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If anyone has solved the error: conflicting types for 'exp' or the equivalent for 'log', I'd be incredibly grateful.
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Is the conflicting types a warning or an error ?
Can you display the full message?
If it's just a warning, don't worry about it.Comment
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phil@phil:~/Desktop/samtools-0.1.18$ make
make[1]: Entering directory `/home/phil/Desktop/samtools-0.1.18'
make[2]: Entering directory `/home/phil/Desktop/samtools-0.1.18'
gcc -c -g -Wall -O2 -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bgzf.c -o bgzf.o
bgzf.c: In function ‘bgzf_close’:
bgzf.c:630:8: warning: variable ‘count’ set but not used [-Wunused-but-set-variable]
gcc -c -g -Wall -O2 -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. kstring.c -o kstring.o
gcc -c -g -Wall -O2 -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_aux.c -o bam_aux.o
gcc -c -g -Wall -O2 -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam.c -o bam.o
gcc -c -g -Wall -O2 -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_import.c -o bam_import.o
gcc -c -g -Wall -O2 -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. sam.c -o sam.o
gcc -c -g -Wall -O2 -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_index.c -o bam_index.o
bam_index.c: In function ‘bam_index_load_core’:
bam_index.c:330:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:337:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:350:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:353:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:357:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:361:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:371:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:375:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
gcc -c -g -Wall -O2 -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_pileup.c -o bam_pileup.o
bam_pileup.c: In function ‘resolve_cigar2’:
bam_pileup.c:75:9: warning: variable ‘is_head’ set but not used [-Wunused-but-set-variable]
gcc -c -g -Wall -O2 -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -Wall -O2 -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_md.c -o bam_md.o
In file included from /usr/include/math.h:146:0,
from bam_md.c:5:
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:101:1: error: conflicting types for ‘exp’
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:110:1: error: conflicting types for ‘log’
make[2]: *** [bam_md.o] Error 1
make[2]: Leaving directory `/home/phil/Desktop/samtools-0.1.18'
make[1]: *** [lib-recur] Error 1
make[1]: Leaving directory `/home/phil/Desktop/samtools-0.1.18'
make: *** [all-recur] Error 1Comment
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I don't quite know what's important, so there's all of it.Comment
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Figured it out! I put in, from somewhere I found online, the -Dexpl=exp -Dlogl=log line in DFLAGS. Got rid of that and it worked! Thanks!Comment
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I was having the same problem running make in Ubuntu 12.04 lts, with errors resulting from problems with both zlib and curses. Ultimately the solution was to do this:
sudo apt-get update
sudo apt-get install zlib1g-dev libncurses5-dev
sudo make clean
sudo makeComment
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Thanks, NRP! I'll pass that onto anyone having a similar problem!Comment
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Originally posted by Richard Finney View Post
On an Ubuntu box if you install the libncurses5 and libncurses5-dev the -I parameter is useless…SysAdmin & ICT consultant
http://about.me/nicola.lositoComment
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there are installation instructions in the file "INSTALL":
The text-based viewer (tview) requires the GNU ncurses library
<http://www.gnu.org/software/ncurses/>, which comes with Mac OS X and most of
the modern Linux/Unix distributions. If you do not have this library installed,
you can still compile the rest of SAMtools by manually changing:
`-D_CURSES_LIB=1' to `-D_CURSES_LIB=0' at the line starting with `DFLAGS=', and
comment out the line starting with `LIBCURSES='.
Worked for me (Ubuntu 12.04)Comment
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When it comes to running packages like samtools, bedtools or any other kind of bioinformatics solution on a Windows box, you're better off getting VMWare and installing Ubuntu. Trying to compile things from source with Cygwin is asking for trouble.Comment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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