Re: [Bioc-devel] Failing to build vignette because of problems with ImageMagick

[Vincent Carey]

On Wed, Oct 9, 2019 at 6:55 AM Andrzej Oleś  wrote:

> Hi Vince,
>
> I briefly communicated with Martin regarding this issue a few days ago.
> The ImageMagick convert tool called by BiocStyle through a knitr figure
> cropping hook can certainly be improved, as pointed out by Yihui in the in
> the GitHub issue linked by Christian. This is something I will look into.
> However, I don't think that your failing builds are related to BiocStyle. I
> can only second on what Herve has already mentioned here: the observed
> convert messages are picked up as warnings by 'R CMD build' and they don't
> actually cause the build to fail.
>

Thank you Andrzej ... I missed this point.  Because it is a
platform-specific failure (no prob on linux or mac)
I assumed that this event was the problem.  I will look more closely at a
windows build attempt.


>
> Cheers,
> Andrzej
>
> On Wed, Oct 9, 2019 at 12:10 PM Vincent Carey 
> wrote:
>
>> Just wondering whether this has been followed up.  I am still seeing build
>> errors for
>> windows related to this.
>>
>> On Tue, Sep 17, 2019 at 10:20 AM Christian Mertes 
>> wrote:
>>
>> > I just came across this issue on rmarkdown which links the same problem
>> to
>> > BiocStyle.
>> > The post is from Nov 2017.
>> >
>> > https://github.com/rstudio/rmarkdown/issues/1207
>> >
>> > Maybe this helps to understand the underlying problem?
>> >
>> > It was suggested to check this in BiocStyle:
>> >
>> > Have you reported to the authors of BiocStyle? It seems they enabled the
>> > *knitr* hook knitr::hook_pdfcrop unconditionally (i.e. without checking
>> > if ImageMagick has been installed).
>> >
>> > Best,
>> >
>> > Christian
>> > On 9/11/19 5:50 PM, Pages, Herve wrote:
>> >
>> > New to me too. But it seems that knitr suggests magick, which itself has
>> >
>> >SystemRequirements: ImageMagick++: ImageMagick-c++-devel (rpm) or
>> > libmagick++-dev (deb)
>> >
>> > Don't know when this knitr dep on magick was introduced tough... Bummer!
>> >
>> > H.
>> >
>> > On 9/11/19 06:13, Kasper Daniel Hansen wrote:
>> >
>> > Yeah, does this imply that the render operation uses (or tries to use)
>> > ImageMagick? That's news to me, but I am not following this closely.
>> >
>> > On Wed, Sep 11, 2019 at 5:21 AM Pages, Herve >  > wrote:
>> >
>> > On 9/11/19 00:50, Vincent Carey wrote:
>> >  > I seem to be running into a similar problem with BiocOncoTK on
>> > windows
>> >  >
>> >  > The build report for tokay1 shows:
>> >  >
>> >  > Loading required package: ontologyIndex
>> >  > Invalid Parameter - /figure-html
>> >  > Warning in shell(paste(c(cmd, args), collapse = " ")) :
>> >  >'convert "BiocOncoTK_files/figure-html/lkgbm-1.png" -trim
>> >  > "BiocOncoTK_files/figure-html/lkgbm-1.png"' execution failed with
>> >  > error code 4
>> >  > Invalid Parameter - /figure-html
>> >  >
>> >  > The figure code is introduced with ```{r
>> > lkgbm,fig=TRUE,message=FALSE}
>> >  > ... the 'convert' process is not requested by me
>> >  >
>> >  > Is the fig=TRUE problematic for windows?  It seems unnecessary.
>> >
>> > Not sure what's going on. A few observations:
>> >
>> > a) About 500 software packages use fig=TRUE.
>> >
>> > b) The convert warning is just a warning. The actual error in the
>> case
>> > of BiocOncoTK is:
>> >
>> > Error: processing vignette 'BiocOncoTK.Rmd' failed with
>> diagnostics:
>> > argument is of length zero
>> >
>> > Note that the ndexr vignette also fails with this error on
>> tokay1
>> > only but it doesn't have the convert warning (this vignette does not
>> > use
>> > 'fig' at all). So it's not clear to me that the "argument is of
>> length
>> > zero" error is related to the convert warning.
>> >
>> > c) The devel build report shows the convert warning for 4 other
>> > packages
>> > (CAGEfightR, CATALYST, CTDquerier, specL) but each of them actually
>> > fails with a different error message:
>> >
>> > CAGEfightR:
>> >   colData(object1) not identical to colData(object2)
>> >
>> > CATALYST:
>> >   no slot of name "reducedDims" for this object of class
>> "daFrame"
>> >
>> > CTDquerier:
>> >   bfcadd() failed; see warnings()
>> >
>> > specL:
>> >   pandoc.exe: Out of memory
>> >
>> > These errors don't seem related to the convert warning either.
>> >
>> > So I'm wondering: could it be that the convert warning is actually
>> > common but we generally don't see it because 'R CMD build' doesn't
>> > report warnings? And that we just happen to see the warning when 'R
>> CMD
>> > build' fails to build a vignette.
>> >
>> > We'll investigate more.
>> >
>> > H.
>> >
>> >
>> >  >
>> >  > On Tue, Sep 10, 2019 at 11:35 AM Christian Mertes
>> > mailto:mer...@in.tum.de> >
>> wrote:
>> >  >
>> >  >> Thanks a lot for t

