Hi, I'm working on a new package. The 'build' is ok, but when running 'check' I get a warning that I'm not sure on how to eliminate it. The warning is : * checking for unstated dependencies in R code ... WARNING 'library' or 'require' calls not declared from: BSgenome.Hsapiens.UCSC.hg17 BSgenome.Hsapiens.UCSC.hg18 The reason of course is that I'm using the require function and I'm not adding these libraries in 'Depends' or 'Suggests'. The point is that I would not like to oblige users to install both hg17 and hg18 libraries, since they are huge (800Mb). This is going to be even more important if I would support many other annotation libraries. The idea was then to use require to load only the one requested from the user (either hg17 or hg18). I'm going to submit this library to Bioconductor. Can I ignore this warning, should I add all the annotation libraries in 'Depends', or is there another way to fix this warning? Many thanks, mattia
[Bioc-devel] library checking: question on require/depends
5 messages · mattia pelizzola, Laurent Gautier, Sean Davis
On Tue, Jul 29, 2008 at 1:51 PM, mattia pelizzola
<mattia.pelizzola at gmail.com> wrote:
Hi, I'm working on a new package. The 'build' is ok, but when running 'check' I get a warning that I'm not sure on how to eliminate it. The warning is : * checking for unstated dependencies in R code ... WARNING 'library' or 'require' calls not declared from: BSgenome.Hsapiens.UCSC.hg17 BSgenome.Hsapiens.UCSC.hg18 The reason of course is that I'm using the require function and I'm not adding these libraries in 'Depends' or 'Suggests'. The point is that I would not like to oblige users to install both hg17 and hg18 libraries, since they are huge (800Mb). This is going to be even more important if I would support many other annotation libraries. The idea was then to use require to load only the one requested from the user (either hg17 or hg18). I'm going to submit this library to Bioconductor. Can I ignore this warning, should I add all the annotation libraries in 'Depends', or is there another way to fix this warning?
This is what "Suggests" is for. Sean
Adding it in "Suggests" will keep R CMD check happy, as Sean told it. One question, still: Are you using the those packages in examples ? In that case, using a smaller dataset might be a good idea. If there is not any suitable smaller dataset currently avalaible, it could be nice to create a demo-oriented one, with one chromosome for example. This could also be used by other packages needing full genome. 2008/7/29 Sean Davis <sdavis2 at mail.nih.gov>:
On Tue, Jul 29, 2008 at 1:51 PM, mattia pelizzola <mattia.pelizzola at gmail.com> wrote:
Hi, I'm working on a new package. The 'build' is ok, but when running 'check' I get a warning that I'm not sure on how to eliminate it. The warning is : * checking for unstated dependencies in R code ... WARNING 'library' or 'require' calls not declared from: BSgenome.Hsapiens.UCSC.hg17 BSgenome.Hsapiens.UCSC.hg18 The reason of course is that I'm using the require function and I'm not adding these libraries in 'Depends' or 'Suggests'. The point is that I would not like to oblige users to install both hg17 and hg18 libraries, since they are huge (800Mb). This is going to be even more important if I would support many other annotation libraries. The idea was then to use require to load only the one requested from the user (either hg17 or hg18). I'm going to submit this library to Bioconductor. Can I ignore this warning, should I add all the annotation libraries in 'Depends', or is there another way to fix this warning?
This is what "Suggests" is for. Sean
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Hi,
On Tue, Jul 29, 2008 at 2:43 PM, Laurent Gautier <lgautier at gmail.com> wrote:
Adding it in "Suggests" will keep R CMD check happy, as Sean told it.
Thanks, I just did not know that still I needed to have all the "Suggests" library installed. Now the warning is gone.
One question, still: Are you using the those packages in examples ? In that case, using a smaller dataset might be a good idea. If there is not any suitable smaller dataset currently avalaible, it could be nice to create a demo-oriented one, with one chromosome for example. This could also be used by other packages needing full genome.
Yes, I'm using one of the suggested packages in the examples and I'm releasing a small dataset with the library, just for demonstration purposes. Thanks, mattia
2008/7/29 Sean Davis <sdavis2 at mail.nih.gov>:
On Tue, Jul 29, 2008 at 1:51 PM, mattia pelizzola <mattia.pelizzola at gmail.com> wrote:
Hi, I'm working on a new package. The 'build' is ok, but when running 'check' I get a warning that I'm not sure on how to eliminate it. The warning is : * checking for unstated dependencies in R code ... WARNING 'library' or 'require' calls not declared from: BSgenome.Hsapiens.UCSC.hg17 BSgenome.Hsapiens.UCSC.hg18 The reason of course is that I'm using the require function and I'm not adding these libraries in 'Depends' or 'Suggests'. The point is that I would not like to oblige users to install both hg17 and hg18 libraries, since they are huge (800Mb). This is going to be even more important if I would support many other annotation libraries. The idea was then to use require to load only the one requested from the user (either hg17 or hg18). I'm going to submit this library to Bioconductor. Can I ignore this warning, should I add all the annotation libraries in 'Depends', or is there another way to fix this warning?
This is what "Suggests" is for. Sean
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
On Tue, Jul 29, 2008 at 3:40 PM, mattia pelizzola
<mattia.pelizzola at gmail.com> wrote:
Hi, On Tue, Jul 29, 2008 at 2:43 PM, Laurent Gautier <lgautier at gmail.com> wrote:
Adding it in "Suggests" will keep R CMD check happy, as Sean told it.
Thanks, I just did not know that still I needed to have all the "Suggests" library installed. Now the warning is gone.
Just to clarify, the "Suggests" libraries do NOT need to be installed. That is the difference between Suggests and Depends; all libraries in Depends must be installed for the new package to be installed.
One question, still: Are you using the those packages in examples ? In that case, using a smaller dataset might be a good idea. If there is not any suitable smaller dataset currently avalaible, it could be nice to create a demo-oriented one, with one chromosome for example. This could also be used by other packages needing full genome.
Yes, I'm using one of the suggested packages in the examples and I'm releasing a small dataset with the library, just for demonstration purposes.
2008/7/29 Sean Davis <sdavis2 at mail.nih.gov>:
On Tue, Jul 29, 2008 at 1:51 PM, mattia pelizzola <mattia.pelizzola at gmail.com> wrote:
Hi, I'm working on a new package. The 'build' is ok, but when running 'check' I get a warning that I'm not sure on how to eliminate it. The warning is : * checking for unstated dependencies in R code ... WARNING 'library' or 'require' calls not declared from: BSgenome.Hsapiens.UCSC.hg17 BSgenome.Hsapiens.UCSC.hg18 The reason of course is that I'm using the require function and I'm not adding these libraries in 'Depends' or 'Suggests'. The point is that I would not like to oblige users to install both hg17 and hg18 libraries, since they are huge (800Mb). This is going to be even more important if I would support many other annotation libraries. The idea was then to use require to load only the one requested from the user (either hg17 or hg18). I'm going to submit this library to Bioconductor. Can I ignore this warning, should I add all the annotation libraries in 'Depends', or is there another way to fix this warning?
This is what "Suggests" is for. Sean
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel