# This file created by conda-build 3.24.0
# meta.yaml template originally from:
# /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/bioconductor-msnid, last modified Thu May 18 21:48:09 2023
# ------------------------------------------------

package:
  name: bioconductor-msnid
  version: 1.32.0
source:
  md5: a3fbc76e3678abed4b9837d7908a1523
  url:
    - https://bioarchive.galaxyproject.org/MSnID_1.32.0.tar.gz
    - https://bioconductor.org/packages/3.16/bioc/src/contrib/Archive/MSnID/MSnID_1.32.0.tar.gz
    - https://bioconductor.org/packages/3.16/bioc/src/contrib/MSnID_1.32.0.tar.gz
    - https://depot.galaxyproject.org/software/bioconductor-msnid/bioconductor-msnid_1.32.0_src_all.tar.gz
build:
  number: '1'
  rpaths:
    - lib/
    - lib/R/lib/
  string: r42hc0ef7c4_1
requirements:
  build:
    - ca-certificates 2023.5.7 h8857fd0_0
    - cctools_osx-64 973.0.1 h48a5a9d_13
    - clang 15.0.7 h694c41f_2
    - clang-15 15.0.7 default_hdb78580_2
    - clang_osx-64 15.0.7 h03d6864_2
    - clangxx 15.0.7 default_hdb78580_2
    - clangxx_osx-64 15.0.7 h2133e9c_2
    - compiler-rt 15.0.7 he1888fc_1
    - compiler-rt_osx-64 15.0.7 he1888fc_1
    - icu 72.1 h7336db1_0
    - ld64_osx-64 609 h8ce0179_13
    - libclang-cpp15 15.0.7 default_hdb78580_2
    - libcxx 16.0.4 hd57cbcb_0
    - libiconv 1.17 hac89ed1_0
    - libllvm15 15.0.7 he4b1e75_2
    - libxml2 2.11.3 hd95e348_2
    - libzlib 1.2.13 hfd90126_4
    - llvm-tools 15.0.7 he4b1e75_2
    - openssl 3.1.0 h8a1eda9_3
    - sigtool 0.1.3 h88f4db0_0
    - tapi 1100.0.11 h9ce4665_0
    - xz 5.2.6 h775f41a_0
    - zstd 1.5.2 hbc0c0cd_6
  host:
    - _r-mutex 1.0.1 anacondar_1
    - argcomplete 3.0.8 pyhd8ed1ab_0
    - bioconductor-affy 1.76.0 r42h3be46a4_2
    - bioconductor-affyio 1.68.0 r42h4c50009_1
    - bioconductor-annotationdbi 1.60.0 r42hdfd78af_0
    - bioconductor-annotationhub 3.6.0 r42hdfd78af_0
    - bioconductor-biobase 2.58.0 r42h4c50009_1
    - bioconductor-biocfilecache 2.6.0 r42hdfd78af_0
    - bioconductor-biocgenerics 0.44.0 r42hdfd78af_0
    - bioconductor-biocparallel 1.32.5 r42hc0ef7c4_1
    - bioconductor-biocstyle 2.26.0 r42hdfd78af_0
    - bioconductor-biocversion 3.16.0 r42hdfd78af_0
    - bioconductor-biostrings 2.66.0 r42h3be46a4_0
    - bioconductor-data-packages 20230420 hdfd78af_0
    - bioconductor-edger 3.40.0 r42hb890f52_0
    - bioconductor-genomeinfodb 1.34.9 r42hdfd78af_0
    - bioconductor-genomeinfodbdata 1.2.9 r42hdfd78af_0
    - bioconductor-impute 1.72.0 r42h1302f76_1
    - bioconductor-interactivedisplaybase 1.36.0 r42hdfd78af_0
    - bioconductor-iranges 2.32.0 r42h3be46a4_0
    - bioconductor-keggrest 1.38.0 r42hdfd78af_0
    - bioconductor-limma 3.54.0 r42h4c50009_1
    - bioconductor-mscoreutils 1.10.0 r42hb890f52_0
    - bioconductor-msmseda 1.36.0 r42hdfd78af_0
    - bioconductor-msmstests 1.36.0 r42hdfd78af_0
    - bioconductor-msnbase 2.24.0 r42hb890f52_0
    - bioconductor-mzid 1.36.0 r42hdfd78af_0
    - bioconductor-mzr 2.32.0 r42hb890f52_0
    - bioconductor-pcamethods 1.90.0 r42hb890f52_0
    - bioconductor-preprocesscore 1.60.2 r42h4c50009_2
    - bioconductor-protgenerics 1.30.0 r42hdfd78af_0
    - bioconductor-qvalue 2.30.0 r42hdfd78af_0
    - bioconductor-rhdf5lib 1.20.0 r42h4c50009_2
    - bioconductor-s4vectors 0.36.0 r42h4c50009_1
    - bioconductor-vsn 3.66.0 r42h3be46a4_0
    - bioconductor-xvector 0.38.0 r42h3be46a4_0
    - bioconductor-zlibbioc 1.44.0 r42h4c50009_2
    - blosc 1.21.4 heccf04b_0
    - bwidget 1.9.14 h694c41f_1
    - bzip2 1.0.8 h0d85af4_4
    - c-ares 1.19.0 h0dc2134_0
    - ca-certificates 2023.5.7 h8857fd0_0
    - cairo 1.16.0 h297c08e_1015
    - cctools_osx-64 973.0.1 h5676edf_13
    - clang 16.0.3 hc177806_2
    - clang-16 16.0.3 default_h762fdd7_2
    - clang_osx-64 16.0.3 h51755a5_1
    - clangxx 16.0.3 default_h762fdd7_2
    - clangxx_osx-64 16.0.3 hc8f2981_1
    - compiler-rt 16.0.3 he1888fc_1
    - compiler-rt_osx-64 16.0.3 he1888fc_1
    - curl 8.1.0 hbee3ae8_0
    - expat 2.5.0 hf0c8a7f_1
    - font-ttf-dejavu-sans-mono 2.37 hab24e00_0
    - font-ttf-inconsolata 3.000 h77eed37_0
    - font-ttf-source-code-pro 2.038 h77eed37_0
    - font-ttf-ubuntu 0.83 hab24e00_0
    - fontconfig 2.14.2 h5bb23bf_0
    - fonts-conda-ecosystem 1 0
    - fonts-conda-forge 1 0
    - freetype 2.12.1 h3f81eb7_1
    - fribidi 1.0.10 hbcb3906_0
    - gettext 0.21.1 h8a4c099_0
    - gfortran_impl_osx-64 11.3.0 h1f927f5_31
    - gfortran_osx-64 11.3.0 h18f7dce_1
    - gmp 6.2.1 h2e338ed_0
    - graphite2 1.3.13 h2e338ed_1001
    - gsl 2.7 h93259b0_0
    - harfbuzz 7.3.0 h413ba03_0
    - hdf4 4.2.15 h9804679_6
    - hdf5 1.14.0 nompi_hbf0aa07_103
    - icu 72.1 h7336db1_0
    - isl 0.25 hb486fe8_0
    - jq 1.6 hc929b4f_1000
    - krb5 1.20.1 h049b76e_0
    - ld64_osx-64 609 hbfe4790_13
    - lerc 4.0.0 hb486fe8_0
    - libaec 1.0.6 hf0c8a7f_1
    - libblas 3.9.0 5_h0661a58_netlib
    - libcblas 3.9.0 5_h0661a58_netlib
    - libclang-cpp16 16.0.3 default_h762fdd7_2
    - libcurl 8.1.0 hbee3ae8_0
    - libcxx 16.0.4 hd57cbcb_0
    - libdeflate 1.18 hac1461d_0
    - libedit 3.1.20191231 h0678c8f_2
