heathsc
commented
4 years ago Thank you for the report. I have not yet tried with Ubuntu 20.10, but there are some issues with gcc 10. I will look in to the problem.
Simon
On Sat, 31 Oct 2020, 12:53 Stefano Pirrò, notifications@github.com wrote:
Hi there, I am trying to install gemBS from singularity base ubuntu:rolling (20.10). All dependencies are satisfied in my recipe:
apt-get -y install python3 python3-pip python3-dev apt-get install -y build-essential git pigz apt-get install -y zlib1g-dev libbz2-dev apt-get install -y libncurses5-dev liblzma-dev libssl-dev libcurl4-openssl-dev apt-get install -y autoconf pip3 install matplotlib multiprocess git clone --recursive https://github.com/heathsc/gemBS.git cd gemBS && python3 setup.py install
version of gcc and g++ is 10
This is the error I have:
make[1]: Entering directory '/gemBS/tools/utils'
gcc -O3 -g -I. -Icommon -o ../bin/gemBS_cat gemBS_cat.c common/utils.c -lm
gcc -O3 -g -I. -Icommon -o ../bin/readNameClean readNameClean/readNameClean.c common/utils.c -lm
gcc -O3 -g -I. -Icommon -o ../bin/md5_fasta md5_fasta.c common/utils.c -lm -lcrypto
gcc -O3 -g -I. -Icommon -o ../bin/mextr mextr/mextr.c mextr/calc_gt_prob.c mextr/output.c mextr/output_utils.c mextr/output_headers.c mextr/command_line.c mextr/init_params.c mextr/files.c mextr/stats.c mextr/unpack.c mextr/rec.c mextr/bbi.c common/utils.c -I../htslib -Imextr ../htslib/libhts.a -lcurl -lcrypto -llzma -lz -lbz2 -lpthread -lm
mextr/command_line.c: In function ‘handle_command_line’:
mextr/command_line.c:304:31: error: invalid use of undefined type ‘struct bcf_sr_region_t’
304 | memcpy(treg + i, reg->regs + j, sizeof(struct _region_t));
| ^mextr/command_line.c:310:13: warning: assignment to ‘struct bcf_sr_region_t ’ from incompatible pointer type ‘struct _region_t ’ [-Wincompatible-pointer-types]
310 | reg->regs = treg;
| ^mextr/command_line.c:343:14: error: invalid use of undefined type ‘struct bcf_sr_region_t’
343 | reg->regs[i].creg = -1;
| ^mextr/command_line.c:343:17: error: invalid use of undefined type ‘struct bcf_sr_region_t’
343 | reg->regs[i].creg = -1;
| ^mextr/command_line.c:344:14: error: invalid use of undefined type ‘struct bcf_sr_region_t’
344 | reg->regs[i].nregs = reg->regs[i].mregs = 1;
| ^mextr/command_line.c:344:17: error: invalid use of undefined type ‘struct bcf_sr_region_t’
344 | reg->regs[i].nregs = reg->regs[i].mregs = 1;
| ^mextr/command_line.c:344:35: error: invalid use of undefined type ‘struct bcf_sr_region_t’
344 | reg->regs[i].nregs = reg->regs[i].mregs = 1;
| ^mextr/command_line.c:344:38: error: invalid use of undefined type ‘struct bcf_sr_region_t’
344 | reg->regs[i].nregs = reg->regs[i].mregs = 1;
| ^mextr/command_line.c:345:14: error: invalid use of undefined type ‘struct bcf_sr_region_t’
345 | reg->regs[i].regs = malloc(sizeof(region1_t));
| ^mextr/command_line.c:345:17: error: invalid use of undefined type ‘struct bcf_sr_region_t’
345 | reg->regs[i].regs = malloc(sizeof(region1_t));
| ^mextr/command_line.c:346:14: error: invalid use of undefined type ‘struct bcf_sr_region_t’
346 | reg->regs[i].regs->start = 0;
| ^mextr/command_line.c:346:17: error: invalid use of undefined type ‘struct bcf_sr_region_t’
346 | reg->regs[i].regs->start = 0;
| ^mextr/command_line.c:347:14: error: invalid use of undefined type ‘struct bcf_sr_region_t’
347 | reg->regs[i].regs->end = ctgs[i].len - 1;
| ^mextr/command_line.c:347:17: error: invalid use of undefined type ‘struct bcf_sr_region_t’
347 | reg->regs[i].regs->end = ctgs[i].len - 1;
| ^mextr/command_line.c:361:32: error: invalid use of undefined type ‘struct bcf_sr_region_t’
361 | args->cumul_len[0] = reg->regs[0].regs->end + 1;
| ^mextr/command_line.c:361:35: error: invalid use of undefined type ‘struct bcf_sr_region_t’
361 | args->cumul_len[0] = reg->regs[0].regs->end + 1;
| ^mextr/command_line.c:362:88: error: invalid use of undefined type ‘struct bcf_sr_region_t’
362 | for(int i = 1; i < nctgs; i++) args->cumul_len[i] = args->cumul_len[i - 1] + reg->regs[i].regs->end + 1;
| ^mextr/command_line.c:362:91: error: invalid use of undefined type ‘struct bcf_sr_region_t’
362 | for(int i = 1; i < nctgs; i++) args->cumul_len[i] = args->cumul_len[i - 1] + reg->regs[i].regs->end + 1;
| ^mextr/unpack.c: In function ‘process’:
mextr/unpack.c:155:22: warning: too many arguments for format [-Wformat-extra-args]
155 | fprintf(stderr,"Reading %s\n", args->sr->regions->seq_names[id], complete);
| ^~~~~~~~~~~~~~make[1]: *** [Makefile:71: ../bin/mextr] Error 1
make[1]: Leaving directory '/gemBS/tools/utils'
make: *** [Makefile:49: _utils] Error 2
Error while compiling gemBS. That is very unfortunate.
A possible reason might be a missing dependency. Please take a look at the lines
before this one. You need the following programs and libraries installed to compile
the gemBS.
Programms needed:
* make * gccLibraris needed:
* python-dev (the python headers and include files) * libbz2-dev (for bz compression support)On a Debian/Ubuntu system you should be able to get all needed dependencies with:
sudo apt-get install make gcc python-dev libbz2-dev
Could someone please help?
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wynstep
Hi there, I am trying to install gemBS from singularity base ubuntu:rolling (20.10). All dependencies are satisfied in my recipe:
apt-get -y install python3 python3-pip python3-devapt-get install -y build-essential git pigzapt-get install -y zlib1g-dev libbz2-devapt-get install -y libncurses5-dev liblzma-dev libssl-dev libcurl4-openssl-devapt-get install -y autoconfpip3 install matplotlib multiprocessgit clone --recursive https://github.com/heathsc/gemBS.gitcd gemBS && python3 setup.py installversion of gcc and g++ is 10
This is the error I have:
Could someone please help?