Biostar-Tools is a metaport for installing all the tools necessary to work
through the Biostar Handbook, except for bedGrapToBigWig, which has license
restrictions. If you need bedGraphToBigWig, run
cd /usr/ports/biology/ucsc-userapps && make install clean
CSV/TSV formats are basic and ubiquitous file formats in both Bioinformatics
and data science.
People usually use spreadsheet software like MS Excel to process table data.
However this is all by clicking and typing, which is not automated and is
time-consuming to repeat, especially when you want to apply similar operations
with different datasets or purposes.
csvtk is convenient for rapid data investigation and also easy to integrate
into analysis pipelines. It could save you lots of time in (not) writing
Python/R scripts.
Welcome GCC 11.1, the first release of the GCC 11 series!
https://gcc.gnu.org/gcc-11/changes.html has a comprehensive overview
of many improvements and changes and
https://gcc.gnu.org/gcc-11/porting_to.html highlights issues you may
encounter porting to this version. This release series should not
prove too disruptive, mainly C++ defaulting to GNU++17 and some more
libstdc++ headers will need to be included explicitly.
To give a brief overview of some of the more noticable changes:
Some short options of the gcov tool have been renamed: -i to -j and
-j to -H.
Debugging information defaults to DWARF 5.
Vectorizer improvements, a new IPA-modref pass to track side effects
of function calls and improve precision of points-to-analysis, better
interprocedural constant propagation (IP-CP), smaller link-time
optimization (LTO) object files.
OpenMP 4.5 is now fully supported and OpenMP 5.0 support has been
extended.
A set of new warnings including -Wmismatched-dealloc, -Wsizeof-array-div,
-Wstringop-overread, and enhancements to existing warnings.
Several new features from the upcoming C2X revision of the ISO C
standard are supported with -std=c2x and -std=gnu2x.
Several C++20 features have been implemented and even some of the
upcoming C++23 draft features with the -std=c++23 and the like.
libstdc++ features improved C++17 support.
And, last but not least, loads of improvements for all of FreeBSD's
architectures.
gl-device-release.c:33:8: error: unknown type name 'Window'
static Window
^
gl-device-release.c:34:21: error: unknown type name 'Display'
create_test_window (Display *display,
^
gl-device-release.c:35:7: error: unknown type name 'GLXContext'; did you mean 'EGLContext'?
GLXContext glx_context,
^~~~~~~~~~
EGLContext
/usr/local/include/EGL/egl.h:64:15: note: 'EGLContext' declared here
typedef void *EGLContext;
^
gl-device-release.c:36:7: error: unknown type name 'XVisualInfo'
XVisualInfo *visual_info)
^
gl-oversized-surface.c:38:2: error: use of undeclared identifier 'GLX_RGBA'
GLX_RGBA,
^
gl-oversized-surface.c:39:2: error: use of undeclared identifier 'GLX_RED_SIZE'
GLX_RED_SIZE, 1,
^
gl-oversized-surface.c:40:2: error: use of undeclared identifier 'GLX_GREEN_SIZE'
GLX_GREEN_SIZE, 1,
^
gl-oversized-surface.c:41:2: error: use of undeclared identifier 'GLX_BLUE_SIZE'
GLX_BLUE_SIZE, 1,
^
gl-oversized-surface.c:42:2: error: use of undeclared identifier 'GLX_ALPHA_SIZE'
GLX_ALPHA_SIZE, 1,
^
gl-surface-source.c:33:5: error: unknown type name 'Display'
Display *dpy;
^
gl-surface-source.c:34:5: error: unknown type name 'GLXContext'; did you mean 'EGLContext'?
GLXContext ctx;
^~~~~~~~~~
EGLContext
/usr/local/include/EGL/egl.h:64:15: note: 'EGLContext' declared here
typedef void *EGLContext;
^
gl-surface-source.c:42:5: error: implicit declaration of function 'glXDestroyContext' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
glXDestroyContext (arg->dpy, arg->ctx);
^
gl-surface-source.c:42:5: note: did you mean 'eglDestroyContext'?
