MACS (Model-based Analysis of ChIP-Seq) is a tool for identifying
transcription factor (TF) binding sites. Such sites are generated
by CHiP-Seq (CHromatin immuno-Precipitation sequencing) and ATAC-Seq
(Assay for Transposase Accessible Chromatin Sequencing). MACS
identifies "peaks" in the genome sequence, which are areas enriched
in bound TFs or accessible chromatin.
Currently their is a hardcoded dependency on mysql57-client which is
about to be removed. Ports depending on mysql should always use
USES=mysql rather than hardcoded *_DEPENDS. As I do not have a licensed
version of this application for now switch to USES=mysql. This should
not affect the cluster build at all as this is a RESTRICTED ports.
Approved by: portmgr (blanket)
- There are multiple ports which has MYSQL options and are non-DEFAULT.
Most of the time committers actually forget to check with the OPTION
enabled and in some cases they are BROKEN with newr versions of mysql.
So test with different versions of mysql and mark IGNOPRE_WITH_MYSQL
appropriately. Due to the EOL of 5.7 this has not been checked.
- Unbreak sysutils/cfengine* with MySQL 8.0 and later
- The primary purpose of running this check is having statistics of the
MySQL usability over MariaDB to explore the future possibility of
shifting to MariaDB as the default as major ports upstream have moved
their codebase to support MariaDB over MySQL.
- The following actions will also be taken after the sunset of MySQL 5.7
If a port is broken on all instances of MySQL/MariaDB:
- If a port has the option of multiple DB backends and MySQL is the
default then the DEFAULT will be changed to PGSQL/SQLITE before
2024Q1. And the OPTION will be removed before 2024Q2. If a
MAINTAINER is aware about such cases and want to prefer PGSQL over
SQLITE or vice versa please do so at your own accord. Otherwise
PGSQL will be preferred over SQLITE.
- If a port has the option of multiple DB backends and MySQL is not
the default then the the OPTION will be removed before 2024Q1.
Approved by: portmgr (blanket)
Rename the roundup method defined in bwValues.c as it clashes with the
roundup macro defined in sys/param.h
/wrkdirs/usr/ports/biology/libbigwig/work/libBigWig-0.4.7/bwValues.c:9:35:
error: too few arguments provided to function-like macro invocation
static uint32_t roundup(uint32_t v) {
^
/usr/include/sys/param.h:300:9: note: macro 'roundup' defined here
^
/wrkdirs/usr/ports/biology/libbigwig/work/libBigWig-0.4.7/bwValues.c:9:24:
error: expected ';' after top level declarator
static uint32_t roundup(uint32_t v) {
^
;
/wrkdirs/usr/ports/biology/libbigwig/work/libBigWig-0.4.7/bwValues.c:350:30:
error: too few arguments provided to function-like macro invocation
o->m = roundup(o->l+1);
^
/usr/include/sys/param.h:300:9: note: macro 'roundup' defined here
^
/wrkdirs/usr/ports/biology/libbigwig/work/libBigWig-0.4.7/bwValues.c:370:30:
error: too few arguments provided to function-like macro invocation
o->m = roundup(o->l+1);
^
/usr/include/sys/param.h:300:9: note: macro 'roundup' defined here
^
4 errors generated.
Approved by: portmgr (blanket)
The BiocManager package, as the modern successor package to
BiocInstaller, allows users to install and manage packages from the
Bioconductor project. Bioconductor focuses on the statistical analysis
and comprehension of high-throughput genomic data.
WWW: https://bioconductor.github.io/BiocManager/
ajfileio.c:271:7: warning: call to undeclared function 'ajSysFuncFgets'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
cp = ajSysFuncFgets(&buff[ipos], isize, file->fp);
^
ajfileio.c:271:5: error: incompatible integer to pointer conversion assigning to 'const char *' from 'int' [-Wint-conversion]
cp = ajSysFuncFgets(&buff[ipos], isize, file->fp);
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 warning and 1 error generated.
