Hello Nadiya, On Sat, Mar 25, 2017 at 08:31:24PM -0700, Nadiya Sitdykova wrote: > Thank you for instructions for using dch, I hope now I got it right.
I think so (except the blank line in the beginning which was probably a typo). > 1) I edited patch use_debian_packaged_seqtk.patch so I guess the problem > with seqtk should be resolved now. Yes, this works now for me. > 2) I have this error on Ubuntu xenial, Debian jessie and after you > mentioned that it's better to use unstable version, I tried Debian sid > (amd64) and still got problems with RcppGSL. > That stand-alone test returns exit code 1 with message "Missing the > following R library RcppGSL". This is very strange. I can confirm that there is really a problem if I run LANG=C . run-unit-test 2>&1 | tee > run-unit-test.out I get the attached build log - but this does not contain the string Rcpp. This needs to be investigated. > And for commented tests in run-unit-test file > the message is "Cannot use --stats-only with missing R libraries". I think it would be the best to stick to the not commented tests and make sure we get the same results. Could you please also create the exact output if your test? Kind regards Andreas. -- http://fam-tille.de
bash: cd: /tmp/mapdamage-test.lMvam8: No such file or directory gzip: pulse-PKdhtXMmr18n: Permission denied gzip: ssh-pgBy7Zg4S5zX/agent.3114: No such device or address gzip: systemd-private-517cc73010a84c8dbec2b18fedc67d02-apache2.service-grolbu: Permission denied gzip: systemd-private-517cc73010a84c8dbec2b18fedc67d02-colord.service-VKfwve: Permission denied gzip: systemd-private-517cc73010a84c8dbec2b18fedc67d02-rtkit-daemon.service-uoqkYG: Permission denied [fai_load] build FASTA index. .. ---------------------------------------------------------------------- Ran 2 tests in 0.058s OK Started with the command: /usr/bin/mapDamage -i rescale_test/pe_test/pe.sam -r rescale_test/pe_test/ref.fa No length distributions are available, plotting length distribution only works for single-end reads Performing Bayesian estimates The ACGT frequencies must be in the range 0 to 1 Error in getPmat(cu_pa$Theta, cu_pa$Rho, cu_pa$acgt) : Calls: source -> withVisible -> eval -> eval -> getPmat 7: (function (e) { traceback(2) quit(status = 1) })() 6: stop() 5: getPmat(cu_pa$Theta, cu_pa$Rho, cu_pa$acgt) 4: eval(expr, envir, enclos) 3: eval(ei, envir) 2: withVisible(eval(ei, envir)) 1: source(paste(path_to_mapDamage_stats, "main.R", sep = "")) The Bayesian statistics program failed to finish Reading from 'rescale_test/pe_test/pe.sam' Writing results to 'results_pe/' pdf results_pe/Fragmisincorporation_plot.pdf generated Traceback (most recent call last): File "/usr/bin/mapDamage", line 382, in <module> sys.exit(main()) File "/usr/bin/mapDamage", line 365, in main mapdamage.rscript.run_stats(options) File "/usr/lib/python2.7/dist-packages/mapdamage/rscript.py", line 144, in run_stats raise e subprocess.CalledProcessError: Command '['Rscript', '/usr/lib/python2.7/dist-packages/mapdamage/Rscripts/stats/runGeneral.R', '--args', '30', '10000', '10', '50000', '0', '0', '1', '1', '0', '0', '1', '12', 'results_pe/', '/usr/lib/python2.7/dist-packages/mapdamage/Rscripts/stats/', 'results_pe/Stats_out', '0', '0', '0', 'results_pe/acgt_ratio.csv', '0', '0']' returned non-zero exit status 1 pdf result exists Started with the command: /usr/bin/mapDamage -d results_pe -y 0.1 --plot-only No length distributions are available, plotting length distribution only works for single-end reads pdf results_pe/Fragmisincorporation_plot.pdf generated checking stdin redirect... Started with the command: /usr/bin/mapDamage -i - -r rescale_test/pe_test/ref.fa No length distributions are available, plotting length distribution only works for single-end reads Performing Bayesian estimates The ACGT frequencies must be in the range 0 to 1 Error in getPmat(cu_pa$Theta, cu_pa$Rho, cu_pa$acgt) : Calls: source -> withVisible -> eval -> eval -> getPmat 7: (function (e) { traceback(2) quit(status = 1) })() 6: stop() 5: getPmat(cu_pa$Theta, cu_pa$Rho, cu_pa$acgt) 4: eval(expr, envir, enclos) 3: eval(ei, envir) 2: withVisible(eval(ei, envir)) 1: source(paste(path_to_mapDamage_stats, "main.R", sep = "")) The Bayesian statistics program failed to finish Reading from '-' Writing results to 'results_-/' pdf results_-/Fragmisincorporation_plot.pdf generated Traceback (most recent call last): File "/usr/bin/mapDamage", line 382, in <module> sys.exit(main()) File "/usr/bin/mapDamage", line 365, in main mapdamage.rscript.run_stats(options) File "/usr/lib/python2.7/dist-packages/mapdamage/rscript.py", line 144, in run_stats raise e subprocess.CalledProcessError: Command '['Rscript', '/usr/lib/python2.7/dist-packages/mapdamage/Rscripts/stats/runGeneral.R', '--args', '30', '10000', '10', '50000', '0', '0', '1', '1', '0', '0', '1', '12', 'results_-/', '/usr/lib/python2.7/dist-packages/mapdamage/Rscripts/stats/', 'results_-/Stats_out', '0', '0', '0', 'results_-/acgt_ratio.csv', '0', '0']' returned non-zero exit status 1