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A pipeline for detecting Somatic Insertion of DE novo RETROcopies

Home Page: https://sideretro.readthedocs.io

License: GNU General Public License v3.0

C 98.80% Meson 1.10% Dockerfile 0.10%

cnv genotype mobile-elements next-generation-sequencing polimorphism pseudogenes retrocopy wes wgs

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sideretro's Issues

Error when installing sideRETRO

Hi,
I am installing sideRETRO, I used anaconda to install ninja and meson.

I have managed to build with meson, I have the "build" directory.

meson build
The Meson build system
Version: 0.53.2
Source dir: /home/kgagalova/src/sideRETRO
Build dir: /home/kgagalova/src/sideRETRO/build
Build type: native build
Project name: sideRETRO
Project version: 0.14.0
Appending CFLAGS from environment: '-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/include'
Appending LDFLAGS from environment: ['-Wl,-O2', '-Wl,--sort-common', '-Wl,--as-needed', '-Wl,-z,relro', '-Wl,-z,now', '-Wl,--disable-new-dtags', '-Wl,--gc-sections', '-Wl,-rpath,/projects/spruceup_scratch/dev/anaconda3/envs/py3.8/lib', '-Wl,-rpath-link,/projects/spruceup_scratch/dev/anaconda3/envs/py3.8/lib', '-L/projects/spruceup_scratch/dev/anaconda3/envs/py3.8/lib']
Appending CPPFLAGS from environment: '-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/include'
Appending CFLAGS from environment: '-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/include'
Appending LDFLAGS from environment: ['-Wl,-O2', '-Wl,--sort-common', '-Wl,--as-needed', '-Wl,-z,relro', '-Wl,-z,now', '-Wl,--disable-new-dtags', '-Wl,--gc-sections', '-Wl,-rpath,/projects/spruceup_scratch/dev/anaconda3/envs/py3.8/lib', '-Wl,-rpath-link,/projects/spruceup_scratch/dev/anaconda3/envs/py3.8/lib', '-L/projects/spruceup_scratch/dev/anaconda3/envs/py3.8/lib']
Appending CPPFLAGS from environment: '-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/include'
C compiler for the host machine: /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/bin/x86_64-conda_cos6-linux-gnu-cc (gcc 7.3.0 "x86_64-conda_cos6-linux-gnu-cc (crosstool-NG 1.23.0.449-a04d0) 7.3.0")
C linker for the host machine: /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/bin/x86_64-conda_cos6-linux-gnu-cc ld.bfd 2.33.1
Host machine cpu family: x86_64
Host machine cpu: x86_64
Configuring config.h.in using configuration
Library m found: YES
Library dl found: YES
Run-time dependency threads found: YES
Found pkg-config: /usr/bin/pkg-config (0.27.1)
Run-time dependency zlib found: YES 1.2.7
Dependency sqlite3 found: NO found 3.7.17 but need: '>= 3.28.0'
Did not find CMake 'cmake'
Found CMake: NO
Run-time dependency sqlite3 found: NO (tried pkgconfig and cmake)
Looking for a fallback subproject for the dependency sqlite3
Downloading sqlite source from https://github.com/azadkuh/sqlite-amalgamation/archive/3.29.0.tar.gz
Downloading file of unknown size.
Downloading sqlite patch from https://github.com/galantelab/sqlite-amalgamation/archive/3.29.0.tar.gz
Downloading file of unknown size.

|Executing subproject sqlite method meson 
|
|Project name: sqlite
|Project version: 3.29.0
|C compiler for the host machine: /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/bin/x86_64-conda_cos6-linux-gnu-cc (gcc 7.3.0 "x86_64-conda_cos6-linux-gnu-cc (crosstool-NG 1.23.0.449-a04d0) 7.3.0")
|C linker for the host machine: /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/bin/x86_64-conda_cos6-linux-gnu-cc ld.bfd 2.33.1
|Library dl found: YES
|Dependency threads found: YES unknown (cached)
|Build targets in project: 2
|Subproject sqlite finished.

