minimap2 error with make - argp.h not found
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anita-brzoza commented
Hi, I past this cd LongQC/minimap2-coverage && make arm_neon=1 aarch64=1 to the terminal and got this error message:
cc -c -g -O2 -Wall -Wc++-compat -D_FILE_OFFSET_BITS=64 -fsigned-char -DHAVE_KALLOC -Isse2neon minimap2-coverage.c -o minimap2-coverage.o
minimap2-coverage.c:12:10: fatal error: 'argp.h' file not found
#include <argp.h>
^~~~~~~~
1 error generated.
make: *** [minimap2-coverage.o] Error 1
I'm using Mac M1 Max (MacBook Pro) Sonoma 14.3.1. and anaconda env. I installed argp-standalone as shown below and found the argp.h file in this environment, so it is present.
conda list -n env1
# packages in environment at /Users/anitabrzoza/anaconda3/envs/env1:
#
# Name Version Build Channel
argp-standalone 1.5.0 he4db4b2_0 conda-forge
bzip2 1.0.8 h10d778d_5 conda-forge
ca-certificates 2024.2.2 hf0a4a13_0 conda-forge
contourpy 1.2.0 pypi_0 pypi
cycler 0.12.1 pypi_0 pypi
edlib 1.3.9 pypi_0 pypi
fonttools 4.48.1 pypi_0 pypi
h5py 3.10.0 pypi_0 pypi
importlib-resources 6.1.1 pypi_0 pypi
jinja2 3.1.3 pypi_0 pypi
joblib 1.3.2 pypi_0 pypi
kiwisolver 1.4.5 pypi_0 pypi
libffi 3.4.2 h0d85af4_5 conda-forge
libsqlite 3.45.1 h92b6c6a_0 conda-forge
libtool 2.4.6 h313beb8_1009 anaconda
libzlib 1.2.13 h8a1eda9_5 conda-forge
markupsafe 2.1.5 pypi_0 pypi
matplotlib 3.8.2 pypi_0 pypi
ncurses 6.4 h93d8f39_2 conda-forge
numpy 1.26.4 pypi_0 pypi
openssl 3.2.1 hd75f5a5_0 conda-forge
packaging 23.2 pypi_0 pypi
pillow 10.2.0 pypi_0 pypi
pip 24.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.1.1 pypi_0 pypi
pysam 0.22.0 pypi_0 pypi
python 3.9.18 h7a9c478_1_cpython conda-forge
python-dateutil 2.8.2 pypi_0 pypi
readline 8.2 h9e318b2_1 conda-forge
scikit-learn 1.4.0 pypi_0 pypi
scipy 1.12.0 pypi_0 pypi
setuptools 69.0.3 pyhd8ed1ab_0 conda-forge
six 1.16.0 pypi_0 pypi
threadpoolctl 3.2.0 pypi_0 pypi
tk 8.6.13 h1abcd95_1 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h775f41a_0 conda-forge
zipp 3.17.0 pypi_0 pypi
ls anaconda3/envs/env1/include
X11 odbcStubs.h tkDecls.h
argp.h openssl tkEntry.h
bzlib.h panel.h tkFileFilter.h
curses.h pqStubs.h tkFont.h
cursesapp.h python3.9 tkImgPhoto.h
cursesf.h readline tkInt.h
cursesm.h sqlite3.h tkIntDecls.h
cursesp.h sqlite3ext.h tkIntPlatDecls.h
cursesw.h tcl.h tkIntXlibDecls.h
cursslk.h tclDecls.h tkMacOSX.h
default.h tclInt.h tkMacOSXColor.h
eti.h tclIntDecls.h tkMacOSXConstants.h
etip.h tclIntPlatDecls.h tkMacOSXCursors.h
fakemysql.h tclOO.h tkMacOSXDebug.h
fakepq.h tclOODecls.h tkMacOSXDefault.h
fakesql.h tclOOInt.h tkMacOSXEvent.h
ffi.h tclOOIntDecls.h tkMacOSXFileTypes.h
ffitarget.h tclPlatDecls.h tkMacOSXFont.h
form.h tclPort.h tkMacOSXInt.h
itcl.h tclThread.h tkMacOSXKeysyms.h
itcl2TclOO.h tclTomMath.h tkMacOSXPort.h
itclDecls.h tclTomMathDecls.h tkMacOSXPrivate.h
itclInt.h tclUnixPort.h tkMacOSXWm.h
itclIntDecls.h tdbc.h tkMacOSXXCursors.h
itclMigrate2TclCore.h tdbcDecls.h tkMenu.h
itclTclIntStubsFcn.h tdbcInt.h tkMenubutton.h
ks_names.h term.h tkPlatDecls.h
libltdl term_entry.h tkPort.h
ltdl.h termcap.h tkScale.h
lzma tic.h tkScrollbar.h
lzma.h tk.h tkSelect.h
menu.h tk3d.h tkText.h
mysqlStubs.h tkArray.h tkUndo.h
nc_tparm.h tkBusy.h tkUnixDefault.h
ncurses tkButton.h tkUnixInt.h
ncurses.h tkCanvas.h tkUnixPort.h
ncurses_dll.h tkColor.h tkUuid.h
ncursesw tkDList.h unctrl.h
yfukasawa commented
Hi @anita-brzoza,
Thank you for your interest in our tool!
To get the root path for your conda environment, simply use $CONDA_PREFIX and try below.
This would be ad hoc but worked for me.
make arm_neon=1 aarch64=1 CFLAGS+="-L${CONDA_PREFIX}/lib -I${CONDA_PREFIX}/include"
Yoshinori