Thank you Morgan, this is indeed working Quoting Martin Morgan <martin.mor...@roswellpark.org>:
> On 09/27/2017 08:11 AM, sergi.pic...@upc.edu wrote: >> Dear developers, >> Sorry if the e-mail is duplicated, I had an issue sending it. >> I have been struggling with problems building my package DIFFUSTATS a >> The problem is related to the usage of Rcpp. >> In my current machine, I am unable to build the DIFFUSTATS in the >> devel bioconductor: >> ############## >> >> > build() > > Not really any solution or insight here, but I suggest removing > devtool from the equation, and making sure that you are working from > a clean source tree without artifacts (.o, .so, .dylib, etc.) from > previous builds. On my linux I did > > R -e "BiocInstaller::biocVersion()" # 3.6 > R -e "BiocInstaller::isDevel()" # TRUE > R -e "BiocInstaller::isValid()" # yup > cd /tmp > git clone https://git.bioconductor.org/packages/diffuStats > ## check in diffuStats/src directory for build artifacts -- none > R CMD buld diffuStats > R CMD check diffuStats_0.99.12.tar.gz > > Martin > >> '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save >> --no-restore --quiet \ >> CMD build '/home/sergi/eraseme3/diffuStats' --no-resave-data --no-manual >> >> * checking for file ‘/home/sergi/eraseme3/diffuStats/DESCRIPTION’ ... OK >> * preparing ‘diffuStats’: >> * checking DESCRIPTION meta-information ... OK >> * cleaning src >> * installing the package to build vignettes >> ----------------------------------- >> * installing *source* package ‘diffuStats’ ... >> ** libs >> g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG >> -I"/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" >> -I"/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/inc >> lude" >> -I"/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppParallel/include" >> -fpic -g -O2 -fstack-protector-strong -Wformat >> -Werror=format-security -Wdate-time -D_FORTIFY_SOUR >> CE=2 -g -c RcppExports.cpp -o RcppExports.o >> In file included from >> /home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/include/armadillo:52:0, >> from >> /home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/include/RcppArmadilloForward.h:46, >> from >> /home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/include/RcppArmadillo.h:31, >> from RcppExports.cpp:4: >> /home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:474:96: >> note: #pragma message: WARNING: use of OpenMP disabled; >> this >> compiler >> doesn't support OpenMP 3.0+ >> #pragma message ("WARNING: use of OpenMP disabled; this compiler >> doesn't support OpenMP 3.0+") >> >> ^ >> g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG >> -I"/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" >> -I"/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/inc >> lude" >> -I"/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppParallel/include" >> -fpic -g -O2 -fstack-protector-strong -Wformat >> -Werror=format-security -Wdate-time -D_FORTIFY_SOUR >> CE=2 -g -c diffuse_parallel.cpp -o diffuse_parallel.o >> In file included from >> /home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/include/armadillo:52:0, >> from >> /home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/include/RcppArmadilloForward.h:46, >> from >> /home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/include/RcppArmadillo.h:31, >> from diffuse_parallel.cpp:1: >> /home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:474:96: >> note: #pragma message: WARNING: use of OpenMP disabled; >> this >> compiler >> doesn't support OpenMP 3.0+ >> #pragma message ("WARNING: use of OpenMP disabled; this compiler >> doesn't support OpenMP 3.0+") >> >> ^ >> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG >> -I"/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" >> -I"/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppArmadillo/inclu >> de" >> -I"/home/sergi/R/x86_64-pc-linux-gnu-library/3.4/RcppParallel/include" >> -fpic -g -O2 -fstack-protector-strong -Wformat >> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE >> =2 -g -c init.c -o init.o >> g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions >> -Wl,-z,relro -o diffuStats.so RcppExports.o diffuse_parallel.o init.o >> -L/usr/lib/R/lib -lR >> installing to /tmp/RtmpRLy9NN/Rinst4d19c0dca4b/diffuStats/libs >> ** R >> ** data >> *** moving datasets to lazyload DB >> ** preparing package for lazy loading >> ** help >> *** installing help indices >> ** building package indices >> ** installing vignettes >> ** testing if installed package can be loaded >> Error: package or namespace load failed for ‘diffuStats’ in >> dyn.load(file, DLLpath = DLLpath, ...): >> unable to load shared object >> '/tmp/RtmpRLy9NN/Rinst4d19c0dca4b/diffuStats/libs/diffuStats.so': >> /tmp/RtmpRLy9NN/Rinst4d19c0dca4b/diffuStats/libs/diffuStats.so: >> undefined symbol: diffuStats_convertSparse >> Error: loading failed >> Execution halted >> ERROR: loading failed >> * removing ‘/tmp/RtmpRLy9NN/Rinst4d19c0dca4b/diffuStats’ >> ----------------------------------- >> ERROR: package installation failed >> Error: Command failed (1) >> However, this is successful when build(vignettes=FALSE) >> ############## >> > sessionInfo() >> R version 3.4.1 (2017-06-30) >> Platform: x86_64-pc-linux-gnu (64-bit) >> Running under: Ubuntu 16.04.3 LTS >> >> Matrix products: default >> BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0 >> LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0 >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> loaded via a namespace (and not attached): >> [1] compiler_3.4.1 tools_3.4.1 >> [3] RcppArmadillo_0.7.960.1.2 withr_2.0.0 >> [5] Rcpp_0.12.12 memoise_1.1.0 >> [7] digest_0.6.12 RcppParallel_4.3.20 >> [9] devtools_1.13.3 >> >> ############## >> The local installation of Rcpp, RcppParallel, RcppArmadillo or >> devtools seems to have something to do with it, because a machine with >> the following configuration (which I cannot use for developing in a >> regular basis) works just fine: >> > sessionInfo() >> R version 3.4.1 (2017-06-30) >> Platform: x86_64-pc-linux-gnu (64-bit) >> Running under: Ubuntu 14.04.5 LTS >> >> Matrix products: default >> BLAS: /usr/lib/openblas-base/libblas.so.3 >> LAPACK: /usr/lib/lapack/liblapack.so.3.0 >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=es_ES.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=es_ES.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] devtools_1.13.2 >> >> loaded via a namespace (and not attached): >> [1] compiler_3.4.1 tools_3.4.1 >> [3] RcppArmadillo_0.7.900.2.0 withr_1.0.2 >> [5] Rcpp_0.12.11 memoise_1.1.0 >> [7] digest_0.6.12 RcppParallel_4.3.20 >> ############## >> If I try other actions, such as devtools::document or load_all: >> Error in dyn.load(dllfile) : >> unable to load shared object >> '/home/sergi/all/devel/rpackages/diffuStats/src/diffuStats.so': >> /home/sergi/all/devel/rpackages/diffuStats/src/diffuStats.so: >> undefined symbol: diffuStats_convertSparse >> Where convertSparse is the first function in the >> exported c++ functions >> ############## >> >> I have tried addressing the OpenMP 3.0 warning without success. >> However, I think the problem lies in the compilation. >> I have updated the R version, also re-run >> Rcpp::compileAttributes() >> And the problem persists whatever I do. I might be missing something >> obvious... >> Any help will be appreciated, >> >> Sergio >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > This email message may contain legally privileged and/or > confidential information. If you are not the intended recipient(s), > or the employee or agent responsible for the delivery of this > message to the intended recipient(s), you are hereby notified that > any disclosure, copying, distribution, or use of this email message > is prohibited. If you have received this message in error, please > notify the sender immediately by e-mail and delete this email > message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