Dependency sqlite3 from subproject subprojects/sqlite found: YES 3.29.0
Run-time dependency htslib found: NO (tried pkgconfig and cmake)
Looking for a fallback subproject for the dependency htslib
Downloading htslib source from https://github.com/samtools/htslib/archive/1.9.tar.gz
Downloading file of unknown size.
Downloading htslib patch from https://github.com/galantelab/htslib/archive/1.9.tar.gz
Downloading file of unknown size.

|Executing subproject htslib method meson 
|
|Project name: htslib
|Project version: 1.9
|C compiler for the host machine: /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/bin/x86_64-conda_cos6-linux-gnu-cc (gcc 7.3.0 "x86_64-conda_cos6-linux-gnu-cc (crosstool-NG 1.23.0.449-a04d0) 7.3.0")
|C linker for the host machine: /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/bin/x86_64-conda_cos6-linux-gnu-cc ld.bfd 2.33.1
|Library m found: YES
|Dependency threads found: YES unknown (cached)
|Dependency zlib found: YES 1.2.7 (cached)
|Configuring config.h using configuration
|Configuring version.h using configuration
|Build targets in project: 3
|Subproject htslib finished.

Dependency htslib from subproject subprojects/htslib found: YES 1.9
Run-time dependency check found: NO (tried pkgconfig and cmake)
Program sphinx-build found: YES (/projects/spruceup_scratch/dev/anaconda3/bin/sphinx-build)
tests/meson.build:55: WARNING: Testing is disabled without 'libcheck'
Build targets in project: 6

sideRETRO 0.14.0

  Subprojects
    htslib: YES
    sqlite: YES

Found ninja-1.10.0 at /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/bin/ninja

However after running ninja I have the following error

ninja -C build
ninja: Entering directory `build'
[1/79] Compiling C object 'src/25a6634@@sider@exe/main.c.o'.
FAILED: src/25a6634@@sider@exe/main.c.o 
/projects/spruceup_scratch/dev/anaconda3/envs/py3.8/bin/x86_64-conda_cos6-linux-gnu-cc -Isrc/25a6634@@sider@exe -Isrc -I../src -I. -I../ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -g -DHAVE_CONFIG_H -D_GNU_SOURCE -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -isystem /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/include -MD -MQ 'src/25a6634@@sider@exe/main.c.o' -MF 'src/25a6634@@sider@exe/main.c.o.d' -o 'src/25a6634@@sider@exe/main.c.o' -c ../src/main.c
../src/main.c:1:10: fatal error: config.h: No such file or directory
 #include "config.h"
          ^~~~~~~~~~
compilation terminated.
[13/79] Compiling C object 'src/25a6634@@sider@sta/db.c.o'.
FAILED: src/25a6634@@sider@sta/db.c.o 
/projects/spruceup_scratch/dev/anaconda3/envs/py3.8/bin/x86_64-conda_cos6-linux-gnu-cc -Isrc/25a6634@@sider@sta -Isrc -I../src -I. -I../ -Isubprojects/sqlite-amalgamation-3.29.0 -I../subprojects/sqlite-amalgamation-3.29.0 -Isubprojects/htslib-1.9 -I../subprojects/htslib-1.9 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -g -DHAVE_CONFIG_H -D_GNU_SOURCE -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -isystem /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/include -fPIC -pthread -MD -MQ 'src/25a6634@@sider@sta/db.c.o' -MF 'src/25a6634@@sider@sta/db.c.o.d' -o 'src/25a6634@@sider@sta/db.c.o' -c ../src/db.c
In file included from ../src/db.c:5:0:
../src/db.c: In function 'db_check_schema_version':
../src/db.c:480:55: error: 'PACKAGE_STRING' undeclared (first use in this function); did you mean '__STRING'?
     DB_SCHEMA_MAJOR_VERSION, DB_SCHEMA_MINOR_VERSION, PACKAGE_STRING);
                                                       ^
../src/log.h:45:47: note: in definition of macro 'log_fatal'
   log_log (LOG_FATAL, __FILENAME__, __LINE__, __VA_ARGS__); \
                                               ^~~~~~~~~~~
../src/db.c:480:55: note: each undeclared identifier is reported only once for each function it appears in
     DB_SCHEMA_MAJOR_VERSION, DB_SCHEMA_MINOR_VERSION, PACKAGE_STRING);
                                                       ^
../src/log.h:45:47: note: in definition of macro 'log_fatal'
   log_log (LOG_FATAL, __FILENAME__, __LINE__, __VA_ARGS__); \
                                               ^~~~~~~~~~~
[24/79] Compiling C object 'src/25a6634@@sider@sta/vcf.c.o'.
FAILED: src/25a6634@@sider@sta/vcf.c.o 
/projects/spruceup_scratch/dev/anaconda3/envs/py3.8/bin/x86_64-conda_cos6-linux-gnu-cc -Isrc/25a6634@@sider@sta -Isrc -I../src -I. -I../ -Isubprojects/sqlite-amalgamation-3.29.0 -I../subprojects/sqlite-amalgamation-3.29.0 -Isubprojects/htslib-1.9 -I../subprojects/htslib-1.9 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -g -DHAVE_CONFIG_H -D_GNU_SOURCE -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -isystem /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/include -fPIC -pthread -MD -MQ 'src/25a6634@@sider@sta/vcf.c.o' -MF 'src/25a6634@@sider@sta/vcf.c.o.d' -o 'src/25a6634@@sider@sta/vcf.c.o' -c ../src/vcf.c
../src/vcf.c: In function 'vcf_print_header':
../src/vcf.c:201:27: error: 'PACKAGE_NAME' undeclared (first use in this function)
   VCF_VERSION, timestamp, PACKAGE_NAME, PACKAGE_VERSION);
                           ^~~~~~~~~~~~
../src/vcf.c:201:27: note: each undeclared identifier is reported only once for each function it appears in
../src/vcf.c:201:41: error: 'PACKAGE_VERSION' undeclared (first use in this function); did you mean '_SC_REGEX_VERSION'?