/usr/local/include/EGL/egl.h:156:31: note: 'eglDestroyContext' declared here
EGLAPI EGLBoolean EGLAPIENTRY eglDestroyContext (EGLDisplay dpy, EGLContext ctx);
^
gl-surface-source.c:43:5: error: implicit declaration of function 'XCloseDisplay' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
XCloseDisplay (arg->dpy);
^
gl-device-release.c:38:5: error: use of undeclared identifier 'Colormap'
Colormap colormap;
^
gl-device-release.c:39:5: error: use of undeclared identifier 'XSetWindowAttributes'
XSetWindowAttributes window_attributes;
^
gl-device-release.c:40:5: error: use of undeclared identifier 'Window'
Window window = None;
^
gl-device-release.c:42:5: error: use of undeclared identifier 'colormap'
colormap = XCreateColormap (display,
^
gl-device-release.c:42:16: error: implicit declaration of function 'XCreateColormap' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
colormap = XCreateColormap (display,
^
gl-device-release.c:43:8: error: implicit declaration of function 'RootWindow' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
RootWindow (display, visual_info->screen),
^
gl-device-release.c:45:8: error: use of undeclared identifier 'AllocNone'
AllocNone);
^
gl-oversized-surface.c:43:2: error: use of undeclared identifier 'GLX_DOUBLEBUFFER'
GLX_DOUBLEBUFFER,
^
gl-oversized-surface.c:44:2: error: use of undeclared identifier 'None'
None
^
gl-oversized-surface.c:47:5: error: use of undeclared identifier 'Display'
Display *display;
^
gl-oversized-surface.c:47:14: error: use of undeclared identifier 'display'
Display *display;
^
gl-oversized-surface.c:48:5: error: use of undeclared identifier 'XVisualInfo'
XVisualInfo *visual_info;
^
gl-oversized-surface.c:48:18: error: use of undeclared identifier 'visual_info'
XVisualInfo *visual_info;
^
gl-oversized-surface.c:49:5: error: unknown type name 'GLXContext'; did you mean 'EGLContext'?
GLXContext glx_context;
^~~~~~~~~~
EGLContext
/usr/local/include/EGL/egl.h:64:15: note: 'EGLContext' declared here
typedef void *EGLContext;
^
gl-oversized-surface.c:54:5: error: use of undeclared identifier 'display'
display = XOpenDisplay (NULL);
^
gl-surface-source.c:52:2: error: use of undeclared identifier 'GLX_RGBA'
GLX_RGBA,
^
gl-surface-source.c:53:2: error: use of undeclared identifier 'GLX_RED_SIZE'
GLX_RED_SIZE, 1,
^
gl-surface-source.c:54:2: error: use of undeclared identifier 'GLX_GREEN_SIZE'
GLX_GREEN_SIZE, 1,
^
gl-surface-source.c:55:2: error: use of undeclared identifier 'GLX_BLUE_SIZE'
GLX_BLUE_SIZE, 1,
^
gl-surface-source.c:56:2: error: use of undeclared identifier 'GLX_ALPHA_SIZE'
GLX_ALPHA_SIZE, 1,
^
gl-surface-source.c:57:2: error: use of undeclared identifier 'GLX_DOUBLEBUFFER'
GLX_DOUBLEBUFFER,
^
gl-surface-source.c:58:2: error: use of undeclared identifier 'None'
None
^
gl-surface-source.c:60:5: error: use of undeclared identifier 'XVisualInfo'
XVisualInfo *visinfo;
^
gl-surface-source.c:60:18: error: use of undeclared identifier 'visinfo'
XVisualInfo *visinfo;
^
gl-device-release.c:46:5: error: use of undeclared identifier 'window_attributes'
window_attributes.colormap = colormap;
^
gl-device-release.c:46:34: error: use of undeclared identifier 'colormap'
window_attributes.colormap = colormap;
^
gl-device-release.c:47:5: error: use of undeclared identifier 'window_attributes'
window_attributes.border_pixel = 0;
^
gl-device-release.c:48:5: error: use of undeclared identifier 'window'
window = XCreateWindow (display, RootWindow (display, visual_info->screen),
^
gl-device-release.c:48:14: error: implicit declaration of function 'XCreateWindow' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
window = XCreateWindow (display, RootWindow (display, visual_info->screen),
^
gl-oversized-surface.c:54:15: error: implicit declaration of function 'XOpenDisplay' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
display = XOpenDisplay (NULL);
^
gl-oversized-surface.c:55:9: error: use of undeclared identifier 'display'
if (display == NULL)
^
gl-oversized-surface.c:58:5: error: use of undeclared identifier 'visual_info'
visual_info = glXChooseVisual (display, DefaultScreen (display), rgba_attribs);
^
gl-oversized-surface.c:58:19: error: implicit declaration of function 'glXChooseVisual' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
visual_info = glXChooseVisual (display, DefaultScreen (display), rgba_attribs);
^
gl-oversized-surface.c:58:45: error: implicit declaration of function 'DefaultScreen' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
visual_info = glXChooseVisual (display, DefaultScreen (display), rgba_attribs);
gl-surface-source.c:61:5: error: unknown type name 'GLXContext'; did you mean 'EGLContext'?
