Thank you very much Martin, adding the Makevars did the trick. > On 21 Jun 2017, at 1:05 pm, Martin Morgan <martin.mor...@roswellpark.org> > wrote: > > On 06/20/2017 10:57 PM, Shian Su wrote: >> Thanks Martin, >> Should this be as simple as removing all my local htslib files, adding the >> LinkingTo specifiers and rebuilding? Currently getting >> Error in dyn.load(dllfile) : >> unable to load shared object ‘~/Programs/R/scPipe/src/scPipe.so': >> dlopen(~/Programs/R/scPipe/src/scPipe.so, 6): Symbol not found: >> _seq_nt16_table >> Referenced from: ~/Programs/R/scPipe/src/scPipe.so >> Expected in: flat namespace >> in ~/Programs/R/scPipe/src/scPipe.so >> Perhaps I’ve done something silly. > > There's a short vignette > > http://bioconductor.org/packages/devel/bioc/vignettes/Rhtslib/inst/doc/Rhtslib.html > > describing use; LinkingTo gives you the headers, but you still need to tell R > where to find the compiled binaries via a src/Makevars > > Martin > >> Shian >>> On 21 Jun 2017, at 12:12 pm, Martin Morgan <martin.mor...@roswellpark.org >>> <mailto:martin.mor...@roswellpark.org>> wrote: >>> >>> On 06/20/2017 09:38 PM, Shian Su wrote: >>>> My warning is >>>> checking compiled code ... WARNING >>>> File ‘scPipe/libs/scPipe.so’: >>>> Found ‘___stderrp’, possibly from ‘stderr’ (C) >>>> Objects: ‘bgzf.o’, ‘hts.o’, ‘sam.o’ >>>> Found ‘_abort’, possibly from ‘abort’ (C) >>>> Object: ‘sam.o’ >>>> Found ‘_exit’, possibly from ‘exit’ (C) >>>> Object: ‘bgzf.o’ >>>> Compiled code should not call entry points which might terminate R nor >>>> write to stdout/stderr instead of to the console, nor the system RNG. >>>> As far as I can tell my source files are identical to the ones in Rhtslib, >>>> how does Rhtslib avoid this warning? I feel safer with one less dependency >>>> but I’ll consider linking to Rhtslib, thanks! >>> >>> please reuse Rhtslib instead of adding code that requires independent >>> maintenance; in particular considerable effort is required to make htslib >>> available across platforms. If there are issues with Rhtslib then report >>> them and, especially if a patch is provided, they will be fixed. >>> >>> Rhtslib builds the library in src/htslib/.libs/libhts.so whereas R checks >>> src/Rhstlib.so, which contains a single function that reports the version. >>> So R doesn't find the use of stderr, etc. >>> >>> A previous discussion of similar issues is at >>> >>> https://stat.ethz.ch/pipermail/bioc-devel/2017-April/010837.html >>> >>> and other posts in the same thread. >>> >>> For Rsamtools I had introduced in src/Makevars.common a macro that >>> redirects fprintf / exit / abort to code that does not use these macros, >>> but to do so requires unsetting _FORTIFY_SOURCE >>> >>> DFLAGS = -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 \ >>> -U_FORTIFY_SOURCE -DBGZF_CACHE \ >>> -Dfprintf=_samtools_fprintf \ >>> -Dexit=_samtools_exit \ >>> -Dabort=_samtools_abort >>> >>> but this is not a perfect solution. >>> >>> Martin >>> >>>> On 20 Jun 2017, at 8:03 pm, Vincent Carey <st...@channing.harvard.edu >>>> <mailto:st...@channing.harvard.edu><mailto:st...@channing.harvard.edu>> >>>> wrote: >>>> Have you looked at the Bioconductor package Rhtslib? >>>> Is your package's source visible on github? If so please provide the URL. >>>> If not, please provide more details on the error messages observed. >>>> It would seem to me that the best way to proceed would be to link to >>>> Rhtslib. >>>> On Tue, Jun 20, 2017 at 2:29 AM, Shian Su <s...@wehi.edu.au >>>> <mailto:s...@wehi.edu.au><mailto:s...@wehi.edu.au>> wrote: >>>> Hi all, >>>> I am using parts of htslib in a new package. R CMD check gives me warnings >>>> about R terminating entry points and such resulting from htslib’s calls. >>>> Is there a way to get around this or do I have to go into the source code >>>> of htslib and change all their calls. >>>> Also, Hadley’s best practices recommends using “error” instead of “exit” >>>> however I am using Rcpp to glue things together which only seems to >>>> provide “stop” for this purpose. Can exits be simply swapped out with >>>> Rcpp::stop? >>>> Kind regards, >>>> Shian Su >>>> _______________________________________________ >>>> Bioc-devel@r-project.org >>>> <mailto:Bioc-devel@r-project.org><mailto:Bioc-devel@r-project.org> mailing >>>> list >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>> [[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. > > > 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.
_______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
