Entering edit mode

20 months ago

mohammedtoufiq91
▴
260

Hi,

I downloaded the `RSEM`

software package for estimating gene and isoform expression levels from RNA-Seq data, then compiled RSEM using `make`

in the same directory, throws many errors and warnings:

```
In file included from simulation.cpp:22:
In file included from ./SingleModel.h:16:
In file included from ./Orientation.h:8:
In file included from ./simul.h:6:
In file included from ./boost/random.hpp:52:
In file included from ./boost/random/generate_canonical.hpp:22:
In file included from ./boost/math/special_functions.hpp:15:
In file included from ./boost/math/special_functions/airy.hpp:10:
In file included from ./boost/math/special_functions/bessel.hpp:21:
In file included from ./boost/math/special_functions/detail/bessel_jy_zero.hpp:25:
./boost/math/special_functions/detail/airy_ai_bi_zero.hpp:91:24: error: no template named 'tuple' in namespace 'boost::math'
boost::math::tuple<T, T> operator()(const T& x) const
~~~~~~~~~~~~~^
./boost/math/special_functions/detail/airy_ai_bi_zero.hpp:94:33: error: no member named 'make_tuple' in namespace 'boost::math'
return boost::math::make_tuple(
~~~~~~~~~~~~~^
./boost/math/special_functions/detail/airy_ai_bi_zero.hpp:142:24: error: no template named 'tuple' in namespace 'boost::math'
boost::math::tuple<T, T> operator()(const T& x) const
~~~~~~~~~~~~~^
./boost/math/special_functions/detail/airy_ai_bi_zero.hpp:145:33: error: no member named 'make_tuple' in namespace 'boost::math'
return boost::math::make_tuple(
~~~~~~~~~~~~~^
In file included from simulation.cpp:22:
In file included from ./SingleModel.h:16:
In file included from ./Orientation.h:8:
In file included from ./simul.h:6:
In file included from ./boost/random.hpp:52:
In file included from ./boost/random/generate_canonical.hpp:22:
In file included from ./boost/math/special_functions.hpp:15:
In file included from ./boost/math/special_functions/airy.hpp:10:
In file included from ./boost/math/special_functions/bessel.hpp:21:
./boost/math/special_functions/detail/bessel_jy_zero.hpp:62:22: error: no template named 'tuple' in namespace 'boost::math'
boost::math::tuple<T, T> operator()(const T& z) const
~~~~~~~~~~~~~^
./boost/math/special_functions/detail/bessel_jy_zero.hpp:78:31: error: no member named 'tuple' in namespace 'boost::math'
return boost::math::tuple<T, T>(the_function, its_derivative);
~~~~~~~~~~~~~^
./boost/math/special_functions/detail/bessel_jy_zero.hpp:78:37: error: 'T' does not refer to a value
return boost::math::tuple<T, T>(the_function, its_derivative);
^
./boost/math/special_functions/detail/bessel_jy_zero.hpp:56:25: note: declared here
template<typename T>
^
./boost/math/special_functions/detail/bessel_jy_zero.hpp:211:24: error: no template named 'tuple' in namespace 'boost::math'
boost::math::tuple<T, T> operator()(const T& x) const
~~~~~~~~~~~~~^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
6 warnings and 20 errors generated.
make: *** [simulation.o] Error 1
```

Then, tried running `RSEM`

```
./rsem-calculate-expression --bowtie2 --bowtie2-path /Users/Documents/Bioinformatics_tools/Bowtie2/bowtie2-2.5.0-macos-x86_64 -p 8 --output-genome-bam --paired-end /Users/Documents/Bioinformatics_tools/SRA/fastq_dir/SRR1039508_1.fastq /Users/Documents/Bioinformatics_tools/SRA/fastq_dir/SRR1039508_2.fastq /Users/Documents/Bioinformatics_tools/Bowtie2/index/GRCh38_noalt_as/GRCh38_noalt_as hg_paired_end_quals
```

but it shows the below error, I guess this is searching for this file, but this not generated after compiling using `make`

command?

`rsem-parse-alignments : No such file or directory!`

I tried to trouble shoot the issue using this link but unsuccessful rsem-calculate-expression error

Best Regards, Toufiq

same (unsolved) error on github : https://github.com/deweylab/RSEM/issues/189

Pierre Lindenbaum, thank you for the response. Does posting this question on

`stackoverflow`

should help me resolve this? This tool is very important for my analysis.Well I would say that a compilation flag is missing in the Makefile, or you're using an old version of gcc, but you can always post to SO.

Pierre Lindenbaum thank you very much.