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) 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? Any suggestions about it? Or I should wait until those imported package passed the check and then submit again? Thanks, Miao -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 833 bytes Desc: Message signed with OpenPGP URL: <https://stat.ethz.ch/pipermail/r-package-devel/attachments/20180110/2600f759/attachment.sig>
[R-pkg-devel] package dependencies are not available on some check severs
3 messages · Miao YU, Duncan Murdoch
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
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. Miao
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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