Re: [Bioc-devel] Failing to build vignette because of problems with ImageMagick

[Andrzej Oleś]

Hi Vince,

I briefly communicated with Martin regarding this issue a few days ago. The
ImageMagick convert tool called by BiocStyle through a knitr figure
cropping hook can certainly be improved, as pointed out by Yihui in the in
the GitHub issue linked by Christian. This is something I will look into.
However, I don't think that your failing builds are related to BiocStyle. I
can only second on what Herve has already mentioned here: the observed
convert messages are picked up as warnings by 'R CMD build' and they don't
actually cause the build to fail.

Cheers,
Andrzej

On Wed, Oct 9, 2019 at 12:10 PM Vincent Carey 
wrote:

> Just wondering whether this has been followed up.  I am still seeing build
> errors for
> windows related to this.
>
> On Tue, Sep 17, 2019 at 10:20 AM Christian Mertes 
> wrote:
>
> > I just came across this issue on rmarkdown which links the same problem
> to
> > BiocStyle.
> > The post is from Nov 2017.
> >
> > https://github.com/rstudio/rmarkdown/issues/1207
> >
> > Maybe this helps to understand the underlying problem?
> >
> > It was suggested to check this in BiocStyle:
> >
> > Have you reported to the authors of BiocStyle? It seems they enabled the
> > *knitr* hook knitr::hook_pdfcrop unconditionally (i.e. without checking
> > if ImageMagick has been installed).
> >
> > Best,
> >
> > Christian
> > On 9/11/19 5:50 PM, Pages, Herve wrote:
> >
> > New to me too. But it seems that knitr suggests magick, which itself has
> >
> >SystemRequirements: ImageMagick++: ImageMagick-c++-devel (rpm) or
> > libmagick++-dev (deb)
> >
> > Don't know when this knitr dep on magick was introduced tough... Bummer!
> >
> > H.
> >
> > On 9/11/19 06:13, Kasper Daniel Hansen wrote:
> >
> > Yeah, does this imply that the render operation uses (or tries to use)
> > ImageMagick? That's news to me, but I am not following this closely.
> >
> > On Wed, Sep 11, 2019 at 5:21 AM Pages, Herve   > wrote:
> >
> > On 9/11/19 00:50, Vincent Carey wrote:
> >  > I seem to be running into a similar problem with BiocOncoTK on
> > windows
> >  >
> >  > The build report for tokay1 shows:
> >  >
> >  > Loading required package: ontologyIndex
> >  > Invalid Parameter - /figure-html
> >  > Warning in shell(paste(c(cmd, args), collapse = " ")) :
> >  >'convert "BiocOncoTK_files/figure-html/lkgbm-1.png" -trim
> >  > "BiocOncoTK_files/figure-html/lkgbm-1.png"' execution failed with
> >  > error code 4
> >  > Invalid Parameter - /figure-html
> >  >
> >  > The figure code is introduced with ```{r
> > lkgbm,fig=TRUE,message=FALSE}
> >  > ... the 'convert' process is not requested by me
> >  >
> >  > Is the fig=TRUE problematic for windows?  It seems unnecessary.
> >
> > Not sure what's going on. A few observations:
> >
> > a) About 500 software packages use fig=TRUE.
> >
> > b) The convert warning is just a warning. The actual error in the
> case
> > of BiocOncoTK is:
> >
> > Error: processing vignette 'BiocOncoTK.Rmd' failed with
> diagnostics:
> > argument is of length zero
> >
> > Note that the ndexr vignette also fails with this error on tokay1
> > only but it doesn't have the convert warning (this vignette does not
> > use
> > 'fig' at all). So it's not clear to me that the "argument is of
> length
> > zero" error is related to the convert warning.
> >
> > c) The devel build report shows the convert warning for 4 other
> > packages
> > (CAGEfightR, CATALYST, CTDquerier, specL) but each of them actually
> > fails with a different error message:
> >
> > CAGEfightR:
> >   colData(object1) not identical to colData(object2)
> >
> > CATALYST:
> >   no slot of name "reducedDims" for this object of class
> "daFrame"
> >
> > CTDquerier:
> >   bfcadd() failed; see warnings()
> >
> > specL:
> >   pandoc.exe: Out of memory
> >
> > These errors don't seem related to the convert warning either.
> >
> > So I'm wondering: could it be that the convert warning is actually
> > common but we generally don't see it because 'R CMD build' doesn't
> > report warnings? And that we just happen to see the warning when 'R
> CMD
> > build' fails to build a vignette.
> >
> > We'll investigate more.
> >
> > H.
> >
> >
> >  >
> >  > On Tue, Sep 10, 2019 at 11:35 AM Christian Mertes
> > mailto:mer...@in.tum.de> >
> wrote:
> >  >
> >  >> Thanks a lot for the info! So from my understanding we dont use
> any
> >  >> trimming or editing function from ImageMagick directly. I think
> > this is
> >  >> rather knitr based since we just include png files in the
> vignette.
> >  >>
> >  >> I guess it was an hickup since now the error is gone over night.
> >  >>
> >  >> Best regards,
> >  >>
> >  >> Christian
> >  >>
> >  >> On 9/9/19

Re: [Bioc-devel] Failing to build vignette because of problems with ImageMagick

[Vincent Carey]

Just wondering whether this has been followed up.  I am still seeing build
errors for
windows related to this.

On Tue, Sep 17, 2019 at 10:20 AM Christian Mertes  wrote:

> I just came across this issue on rmarkdown which links the same problem to
> BiocStyle.
> The post is from Nov 2017.
>
> https://github.com/rstudio/rmarkdown/issues/1207
>
> Maybe this helps to understand the underlying problem?
>
> It was suggested to check this in BiocStyle:
>
> Have you reported to the authors of BiocStyle? It seems they enabled the
> *knitr* hook knitr::hook_pdfcrop unconditionally (i.e. without checking
> if ImageMagick has been installed).
>
> Best,
>
> Christian
> On 9/11/19 5:50 PM, Pages, Herve wrote:
>
> New to me too. But it seems that knitr suggests magick, which itself has
>
>SystemRequirements: ImageMagick++: ImageMagick-c++-devel (rpm) or
> libmagick++-dev (deb)
>
> Don't know when this knitr dep on magick was introduced tough... Bummer!
>
> H.
>
> On 9/11/19 06:13, Kasper Daniel Hansen wrote:
>
> Yeah, does this imply that the render operation uses (or tries to use)
> ImageMagick? That's news to me, but I am not following this closely.
>
> On Wed, Sep 11, 2019 at 5:21 AM Pages, Herve   > wrote:
>
> On 9/11/19 00:50, Vincent Carey wrote:
>  > I seem to be running into a similar problem with BiocOncoTK on
> windows
>  >
>  > The build report for tokay1 shows:
>  >
>  > Loading required package: ontologyIndex
>  > Invalid Parameter - /figure-html
>  > Warning in shell(paste(c(cmd, args), collapse = " ")) :
>  >'convert "BiocOncoTK_files/figure-html/lkgbm-1.png" -trim
>  > "BiocOncoTK_files/figure-html/lkgbm-1.png"' execution failed with
>  > error code 4
>  > Invalid Parameter - /figure-html
>  >
>  > The figure code is introduced with ```{r
> lkgbm,fig=TRUE,message=FALSE}
>  > ... the 'convert' process is not requested by me
>  >
>  > Is the fig=TRUE problematic for windows?  It seems unnecessary.
>
> Not sure what's going on. A few observations:
>
> a) About 500 software packages use fig=TRUE.
>
> b) The convert warning is just a warning. The actual error in the case
> of BiocOncoTK is:
>
> Error: processing vignette 'BiocOncoTK.Rmd' failed with diagnostics:
> argument is of length zero
>
> Note that the ndexr vignette also fails with this error on tokay1
> only but it doesn't have the convert warning (this vignette does not
> use
> 'fig' at all). So it's not clear to me that the "argument is of length
> zero" error is related to the convert warning.
>
> c) The devel build report shows the convert warning for 4 other
> packages
> (CAGEfightR, CATALYST, CTDquerier, specL) but each of them actually
> fails with a different error message:
>
> CAGEfightR:
>   colData(object1) not identical to colData(object2)
>
> CATALYST:
>   no slot of name "reducedDims" for this object of class "daFrame"
>
> CTDquerier:
>   bfcadd() failed; see warnings()
