, 2007 * * This program is free software; you can redistribute it and/or @@ -28,9 +28,11 @@ * **********************************************************************/ +#define USE_FC_LEN_T #include #include #include +#include #include #include #include @@ -38,6 +40,9 @@ #include #include "effectscan.h" #include "util.h" +#ifndef FCONE +# define FCONE +#endif /* R_effectscan: wrapper for effectscan */ @@ -126,7 +131,7 @@ if(!flag[i]) { /* linear regression */ F77_CALL(dgels)("N", &nind, &ngen, &nphe, x, &nind, resid, &nind, - dwork, &lwork, &info); + dwork, &lwork, &info FCONE); /* coefficient estimates */ for(j=0; j #include #include +#include #include #include #include @@ -37,6 +39,9 @@ #include #include "lapackutil.h" #define TOL 1e-12 +#ifndef FCONE +# define FCONE +#endif /* DGELSS function */ @@ -48,7 +53,7 @@ /* use dgels first */ F77_CALL(dgels)("N", n_ind, ncolx0, nphe, x0, n_ind, tmppheno, n_ind, - work, lwork, info); + work, lwork, info FCONE); /* if there's problem like singular, use dgelss */ /* note that x0 will contain the result for QR decomposition. @@ -81,21 +86,15 @@ double *beta, double *rss_det) { F77_CALL(dgemm)("T", "N", nphe, nphe, n_ind, alpha, tmppheno, n_ind, - tmppheno, n_ind, beta, rss_det, nphe); + tmppheno, n_ind, beta, rss_det, nphe FCONE FCONE); } /* DPOTRF */ void mydpotrf(int *nphe, double *rss_det, int *info) { - F77_CALL(dpotrf)("U", nphe, rss_det, nphe, info); + F77_CALL(dpotrf)("U", nphe, rss_det, nphe, info FCONE); } -/*DPOTRS */ -void mydpotrs(char *uplo, int *n, int *nrhs, double *A, - int *lda, double *B, int *ldb, int *info) -{ - F77_CALL(dpotrs)(uplo, n, nrhs, A, lda, B, ldb, info); -} /* end of lapackutil.c */ diff -Nru r-cran-qtl-1.47-9/src/lapackutil.h r-cran-qtl-1.50/src/lapackutil.h --- r-cran-qtl-1.47-9/src/lapackutil.h 2016-09-19 17:12:54.000000000 +0000 +++ r-cran-qtl-1.50/src/lapackutil.h 2021-09-25 21:11:15.000000000 +0000 @@ -23,7 +23,7 @@ * * These are some wrapper functions for several LAPACK routines. * - * Contains: mydgelss, mydgemm, mydpotrf, mydpotrs + * Contains: mydgelss, mydgemm, mydpotrf * **********************************************************************/ @@ -39,8 +39,4 @@ /* DPOTRF */ void mydpotrf(int *nphe1, double *rss_det, int *info); -/* DPOTRS */ -void mydpotrs(char *uplo, int *n, int *nrhs, double *A, - int *lda, double *B, int *ldb, int *info); - /* end of lapackutil.h */ diff -Nru r-cran-qtl-1.47-9/src/util.c r-cran-qtl-1.50/src/util.c --- r-cran-qtl-1.47-9/src/util.c 2018-10-03 11:55:17.000000000 +0000 +++ r-cran-qtl-1.50/src/util.c 2021-09-25 21:11:15.000000000 +0000 @@ -41,7 +41,6 @@ **********************************************************************/ #include -/* #include */ #include "util.h" #define THRESH 200.0 @@ -702,17 +701,6 @@ } /* end loop over individuals */ } -/* multiply two matrices - I'm using dgemm from lapack here */ -/* - void matmult2(double *result, double *a, int nrowa, - int ncola, double *b, int ncolb) - - { - double alpha=1.0, beta=1.0; - F77_CALL(dgemm)("N", "N", &nrowa, &ncolb, &ncola, &alpha, a, &nrowa, - b, &ncola, &beta, result, &nrowa); - } -*/ void matmult(double *result, double *a, int nrowa, int ncola, double *b, int ncolb)