   VCF_VERSION, timestamp, PACKAGE_NAME, PACKAGE_VERSION);
                                         ^~~~~~~~~~~~~~~
                                         _SC_REGEX_VERSION
[36/79] Compiling C object 'src/25a6634@@sider@sta/make_vcf.c.o'.
FAILED: src/25a6634@@sider@sta/make_vcf.c.o 
/projects/spruceup_scratch/dev/anaconda3/envs/py3.8/bin/x86_64-conda_cos6-linux-gnu-cc -Isrc/25a6634@@sider@sta -Isrc -I../src -I. -I../ -Isubprojects/sqlite-amalgamation-3.29.0 -I../subprojects/sqlite-amalgamation-3.29.0 -Isubprojects/htslib-1.9 -I../subprojects/htslib-1.9 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -g -DHAVE_CONFIG_H -D_GNU_SOURCE -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -isystem /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/include -fPIC -pthread -MD -MQ 'src/25a6634@@sider@sta/make_vcf.c.o' -MF 'src/25a6634@@sider@sta/make_vcf.c.o.d' -o 'src/25a6634@@sider@sta/make_vcf.c.o' -c ../src/make_vcf.c
../src/make_vcf.c: In function 'print_usage':
../src/make_vcf.c:81:24: error: 'PACKAGE' undeclared (first use in this function)
  int pkg_len = strlen (PACKAGE);
                        ^~~~~~~
../src/make_vcf.c:81:24: note: each undeclared identifier is reported only once for each function it appears in
../src/make_vcf.c:121:3: error: 'PACKAGE_STRING' undeclared (first use in this function); did you mean 'PACKAGE'?
   PACKAGE_STRING, PACKAGE, pkg_len, ' ', pkg_len, ' ',
   ^~~~~~~~~~~~~~
   PACKAGE
../src/make_vcf.c: In function 'print_try_help':
../src/make_vcf.c:130:4: error: 'PACKAGE' undeclared (first use in this function)
    PACKAGE);
    ^~~~~~~
../src/make_vcf.c: In function 'make_vcf_validate':
../src/make_vcf.c:174:6: error: 'PACKAGE' undeclared (first use in this function)
      PACKAGE, vcf->db_file);
      ^~~~~~~
../src/make_vcf.c: In function 'make_vcf_print':
../src/make_vcf.c:244:3: error: 'PACKAGE_STRING' undeclared (first use in this function); did you mean '__STRING'?
   PACKAGE_STRING, PACKAGE, PACKAGE,
   ^~~~~~~~~~~~~~
   __STRING
../src/make_vcf.c:244:19: error: 'PACKAGE' undeclared (first use in this function)
   PACKAGE_STRING, PACKAGE, PACKAGE,
                   ^~~~~~~
[37/79] Compiling C object 'src/25a6634@@sider@sta/process_sample.c.o'.
FAILED: src/25a6634@@sider@sta/process_sample.c.o 
/projects/spruceup_scratch/dev/anaconda3/envs/py3.8/bin/x86_64-conda_cos6-linux-gnu-cc -Isrc/25a6634@@sider@sta -Isrc -I../src -I. -I../ -Isubprojects/sqlite-amalgamation-3.29.0 -I../subprojects/sqlite-amalgamation-3.29.0 -Isubprojects/htslib-1.9 -I../subprojects/htslib-1.9 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -g -DHAVE_CONFIG_H -D_GNU_SOURCE -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -isystem /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/include -fPIC -pthread -MD -MQ 'src/25a6634@@sider@sta/process_sample.c.o' -MF 'src/25a6634@@sider@sta/process_sample.c.o.d' -o 'src/25a6634@@sider@sta/process_sample.c.o' -c ../src/process_sample.c
../src/process_sample.c: In function 'print_usage':
../src/process_sample.c:224:24: error: 'PACKAGE' undeclared (first use in this function)
  int pkg_len = strlen (PACKAGE);
                        ^~~~~~~
../src/process_sample.c:224:24: note: each undeclared identifier is reported only once for each function it appears in
../src/process_sample.c:299:3: error: 'PACKAGE_STRING' undeclared (first use in this function); did you mean 'PACKAGE'?
   PACKAGE_STRING, PACKAGE, pkg_len, ' ', pkg_len, ' ', pkg_len, ' ', pkg_len, ' ',
   ^~~~~~~~~~~~~~
   PACKAGE
../src/process_sample.c: In function 'print_try_help':
../src/process_sample.c:309:4: error: 'PACKAGE' undeclared (first use in this function)
    PACKAGE);
    ^~~~~~~
../src/process_sample.c: In function 'process_sample_validate':