    - libev 4.33 haf1e3a3_1
    - libexpat 2.5.0 hf0c8a7f_1
    - libffi 3.4.2 h0d85af4_5
    - libgfortran 5.0.0 11_3_0_h97931a8_31
    - libgfortran-devel_osx-64 11.3.0 h824d247_31
    - libgfortran5 12.2.0 he409387_31
    - libglib 2.76.2 hc62aa5d_0
    - libiconv 1.17 hac89ed1_0
    - libjpeg-turbo 2.1.5.1 hb7f2c08_0
    - liblapack 3.9.0 5_h0661a58_netlib
    - libllvm16 16.0.3 hf646ca0_1
    - libnetcdf 4.9.2 nompi_h4ab8a84_104
    - libnghttp2 1.52.0 he2ab024_0
    - libpng 1.6.39 ha978bb4_0
    - libsqlite 3.42.0 h58db7d2_0
    - libssh2 1.10.0 h47af595_3
    - libtiff 4.5.0 hedf67fa_6
    - libwebp-base 1.3.0 hb7f2c08_0
    - libxml2 2.10.4 h554bb67_0
    - libzip 1.9.2 h6db710c_1
    - libzlib 1.2.13 hfd90126_4
    - llvm-openmp 16.0.4 hff08bdf_0
    - llvm-tools 16.0.3 hf646ca0_1
    - lz4-c 1.9.4 hf0c8a7f_0
    - make 4.3 h22f3db7_1
    - mpc 1.3.1 h81bd1dd_0
    - mpfr 4.2.0 h4f9bd69_0
    - ncurses 6.3 h96cf925_1
    - oniguruma 6.9.8 hac89ed1_0
    - openssl 3.1.0 h8a1eda9_3
    - pandoc 2.19.2 h694c41f_2
    - pango 1.50.14 hbce5e75_1
    - pcre2 10.40 h1c4e4bc_0
    - pixman 0.40.0 hbcb3906_0
    - python 3.11.3 h99528f9_0_cpython
    - python_abi 3.11 3_cp311
    - pyyaml 6.0 py311h5547dcb_5
    - r-askpass 1.1 r42h815d134_3
    - r-base 4.2.3 h29e1f52_2
    - r-base64enc 0.1_3 r42h815d134_1005
    - r-bh 1.81.0_1 r42hc72bb7e_0
    - r-biocmanager 1.30.20 r42hc72bb7e_0
    - r-bit 4.0.5 r42h815d134_0
    - r-bit64 4.0.5 r42h815d134_1
    - r-bitops 1.0_7 r42h815d134_1
    - r-blob 1.2.4 r42hc72bb7e_0
    - r-bookdown 0.34 r42hc72bb7e_0
    - r-bslib 0.4.2 r42hc72bb7e_0
    - r-cachem 1.0.8 r42h6dc245f_0
    - r-catools 1.18.2 r42h49197e3_1
    - r-cli 3.6.1 r42h49197e3_0
    - r-clue 0.3_64 r42h815d134_0
    - r-cluster 2.1.4 r42h1e4e481_0
    - r-codetools 0.2_19 r42hc72bb7e_0
    - r-colorspace 2.1_0 r42h815d134_0
    - r-commonmark 1.9.0 r42h815d134_0
    - r-cpp11 0.4.3 r42hc72bb7e_0
    - r-crayon 1.5.2 r42hc72bb7e_1
    - r-crosstalk 1.2.0 r42hc72bb7e_1
    - r-curl 4.3.3 r42h0100ac3_2
    - r-data.table 1.14.8 r42h557251b_0
    - r-dbi 1.1.3 r42hc72bb7e_1
    - r-dbplyr 2.3.2 r42hc72bb7e_0
    - r-digest 0.6.31 r42h49197e3_0
    - r-doparallel 1.0.17 r42hc72bb7e_1
    - r-dplyr 1.1.2 r42hac7d2d5_0
    - r-dt 0.28 r42hc72bb7e_0
    - r-ellipsis 0.3.2 r42h815d134_1
    - r-evaluate 0.21 r42hc72bb7e_0
    - r-fansi 1.0.4 r42h815d134_0
    - r-farver 2.1.1 r42h49197e3_1
    - r-fastmap 1.1.1 r42h49197e3_0
    - r-filelock 1.0.2 r42h815d134_1003
    - r-fontawesome 0.5.1 r42hc72bb7e_0
    - r-foreach 1.5.2 r42hc72bb7e_1
    - r-formatr 1.14 r42hc72bb7e_0
    - r-fs 1.6.2 r42hac7d2d5_0
    - r-futile.logger 1.4.3 r42hc72bb7e_1004
    - r-futile.options 1.0.1 r42hc72bb7e_1003
    - r-generics 0.1.3 r42hc72bb7e_1
    - r-ggplot2 3.4.2 r42hc72bb7e_0
    - r-glue 1.6.2 r42h815d134_1
    - r-gplots 3.1.3 r42hc72bb7e_1
    - r-gtable 0.3.3 r42hc72bb7e_0
    - r-gtools 3.9.4 r42h815d134_0
    - r-highr 0.10 r42hc72bb7e_0
    - r-htmltools 0.5.5 r42h49197e3_0
    - r-htmlwidgets 1.6.2 r42hc72bb7e_0
    - r-httpuv 1.6.11 r42hac7d2d5_0
    - r-httr 1.4.6 r42hc72bb7e_0
    - r-isoband 0.2.7 r42h49197e3_1
    - r-iterators 1.0.14 r42hc72bb7e_1
    - r-jquerylib 0.1.4 r42hc72bb7e_1
    - r-jsonlite 1.8.4 r42h815d134_0
    - r-kernsmooth 2.23_21 r42h06293e5_0
    - r-knitr 1.42 r42hc72bb7e_1
    - r-labeling 0.4.2 r42hc72bb7e_2
    - r-lambda.r 1.2.4 r42hc72bb7e_2
    - r-later 1.3.1 r42h670e93c_0
    - r-lattice 0.21_8 r42h815d134_0
    - r-lazyeval 0.2.2 r42h815d134_3
    - r-lifecycle 1.0.3 r42hc72bb7e_1
    - r-locfit 1.5_9.7 r42h815d134_0
    - r-magrittr 2.0.3 r42h815d134_1
    - r-maldiquant 1.22.1 r42h815d134_0
    - r-mass 7.3_60 r42h6dc245f_0
    - r-matrix 1.5_4 r42hce01bf1_0
    - r-memoise 2.0.1 r42hc72bb7e_1
    - r-mgcv 1.8_42 r42h40f944a_0
    - r-mime 0.12 r42h815d134_1
    - r-munsell 0.5.0 r42hc72bb7e_1005
    - r-ncdf4 1.21 r42hb51f3f3_3
    - r-nlme 3.1_162 r42h1e4e481_0
    - r-openssl 2.0.6 r42hfeb9312_0
    - r-pillar 1.9.0 r42hc72bb7e_0
    - r-pkgconfig 2.0.3 r42hc72bb7e_2
    - r-plogr 0.2.0 r42hc72bb7e_1004
    - r-plyr 1.8.8 r42h49197e3_0
    - r-png 0.1_8 r42hbf2103b_0
    - r-promises 1.2.0.1 r42h49197e3_1
    - r-purrr 1.0.1 r42h815d134_0
    - r-r.cache 0.16.0 r42hc72bb7e_1
    - r-r.methodss3 1.8.2 r42hc72bb7e_1
    - r-r.oo 1.25.0 r42hc72bb7e_1
    - r-r.utils 2.12.2 r42hc72bb7e_0
    - r-r6 2.5.1 r42hc72bb7e_1
    - r-rappdirs 0.3.3 r42h815d134_1
    - r-rcolorbrewer 1.1_3 r42h785f33e_1
    - r-rcpp 1.0.10 r42h49197e3_0
    - r-rcurl 1.98_1.12 r42h0100ac3_1
    - r-reshape2 1.4.4 r42h49197e3_2
    - r-rlang 1.1.1 r42hac7d2d5_0
    - r-rmarkdown 2.21 r42hc72bb7e_0
    - r-rsqlite 2.3.1 r42h49197e3_0
    - r-runit 0.4.32 r42hc72bb7e_1003
    - r-sass 0.4.6 r42hac7d2d5_0
    - r-scales 1.2.1 r42hc72bb7e_1
    - r-shiny 1.7.4 r42h785f33e_0
    - r-snow 0.4_4 r42hc72bb7e_1
    - r-sourcetools 0.1.7_1 r42h49197e3_0
    - r-stringi 1.7.12 r42hf939c12_1
    - r-stringr 1.5.0 r42h785f33e_0
    - r-sys 3.4.1 r42h815d134_0
    - r-tibble 3.2.1 r42h815d134_1
    - r-tidyr 1.3.0 r42h49197e3_0