GLXContext ctx;
^~~~~~~~~~
EGLContext
/usr/local/include/EGL/egl.h:64:15: note: 'EGLContext' declared here
typedef void *EGLContext;
^
gl-surface-source.c:65:5: error: use of undeclared identifier 'Display'
Display *dpy;
^
gl-surface-source.c:65:14: error: use of undeclared identifier 'dpy'
Display *dpy;
^
gl-surface-source.c:67:5: error: use of undeclared identifier 'dpy'
dpy = XOpenDisplay (NULL);
^
gl-surface-source.c:67:11: error: implicit declaration of function 'XOpenDisplay' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
dpy = XOpenDisplay (NULL);
^
gl-surface-source.c:68:9: error: use of undeclared identifier 'dpy'
if (dpy == NULL)
^
gl-oversized-surface.c:58:60: error: use of undeclared identifier 'display'
visual_info = glXChooseVisual (display, DefaultScreen (display), rgba_attribs);
^
PR: 256180
Reported by: shrdlu19@gmail.com
Approved by: maintainer timeout (3 weeks)
- Make an option for FFMPEG, and do not enable it by default.
- Do not bump PORTREVISION: pkg will take care of it, and ports users
may rebuild it if needed.
- Note: there is no simple way to deactivate this option when ffmpeg is
already installed.
PR: 256215
Reported by: Toshimichi Masubuchi (ImageMagick7) and gessel (6)
Approved by: maintainer’s time-out
Fix a regression in the previous release that could cause
a crash when changing layouts and mousing.
Changelog: https://sw.kovidgoyal.net/kitty/changelog.html#id1
PR: 256678
Reported by: Alexis Praga <alexis.praga@free.fr> (maintainer)
These have been supplanted by the devel/freebsd-gcc6 port which uses
separate flavors for each target architecture and bundles the
CROSS_TOOLCHAIN makefile.
Feedback from: jrm
Reviewed by: lwhsu, bapt
Differential Revision: https://reviews.freebsd.org/D30765
Unlike most of the terminal file managers, CliFM replaces the
traditional curses interface by a simple command-line interface.
It is a file manager, but also a shell extension.
WWW: https://github.com/leo-arch/clifm
The following ports part of security gvm were updated
security/gvmd: Update to 21.4.0
security/gvm-libs: Update to 21.4.0
security/openvas: Update to 21.4.0
security/py-ospd-openvas: Update to 21.4.0
security/py-ospd: Update to 21.4.0
security/greenbone-security-assistant: Update to 21.4.0
security/py-python-gvm: Update to 21.5.2
security/py-gvm-tools: Update to 21.6.0
Notable Changes in this Release
- All components and the feed support CVSSv3/CVSSv3.1
- GSA contains a new calculator for these CVSS versions
- Rework of the login page in GSA to have a better entry point into our software
- Dropped support for Internet Explorer
- Dropped support for Microsoft Edge <= 18
- Removed auto false positive feature
- Removed GMP scanner support
- Dropped dynamic severity classes
- Removed support for Python 3.5 and lower
PR: 254630 254632
Reported by: Eirik Oeverby <ltning-freebsd at anduin.net>
