Log Wording Ambiguous
Created by: DarioS
I get an error such as
Configuring Bio-DB-HTS-3.01 ... N/A ! Configure failed for Bio-DB-HTS-3.01. See /users/stgrad/dario/.cpanm/work/1585179865.8235/build.log for details.
cpanm to install it. When I look at the log file it's not clear what the error is
Running Build.PL This module requires HTSlib (http://htslib.org/) Install it if you have not done so already. This script will attempt to locate HTSlib by looking for htslib/hts.h and libhts.a / libhts.so in: 1. --htslib command line argument 2. HTSLIB_DIR environment variable 3. --prefix command line argument (which also sets installation location) 4. Alien::HTSlib dependency resolver 5. pkg-config (extra directories can be set in PKG_CONFIG_PATH environment variable) 6. common library locations: /usr /usr/local, /usr/share, /opt/local -> N/A -> FAIL Configure failed for Bio-DB-HTS-3.01. See /users/stgrad/dario/.cpanm/work/1585179865.8235/build.log for details.
"This script will attempt to locate HTSlib ..." doesn't explain whether the script successfully found HTSlib or not for my particular instance. Also, the end of the log file advises "See /users/stgrad/dario/.cpanm/work/1585179865.8235/build.log for details." But, I am already viewing that file, so the user should not be instructed to re-open the log file they already opened.
I'm baffled why this script can't detect HTSlib on the server I'm using:
~$ dpkg --list | grep hts ii libhts-dev:amd64 1.9-11 amd64 development files for the HTSlib ii libhts2:amd64 1.9-11 amd64 C library for high-throughput sequencing data formats ii python-htseq 0.11.2-1 amd64 Python high-throughput genome sequencing read analysis utilities