[package - main-amd64-default][biology/igv] Failed for igv-2.16.0_3 in build-depends
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Date: Tue, 01 Sep 2026 08:33:23 UTC
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: yuri@FreeBSD.org Log URL: https://pkg-status.freebsd.org/beefy24/data/main-amd64-default/pc3d47bb8f5ff_see44a57e34/logs/igv-2.16.0_3.log Build URL: https://pkg-status.freebsd.org/beefy24/build.html?mastername=main-amd64-default&build=pc3d47bb8f5ff_see44a57e34 Log: =>> Building biology/igv build started at Tue Sep 1 08:33:09 UTC 2026 port directory: /usr/ports/biology/igv package name: igv-2.16.0_3 building for: FreeBSD main-amd64-default-job-37 16.0-CURRENT FreeBSD 16.0-CURRENT 1600021 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 2394 Apr 4 01:01 /usr/ports/biology/igv/Makefile Ports top last git commit: c3d47bb8f5ff8b7332d3187e0f5edd71286027b8 Ports top unclean checkout: no Port dir last git commit: 86813e9ccf597695e26c8104e678f913689f1e93 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.8-2-g2e891d4a Host OSVERSION: 1600019 Jail OSVERSION: 1600021 Job Id: 37 !!! Jail is newer than host. (Jail: 1600021, Host: 1600019) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1600021 UNAME_v=FreeBSD 16.0-CURRENT 1600021 UNAME_r=16.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.8-2-g2e891d4a MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/main-amd64-default/37/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=main-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.8-2-g2e891d4a SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/igv/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/igv/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/igv/work/.cache HOME=/wrkdirs/usr/ports/biology/igv/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/igv/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/igv/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- GRADLE_USER_HOME=/wrkdirs/usr/ports/biology/igv/work JAVA_HOME=/usr/local/openjdk11 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/igv/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/igv/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/igv/work/.cache HOME=/wrkdirs/usr/ports/biology/igv/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/igv/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/igv/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" B SD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=16.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/igv" EXAMPLESDIR="share/examples/igv" DATADIR="share/igv" WWWDIR="www/igv" ETCDIR="etc/igv" --End PLIST_SUB-- --SUB_LIST-- JAVA_HOME=/usr/local/openjdk11 JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" JAVA_VERSION="11" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/igv DOCSDIR=/usr/local/share/doc/igv EXAMPLESDIR=/usr/local/share/examples/igv WWWDIR=/usr/local/www/igv ETCDIR=/usr/local/etc/igv --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (kbytes, -y) unlimited virtual machines (-V) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> igv-2.16.0_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.8.4.pkg [main-amd64-default-job-37] Installing pkg-2.8.4... [main-amd64-default-job-37] Extracting pkg-2.8.4: .......... done ===> igv-2.16.0_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of igv-2.16.0_3 =========================================================================== =======================<phase: fetch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: fetch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by igv-2.16.0_3 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by igv-2.16.0_3 for building => SHA256 Checksum OK for igv-2.16.0/tools.png. => SHA256 Checksum OK for igv-2.16.0/igv-2.16.0-deps.tar.gz. => SHA256 Checksum OK for igv-2.16.0/igvteam-igv-v2.16.0_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: extract >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License MIT accepted by the user ===> Fetching all distfiles required by igv-2.16.0_3 for building ===> Extracting for igv-2.16.0_3 => SHA256 Checksum OK for igv-2.16.0/tools.png. => SHA256 Checksum OK for igv-2.16.0/igv-2.16.0-deps.tar.gz. => SHA256 Checksum OK for igv-2.16.0/igvteam-igv-v2.16.0_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: patch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for igv-2.16.0_3 =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> igv-2.16.0_3 depends on package: openjfx14>0 - not found ===> Installing existing package /packages/All/openjfx14-14.0.2.1+1_20.pkg [main-amd64-default-job-37] Installing openjfx14-14.0.2.1+1_20... [main-amd64-default-job-37] `-- Installing alsa-lib-1.2.16.1... [main-amd64-default-job-37] `-- Extracting alsa-lib-1.2.16.1: .......... done [main-amd64-default-job-37] `-- Installing at-spi2-core-2.60.4... [main-amd64-default-job-37] | `-- Installing dbus-1.16.2_4,1... [main-amd64-default-job-37] | | `-- Installing expat-2.8.3... [main-amd64-default-job-37] | | `-- Extracting expat-2.8.3: .......... done [main-amd64-default-job-37] | | `-- Installing libICE-1.1.2,1... [main-amd64-default-job-37] | | `-- Extracting libICE-1.1.2,1: .......... done <snip> [main-amd64-default-job-37] | `-- Installing libXdamage-1.1.7... [main-amd64-default-job-37] | `-- Extracting libXdamage-1.1.7: ......... done [main-amd64-default-job-37] | `-- Installing libXinerama-1.1.6,1... [main-amd64-default-job-37] | `-- Extracting libXinerama-1.1.6,1: .......... done [main-amd64-default-job-37] | `-- Installing libXrandr-1.5.5... [main-amd64-default-job-37] | `-- Extracting libXrandr-1.5.5: .......... done [main-amd64-default-job-37] | `-- Installing pango-1.57.1... [main-amd64-default-job-37] | | `-- Installing libXft-2.3.9... [main-amd64-default-job-37] | | `-- Extracting libXft-2.3.9: .......... done [main-amd64-default-job-37] | | `-- Installing libthai-0.1.30... [main-amd64-default-job-37] | | `-- Installing libdatrie-0.2.14_1... [main-amd64-default-job-37] | | `-- Extracting libdatrie-0.2.14_1: .......... done [main-amd64-default-job-37] | | `-- Extracting libthai-0.1.30: .......... done [main-amd64-default-job-37] | `-- Extracting pango-1.57.1: .......... done [main-amd64-default-job-37] `-- Extracting gtk2-2.24.33_1: .......... done [main-amd64-default-job-37] `-- Installing gtk3-3.24.52... [main-amd64-default-job-37] | `-- Installing adwaita-icon-theme-47.0... [main-amd64-default-job-37] | | `-- Installing adwaita-icon-theme-legacy-46.2... [main-amd64-default-job-37] | | `-- Extracting adwaita-icon-theme-legacy-46.2: .......... done [main-amd64-default-job-37] | `-- Extracting adwaita-icon-theme-47.0: .......... done [main-amd64-default-job-37] | `-- Installing colord-1.4.8_2... [main-amd64-default-job-37] | | `-- Installing lcms2-2.19.1... [main-amd64-default-job-37] | | `-- Extracting lcms2-2.19.1: .......... done [main-amd64-default-job-37] | | `-- Installing libgudev-237... [main-amd64-default-job-37] | | `-- Extracting libgudev-237: .......... done [main-amd64-default-job-37] | | `-- Installing libgusb-0.4.9_1... [main-amd64-default-job-37] | | `-- Installing json-glib-1.10.8... [main-amd64-default-job-37] | | | `-- Installing gobject-introspection-1.86.0,1... [main-amd64-default-job-37] | | | `-- Installing py312-setuptools-63.1.0_3... [main-amd64-default-job-37] | | | `-- Extracting py312-setuptools-63.1.0_3: .......... done [main-amd64-default-job-37] | | | `-- Extracting gobject-introspection-1.86.0,1: .......... done [main-amd64-default-job-37] | | `-- Extracting json-glib-1.10.8: .......... done [main-amd64-default-job-37] | | `-- Extracting libgusb-0.4.9_1: .......... done [main-amd64-default-job-37] | | `-- Installing polkit-127... [main-amd64-default-job-37] | | `-- Installing duktape-lib-2.7.0_1... [main-amd64-default-job-37] | | `-- Extracting duktape-lib-2.7.0_1: ......... done ===> Creating groups Creating group 'polkitd' with gid '565' ===> Creating users Creating user 'polkitd' with uid '565' [main-amd64-default-job-37] | | `-- Extracting polkit-127: ......... done [main-amd64-default-job-37] | | `-- Installing sqlite3-3.53.4,1... [main-amd64-default-job-37] | | `-- Installing libedit-3.1.20260512,1... [main-amd64-default-job-37] | | `-- Extracting libedit-3.1.20260512,1: .......... done [main-amd64-default-job-37] | | `-- Extracting sqlite3-3.53.4,1: .......... done ===> Creating groups Creating group 'colord' with gid '970' ===> Creating users Creating user 'colord' with uid '970' [main-amd64-default-job-37] | `-- Extracting colord-1.4.8_2: .......... done [main-amd64-default-job-37] | `-- Installing libepoxy-1.5.10... [main-amd64-default-job-37] | `-- Extracting libepoxy-1.5.10: .......... done [main-amd64-default-job-37] | `-- Installing librsvg2-rust-2.62.3_1... [main-amd64-default-job-37] | `-- Extracting librsvg2-rust-2.62.3_1: .......... done [main-amd64-default-job-37] | `-- Installing libxkbcommon-1.13.2... [main-amd64-default-job-37] | | `-- Installing xkeyboard-config-2.48... [main-amd64-default-job-37] | | `-- Extracting xkeyboard-config-2.48: .......... done [main-amd64-default-job-37] | `-- Extracting libxkbcommon-1.13.2: .......... done [main-amd64-default-job-37] `-- Extracting gtk3-3.24.52: .......... done [main-amd64-default-job-37] `-- Installing icu-76.1,1... [main-amd64-default-job-37] `-- Extracting icu-76.1,1: .......... done [main-amd64-default-job-37] `-- Installing libXt-1.3.1,1... [main-amd64-default-job-37] `-- Extracting libXt-1.3.1,1: .......... done [main-amd64-default-job-37] `-- Installing libXxf86vm-1.1.7... [main-amd64-default-job-37] `-- Extracting libXxf86vm-1.1.7: .......... done [main-amd64-default-job-37] `-- Installing libxslt-1.1.45... [main-amd64-default-job-37] | `-- Installing libgcrypt-1.12.3_2... [main-amd64-default-job-37] | | `-- Installing libgpg-error-1.61... [main-amd64-default-job-37] | | `-- Extracting libgpg-error-1.61: .......... done [main-amd64-default-job-37] | `-- Extracting libgcrypt-1.12.3_2: .......... done [main-amd64-default-job-37] `-- Extracting libxslt-1.1.45: .......... done [main-amd64-default-job-37] `-- Installing openjdk11-11.0.32+9.2_1... [main-amd64-default-job-37] | `-- Installing javavmwrapper-2.7.10_2... [main-amd64-default-job-37] | `-- Extracting javavmwrapper-2.7.10_2: .......... done [main-amd64-default-job-37] | `-- Installing xorg-fonts-truetype-7.7_1... [main-amd64-default-job-37] | | `-- Installing dejavu-2.37_4... [main-amd64-default-job-37] | | `-- Installing mkfontscale-1.2.4... [main-amd64-default-job-37] | | | `-- Installing libfontenc-1.1.9... [main-amd64-default-job-37] | | | `-- Extracting libfontenc-1.1.9: ......... done [main-amd64-default-job-37] | | `-- Extracting mkfontscale-1.2.4: ....... done [main-amd64-default-job-37] | | `-- Extracting dejavu-2.37_4: .......... done [main-amd64-default-job-37] | | `-- Installing encodings-1.1.0,1... [main-amd64-default-job-37] | | `-- Extracting encodings-1.1.0,1: .......... done [main-amd64-default-job-37] | | `-- Installing font-bh-ttf-1.0.4... [main-amd64-default-job-37] | | `-- Extracting font-bh-ttf-1.0.4: .......... done [main-amd64-default-job-37] | | `-- Installing font-misc-ethiopic-1.0.5... [main-amd64-default-job-37] | | `-- Extracting font-misc-ethiopic-1.0.5: ...... done [main-amd64-default-job-37] | | `-- Installing font-misc-meltho-1.0.4... [main-amd64-default-job-37] | | `-- Extracting font-misc-meltho-1.0.4: .......... done [main-amd64-default-job-37] | `-- Extracting xorg-fonts-truetype-7.7_1: ... done [main-amd64-default-job-37] `-- Extracting openjdk11-11.0.32+9.2_1: .......... done [main-amd64-default-job-37] `-- Installing sndio-1.10.0_1... ===> Creating groups Creating group '_sndio' with gid '702' ===> Creating users Creating user '_sndio' with uid '702' [main-amd64-default-job-37] `-- Extracting sndio-1.10.0_1: .......... done pkg-static: Missing shlib libjvm.so required by openjfx14 Failed to install the following 1 package(s): /packages/All/openjfx14-14.0.2.1+1_20.pkg ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ==> Running trigger: gdk-pixbuf-query-loaders.ucl Generating gdk-pixbuf modules cache ==> Running trigger: gio-modules.ucl Generating GIO modules cache ==> Running trigger: gtk-update-icon-cache.ucl Generating GTK icon cache for /usr/local/share/icons/hicolor Generating GTK icon cache for /usr/local/share/icons/Adwaita Generating GTK icon cache for /usr/local/share/icons/AdwaitaLegacy ==> Running trigger: glib-schemas.ucl Compiling glib schemas Warning: Schema “org.gnome.system.locale” has path “/system/locale/”. Paths starting with “/apps/”, “/desktop/” or “/system/” are deprecated. Warning: Schema “org.gnome.system.proxy” has path “/system/proxy/”. Paths starting with “/apps/”, “/desktop/” or “/system/” are deprecated. Warning: Schema “org.gnome.system.proxy.http” has path “/system/proxy/http/”. Paths starting with “/apps/”, “/desktop/” or “/system/” are deprecated. Warning: Schema “org.gnome.system.proxy.https” has path “/system/proxy/https/”. Paths starting with “/apps/”, “/desktop/” or “/system/” are deprecated. Warning: Schema “org.gnome.system.proxy.ftp” has path “/system/proxy/ftp/”. Paths starting with “/apps/”, “/desktop/” or “/system/” are deprecated. Warning: Schema “org.gnome.system.proxy.socks” has path “/system/proxy/socks/”. Paths starting with “/apps/”, “/desktop/” or “/system/” are deprecated. ==> Running trigger: shared-mime-info.ucl Building the Shared MIME-Info database cache ===== Message from python312-3.12.14: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py312-gdbm databases/py-gdbm@py312 py312-sqlite3 databases/py-sqlite3@py312 py312-tkinter x11-toolkits/py-tkinter@py312 ===== Message from freetype2-2.14.3: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/index.html, if documentation was installed). ===== Message from wayland-1.26.0: -- Wayland requires XDG_RUNTIME_DIR to be defined to a path that will contain "wayland-%d" unix(4) sockets. This is usually handled by consolekit2 (via ck-launch-session) or pam_xdg (via login). ===== Message from libxkbcommon-1.13.2: -- If arrow keys don't work under X11 switch to legacy rules e.g., For sh/bash/ksh/zsh run and (optionally) add into ~/.profile: export XKB_DEFAULT_RULES=xorg For csh/tcsh run and (optionally) add into ~/.login: setenv XKB_DEFAULT_RULES xorg ===== Message from openjdk11-11.0.32+9.2_1: -- This OpenJDK implementation may require procfs(5) mounted on /proc for some applications. If you have not done it yet, please do the following: mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: proc /proc procfs rw 0 0 *** Error code 1 Stop. make: stopped making "build-depends" in /usr/ports/biology/igv