=> Building science/hs-bio Started : Thursday, 19 APR 2018 at 05:31:39 UTC Platform: 5.3-DEVELOPMENT DragonFly v5.3.0.81.g32506c-DEVELOPMENT #29: Tue Apr 10 08:49:52 PDT 2018 marino@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.0-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.0-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- ===> The following configuration options are available for hs-bio-0.5.3_4: DOCS=on: Build and/or install documentation DYNAMIC=on: Add support for dynamic linking HSCOLOUR=off: Colorize generated documentation by HsColour PROFILE=off: Add support for profiling ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/science/hs-bio XDG_CONFIG_HOME=/construction/science/hs-bio HOME=/construction/science/hs-bio TMPDIR="/construction/science/hs-bio/tmp" PATH=/construction/science/hs-bio/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --libdir=/usr/local/lib/cabal/ghc-8.0.2 --libsubdir=bio-0.5.3 --with-gcc=cc --with-ld=ld --with-ar=ar --enable-executable-stripping --haddock-options=-w --with-haddock=/usr/local/bin/haddock --enable-shared --enable-executable-dynamic --disable-profiling --disable-library-profiling -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- DESTDIR=/construction/science/hs-bio/stage TMPDIR=/construction/science/hs-bio/tmp XDG_DATA_HOME=/construction/science/hs-bio XDG_CONFIG_HOME=/construction/science/hs-bio HOME=/construction/science/hs-bio TMPDIR="/construction/science/hs-bio/tmp" PATH=/construction/science/hs-bio/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" NOPROFILE=1 CC="cc" CFLAGS="-pipe -I/usr/local/include -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="-I/usr/local/include" LDFLAGS=" -L/usr/local/lib" LIBS="" CXX="c++" CXXFLAGS=" -pipe -I/usr/local/include -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/science/hs-bio/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- GHC_VERSION=8.0.2 PORTNAME=bio PORTVERSION=0.5.3 LIBDIR_REL=lib/cabal/ghc-8.0.2/bio-0.5.3 PORTDOCS="" PORTEXAMPLES="" OSREL=5.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/cabal/ghc-8.0.2/bio-0.5.3" EXAMPLESDIR="share/examples/cabal/ghc-8.0.2/bio-0.5.3" DATADIR="share/cabal/ghc-8.0.2/bio-0.5.3" WWWDIR="www/bio" ETCDIR="etc/bio" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/cabal/ghc-8.0.2/bio-0.5.3 DOCSDIR=/usr/local/share/doc/cabal/ghc-8.0.2/bio-0.5.3 EXAMPLESDIR=/usr/local/share/examples/cabal/ghc-8.0.2/bio-0.5.3 WWWDIR=/usr/local/www/bio ETCDIR=/usr/local/etc/bio -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.0 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500000 OSVERSION=9999999 OSREL=5.0 _OSRELEASE=5.0-SYNTH -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License LGPL21 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> hs-bio-0.5.3_4 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5.txz Installing pkg-1.10.5... Extracting pkg-1.10.5: .......... done ===> hs-bio-0.5.3_4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of hs-bio-0.5.3_4 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by hs-bio-0.5.3_4 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by hs-bio-0.5.3_4 for building => SHA256 Checksum OK for cabal/bio-0.5.3.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by hs-bio-0.5.3_4 for building ===> Extracting for hs-bio-0.5.3_4 ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by hs-bio-0.5.3_4 for building => SHA256 Checksum OK for cabal/bio-0.5.3.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for hs-bio-0.5.3_4 ===> Applying ports patches for hs-bio-0.5.3_4 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> hs-bio-0.5.3_4 depends on executable: ghc - not found ===> Installing existing package /packages/All/ghc-8.0.2_3.txz Installing ghc-8.0.2_3... `-- Installing gmp-6.1.2... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gmp-6.1.2: .......... done `-- Installing libffi-3.2.1_2... `-- Extracting libffi-3.2.1_2: .......... done `-- Installing libiconv-1.14_11... `-- Extracting libiconv-1.14_11: .......... done `-- Installing ncurses-6.0.0s20171223_1... `-- Extracting ncurses-6.0.0s20171223_1: .......... done Extracting ghc-8.0.2_3: .......... done ===> hs-bio-0.5.3_4 depends on executable: ghc - found ===> Returning to build of hs-bio-0.5.3_4 ===> hs-bio-0.5.3_4 depends on package: ghc>=8.0.2 - found ===> hs-bio-0.5.3_4 depends on package: hs-mtl>=0 - not found ===> Installing existing package /packages/All/hs-mtl-2.2.1_2.txz Installing hs-mtl-2.2.1_2... Extracting hs-mtl-2.2.1_2: .......... done ===> hs-bio-0.5.3_4 depends on package: hs-mtl>=0 - found ===> Returning to build of hs-bio-0.5.3_4 ===> hs-bio-0.5.3_4 depends on package: hs-old-time>=0 - not found ===> Installing existing package /packages/All/hs-old-time-1.1.0.3_2.txz Installing hs-old-time-1.1.0.3_2... `-- Installing hs-old-locale-1.0.0.7_2... `-- Extracting hs-old-locale-1.0.0.7_2: .......... done Extracting hs-old-time-1.1.0.3_2: .......... done ===> hs-bio-0.5.3_4 depends on package: hs-old-time>=0 - found ===> Returning to build of hs-bio-0.5.3_4 ===> hs-bio-0.5.3_4 depends on package: hs-parallel>=0 - not found ===> Installing existing package /packages/All/hs-parallel-3.2.1.1_1.txz Installing hs-parallel-3.2.1.1_1... Extracting hs-parallel-3.2.1.1_1: .......... done ===> hs-bio-0.5.3_4 depends on package: hs-parallel>=0 - found ===> Returning to build of hs-bio-0.5.3_4 ===> hs-bio-0.5.3_4 depends on package: hs-parsec>=0 - not found ===> Installing existing package /packages/All/hs-parsec-3.1.11_1.txz Installing hs-parsec-3.1.11_1... `-- Installing hs-text-1.2.2.2_1... `-- Extracting hs-text-1.2.2.2_1: .......... done Extracting hs-parsec-3.1.11_1: .......... done ===> hs-bio-0.5.3_4 depends on package: hs-parsec>=0 - found ===> Returning to build of hs-bio-0.5.3_4 ===> hs-bio-0.5.3_4 depends on package: hs-QuickCheck>=2 - not found ===> Installing existing package /packages/All/hs-QuickCheck-2.10.0.1_1.txz Installing hs-QuickCheck-2.10.0.1_1... `-- Installing hs-extensible-exceptions-0.1.1.4_9... `-- Extracting hs-extensible-exceptions-0.1.1.4_9: .......... done `-- Installing hs-random-1.1_2... `-- Extracting hs-random-1.1_2: .......... done `-- Installing hs-tf-random-0.5_4... | `-- Installing hs-primitive-0.6.2.0_1... | `-- Extracting hs-primitive-0.6.2.0_1: .......... done `-- Extracting hs-tf-random-0.5_4: .......... done Extracting hs-QuickCheck-2.10.0.1_1: .......... done ===> hs-bio-0.5.3_4 depends on package: hs-QuickCheck>=2 - found ===> Returning to build of hs-bio-0.5.3_4 ===> hs-bio-0.5.3_4 depends on package: hs-random>=0 - found ===> hs-bio-0.5.3_4 depends on package: hs-tagsoup>=0.8 - not found ===> Installing existing package /packages/All/hs-tagsoup-0.14.1_1.txz Installing hs-tagsoup-0.14.1_1... Extracting hs-tagsoup-0.14.1_1: .......... done ===> hs-bio-0.5.3_4 depends on package: hs-tagsoup>=0.8 - found ===> Returning to build of hs-bio-0.5.3_4 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> hs-bio-0.5.3_4 depends on shared library: libgmp.so - found (/usr/local/lib/libgmp.so) ===> hs-bio-0.5.3_4 depends on shared library: libiconv.so - found (/usr/local/lib/libiconv.so) -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for hs-bio-0.5.3_4 [1 of 1] Compiling Main ( Setup.hs, Setup.o ) Linking ./setup ... Configuring bio-0.5.3... -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for hs-bio-0.5.3_4 Building bio-0.5.3... Preprocessing library bio-0.5.3... [ 1 of 46] Compiling Bio.Util.Parsex ( Bio/Util/Parsex.hs, dist/build/Bio/Util/Parsex.o ) [ 2 of 46] Compiling Bio.Util ( Bio/Util.hs, dist/build/Bio/Util.o ) [ 3 of 46] Compiling Bio.Sequence.SeqData ( Bio/Sequence/SeqData.hs, dist/build/Bio/Sequence/SeqData.o ) [ 4 of 46] Compiling Bio.Sequence.TwoBit ( Bio/Sequence/TwoBit.hs, dist/build/Bio/Sequence/TwoBit.o ) Bio/Sequence/TwoBit.hs:256:26: warning: [-Wname-shadowing] This binding for ‘ns’ shadows the existing binding bound at Bio/Sequence/TwoBit.hs:234:8 Bio/Sequence/TwoBit.hs:261:21: warning: [-Wname-shadowing] This binding for ‘ns’ shadows the existing binding bound at Bio/Sequence/TwoBit.hs:234:8 Bio/Sequence/TwoBit.hs:360:29: warning: [-Wincomplete-patterns] Pattern match(es) are non-exhaustive In a case alternative: Patterns not matched: p where p is not one of {'G', 'A', 'C', 'T'} Bio/Sequence/TwoBit.hs:396:51: warning: [-Wincomplete-patterns] Pattern match(es) are non-exhaustive In a case alternative: Patterns not matched: p where p is not one of {4, 3, 2, 1} [ 5 of 46] Compiling Bio.Sequence.SFF_name ( Bio/Sequence/SFF_name.hs, dist/build/Bio/Sequence/SFF_name.o ) [ 6 of 46] Compiling Bio.Sequence.SFF ( Bio/Sequence/SFF.hs, dist/build/Bio/Sequence/SFF.o ) [ 7 of 46] Compiling Bio.Sequence.SFF_filters ( Bio/Sequence/SFF_filters.hs, dist/build/Bio/Sequence/SFF_filters.o ) [ 8 of 46] Compiling Bio.Sequence.Phd ( Bio/Sequence/Phd.hs, dist/build/Bio/Sequence/Phd.o ) [ 9 of 46] Compiling Bio.Sequence.HashWord ( Bio/Sequence/HashWord.lhs, dist/build/Bio/Sequence/HashWord.o ) [10 of 46] Compiling Bio.Sequence.GeneOntology ( Bio/Sequence/GeneOntology.hs, dist/build/Bio/Sequence/GeneOntology.o ) Bio/Sequence/GeneOntology.hs:162:1: warning: [-Wtabs] Tab character found here, and in 12 further locations. Please use spaces instead. [11 of 46] Compiling Bio.Sequence.KEGG ( Bio/Sequence/KEGG.hs, dist/build/Bio/Sequence/KEGG.o ) [12 of 46] Compiling Bio.Sequence.GOA ( Bio/Sequence/GOA.hs, dist/build/Bio/Sequence/GOA.o ) [13 of 46] Compiling Bio.Sequence.Fasta ( Bio/Sequence/Fasta.hs, dist/build/Bio/Sequence/Fasta.o ) Bio/Sequence/Fasta.hs:31:1: warning: [-Wunused-imports] The import of ‘chr’ from module ‘Data.Char’ is redundant [14 of 46] Compiling Bio.Sequence.FastQ ( Bio/Sequence/FastQ.hs, dist/build/Bio/Sequence/FastQ.o ) [15 of 46] Compiling Bio.Sequence.Entropy ( Bio/Sequence/Entropy.hs, dist/build/Bio/Sequence/Entropy.o ) [16 of 46] Compiling Bio.Sequence.AminoProperties ( Bio/Sequence/AminoProperties.hs, dist/build/Bio/Sequence/AminoProperties.o ) [17 of 46] Compiling Bio.Sequence ( Bio/Sequence.hs, dist/build/Bio/Sequence.o ) [18 of 46] Compiling Bio.Location.Strand ( Bio/Location/Strand.hs, dist/build/Bio/Location/Strand.o ) [19 of 46] Compiling Bio.Location.Position ( Bio/Location/Position.hs, dist/build/Bio/Location/Position.o ) Bio/Location/Position.hs:21:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/Location/Position.hs:24:1: warning: [-Wunused-imports] The import of ‘Data.List’ is redundant except perhaps to import instances from ‘Data.List’ To import instances alone, use: import Data.List() Bio/Location/Position.hs:52:11: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Location/Position.hs:54:53: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" [20 of 46] Compiling Bio.Location.OnSeq ( Bio/Location/OnSeq.hs, dist/build/Bio/Location/OnSeq.o ) Bio/Location/OnSeq.hs:19:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/Location/OnSeq.hs:21:1: warning: [-Wunused-imports] The import of ‘Data.List’ is redundant except perhaps to import instances from ‘Data.List’ To import instances alone, use: import Data.List() Bio/Location/OnSeq.hs:23:1: warning: [-Wunused-imports] The import of ‘Data.Monoid’ is redundant except perhaps to import instances from ‘Data.Monoid’ To import instances alone, use: import Data.Monoid() Bio/Location/OnSeq.hs:54:15: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Location/OnSeq.hs:57:37: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" [21 of 46] Compiling Bio.Location.ContigLocation ( Bio/Location/ContigLocation.hs, dist/build/Bio/Location/ContigLocation.o ) Bio/Location/ContigLocation.hs:29:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/Location/ContigLocation.hs:100:13: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Location/ContigLocation.hs:106:38: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" [22 of 46] Compiling Bio.Location.Location ( Bio/Location/Location.hs, dist/build/Bio/Location/Location.o ) Bio/Location/Location.hs:30:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/Location/Location.hs:75:13: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" [23 of 46] Compiling Bio.Location.LocMap ( Bio/Location/LocMap.hs, dist/build/Bio/Location/LocMap.o ) Bio/Location/LocMap.hs:29:1: warning: [-Wunused-imports] The import of ‘Data.Maybe’ is redundant except perhaps to import instances from ‘Data.Maybe’ To import instances alone, use: import Data.Maybe() Bio/Location/LocMap.hs:30:1: warning: [-Wunused-imports] The import of ‘Data.Monoid’ is redundant except perhaps to import instances from ‘Data.Monoid’ To import instances alone, use: import Data.Monoid() Bio/Location/LocMap.hs:50:10: warning: [-Wunused-matches] Defined but not used: ‘zonesize’ [24 of 46] Compiling Bio.Location.SeqLocation ( Bio/Location/SeqLocation.hs, dist/build/Bio/Location/SeqLocation.o ) Bio/Location/SeqLocation.hs:28:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/Location/SeqLocation.hs:77:13: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" [25 of 46] Compiling Bio.Location.SeqLocMap ( Bio/Location/SeqLocMap.hs, dist/build/Bio/Location/SeqLocMap.o ) [26 of 46] Compiling Bio.GFF3.Escape ( Bio/GFF3/Escape.hs, dist/build/Bio/GFF3/Escape.o ) Bio/GFF3/Escape.hs:6:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/GFF3/Escape.hs:16:24: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Escape.hs:28:42: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Escape.hs:29:38: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" [27 of 46] Compiling Bio.GFF3.Feature ( Bio/GFF3/Feature.hs, dist/build/Bio/GFF3/Feature.o ) Bio/GFF3/Feature.hs:13:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/GFF3/Feature.hs:46:11: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Feature.hs:59:35: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Feature.hs:62:52: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Feature.hs:66:50: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Feature.hs:69:55: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Feature.hs:77:60: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Feature.hs:109:20: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Feature.hs:138:10: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Feature.hs:139:30: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" [28 of 46] Compiling Bio.GFF3.FeatureHier ( Bio/GFF3/FeatureHier.hs, dist/build/Bio/GFF3/FeatureHier.o ) Bio/GFF3/FeatureHier.hs:11:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/GFF3/FeatureHier.hs:30:14: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:32:37: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:34:22: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:36:37: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:38:14: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:59:12: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:65:56: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:70:57: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:72:12: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:77:48: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:81:56: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:83:49: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:86:57: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" [29 of 46] Compiling Bio.GFF3.FeatureHierSequences ( Bio/GFF3/FeatureHierSequences.hs, dist/build/Bio/GFF3/FeatureHierSequences.o ) Bio/GFF3/FeatureHierSequences.hs:12:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/GFF3/FeatureHierSequences.hs:32:11: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:36:15: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:42:45: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:52:14: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:61:13: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:65:17: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:67:40: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:69:21: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:74:26: warning: [-Wdeprecations] In the use of type constructor or class ‘ErrorT’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:75:19: warning: [-Wdeprecations] In the use of data constructor ‘ErrorT’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:75:28: warning: [-Wdeprecations] In the use of ‘runErrorT’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:77:24: warning: [-Wdeprecations] In the use of type constructor or class ‘ErrorT’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:77:74: warning: [-Wdeprecations] In the use of type constructor or class ‘ErrorT’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:80:61: warning: [-Wdeprecations] In the use of ‘runErrorT’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:82:26: warning: [-Wdeprecations] In the use of type constructor or class ‘ErrorT’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:82:80: warning: [-Wdeprecations] In the use of type constructor or class ‘ErrorT’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:85:26: warning: [-Wdeprecations] In the use of ‘mapErrorT’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:87:13: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" [30 of 46] Compiling Bio.GFF3.SGD ( Bio/GFF3/SGD.hs, dist/build/Bio/GFF3/SGD.o ) Bio/GFF3/SGD.hs:10:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/GFF3/SGD.hs:48:18: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:50:56: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:53:16: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:60:23: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:62:62: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:65:21: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:72:15: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:75:44: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:79:16: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:80:30: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:85:28: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:91:17: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" [31 of 46] Compiling Bio.Clustering ( Bio/Clustering.hs, dist/build/Bio/Clustering.o ) [32 of 46] Compiling Bio.Alignment.Soap ( Bio/Alignment/Soap.hs, dist/build/Bio/Alignment/Soap.o ) Bio/Alignment/Soap.hs:9:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/Alignment/Soap.hs:63:11: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:77:28: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:78:78: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:82:46: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:84:19: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:92:36: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:95:18: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:98:41: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:100:21: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:103:44: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:105:19: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:107:48: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" [33 of 46] Compiling Bio.Alignment.PSL ( Bio/Alignment/PSL.hs, dist/build/Bio/Alignment/PSL.o ) [34 of 46] Compiling Bio.Alignment.Bowtie ( Bio/Alignment/Bowtie.hs, dist/build/Bio/Alignment/Bowtie.o ) Bio/Alignment/Bowtie.hs:32:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/Alignment/Bowtie.hs:36:1: warning: [-Wunused-imports] The import of ‘Data.Char’ is redundant except perhaps to import instances from ‘Data.Char’ To import instances alone, use: import Data.Char() Bio/Alignment/Bowtie.hs:74:27: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" [35 of 46] Compiling Bio.Alignment.BlastData ( Bio/Alignment/BlastData.hs, dist/build/Bio/Alignment/BlastData.o ) [36 of 46] Compiling Bio.Alignment.BlastXML ( Bio/Alignment/BlastXML.hs, dist/build/Bio/Alignment/BlastXML.o ) [37 of 46] Compiling Bio.Alignment.BlastFlat ( Bio/Alignment/BlastFlat.hs, dist/build/Bio/Alignment/BlastFlat.o ) [38 of 46] Compiling Bio.Alignment.Blast ( Bio/Alignment/Blast.hs, dist/build/Bio/Alignment/Blast.o ) [39 of 46] Compiling Bio.Alignment.BED ( Bio/Alignment/BED.hs, dist/build/Bio/Alignment/BED.o ) [40 of 46] Compiling Bio.Alignment.AlignData ( Bio/Alignment/AlignData.hs, dist/build/Bio/Alignment/AlignData.o ) Bio/Alignment/AlignData.hs:59:1: warning: [-Wmissing-signatures] Top-level binding with no type signature: showalign :: EditList -> [Char] Bio/Alignment/AlignData.hs:112:9: warning: [-Wincomplete-patterns] Pattern match(es) are non-exhaustive In an equation for ‘mkcol’: Patterns not matched: ([], _) Bio/Alignment/AlignData.hs:121:1: warning: [-Wmissing-signatures] Top-level binding with no type signature: on :: (t2 -> t2 -> t1) -> (t -> t2) -> t -> t -> t1 [41 of 46] Compiling Bio.Alignment.Matrices ( Bio/Alignment/Matrices.hs, dist/build/Bio/Alignment/Matrices.o ) [42 of 46] Compiling Bio.Alignment.Multiple ( Bio/Alignment/Multiple.hs, dist/build/Bio/Alignment/Multiple.o ) [43 of 46] Compiling Bio.Alignment.QAlign ( Bio/Alignment/QAlign.hs, dist/build/Bio/Alignment/QAlign.o ) Bio/Alignment/QAlign.hs:70:9: warning: [-Wincomplete-patterns] Pattern match(es) are non-exhaustive In an equation for ‘mkcol’: Patterns not matched: (_, [], _) Bio/Alignment/QAlign.hs:103:72: warning: [-Wname-shadowing] This binding for ‘x’ shadows the existing binding bound at Bio/Alignment/QAlign.hs:94:15 Bio/Alignment/QAlign.hs:103:86: warning: [-Wname-shadowing] This binding for ‘y’ shadows the existing binding bound at Bio/Alignment/QAlign.hs:94:17 Bio/Alignment/QAlign.hs:104:73: warning: [-Wname-shadowing] This binding for ‘x’ shadows the existing binding bound at Bio/Alignment/QAlign.hs:94:15 Bio/Alignment/QAlign.hs:104:87: warning: [-Wname-shadowing] This binding for ‘y’ shadows the existing binding bound at Bio/Alignment/QAlign.hs:94:17 Bio/Alignment/QAlign.hs:140:11: warning: [-Wincomplete-patterns] Pattern match(es) are non-exhaustive In an equation for ‘overlap_score_select’: Patterns not matched: [] [_, _] (_:_:_:_:_) Bio/Alignment/QAlign.hs:145:14: warning: [-Wname-shadowing] This binding for ‘minf’ shadows the existing binding defined at Bio/Alignment/QAlign.hs:89:1 Bio/Alignment/QAlign.hs:183:11: warning: [-Wincomplete-patterns] Pattern match(es) are non-exhaustive In an equation for ‘overlap_align_select’: Patterns not matched: [] [_, _] (_:_:_:_:_) Bio/Alignment/QAlign.hs:188:1: warning: [-Wunused-top-binds] Defined but not used: ‘overlap_align'’ Bio/Alignment/QAlign.hs:192:11: warning: [-Wincomplete-patterns] Pattern match(es) are non-exhaustive In an equation for ‘overlap_align_select’: Patterns not matched: [] [(((_, _), (_, _)), _, _, _), _] ((((_, _), (_, _)), _, _, _):_:_:_:_) Bio/Alignment/QAlign.hs:193:36: warning: [-Wname-shadowing] This binding for ‘s1’ shadows the existing binding bound at Bio/Alignment/QAlign.hs:188:21 Bio/Alignment/QAlign.hs:193:36: warning: [-Wunused-matches] Defined but not used: ‘s1’ Bio/Alignment/QAlign.hs:193:39: warning: [-Wunused-matches] Defined but not used: ‘es1’ Bio/Alignment/QAlign.hs:193:45: warning: [-Wname-shadowing] This binding for ‘s2’ shadows the existing binding bound at Bio/Alignment/QAlign.hs:188:24 Bio/Alignment/QAlign.hs:193:45: warning: [-Wunused-matches] Defined but not used: ‘s2’ Bio/Alignment/QAlign.hs:196:1: warning: [-Wmissing-signatures] Top-level binding with no type signature: revsnd :: (t, [a]) -> (t, [a]) Bio/Alignment/QAlign.hs:200:14: warning: [-Wname-shadowing] This binding for ‘minf’ shadows the existing binding defined at Bio/Alignment/QAlign.hs:89:1 Bio/Alignment/QAlign.hs:208:1: warning: [-Wmissing-signatures] Top-level binding with no type signature: snd' :: (t2, t3, t1, t) -> t3 Bio/Alignment/QAlign.hs:222:7: warning: [-Wname-shadowing] This binding for ‘or’ shadows the existing binding imported from ‘Prelude’ at Bio/Alignment/QAlign.hs:19:8-27 (and originally defined in ‘Data.Foldable’) [44 of 46] Compiling Bio.Alignment.SAlign ( Bio/Alignment/SAlign.hs, dist/build/Bio/Alignment/SAlign.o ) [45 of 46] Compiling Bio.Alignment.ACE ( Bio/Alignment/ACE.hs, dist/build/Bio/Alignment/ACE.o ) [46 of 46] Compiling Bio.Alignment.AAlign ( Bio/Alignment/AAlign.hs, dist/build/Bio/Alignment/AAlign.o ) Bio/Alignment/AAlign.hs:40:14: warning: [-Wname-shadowing] This binding for ‘minf’ shadows the existing binding defined at Bio/Alignment/AAlign.hs:23:1 Bio/Alignment/AAlign.hs:50:1: warning: [-Wmissing-signatures] Top-level binding with no type signature: max' :: Ord t1 => (t1, t) -> (t1, t) -> (t1, t) Bio/Alignment/AAlign.hs:51:1: warning: [-Wmissing-signatures] Top-level binding with no type signature: fp :: Num t => (t, [a]) -> (t, a) -> (t, [a]) Bio/Alignment/AAlign.hs:64:1: warning: [-Wmissing-signatures] Top-level binding with no type signature: revsnd :: (t, [a]) -> (t, [a]) Bio/Alignment/AAlign.hs:68:14: warning: [-Wname-shadowing] This binding for ‘minf’ shadows the existing binding defined at Bio/Alignment/AAlign.hs:23:1 Preprocessing executable 'flx' for bio-0.5.3... [1 of 4] Compiling Bio.Sequence.SeqData ( Bio/Sequence/SeqData.hs, dist/build/flx/flx-tmp/Bio/Sequence/SeqData.dyn_o ) [2 of 4] Compiling Bio.Sequence.SFF_name ( Bio/Sequence/SFF_name.hs, dist/build/flx/flx-tmp/Bio/Sequence/SFF_name.dyn_o ) [3 of 4] Compiling Bio.Sequence.SFF ( Bio/Sequence/SFF.hs, dist/build/flx/flx-tmp/Bio/Sequence/SFF.dyn_o ) [4 of 4] Compiling Main ( examples/Flx.hs, dist/build/flx/flx-tmp/Main.dyn_o ) Linking dist/build/flx/flx ... Preprocessing executable 'fastout' for bio-0.5.3... [ 1 of 11] Compiling Bio.Sequence.SeqData ( Bio/Sequence/SeqData.hs, dist/build/fastout/fastout-tmp/Bio/Sequence/SeqData.dyn_o ) [ 2 of 11] Compiling Bio.Sequence.TwoBit ( Bio/Sequence/TwoBit.hs, dist/build/fastout/fastout-tmp/Bio/Sequence/TwoBit.dyn_o ) [ 3 of 11] Compiling Bio.Sequence.SFF_name ( Bio/Sequence/SFF_name.hs, dist/build/fastout/fastout-tmp/Bio/Sequence/SFF_name.dyn_o ) [ 4 of 11] Compiling Bio.Sequence.SFF ( Bio/Sequence/SFF.hs, dist/build/fastout/fastout-tmp/Bio/Sequence/SFF.dyn_o ) [ 5 of 11] Compiling Bio.Sequence.Phd ( Bio/Sequence/Phd.hs, dist/build/fastout/fastout-tmp/Bio/Sequence/Phd.dyn_o ) [ 6 of 11] Compiling Bio.Sequence.HashWord ( Bio/Sequence/HashWord.lhs, dist/build/fastout/fastout-tmp/Bio/Sequence/HashWord.dyn_o ) [ 7 of 11] Compiling Bio.Sequence.Fasta ( Bio/Sequence/Fasta.hs, dist/build/fastout/fastout-tmp/Bio/Sequence/Fasta.dyn_o ) [ 8 of 11] Compiling Bio.Sequence.FastQ ( Bio/Sequence/FastQ.hs, dist/build/fastout/fastout-tmp/Bio/Sequence/FastQ.dyn_o ) [ 9 of 11] Compiling Bio.Sequence.Entropy ( Bio/Sequence/Entropy.hs, dist/build/fastout/fastout-tmp/Bio/Sequence/Entropy.dyn_o ) [10 of 11] Compiling Bio.Sequence ( Bio/Sequence.hs, dist/build/fastout/fastout-tmp/Bio/Sequence.dyn_o ) [11 of 11] Compiling Main ( examples/FastOut.hs, dist/build/fastout/fastout-tmp/Main.dyn_o ) Linking dist/build/fastout/fastout ... Preprocessing executable 'frecover' for bio-0.5.3... [1 of 4] Compiling Bio.Sequence.SeqData ( Bio/Sequence/SeqData.hs, dist/build/frecover/frecover-tmp/Bio/Sequence/SeqData.dyn_o ) [2 of 4] Compiling Bio.Sequence.SFF_name ( Bio/Sequence/SFF_name.hs, dist/build/frecover/frecover-tmp/Bio/Sequence/SFF_name.dyn_o ) [3 of 4] Compiling Bio.Sequence.SFF ( Bio/Sequence/SFF.hs, dist/build/frecover/frecover-tmp/Bio/Sequence/SFF.dyn_o ) [4 of 4] Compiling Main ( examples/FRecover.hs, dist/build/frecover/frecover-tmp/Main.dyn_o ) Linking dist/build/frecover/frecover ... Preprocessing executable 'frename' for bio-0.5.3... [1 of 4] Compiling Bio.Sequence.SeqData ( Bio/Sequence/SeqData.hs, dist/build/frename/frename-tmp/Bio/Sequence/SeqData.dyn_o ) [2 of 4] Compiling Bio.Sequence.SFF_name ( Bio/Sequence/SFF_name.hs, dist/build/frename/frename-tmp/Bio/Sequence/SFF_name.dyn_o ) [3 of 4] Compiling Bio.Sequence.SFF ( Bio/Sequence/SFF.hs, dist/build/frename/frename-tmp/Bio/Sequence/SFF.dyn_o ) [4 of 4] Compiling Main ( examples/FRename.hs, dist/build/frename/frename-tmp/Main.dyn_o ) Linking dist/build/frename/frename ... Preprocessing executable 'flowclip' for bio-0.5.3... [1 of 4] Compiling Bio.Sequence.SeqData ( Bio/Sequence/SeqData.hs, dist/build/flowclip/flowclip-tmp/Bio/Sequence/SeqData.dyn_o ) [2 of 4] Compiling Bio.Sequence.SFF_name ( Bio/Sequence/SFF_name.hs, dist/build/flowclip/flowclip-tmp/Bio/Sequence/SFF_name.dyn_o ) [3 of 4] Compiling Bio.Sequence.SFF ( Bio/Sequence/SFF.hs, dist/build/flowclip/flowclip-tmp/Bio/Sequence/SFF.dyn_o ) [4 of 4] Compiling Main ( examples/FlowClip.hs, dist/build/flowclip/flowclip-tmp/Main.dyn_o ) Linking dist/build/flowclip/flowclip ... Preprocessing executable 'orf' for bio-0.5.3... [ 1 of 11] Compiling Bio.Sequence.SeqData ( Bio/Sequence/SeqData.hs, dist/build/orf/orf-tmp/Bio/Sequence/SeqData.dyn_o ) [ 2 of 11] Compiling Bio.Sequence.TwoBit ( Bio/Sequence/TwoBit.hs, dist/build/orf/orf-tmp/Bio/Sequence/TwoBit.dyn_o ) Bio/Sequence/TwoBit.hs:256:26: warning: [-Wname-shadowing] This binding for ‘ns’ shadows the existing binding bound at Bio/Sequence/TwoBit.hs:234:8 Bio/Sequence/TwoBit.hs:261:21: warning: [-Wname-shadowing] This binding for ‘ns’ shadows the existing binding bound at Bio/Sequence/TwoBit.hs:234:8 Bio/Sequence/TwoBit.hs:360:29: warning: [-Wincomplete-patterns] Pattern match(es) are non-exhaustive In a case alternative: Patterns not matched: p where p is not one of {'G', 'A', 'C', 'T'} Bio/Sequence/TwoBit.hs:396:51: warning: [-Wincomplete-patterns] Pattern match(es) are non-exhaustive In a case alternative: Patterns not matched: p where p is not one of {4, 3, 2, 1} [ 3 of 11] Compiling Bio.Sequence.SFF_name ( Bio/Sequence/SFF_name.hs, dist/build/orf/orf-tmp/Bio/Sequence/SFF_name.dyn_o ) [ 4 of 11] Compiling Bio.Sequence.SFF ( Bio/Sequence/SFF.hs, dist/build/orf/orf-tmp/Bio/Sequence/SFF.dyn_o ) [ 5 of 11] Compiling Bio.Sequence.Phd ( Bio/Sequence/Phd.hs, dist/build/orf/orf-tmp/Bio/Sequence/Phd.dyn_o ) [ 6 of 11] Compiling Bio.Sequence.HashWord ( Bio/Sequence/HashWord.lhs, dist/build/orf/orf-tmp/Bio/Sequence/HashWord.dyn_o ) [ 7 of 11] Compiling Bio.Sequence.Fasta ( Bio/Sequence/Fasta.hs, dist/build/orf/orf-tmp/Bio/Sequence/Fasta.dyn_o ) Bio/Sequence/Fasta.hs:31:1: warning: [-Wunused-imports] The import of ‘chr’ from module ‘Data.Char’ is redundant [ 8 of 11] Compiling Bio.Sequence.FastQ ( Bio/Sequence/FastQ.hs, dist/build/orf/orf-tmp/Bio/Sequence/FastQ.dyn_o ) [ 9 of 11] Compiling Bio.Sequence.Entropy ( Bio/Sequence/Entropy.hs, dist/build/orf/orf-tmp/Bio/Sequence/Entropy.dyn_o ) [10 of 11] Compiling Bio.Sequence ( Bio/Sequence.hs, dist/build/orf/orf-tmp/Bio/Sequence.dyn_o ) [11 of 11] Compiling Main ( examples/Orf.hs, dist/build/orf/orf-tmp/Main.dyn_o ) examples/Orf.hs:11:1: warning: [-Wmissing-signatures] Top-level binding with no type signature: doit :: Sequence Nuc -> String examples/Orf.hs:21:1: warning: [-Wmissing-signatures] Top-level binding with no type signature: comp_orflength :: Ord a => (t3, a, t2) -> (t1, a, t) -> Ordering examples/Orf.hs:39:1: warning: [-Wmissing-signatures] Top-level binding with no type signature: takeUntil :: (a -> Bool) -> [a] -> [a] Linking dist/build/orf/orf ... Preprocessing executable 'rselect-pe' for bio-0.5.3... [ 1 of 11] Compiling Bio.Sequence.SeqData ( Bio/Sequence/SeqData.hs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence/SeqData.dyn_o ) [ 2 of 11] Compiling Bio.Sequence.TwoBit ( Bio/Sequence/TwoBit.hs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence/TwoBit.dyn_o ) Bio/Sequence/TwoBit.hs:256:26: warning: [-Wname-shadowing] This binding for ‘ns’ shadows the existing binding bound at Bio/Sequence/TwoBit.hs:234:8 Bio/Sequence/TwoBit.hs:261:21: warning: [-Wname-shadowing] This binding for ‘ns’ shadows the existing binding bound at Bio/Sequence/TwoBit.hs:234:8 Bio/Sequence/TwoBit.hs:360:29: warning: [-Wincomplete-patterns] Pattern match(es) are non-exhaustive In a case alternative: Patterns not matched: p where p is not one of {'G', 'A', 'C', 'T'} Bio/Sequence/TwoBit.hs:396:51: warning: [-Wincomplete-patterns] Pattern match(es) are non-exhaustive In a case alternative: Patterns not matched: p where p is not one of {4, 3, 2, 1} [ 3 of 11] Compiling Bio.Sequence.SFF_name ( Bio/Sequence/SFF_name.hs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence/SFF_name.dyn_o ) [ 4 of 11] Compiling Bio.Sequence.SFF ( Bio/Sequence/SFF.hs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence/SFF.dyn_o ) [ 5 of 11] Compiling Bio.Sequence.Phd ( Bio/Sequence/Phd.hs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence/Phd.dyn_o ) [ 6 of 11] Compiling Bio.Sequence.HashWord ( Bio/Sequence/HashWord.lhs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence/HashWord.dyn_o ) [ 7 of 11] Compiling Bio.Sequence.Fasta ( Bio/Sequence/Fasta.hs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence/Fasta.dyn_o ) Bio/Sequence/Fasta.hs:31:1: warning: [-Wunused-imports] The import of ‘chr’ from module ‘Data.Char’ is redundant [ 8 of 11] Compiling Bio.Sequence.FastQ ( Bio/Sequence/FastQ.hs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence/FastQ.dyn_o ) [ 9 of 11] Compiling Bio.Sequence.Entropy ( Bio/Sequence/Entropy.hs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence/Entropy.dyn_o ) [10 of 11] Compiling Bio.Sequence ( Bio/Sequence.hs, dist/build/rselect-pe/rselect-pe-tmp/Bio/Sequence.dyn_o ) [11 of 11] Compiling Main ( examples/RSelectPE.hs, dist/build/rselect-pe/rselect-pe-tmp/Main.dyn_o ) examples/RSelectPE.hs:9:1: warning: [-Wmissing-signatures] Top-level binding with no type signature: main :: IO () examples/RSelectPE.hs:24:1: warning: [-Wincomplete-patterns] Pattern match(es) are non-exhaustive In an equation for ‘writer’: Patterns not matched: _ _ (_, _) examples/RSelectPE.hs:35:1: warning: [-Wmissing-signatures] Top-level binding with no type signature: sufchk :: [Char] -> [Char] -> Bool examples/RSelectPE.hs:37:1: warning: [-Wmissing-signatures] Top-level binding with no type signature: hdchk :: Sequence a1 -> Sequence a -> Bool Linking dist/build/rselect-pe/rselect-pe ... Creating package registration script: register.sh Running Haddock for bio-0.5.3... Preprocessing library bio-0.5.3... Bio/Sequence/TwoBit.hs:256:26: warning: [-Wname-shadowing] This binding for ‘ns’ shadows the existing binding bound at Bio/Sequence/TwoBit.hs:234:8 Bio/Sequence/TwoBit.hs:261:21: warning: [-Wname-shadowing] This binding for ‘ns’ shadows the existing binding bound at Bio/Sequence/TwoBit.hs:234:8 Bio/Sequence/GeneOntology.hs:162:1: warning: [-Wtabs] Tab character found here, and in 12 further locations. Please use spaces instead. Bio/Sequence/Fasta.hs:31:1: warning: [-Wunused-imports] The import of ‘chr’ from module ‘Data.Char’ is redundant Bio/Location/Position.hs:21:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/Location/Position.hs:24:1: warning: [-Wunused-imports] The import of ‘Data.List’ is redundant except perhaps to import instances from ‘Data.List’ To import instances alone, use: import Data.List() Bio/Location/Position.hs:52:11: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Location/Position.hs:54:53: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Location/OnSeq.hs:19:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/Location/OnSeq.hs:21:1: warning: [-Wunused-imports] The import of ‘Data.List’ is redundant except perhaps to import instances from ‘Data.List’ To import instances alone, use: import Data.List() Bio/Location/OnSeq.hs:23:1: warning: [-Wunused-imports] The import of ‘Data.Monoid’ is redundant except perhaps to import instances from ‘Data.Monoid’ To import instances alone, use: import Data.Monoid() Bio/Location/OnSeq.hs:54:15: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Location/OnSeq.hs:57:37: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Location/ContigLocation.hs:29:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/Location/ContigLocation.hs:100:13: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Location/ContigLocation.hs:106:38: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Location/Location.hs:30:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/Location/Location.hs:75:13: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Location/LocMap.hs:29:1: warning: [-Wunused-imports] The import of ‘Data.Maybe’ is redundant except perhaps to import instances from ‘Data.Maybe’ To import instances alone, use: import Data.Maybe() Bio/Location/LocMap.hs:30:1: warning: [-Wunused-imports] The import of ‘Data.Monoid’ is redundant except perhaps to import instances from ‘Data.Monoid’ To import instances alone, use: import Data.Monoid() Bio/Location/LocMap.hs:50:10: warning: [-Wunused-matches] Defined but not used: ‘zonesize’ Bio/Location/SeqLocation.hs:28:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/Location/SeqLocation.hs:77:13: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Escape.hs:6:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/GFF3/Escape.hs:16:24: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Escape.hs:28:42: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Escape.hs:29:38: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Feature.hs:13:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/GFF3/Feature.hs:46:11: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Feature.hs:59:35: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Feature.hs:62:52: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Feature.hs:66:50: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Feature.hs:69:55: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Feature.hs:77:60: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Feature.hs:109:20: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Feature.hs:138:10: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/Feature.hs:139:30: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:11:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/GFF3/FeatureHier.hs:30:14: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:32:37: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:34:22: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:36:37: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:38:14: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:59:12: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:65:56: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:70:57: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:72:12: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:77:48: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:81:56: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:83:49: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHier.hs:86:57: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:12:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/GFF3/FeatureHierSequences.hs:32:11: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:36:15: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:42:45: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:52:14: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:61:13: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:65:17: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:67:40: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:69:21: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:74:26: warning: [-Wdeprecations] In the use of type constructor or class ‘ErrorT’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:75:19: warning: [-Wdeprecations] In the use of data constructor ‘ErrorT’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:75:28: warning: [-Wdeprecations] In the use of ‘runErrorT’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:77:24: warning: [-Wdeprecations] In the use of type constructor or class ‘ErrorT’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:77:74: warning: [-Wdeprecations] In the use of type constructor or class ‘ErrorT’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:80:61: warning: [-Wdeprecations] In the use of ‘runErrorT’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:82:26: warning: [-Wdeprecations] In the use of type constructor or class ‘ErrorT’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:82:80: warning: [-Wdeprecations] In the use of type constructor or class ‘ErrorT’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:85:26: warning: [-Wdeprecations] In the use of ‘mapErrorT’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/FeatureHierSequences.hs:87:13: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Haddock coverage: 50% ( 1 / 2) in 'Bio.Util.Parsex' Missing documentation for: lazyMany (Bio/Util/Parsex.hs:7) 100% ( 6 / 6) in 'Bio.Util' 90% ( 43 / 48) in 'Bio.Sequence.SeqData' Missing documentation for: ? (Bio/Sequence/SeqData.hs:278) castToNuc (Bio/Sequence/SeqData.hs:94) Amino (Bio/Sequence/SeqData.hs:391) castToAmino (Bio/Sequence/SeqData.hs:97) Unknown (Bio/Sequence/SeqData.hs:88) 100% ( 7 / 7) in 'Bio.Sequence.TwoBit' 7% ( 1 / 14) in 'Bio.Sequence.SFF_name' Missing documentation for: Module header decodeReadName (Bio/Sequence/SFF_name.hs:17) decodeLocation (Bio/Sequence/SFF_name.hs:26) decodeDate (Bio/Sequence/SFF_name.hs:29) encodeReadName (Bio/Sequence/SFF_name.hs:37) encodeLocation (Bio/Sequence/SFF_name.hs:42) encodeRegion (Bio/Sequence/SFF_name.hs:45) encodeDate (Bio/Sequence/SFF_name.hs:48) divMods (Bio/Sequence/SFF_name.hs:53) decode36 (Bio/Sequence/SFF_name.hs:61) decCh (Bio/Sequence/SFF_name.hs:71) encode36 (Bio/Sequence/SFF_name.hs:76) b36 (Bio/Sequence/SFF_name.hs:83) 91% ( 29 / 32) in 'Bio.Sequence.SFF' Missing documentation for: Index (Bio/Sequence/SFF.hs:52) decodeReadName (Bio/Sequence/SFF_name.hs:17) encodeReadName (Bio/Sequence/SFF_name.hs:37) 66% ( 19 / 29) in 'Bio.Sequence.SFF_filters' Missing documentation for: sigint (Bio/Sequence/SFF_filters.hs:65) find_primer (Bio/Sequence/SFF_filters.hs:79) qual20 (Bio/Sequence/SFF_filters.hs:93) flx_linker (Bio/Sequence/SFF_filters.hs:123) ti_linker (Bio/Sequence/SFF_filters.hs:123) rna_adapter (Bio/Sequence/SFF_filters.hs:123) rna_adapter2 (Bio/Sequence/SFF_filters.hs:123) rna_adapter3 (Bio/Sequence/SFF_filters.hs:123) rapid_adapter (Bio/Sequence/SFF_filters.hs:123) ti_adapter_b (Bio/Sequence/SFF_filters.hs:123) 100% ( 3 / 3) in 'Bio.Sequence.Phd' 29% ( 5 / 17) in 'Bio.Sequence.HashWord' Missing documentation for: Module header compact (Bio/Sequence/HashWord.lhs:118) Shape (Bio/Sequence/HashWord.lhs:168) gapped (Bio/Sequence/HashWord.lhs:169) isN (Bio/Sequence/HashWord.lhs:184) n2k (Bio/Sequence/HashWord.lhs:189) n2i' (Bio/Sequence/HashWord.lhs:192) k2n (Bio/Sequence/HashWord.lhs:196) k2n' (Bio/Sequence/HashWord.lhs:199) val (Bio/Sequence/HashWord.lhs:209) unval (Bio/Sequence/HashWord.lhs:213) complement (Bio/Sequence/HashWord.lhs:217) 89% ( 16 / 18) in 'Bio.Sequence.GeneOntology' Missing documentation for: GoClass (Bio/Sequence/GeneOntology.hs:108) decomment (Bio/Sequence/GeneOntology.hs:60) 71% ( 5 / 7) in 'Bio.Sequence.KEGG' Missing documentation for: KO (Bio/Sequence/KEGG.hs:31) (Bio/Sequence/KEGG.hs:32) Warning: Bio.Sequence.GOA: Could not find documentation for exported module: GO 50% ( 1 / 2) in 'Bio.Sequence.GOA' Missing documentation for: readGO (Bio/Sequence/GOA.hs:6) 85% ( 17 / 20) in 'Bio.Sequence.Fasta' Missing documentation for: hWriteQual (Bio/Sequence/Fasta.hs:137) hWriteFastaQual (Bio/Sequence/Fasta.hs:112) countSeqs (Bio/Sequence/Fasta.hs:180) 32% ( 6 / 19) in 'Bio.Sequence.FastQ' Missing documentation for: readFastQ (Bio/Sequence/FastQ.hs:69) hReadFastQ (Bio/Sequence/FastQ.hs:72) writeFastQ (Bio/Sequence/FastQ.hs:96) hWriteFastQ (Bio/Sequence/FastQ.hs:99) unparse (Bio/Sequence/FastQ.hs:103) readSangerQ (Bio/Sequence/FastQ.hs:50) hReadSangerQ (Bio/Sequence/FastQ.hs:54) writeSangerQ (Bio/Sequence/FastQ.hs:58) hWriteSangerQ (Bio/Sequence/FastQ.hs:62) readIllumina (Bio/Sequence/FastQ.hs:50) hReadIllumina (Bio/Sequence/FastQ.hs:54) writeIllumina (Bio/Sequence/FastQ.hs:58) hWriteIllumina (Bio/Sequence/FastQ.hs:62) 0% ( 0 / 3) in 'Bio.Sequence.Entropy' Missing documentation for: Module header KWords (Bio/Sequence/Entropy.hs:5) entropy (Bio/Sequence/Entropy.hs:15) 18% ( 3 / 17) in 'Bio.Sequence.AminoProperties' Missing documentation for: AAProp (Bio/Sequence/AminoProperties.hs:12) oneOf (Bio/Sequence/AminoProperties.hs:14) or (Bio/Sequence/AminoProperties.hs:17) aliphatic (Bio/Sequence/AminoProperties.hs:20) aromatic (Bio/Sequence/AminoProperties.hs:20) hydrophobic (Bio/Sequence/AminoProperties.hs:20) polar (Bio/Sequence/AminoProperties.hs:20) small (Bio/Sequence/AminoProperties.hs:20) tiny (Bio/Sequence/AminoProperties.hs:20) charged (Bio/Sequence/AminoProperties.hs:20) negative (Bio/Sequence/AminoProperties.hs:20) positive (Bio/Sequence/AminoProperties.hs:20) hydropathy (Bio/Sequence/AminoProperties.hs:36) mass (Bio/Sequence/AminoProperties.hs:60) 76% ( 63 / 83) in 'Bio.Sequence' Missing documentation for: Unknown (Bio/Sequence/SeqData.hs:88) castToNuc (Bio/Sequence/SeqData.hs:94) Amino (Bio/Sequence/SeqData.hs:391) castToAmino (Bio/Sequence/SeqData.hs:97) hWriteQual (Bio/Sequence/Fasta.hs:137) hWriteFastaQual (Bio/Sequence/Fasta.hs:112) readFastQ (Bio/Sequence/FastQ.hs:69) writeFastQ (Bio/Sequence/FastQ.hs:96) hReadFastQ (Bio/Sequence/FastQ.hs:72) hWriteFastQ (Bio/Sequence/FastQ.hs:99) readSangerQ (Bio/Sequence/FastQ.hs:50) writeSangerQ (Bio/Sequence/FastQ.hs:58) hReadSangerQ (Bio/Sequence/FastQ.hs:54) hWriteSangerQ (Bio/Sequence/FastQ.hs:62) readIllumina (Bio/Sequence/FastQ.hs:50) writeIllumina (Bio/Sequence/FastQ.hs:58) hReadIllumina (Bio/Sequence/FastQ.hs:54) hWriteIllumina (Bio/Sequence/FastQ.hs:62) KWords (Bio/Sequence/Entropy.hs:5) entropy (Bio/Sequence/Entropy.hs:15) 100% ( 4 / 4) in 'Bio.Location.Strand' 100% ( 10 / 10) in 'Bio.Location.Position' 100% ( 13 / 13) in 'Bio.Location.OnSeq' 100% ( 21 / 21) in 'Bio.Location.ContigLocation' 100% ( 19 / 19) in 'Bio.Location.Location' 92% ( 12 / 13) in 'Bio.Location.LocMap' Missing documentation for: checkInvariants (Bio/Location/LocMap.hs:114) 100% ( 17 / 17) in 'Bio.Location.SeqLocation' 100% ( 10 / 10) in 'Bio.Location.SeqLocMap' 0% ( 0 / 5) in 'Bio.GFF3.Escape' Missing documentation for: Module header unEscapeByteString (Bio/GFF3/Escape.hs:16) escapeByteString (Bio/GFF3/Escape.hs:31) escapeAllBut (Bio/GFF3/Escape.hs:47) escapeAllOf (Bio/GFF3/Escape.hs:52) 0% ( 0 / 14) in 'Bio.GFF3.Feature' Missing documentation for: Module header GFFAttr (Bio/GFF3/Feature.hs:28) Feature (Bio/GFF3/Feature.hs:30) length (Bio/GFF3/Feature.hs:40) parse (Bio/GFF3/Feature.hs:46) unparse (Bio/GFF3/Feature.hs:87) parseWithFasta (Bio/GFF3/Feature.hs:109) attrByTag (Bio/GFF3/Feature.hs:115) ids (Bio/GFF3/Feature.hs:123) parentIds (Bio/GFF3/Feature.hs:126) contigLoc (Bio/GFF3/Feature.hs:129) loc (Bio/GFF3/Feature.hs:132) seqLoc (Bio/GFF3/Feature.hs:135) name (Bio/GFF3/Feature.hs:138) 0% ( 0 / 13) in 'Bio.GFF3.FeatureHier' Missing documentation for: Module header FeatureHier (Bio/GFF3/FeatureHier.hs:22) features (Bio/GFF3/FeatureHier.hs:22) lookupId (Bio/GFF3/FeatureHier.hs:30) lookupIdChildren (Bio/GFF3/FeatureHier.hs:34) fromList (Bio/GFF3/FeatureHier.hs:38) insert (Bio/GFF3/FeatureHier.hs:59) delete (Bio/GFF3/FeatureHier.hs:72) parents (Bio/GFF3/FeatureHier.hs:89) children (Bio/GFF3/FeatureHier.hs:94) parentsM (Bio/GFF3/FeatureHier.hs:98) childrenM (Bio/GFF3/FeatureHier.hs:101) checkInvariants (Bio/GFF3/FeatureHier.hs:104) 0% ( 0 / 15) in 'Bio.GFF3.FeatureHierSequences' Missing documentation for: Module header FeatureHierSequences (Bio/GFF3/FeatureHierSequences.hs:28) features (Bio/GFF3/FeatureHierSequences.hs:45) sequences (Bio/GFF3/FeatureHierSequences.hs:48) fromLists (Bio/GFF3/FeatureHierSequences.hs:36) parse (Bio/GFF3/FeatureHierSequences.hs:32) lookupId (Bio/GFF3/FeatureHierSequences.hs:52) parents (Bio/GFF3/FeatureHierSequences.hs:58) children (Bio/GFF3/FeatureHierSequences.hs:55) seqData (Bio/GFF3/FeatureHierSequences.hs:61) getSequence Bio/GFF3/SGD.hs:10:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/GFF3/SGD.hs:48:18: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:50:56: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:53:16: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:60:23: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:62:62: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:65:21: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:72:15: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:75:44: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:79:16: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:80:30: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:85:28: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/GFF3/SGD.hs:91:17: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:9:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/Alignment/Soap.hs:63:11: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:77:28: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:78:78: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:82:46: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:84:19: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:92:36: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:95:18: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:98:41: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:100:21: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:103:44: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:105:19: warning: [-Wdeprecations] In the use of type constructor or class ‘Error’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Soap.hs:107:48: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/Bowtie.hs:32:1: warning: [-Wdeprecations] Module ‘Control.Monad.Error’ is deprecated: Use Control.Monad.Except instead Bio/Alignment/Bowtie.hs:36:1: warning: [-Wunused-imports] The import of ‘Data.Char’ is redundant except perhaps to import instances from ‘Data.Char’ To import instances alone, use: import Data.Char() Bio/Alignment/Bowtie.hs:74:27: warning: [-Wdeprecations] In the use of ‘strMsg’ (imported from Control.Monad.Error, but defined in transformers-0.5.2.0:Control.Monad.Trans.Error): Deprecated: "Use Control.Monad.Trans.Except instead" Bio/Alignment/AlignData.hs:59:1: warning: [-Wmissing-signatures] Top-level binding with no type signature: showalign :: EditList -> [Char] Bio/Alignment/AlignData.hs:121:1: warning: [-Wmissing-signatures] Top-level binding with no type signature: on :: (t2 -> t2 -> t1) -> (t -> t2) -> t -> t -> t1 Bio/Alignment/QAlign.hs:103:72: warning: [-Wname-shadowing] This binding for ‘x’ shadows the existing binding bound at Bio/Alignment/QAlign.hs:94:15 Bio/Alignment/QAlign.hs:103:86: warning: [-Wname-shadowing] This binding for ‘y’ shadows the existing binding bound at Bio/Alignment/QAlign.hs:94:17 Bio/Alignment/QAlign.hs:104:73: warning: [-Wname-shadowing] This binding for ‘x’ shadows the existing binding bound at Bio/Alignment/QAlign.hs:94:15 Bio/Alignment/QAlign.hs:104:87: warning: [-Wname-shadowing] This binding for ‘y’ shadows the existing binding bound at Bio/Alignment/QAlign.hs:94:17 Bio/Alignment/QAlign.hs:145:14: warning: [-Wname-shadowing] This binding for ‘minf’ shadows the existing binding defined at Bio/Alignment/QAlign.hs:89:1 Bio/Alignment/QAlign.hs:188:1: warning: [-Wunused-top-binds] Defined but not used: ‘overlap_align'’ Bio/Alignment/QAlign.hs:193:36: warning: [-Wname-shadowing] This binding for ‘s1’ shadows the existing binding bound at Bio/Alignment/QAlign.hs:188:21 Bio/Alignment/QAlign.hs:193:36: warning: [-Wunused-matches] Defined but not used: ‘s1’ Bio/Alignment/QAlign.hs:193:39: warning: [-Wunused-matches] Defined but not used: ‘es1’ Bio/Alignment/QAlign.hs:193:45: warning: [-Wname-shadowing] This binding for ‘s2’ shadows the existing binding bound at Bio/Alignment/QAlign.hs:188:24 Bio/Alignment/QAlign.hs:193:45: warning: [-Wunused-matches] Defined but not used: ‘s2’ Bio/Alignment/QAlign.hs:196:1: warning: [-Wmissing-signatures] Top-level binding with no type signature: revsnd :: (t, [a]) -> (t, [a]) Bio/Alignment/QAlign.hs:200:14: warning: [-Wname-shadowing] This binding for ‘minf’ shadows the existing binding defined at Bio/Alignment/QAlign.hs:89:1 Bio/Alignment/QAlign.hs:208:1: warning: [-Wmissing-signatures] Top-level binding with no type signature: snd' :: (t2, t3, t1, t) -> t3 Bio/Alignment/QAlign.hs:222:7: warning: [-Wname-shadowing] This binding for ‘or’ shadows the existing binding imported from ‘Prelude’ at Bio/Alignment/QAlign.hs:19:8-27 (and originally defined in ‘Data.Foldable’) Bio/Alignment/AAlign.hs:40:14: warning: [-Wname-shadowing] This binding for ‘minf’ shadows the existing binding defined at Bio/Alignment/AAlign.hs:23:1 Bio/Alignment/AAlign.hs:50:1: warning: [-Wmissing-signatures] Top-level binding with no type signature: max' :: Ord t1 => (t1, t) -> (t1, t) -> (t1, t) Bio/Alignment/AAlign.hs:51:1: warning: [-Wmissing-signatures] Top-level binding with no type signature: fp :: Num t => (t, [a]) -> (t, a) -> (t, [a]) Bio/Alignment/AAlign.hs:64:1: warning: [-Wmissing-signatures] Top-level binding with no type signature: revsnd :: (t, [a]) -> (t, [a]) Bio/Alignment/AAlign.hs:68:14: warning: [-Wname-shadowing] This binding for ‘minf’ shadows the existing binding defined at Bio/Alignment/AAlign.hs:23:1 (Bio/GFF3/FeatureHierSequences.hs:65) featureSequence (Bio/GFF3/FeatureHierSequences.hs:69) runGFF (Bio/GFF3/FeatureHierSequences.hs:77) runGFFIO (Bio/GFF3/FeatureHierSequences.hs:82) asksGFF (Bio/GFF3/FeatureHierSequences.hs:87) 0% ( 0 / 13) in 'Bio.GFF3.SGD' Missing documentation for: Module header chromosomes (Bio/GFF3/SGD.hs:35) genes (Bio/GFF3/SGD.hs:39) rRNAs (Bio/GFF3/SGD.hs:43) sortExons (Bio/GFF3/SGD.hs:72) geneSequence (Bio/GFF3/SGD.hs:48) geneSeqLoc (Bio/GFF3/SGD.hs:53) geneCDSes (Bio/GFF3/SGD.hs:56) noncodingSequence (Bio/GFF3/SGD.hs:60) noncodingSeqLoc (Bio/GFF3/SGD.hs:65) noncodingExons (Bio/GFF3/SGD.hs:68) namedSLM (Bio/GFF3/SGD.hs:87) geneCDS_SLM (Bio/GFF3/SGD.hs:91) 100% ( 3 / 3) in 'Bio.Clustering' 8% ( 1 / 12) in 'Bio.Alignment.Soap' Missing documentation for: Module header SoapAlignMismatch (Bio/Alignment/Soap.hs:39) refSeqPos (Bio/Alignment/Soap.hs:48) refCSeqLoc (Bio/Alignment/Soap.hs:51) refSeqLoc (Bio/Alignment/Soap.hs:57) mismatchSeqPos (Bio/Alignment/Soap.hs:45) parse (Bio/Alignment/Soap.hs:63) unparse (Bio/Alignment/Soap.hs:109) parseMismatch (Bio/Alignment/Soap.hs:84) unparseMismatch (Bio/Alignment/Soap.hs:124) group (Bio/Alignment/Soap.hs:132) 12% ( 1 / 8) in 'Bio.Alignment.PSL' Missing documentation for: PSL (Bio/Alignment/PSL.hs:15) (Bio/Alignment/PSL.hs:23) readPSL (Bio/Alignment/PSL.hs:26) writePSL (Bio/Alignment/PSL.hs:29) parsePSL (Bio/Alignment/PSL.hs:32) unparsePSL (Bio/Alignment/PSL.hs:46) pslHeader (Bio/Alignment/PSL.hs:58) 94% ( 17 / 18) in 'Bio.Alignment.Bowtie' Missing documentation for: Align (Bio/Alignment/Bowtie.hs:48) 100% ( 8 / 8) in 'Bio.Alignment.BlastData' 100% ( 2 / 2) in 'Bio.Alignment.BlastXML' 53% ( 10 / 19) in 'Bio.Alignment.BlastFlat' Missing documentation for: readXML (Bio/Alignment/BlastFlat.hs:45) blastprogram (Bio/Alignment/BlastData.hs:40) blastversion (Bio/Alignment/BlastData.hs:40) blastdate (Bio/Alignment/BlastData.hs:40) blastreferences (Bio/Alignment/BlastData.hs:41) database (Bio/Alignment/BlastData.hs:42) dbsequences (Bio/Alignment/BlastData.hs:43) dbchars (Bio/Alignment/BlastData.hs:43) results (Bio/Alignment/BlastData.hs:44) 50% ( 1 / 2) in 'Bio.Alignment.Blast' Missing documentation for: parse (Bio/Alignment/Blast.hs:67) 60% ( 3 / 5) in 'Bio.Alignment.BED' Missing documentation for: readBED (Bio/Alignment/BED.hs:40) writeBED (Bio/Alignment/BED.hs:57) 71% ( 15 / 21) in 'Bio.Alignment.AlignData' Missing documentation for: Dir (Bio/Alignment/AlignData.hs:38) Gaps (Bio/Alignment/AlignData.hs:39) Alignment (Bio/Alignment/AlignData.hs:40) insertGaps (Bio/Alignment/AlignData.hs:50) on (Bio/Alignment/AlignData.hs:121) showalign (Bio/Alignment/AlignData.hs:59) 100% ( 14 / 14) in 'Bio.Alignment.Matrices' 100% ( 3 / 3) in 'Bio.Alignment.Multiple' 88% ( 15 / 17) in 'Bio.Alignment.QAlign' Missing documentation for: qualMx (Bio/Alignment/QAlign.hs:93) test (Bio/Alignment/QAlign.hs:210) 86% ( 6 / 7) in 'Bio.Alignment.SAlign' Missing documentation for: local_align (Bio/Alignment/SAlign.hs:56) 50% ( 3 / 6) in 'Bio.Alignment.ACE' Missing documentation for: writeACE (Bio/Alignment/ACE.hs:259) Assembly (Bio/Alignment/ACE.hs:52) reads (Bio/Alignment/ACE.hs:56) 100% ( 7 / 7) in 'Bio.Alignment.AAlign' Documentation created: dist/doc/html/bio/index.html Preprocessing executable 'flx' for bio-0.5.3... Preprocessing executable 'fastout' for bio-0.5.3... Preprocessing executable 'frecover' for bio-0.5.3... Preprocessing executable 'frename' for bio-0.5.3... Preprocessing executable 'flowclip' for bio-0.5.3... Preprocessing executable 'orf' for bio-0.5.3... Preprocessing executable 'rselect-pe' for bio-0.5.3... -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> hs-bio-0.5.3_4 depends on executable: ghc - found ===> hs-bio-0.5.3_4 depends on package: ghc>=8.0.2 - found ===> hs-bio-0.5.3_4 depends on package: hs-mtl>=0 - found ===> hs-bio-0.5.3_4 depends on package: hs-old-time>=0 - found ===> hs-bio-0.5.3_4 depends on package: hs-parallel>=0 - found ===> hs-bio-0.5.3_4 depends on package: hs-parsec>=0 - found ===> hs-bio-0.5.3_4 depends on package: hs-QuickCheck>=2 - found ===> hs-bio-0.5.3_4 depends on package: hs-random>=0 - found ===> hs-bio-0.5.3_4 depends on package: hs-tagsoup>=0.8 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for hs-bio-0.5.3_4 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-------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for hs-bio-0.5.3_4 file sizes/checksums [236]: ... done packing files [236]: ... done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 19 APR 2018 at 05:39:17 UTC Duration: 00:07:37