[Bioc-devel] What to do about std::cerr/cout warnings in external libraries?

[Martin Morgan]

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.morgan at roswellpark.org <mailto:martin.morgan at 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 <stvjc at channing.harvard.edu 
>>> <mailto:stvjc at channing.harvard.edu><mailto:stvjc at 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 <su.s at wehi.edu.au 
>>> <mailto:su.s at wehi.edu.au><mailto:su.s at 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 at r-project.org 
>>> <mailto:Bioc-devel at r-project.org><mailto:Bioc-devel at r-project.org> 
>>> mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> [[alternative HTML version deleted]]
>>> _______________________________________________
>>> Bioc-devel at 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...{{dropped:2}}