Getting lots of compilation errors on install

[endrebak]

# ... many more error messages removed - last one fatal
bed2vector.cpp:2530:77: error: qualified-id in declaration before 'li'
       hash_map<string, int, hash<string>,equal_to<string> >::const_iterator li=cind_map.find(chr);
                                                                             ^~
bed2vector.cpp:2532:10: error: 'li' was not declared in this scope
       if(li==cind_map.end()) {
          ^~
bed2vector.cpp:2532:23: error: request for member 'end' in 'cind_map', which is of non-class type 'int'
       if(li==cind_map.end()) {
                       ^~~
bed2vector.cpp:2536:10: error: no match for 'operator[]' (operand types are 'int' and 'std::__cxx11::string {aka std::__cxx11::basic_string<char>}')
  cind_map[chr]=cind;
          ^
/mnt/work/endrebak/software/anaconda/lib/R/etc/Makeconf:167: recipe for target 'bed2vector.o' failed
make: *** [bed2vector.o] Error 1
ERROR: compilation failed for package 'spp'
* removing '/mnt/work/endrebak/software/anaconda/lib/R/library/spp'

[leepc12]

What is your R version? and did you install Boost library?

There is a workaround for this issue. You can use a dependency installer in our ChIP-seq pipeline, which includes phantompeakqualtools and its dependencies (R and all R packages related to it).

1) Install Conda first (https://github.com/kundajelab/chipseq_pipeline#conda) 2) Install dependencies for the pipeline (https://github.com/kundajelab/chipseq_pipeline#dependencies) 3) Activate conda environment ($ source activate aquas_chipseq) 4) Run Rscript

[endrebak]

Thank you for replying. I am using anaconda R with boost and R-cpp.

I guess I should try your install script, but I became wary because of this warning:

REMOVE ANY ANACONDA OR OTHER VERSIONS OF CONDA FROM YOUR BASH STARTUP SCRIPT. WE CANNOT GUARANTEE THAT PIPELINE WORKS WITH OTHER VERSIONS OF CONDA. ALSO REMOVE R AND OTHER CONFLICTING MODULES FROM IT TOO. 

There does not seem to be anything in the install script that would mess with my existing conda though - it just install loads of stuff under a new environment.

[leepc12]

Please ignore that warning and proceed to install it, if something wrong happens then let me know.

[endrebak]

So this is not it? https://github.com/kundajelab/chip-seq-pipeline2/blob/master/installers/install_dependencies.sh

I mean, you seem to have a new pipeline, but I should still use the installer in the old repo?

On Mon, Jul 2, 2018 at 3:39 PM Jin Lee notifications@github.com wrote:

Please ignore that warning and proceed to install it, if something wrong happens then let me know.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/kundajelab/phantompeakqualtools/issues/8#issuecomment-401807335, or mute the thread https://github.com/notifications/unsubscribe-auth/AQ9I0mSPytOEiAjSGTnNfzLu8feBcWz2ks5uCiKagaJpZM4U-xBp .

[endrebak]

I get the same error with /mnt/work/endrebak/software/anaconda/envs/aquas_chipseq/bin/R CMD INSTALL spp_1.14.tar.gz.

[leepc12]

spp is already installed in the conda environment aquas_chipseq.

Jin

On Tue, Jul 3, 2018 at 2:16 AM, Endre Bakken Stovner < notifications@github.com> wrote:

I get the same error with /mnt/work/endrebak/software/ anaconda/envs/aquas_chipseq/bin/R CMD INSTALL spp_1.14.tar.gz

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/kundajelab/phantompeakqualtools/issues/8#issuecomment-402070039, or mute the thread https://github.com/notifications/unsubscribe-auth/AIOd_M0zBel59zcTjGXyh0CbHO-UV903ks5uCzZegaJpZM4U-xBp .

[endrebak]

Haha, thanks. I can be dumb XD

[endrebak]

It worked beautifully - thanks for your patience and help :)