Binary files /tmp/tmpJ293AM/6uYyMpSWqE/r-cran-maldiquantforeign-0.11/build/vignette.rds and /tmp/tmpJ293AM/Bqvbfh784S/r-cran-maldiquantforeign-0.11.1/build/vignette.rds differ diff -Nru r-cran-maldiquantforeign-0.11/debian/changelog r-cran-maldiquantforeign-0.11.1/debian/changelog --- r-cran-maldiquantforeign-0.11/debian/changelog 2017-09-30 22:09:40.000000000 +0000 +++ r-cran-maldiquantforeign-0.11.1/debian/changelog 2018-03-11 17:17:38.000000000 +0000 @@ -1,3 +1,13 @@ +r-cran-maldiquantforeign (0.11.1-1) unstable; urgency=medium + + * Team upload. + * New upstream version + * Secure URI in watch file + * Standards-Version: 4.1.3 + * debhelper 11 + + -- Andreas Tille Sun, 11 Mar 2018 18:17:38 +0100 + r-cran-maldiquantforeign (0.11-1) unstable; urgency=medium * Team upload. diff -Nru r-cran-maldiquantforeign-0.11/debian/compat r-cran-maldiquantforeign-0.11.1/debian/compat --- r-cran-maldiquantforeign-0.11/debian/compat 2017-09-30 22:09:40.000000000 +0000 +++ r-cran-maldiquantforeign-0.11.1/debian/compat 2018-03-11 17:17:38.000000000 +0000 @@ -1 +1 @@ -10 +11 diff -Nru r-cran-maldiquantforeign-0.11/debian/control r-cran-maldiquantforeign-0.11.1/debian/control --- r-cran-maldiquantforeign-0.11/debian/control 2017-09-30 22:09:40.000000000 +0000 +++ r-cran-maldiquantforeign-0.11.1/debian/control 2018-03-11 17:17:38.000000000 +0000 @@ -3,7 +3,7 @@ Uploaders: Filippo Rusconi Section: gnu-r Priority: optional -Build-Depends: debhelper (>= 10), +Build-Depends: debhelper (>= 11~), dh-r, r-base-dev (>= 3.2.2), r-cran-base64enc, @@ -13,7 +13,7 @@ r-cran-readbrukerflexdata, r-cran-readmzxmldata, r-cran-xml -Standards-Version: 4.1.1 +Standards-Version: 4.1.3 Vcs-Browser: https://anonscm.debian.org/cgit/debichem/packages/r-cran-maldiquantforeign.git Vcs-Git: https://anonscm.debian.org/git/debichem/packages/r-cran-maldiquantforeign.git Homepage: https://cran.r-project.org/package=MALDIquantForeign @@ -21,7 +21,7 @@ Package: r-cran-maldiquantforeign Architecture: all Depends: ${misc:Depends}, - ${R:Depends}, + ${R:Depends} Recommends: ${R:Recommends} Suggests: ${R:Suggests} Description: GNU R package providing import/export routines for MALDIquant diff -Nru r-cran-maldiquantforeign-0.11/debian/watch r-cran-maldiquantforeign-0.11.1/debian/watch --- r-cran-maldiquantforeign-0.11/debian/watch 2017-09-30 22:09:40.000000000 +0000 +++ r-cran-maldiquantforeign-0.11.1/debian/watch 2018-03-11 17:17:38.000000000 +0000 @@ -1,3 +1,3 @@ -version=3 -http://cran.r-project.org/src/contrib/MALDIquantForeign_([\d\.]*).tar.gz +version=4 +https://cran.r-project.org/src/contrib/MALDIquantForeign_([\d\.]*).tar.gz diff -Nru r-cran-maldiquantforeign-0.11/DESCRIPTION r-cran-maldiquantforeign-0.11.1/DESCRIPTION --- r-cran-maldiquantforeign-0.11/DESCRIPTION 2017-09-06 18:29:52.000000000 +0000 +++ r-cran-maldiquantforeign-0.11.1/DESCRIPTION 2017-12-04 12:30:50.000000000 +0000 @@ -1,6 +1,6 @@ Package: MALDIquantForeign -Version: 0.11 -Date: 2017-09-01 +Version: 0.11.1 +Date: 2017-12-04 Title: Import/Export Routines for 'MALDIquant' Authors@R: c(person("Sebastian", "Gibb", role=c("aut", "cre"), email="mail@sebastiangibb.de"), person("Pietro", "Franceschi", @@ -22,9 +22,9 @@ VignetteBuilder: knitr RoxygenNote: 5.0.1 NeedsCompilation: no -Packaged: 2017-09-06 18:20:52 UTC; sebastian +Packaged: 2017-12-04 12:08:45 UTC; sebastian Author: Sebastian Gibb [aut, cre], Pietro Franceschi [ctb] Maintainer: Sebastian Gibb Repository: CRAN -Date/Publication: 2017-09-06 18:29:52 UTC +Date/Publication: 2017-12-04 12:30:50 UTC Binary files /tmp/tmpJ293AM/6uYyMpSWqE/r-cran-maldiquantforeign-0.11/inst/doc/MALDIquantForeign-intro.pdf and /tmp/tmpJ293AM/Bqvbfh784S/r-cran-maldiquantforeign-0.11.1/inst/doc/MALDIquantForeign-intro.pdf differ diff -Nru r-cran-maldiquantforeign-0.11/MD5 r-cran-maldiquantforeign-0.11.1/MD5 --- r-cran-maldiquantforeign-0.11/MD5 2017-09-06 18:29:52.000000000 +0000 +++ r-cran-maldiquantforeign-0.11.1/MD5 2017-12-04 12:30:50.000000000 +0000 @@ -1,6 +1,6 @@ -759e4f365a2e4eb8873dd5ec3854f1fa *DESCRIPTION +57129369c3eceae00c8ebaf6488e2c5a *DESCRIPTION 239f2ca23dfb8e6e1c412d77e5fef820 *NAMESPACE -7e0651d77ecb4004023d6ddb53f6c9bc *NEWS +24882c2b22392b04f7a44a8625156956 *NEWS 1a7732f3a9b780b00941aca4a1b4c089 *R/AllGenerics.R b09f7c3504a3dd158913ce0eda3d1085 *R/MALDIquantForeign-parallel.R 5de22a3830c2835b77386c3e075472a5 *R/analyze-functions.R @@ -15,7 +15,7 @@ 263ffe0dc55509e70e46dc1427a308b1 *R/exportMzMl-methods.R ecfcf756e38f25fa2621f612ca25b84a *R/exportTab-methods.R c78a3559e9ec87598fd7d6a7a8ddb53a *R/fileFormats.R -71f2cefaad4fcb88d6b136dad6c6bf6d *R/filename-functions.R +5df96127fe7c883d20f2d8116aca4e24 *R/filename-functions.R 62643bebde1acd81fab75bdc3bda857a *R/filename-methods.R 835269077b9e05e808e49a4c2b12c7e4 *R/ibd-functions.R e5d288e6ded053a3a1dbfde848cdd61e *R/import-functions.R @@ -29,7 +29,7 @@ 0880b48b4392bf8adadddcc5315252cc *R/importMzMl-functions.R 247d4c41523ecd95c18f0d9d544ba843 *R/importMzXml-functions.R b47f5e01c2d80d4c5426a7fdb6923b49 *R/importTab-functions.R -6d0a6289f96a249f6890db871f7feaab *R/imzMl-functions.R +35c92145f354caabe55177ea49a6000b *R/imzMl-functions.R eb4a9e6131098dc3ec0a081fad980898 *R/list.files-functions.R 4bb38e350bb16d36e38e3929821bb9a1 *R/msd-functions.R 18b7c73ebc1c6e50944830351b4f3778 *R/msg-functions.R @@ -42,10 +42,10 @@ bdbaecef5012d4164a71525922ec9d4f *R/testChecksum-functions.R 0c2ae5fafc1ae70528f0e5bb02ffac8f *R/uuid-functions.R a4b92b6f309e60be3af2363e2066f47c *R/xml-functions.R -8ea2ff6d03ea2e9b7ec2986b2a198591 *build/vignette.rds +0a583394ee68e2d618a6d6587c250347 *build/vignette.rds 9b47d07debb7bc07b22ff5877a5ad37e *inst/doc/MALDIquantForeign-intro.R fa3507f704915074f42215d1a7acaf19 *inst/doc/MALDIquantForeign-intro.Rnw -60a191ee9f663cd7e38dad0c7d3288e3 *inst/doc/MALDIquantForeign-intro.pdf +0077ce3e25cfd1badf3a181a6afdbd66 *inst/doc/MALDIquantForeign-intro.pdf 9274dd34d675950326a222a952309a17 *inst/exampledata/ascii.txt 85077ca13692b5a2469af51d18cffd64 *inst/exampledata/brukerflex/0_A1/1/1SLin/acqu fe054ad2e7b98bee673f9ff22d50f00c *inst/exampledata/brukerflex/0_A1/1/1SLin/fid @@ -95,7 +95,7 @@ 0b42556a51f96c78b0314e4d79ee07a8 *tests/testthat/test_exportMzMl-methods.R bc154ef954d4012596f14aeeb9f9d90a *tests/testthat/test_exportTab-methods.R c0c445cb3dc0146a53ed5c7cb4326467 *tests/testthat/test_fileFormats.R -c525ed145225cdca63726e9b8386b4de *tests/testthat/test_filename-functions.R +4c794d2aa272d40186b93e7d19ab3d25 *tests/testthat/test_filename-functions.R 2c30aa4314b05352630a6a9a74578475 *tests/testthat/test_ibd-functions.R 84ac426570d99e3a3e4639013b4ca6b7 *tests/testthat/test_importBrukerFlex-functions.R 071c254f1a0870eb09163742840ee3eb *tests/testthat/test_importCdf-functions.R diff -Nru r-cran-maldiquantforeign-0.11/NEWS r-cran-maldiquantforeign-0.11.1/NEWS --- r-cran-maldiquantforeign-0.11/NEWS 2017-09-01 17:12:43.000000000 +0000 +++ r-cran-maldiquantforeign-0.11.1/NEWS 2017-12-04 12:07:58.000000000 +0000 @@ -1,6 +1,15 @@ RELEASE HISTORY OF THE "MALDIquantForeign" PACKAGE ================================================== +CHANGES IN MALDIquantForeign VERSION 0.11.1 [2017-12-04]: +--------------------------------------------------------- + +BUGFIX + +* Fix handling of "processed" argument in `.writeImzMlDocument`; see #21. +* Fix `export` method if there was no filename given. + + CHANGES IN MALDIquantForeign VERSION 0.11 [2017-09-01]: ------------------------------------------------------- diff -Nru r-cran-maldiquantforeign-0.11/R/filename-functions.R r-cran-maldiquantforeign-0.11.1/R/filename-functions.R --- r-cran-maldiquantforeign-0.11/R/filename-functions.R 2016-12-08 22:26:41.000000000 +0000 +++ r-cran-maldiquantforeign-0.11.1/R/filename-functions.R 2017-12-04 12:07:58.000000000 +0000 @@ -56,6 +56,11 @@ .cutFilenames <- function(x) { l <- strsplit(x, split=.Platform$file.sep, fixed=TRUE) + if (any(lengths(l) == 0)) { + return(sprintf(paste0("%0", trunc(log10(length(x))) + 1L, "d"), + seq_along(x))) + } + nCol <- unlist(lapply(l, length)) mCol <- max(nCol) diff -Nru r-cran-maldiquantforeign-0.11/R/imzMl-functions.R r-cran-maldiquantforeign-0.11.1/R/imzMl-functions.R --- r-cran-maldiquantforeign-0.11/R/imzMl-functions.R 2017-08-27 17:54:58.000000000 +0000 +++ r-cran-maldiquantforeign-0.11.1/R/imzMl-functions.R 2017-12-04 12:07:58.000000000 +0000 @@ -52,7 +52,8 @@ .writeIbd(x, ibdFile, uuid=uuid, processed=processed) sha1 <- digest::digest(ibdFile, algo="sha1", file=TRUE) - .writeMzMlDocument(x=.addIbdOffsets(x), file=file, id=id, + .writeMzMlDocument(x=.addIbdOffsets(x, processed=processed), + file=file, id=id, imsArgs=list(uuid=uuid, sha1=sha1, processed=processed), ...) } diff -Nru r-cran-maldiquantforeign-0.11/tests/testthat/test_filename-functions.R r-cran-maldiquantforeign-0.11.1/tests/testthat/test_filename-functions.R --- r-cran-maldiquantforeign-0.11/tests/testthat/test_filename-functions.R 2015-05-10 10:53:11.000000000 +0000 +++ r-cran-maldiquantforeign-0.11.1/tests/testthat/test_filename-functions.R 2017-12-04 12:07:58.000000000 +0000 @@ -55,6 +55,8 @@ expect_identical(MALDIquantForeign:::.uniqueBaseFilenames( c("/home/user/foo.bar", "/home/user/foo.bar"), fileExtension="txt"), c("foo_1.txt", "foo_2.txt")) + expect_identical(MALDIquantForeign:::.uniqueBaseFilenames( + c("", "")), c("1.csv", "2.csv")) }) test_that(".make.unique", {