../src/process_sample.c:365:64: error: 'PACKAGE' undeclared (first use in this function)
    fprintf (stderr, "%s: Missing alignment files (SAM/BAM)\n", PACKAGE);
                                                                ^~~~~~~
../src/process_sample.c: In function 'process_sample_print':
../src/process_sample.c:500:3: error: 'PACKAGE_STRING' undeclared (first use in this function); did you mean '__STRING'?
   PACKAGE_STRING);
   ^~~~~~~~~~~~~~
   __STRING
../src/process_sample.c:514:3: error: 'PACKAGE' undeclared (first use in this function)
   PACKAGE, PACKAGE, ps->gff_file, ps->output_dir, ps->prefix);
   ^~~~~~~
[38/79] Compiling C object 'src/25a6634@@sider@sta/utils.c.o'.
../src/utils.c: In function 'which':
../src/utils.c:213:10: warning: implicit declaration of function 'secure_getenv'; did you mean '__secure_getenv'? [-Wimplicit-function-declaration]
  paths = secure_getenv ("PATH");
          ^~~~~~~~~~~~~
          __secure_getenv
../src/utils.c:213:8: warning: assignment makes pointer from integer without a cast [-Wint-conversion]
  paths = secure_getenv ("PATH");
        ^
[46/79] Compiling C object 'src/25a6634@@sider@sta/merge_call.c.o'.
FAILED: src/25a6634@@sider@sta/merge_call.c.o 
/projects/spruceup_scratch/dev/anaconda3/envs/py3.8/bin/x86_64-conda_cos6-linux-gnu-cc -Isrc/25a6634@@sider@sta -Isrc -I../src -I. -I../ -Isubprojects/sqlite-amalgamation-3.29.0 -I../subprojects/sqlite-amalgamation-3.29.0 -Isubprojects/htslib-1.9 -I../subprojects/htslib-1.9 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c99 -g -DHAVE_CONFIG_H -D_GNU_SOURCE -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -isystem /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /projects/spruceup_scratch/dev/anaconda3/envs/py3.8/include -fPIC -pthread -MD -MQ 'src/25a6634@@sider@sta/merge_call.c.o' -MF 'src/25a6634@@sider@sta/merge_call.c.o.d' -o 'src/25a6634@@sider@sta/merge_call.c.o' -c ../src/merge_call.c
../src/merge_call.c: In function 'print_usage':
../src/merge_call.c:267:24: error: 'PACKAGE' undeclared (first use in this function)
  int pkg_len = strlen (PACKAGE);
                        ^~~~~~~
../src/merge_call.c:267:24: note: each undeclared identifier is reported only once for each function it appears in
../src/merge_call.c:357:3: error: 'PACKAGE_STRING' undeclared (first use in this function); did you mean 'PACKAGE'?
   PACKAGE_STRING, PACKAGE, pkg_len, ' ', pkg_len, ' ', pkg_len, ' ', pkg_len, ' ', pkg_len, ' ',
   ^~~~~~~~~~~~~~
   PACKAGE
../src/merge_call.c: In function 'print_try_help':
../src/merge_call.c:369:4: error: 'PACKAGE' undeclared (first use in this function)
    PACKAGE);
    ^~~~~~~
../src/merge_call.c: In function 'merge_call_validate':
../src/merge_call.c:432:56: error: 'PACKAGE' undeclared (first use in this function)
    fprintf (stderr, "%s: Missing SQLite3 databases\n", PACKAGE);
                                                        ^~~~~~~
../src/merge_call.c: In function 'merge_call_print':
../src/merge_call.c:597:3: error: 'PACKAGE_STRING' undeclared (first use in this function); did you mean '__STRING'?
   PACKAGE_STRING);
   ^~~~~~~~~~~~~~
   __STRING
../src/merge_call.c:613:3: error: 'PACKAGE' undeclared (first use in this function)
   PACKAGE, PACKAGE, mc->output_dir, mc->prefix);
   ^~~~~~~
../src/merge_call.c: In function 'parse_merge_call_command_opt':
../src/merge_call.c:840:38: error: 'PACKAGE' undeclared (first use in this function)
           "Missing complete pair\n", PACKAGE);
                                      ^~~~~~~
[75/79] Compiling C object 'subprojects/sqlite-amalgamation-3.29.0/5a45302@@sqlite3@sta/sqlite3.c.o'.
ninja: build stopped: subcommand failed.

Do you have any suggestions?
Thank you in advance

Recommended maximum number of samples

Dear authors,

First thank you for this nice and very nicely documented tool.

I would like to use sideretro on a large set of samples (several hundred samples).
Running the complete sideretro practical workflow on 15 samples was successful resulting in a valid vcf file.

Running sideretro process-sample on 30 samples was successfull but merged-call failed.
I stopped the program after several days: no output generated after several days.
The last ouput to the log file was
cluster.c:672: Clustering abnormal alignments

What would be the recommended workflow.
Follow your "Practical Workflow" on batches (of 15 samples) and use adhoc script to merge the vcf files (taking advantage of the parental gene information) ?

Thank you in advance for your help,
Thomas

Does sideRETRO work for non-human samples?

Hello,

I was wondering if it is possible to use sideRETRO on non-human samples. When I run sideRetro on my samples, I get the following warning: "WARN merge_call.c:239: No cluster has been found!" I'm not sure if sideRETRO is assuming that the chromosome names will be human chromosome names. The produced database file is about 1GB in size, but the out.vcf file is completely empty. Of course, there may be some other issue. Thanks for any assistance.

Analyze tumor samples

Dear author,

This is a great tool that I want to apply to tumor genomes. Do I need a matched normal sample for detecting somatic retrocopy insertion? If it dose, I guess both the BAM files of the tumor and normal samples should be added to my_files_list.txt.

Looking forward to your reply!

Thanks!

ninja fails on mac

Hello, on mac OS mojave 10.14.6
current version from git clone
seems to fail near the end
any suggestions welcome!
thanks
christos

Christoss-giant-Mac:sideRETRO christos$ meson build && ninja -C build
The Meson build system
Version: 0.58.1
Source dir: /Users/christos/sideRETRO
Build dir: /Users/christos/sideRETRO/build
Build type: native build
Project name: sideRETRO
Project version: 1.0.0
C compiler for the host machine: gcc-11 (gcc 11.1.0 "gcc-11 (Homebrew GCC 11.1.0_1) 11.1.0")
C linker for the host machine: gcc-11 ld64 530
Host machine cpu family: x86_64
Host machine cpu: x86_64
Configuring config.h.in using configuration
Program /usr/local/Cellar/meson/0.58.1/libexec/bin/meson found: YES (/usr/local/Cellar/meson/0.58.1/libexec/bin/meson)
Library m found: YES
Library dl found: YES
Run-time dependency threads found: YES
Found pkg-config: /usr/local/bin/pkg-config (0.29.2)
Run-time dependency zlib found: YES 1.2.11
Dependency sqlite3 found: NO found 3.24.0 but need: '>= 3.28.0'
Found CMake: /usr/local/bin/cmake (3.9.3)
Run-time dependency sqlite3 found: NO (tried pkgconfig, framework and cmake)
Looking for a fallback subproject for the dependency sqlite3

Executing subproject sqlite

Dependency sqlite3 from subproject subprojects/sqlite-amalgamation-3.29.0 found: YES 3.29.0
Run-time dependency htslib found: NO (tried pkgconfig, framework and cmake)
Looking for a fallback subproject for the dependency htslib

Executing subproject htslib

htslib| Project name: htslib
htslib| Project version: 1.9
htslib| C compiler for the host machine: gcc-11 (gcc 11.1.0 "gcc-11 (Homebrew GCC 11.1.0_1) 11.1.0")
htslib| C linker for the host machine: gcc-11 ld64 530
htslib| Library m found: YES
htslib| Dependency threads found: YES unknown (cached)
htslib| Dependency zlib found: YES 1.2.11 (cached)
htslib| Configuring config.h using configuration
htslib| Configuring version.h using configuration
htslib| Build targets in project: 3
htslib| Subproject htslib finished.

Dependency htslib from subproject subprojects/htslib-1.9 found: YES 1.9
Run-time dependency check found: NO (tried pkgconfig, framework and cmake)
Program sphinx-build found: NO
tests/meson.build:56: WARNING: Testing is disabled without 'libcheck'
docs/meson.build:47: WARNING: Documentation is disabled without 'sphinx'
Build targets in project: 5

