benlangmead / bsmooth-align Goto Github PK

When running 'make' in the folder I get following error:

Do you have any idea what could be causing the issue?

Hi,

I've gotten an error of "No reads specified", but I've added the fastq file with all the reads contained, could you please give me any help? Thank you!

perl /home/genefan/tools/bsmooth-align-0.7.0/bin/bswc_bowtie2_align.pl --bowtie2=/home/genefan/tools/bowtie2-2.1.0/ --four-strand --bscpg --fastq --out=./outReads_level/ --sam=./output.SAM/chr -- ./h.sapiens.bsIndex/chr -- ./h.sapiensRef/*.fa -- ./reads/sra_dat31.fastq

Running make in ./merman/ gives several compiler errors in merman.cpp when compiled on
Bio-Linux 8 / Ubuntu 14.04 LTS using GCC 4.8.2 and also on OS X Mavericks (10.9) using XCode with GCC 4.2.1. This compiles correctly, however, using an older version of GCC (4.1.2) on a Red Hat Linux 5.11 system. All test systems were 64 bit.

Errors found when compiling on Ubuntu 14.04 and GCC 4.8.2 64-bit:

mkdir -p ~/src && cd ~/src/ && export BSMOOTH_HOME=~/src/bsmooth-align
git clone https://github.com/BenLangmead/bsmooth-align.git
cd $BSMOOTH_HOME/merman/
make 2>error.log 1>make.log
grep -i error *.log
error.log:merman.cpp:271:2: error: reference to 'begin' is ambiguous
error.log:merman.cpp:872:14: error: reference to 'begin' is ambiguous
error.log:merman.cpp:1139:30: error: reference to 'begin' is ambiguous
error.log:merman.cpp:1139:58: error: extraneous ')' before ';'
error.log:merman.cpp:1255:36: error: reference to 'begin' is ambiguous
error.log:merman.cpp:1271:89: error: expected ':'
error.log:merman.cpp:1271:89: error: expected expression
error.log:5 warnings and 7 errors generated.
error.log:make: *** [merman] Error 1