    - r-tidyselect 1.2.0 r42hbe3e9c8_0
    - r-tinytex 0.45 r42hc72bb7e_0
    - r-utf8 1.2.3 r42h815d134_0
    - r-vctrs 0.6.2 r42hac7d2d5_0
    - r-viridislite 0.4.1 r42hc72bb7e_1
    - r-withr 2.5.0 r42hc72bb7e_1
    - r-xfun 0.39 r42hac7d2d5_0
    - r-xml 3.99_0.14 r42h67ce8dc_0
    - r-xtable 1.8_4 r42hc72bb7e_4
    - r-yaml 2.3.7 r42h815d134_0
    - readline 8.2 h9e318b2_1
    - setuptools 67.7.2 pyhd8ed1ab_0
    - sigtool 0.1.3 h88f4db0_0
    - snappy 1.1.10 h225ccf5_0
    - tapi 1100.0.11 h9ce4665_0
    - tk 8.6.12 h5dbffcc_0
    - tktable 2.10 h49f0cf7_3
    - toml 0.10.2 pyhd8ed1ab_0
    - tomlkit 0.11.8 pyha770c72_0
    - tzdata 2023c h71feb2d_0
    - xmltodict 0.13.0 pyhd8ed1ab_0
    - xz 5.2.6 h775f41a_0
    - yaml 0.2.5 h0d85af4_2
    - yq 3.2.2 pyhd8ed1ab_0
    - zlib 1.2.13 hfd90126_4
    - zstd 1.5.2 hbc0c0cd_6
  run:
    - bioconductor-annotationdbi >=1.60.0,<1.61.0
    - bioconductor-annotationhub >=3.6.0,<3.7.0
    - bioconductor-biobase >=2.58.0,<2.59.0
    - bioconductor-biocgenerics >=0.44.0,<0.45.0
    - bioconductor-biocstyle >=2.26.0,<2.27.0
    - bioconductor-biostrings >=2.66.0,<2.67.0
    - bioconductor-msmstests >=1.36.0,<1.37.0
    - bioconductor-msnbase >=2.24.0,<2.25.0
    - bioconductor-mzid >=1.36.0,<1.37.0
    - bioconductor-mzr >=2.32.0,<2.33.0
    - bioconductor-protgenerics >=1.30.0,<1.31.0
    - libblas >=3.9.0,<4.0a0
    - libcxx >=15.0.7
    - liblapack >=3.9.0,<4.0a0
    - r-base >=4.2,<4.3.0a0
    - r-data.table
    - r-doparallel
    - r-dplyr
    - r-foreach
    - r-ggplot2
    - r-iterators
    - r-purrr
    - r-r.cache
    - r-rcpp
    - r-reshape2
    - r-rlang
    - r-runit
    - r-stringr
    - r-tibble
    - r-xtable
test:
  commands:
    - $R -e "library('MSnID')"
about:
  description: Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or
    text files. After collating the search results from multiple datasets it assesses
    their identification quality and optimize filtering criteria to achieve the maximum
    number of identifications while not exceeding a specified false discovery rate.
    Also contains a number of utilities to explore the MS/MS results and assess missed
    and irregular enzymatic cleavages, mass measurement accuracy, etc.
  home: https://bioconductor.org/packages/3.16/bioc/html/MSnID.html
  license: Artistic-2.0
  summary: Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics
    Identifications
extra:
  copy_test_source_files: true
  final: true
  identifiers:
    - biotools:msnid
    - doi:10.1038/nmeth.3252