sideRETRO 1.0.0

Subprojects
htslib: YES
sqlite: YES

Found ninja-1.10.2 at /usr/local/bin/ninja
ninja: Entering directory `build'
[68/80] Compiling C object src/libsider.a.p/thpool.c.o
../src/thpool.c: In function 'thread_do':
../src/thpool.c:384:9: warning: implicit declaration of function 'pthread_setname_np'; did you mean 'pthread_setcanceltype'? [-Wimplicit-function-declaration]
384 | pthread_setname_np (thread_name);
| ^~~~~~~~~~~~~~~~~~
| pthread_setcanceltype
[70/80] Compiling C object src/libsider.a.p/utils.c.o
../src/utils.c: In function 'which':
../src/utils.c:239:17: warning: implicit declaration of function 'secure_getenv' [-Wimplicit-function-declaration]
239 | paths = secure_getenv ("PATH");
| ^~~~~~~~~~~~~
../src/utils.c:239:15: warning: assignment to 'char *' from 'int' makes pointer from integer without a cast [-Wint-conversion]
239 | paths = secure_getenv ("PATH");
| ^
[73/80] Compiling C object subprojects/htslib-1.9/libhts.a.p/hts.c.o
../subprojects/htslib-1.9/hts.c: In function 'hts_idx_init':
../subprojects/htslib-1.9/hts.c:1386:59: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int' changes value from 'idx->z.last_bin = 4294967295' to '-1' [-Woverflow]
1386 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu;
| ^~~
[78/80] Compiling C object subprojects...tion-3.29.0/libsqlite3.a.p/sqlite3.c.o
../subprojects/sqlite-amalgamation-3.29.0/sqlite3.c: In function 'sqlite3DefaultRowEst':
../subprojects/sqlite-amalgamation-3.29.0/sqlite3.c:111024:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
111024 | if( pIdx->pPartIdxWhere!=0 ) a[0] -= 10; assert( 10==sqlite3LogEst(2) );
| ^~
In file included from ../subprojects/sqlite-amalgamation-3.29.0/sqlite3.c:13700:
../subprojects/sqlite-amalgamation-3.29.0/sqlite3.c:111024:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'i'
111024 | if( pIdx->pPartIdxWhere!=0 ) a[0] -= 10; assert( 10==sqlite3LogEst(2) );
| ^~~~~~
../subprojects/sqlite-amalgamation-3.29.0/sqlite3.c:111025:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
111025 | if( a[0]<33 ) a[0] = 33; assert( 33==sqlite3LogEst(10) );
| ^~
In file included from ../subprojects/sqlite-amalgamation-3.29.0/sqlite3.c:13700:
../subprojects/sqlite-amalgamation-3.29.0/sqlite3.c:111025:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'i'
111025 | if( a[0]<33 ) a[0] = 33; assert( 33==sqlite3LogEst(10) );
| ^~~~~~
../subprojects/sqlite-amalgamation-3.29.0/sqlite3.c: In function 'sqlite3SelectNew':
../subprojects/sqlite-amalgamation-3.29.0/sqlite3.c:125321:10: warning: function may return address of local variable [-Wreturn-local-addr]
125321 | return pNew;
| ^~~~
../subprojects/sqlite-amalgamation-3.29.0/sqlite3.c:125281:10: note: declared here
125281 | Select standin;
| ^~~~~~~
[80/80] Linking target src/sider
FAILED: src/sider
gcc-11 -o src/sider src/sider.p/main.c.o -L/Users/christos/miniconda3/lib -Wl,-dead_strip_dylibs -Wl,-headerpad_max_install_names -Wl,-undefined,error -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/christos/miniconda3/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/christos/miniconda3/include -D_FORTIFY_SOURCE=2 -isystem /Users/christos/miniconda3/include -Wl,-rpath,/usr/lib src/libsider.a subprojects/sqlite-amalgamation-3.29.0/libsqlite3.a subprojects/htslib-1.9/libhts.a /usr/lib/libz.dylib -lm -ldl
Undefined symbols for architecture x86_64:
"_secure_getenv", referenced from:
_which in libsider.a(utils.c.o)
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
ninja: build stopped: subcommand failed.

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