[R-pkg-devel] package dependencies are not available on some check severs

Miao YU yufreecas at gmail.com
Wed Jan 10 19:18:22 CET 2018

Thanks! I checked the error and found the original error came from another package(mzR) which are imported by xcms and MSnbase. Unfortunately, the functions I needed are not so self-contained and also rely on mzR in some certain cases.

Good news is that someone has recently raised same check error issue on Github(https://github.com/sneumann/mzR/issues/143) and the author has shown a solution for this issue. Maybe a few days later mzR could be updated on Bioc without error and then I will try to submit my package again.


> On Jan 10, 2018, at 12:38 PM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
> On 10/01/2018 11:29 AM, Miao YU wrote:
>> Hi everyone,
>> I want to update my package (enviGCMS) and find it can’t pass the check since some imported functions are not available.
>> Here is the check log: <https://win-builder.r-project.org/incoming_pretest/180110_055122_enviGCMS_050/00check.log>
>> Those functions are all from imported bioc packages and I have used biocViews: in DESCRIPTION . I also found current version of enviGCMS has some problems related to certain check flavor (https://CRAN.R-project.org/web/checks/check_results_enviGCMS.html).
>> The main issue would be that the check server just do not have the packages which is actually available on Bioc server such as xcms(http://bioconductor.org/packages/release/bioc/html/xcms.html), MSnbase(http://bioconductor.org/packages/release/bioc/html/MSnbase.html) and faahKO(https://bioconductor.org/packages/release/data/experiment/html/faahKO.html)
> Generally the checks are done against R-devel, so you need to be looking for packages in the 3.7 version of Bioc.  This page:
> http://bioconductor.org/checkResults/devel/bioc-LATEST/
> shows errors in xcms and MSnbase, and there's no sign of faahKO.
>> As far as I could see, all those packages show a warning or error status on bioc build. Maybe the check servers on CRAN just skip those packages. Could I just import certain functions since the waining and error did not affect my imported functions?
> No, if a package has errors it won't be available at all.
>> Any suggestions about it? Or I should wait until those imported package passed the check and then submit again?
> The other choice is to find alternate sources of the functions you need.  If they are small and self-contained, you might be able to copy the source out of those packages and into yours.  If you do that, be sure to give proper credit to the authors.
> Duncan Murdoch
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