>
> specL:
>   pandoc.exe: Out of memory
>
> These errors don't seem related to the convert warning either.
>
> So I'm wondering: could it be that the convert warning is actually
> common but we generally don't see it because 'R CMD build' doesn't
> report warnings? And that we just happen to see the warning when 'R CMD
> build' fails to build a vignette.
>
> We'll investigate more.
>
> H.
>
>
>  >
>  > On Tue, Sep 10, 2019 at 11:35 AM Christian Mertes
> mailto:mer...@in.tum.de> > wrote:
>  >
>  >> Thanks a lot for the info! So from my understanding we dont use any
>  >> trimming or editing function from ImageMagick directly. I think
> this is
>  >> rather knitr based since we just include png files in the vignette.
>  >>
>  >> I guess it was an hickup since now the error is gone over night.
>  >>
>  >> Best regards,
>  >>
>  >> Christian
>  >>
>  >> On 9/9/19 4:34 PM, Kasper Daniel Hansen wrote:
>  >>> You don't declare any systems requirements for ImageMagick
> (doing so
>  >>> will probably not solve your problem, but you really should).
>  >>>
>  >>> Alternatively you could look into using the tools provided by the
>  >>> magick package, which wraps ImageMagick.
>  >>>
>  >>> But it looks like you're editing PNG files for your vignette. I
> would
>  >>> really recommend not doing so. It introduces a system
> dependency which
>  >>> is just going to increase headaches on your end, for (perhaps)
> no real
>  >>> tangible benefits. If you're trimming PNGs, you should be able to
>  >>> achieve the same effect when using the png device(s) in R, and that
>  >>> will make everything more portable anyway.
>  >>>
>  >>> On Mon, Sep 9, 2019 at 9:42 AM Christian Mertes
>   

Re: [Bioc-devel] Failing to build vignette because of problems with ImageMagick

[Christian Mertes]

I just came across this issue on rmarkdown which links the same problem
to BiocStyle.
The post is from Nov 2017.

https://github.com/rstudio/rmarkdown/issues/1207

Maybe this helps to understand the underlying problem?

It was suggested to check this in BiocStyle:

Have you reported to the authors of BiocStyle? It seems they enabled
the *knitr* hook |knitr::hook_pdfcrop| unconditionally (i.e. without
checking if ImageMagick has been installed).

Best,

Christian

On 9/11/19 5:50 PM, Pages, Herve wrote:
> New to me too. But it seems that knitr suggests magick, which itself has
>
>SystemRequirements: ImageMagick++: ImageMagick-c++-devel (rpm) or 
> libmagick++-dev (deb)
>
> Don't know when this knitr dep on magick was introduced tough... Bummer!
>
> H.
>
> On 9/11/19 06:13, Kasper Daniel Hansen wrote:
>> Yeah, does this imply that the render operation uses (or tries to use) 
>> ImageMagick? That's news to me, but I am not following this closely.
>>
>> On Wed, Sep 11, 2019 at 5:21 AM Pages, Herve > > wrote:
>>
>> On 9/11/19 00:50, Vincent Carey wrote:
>>  > I seem to be running into a similar problem with BiocOncoTK on
>> windows
>>  >
>>  > The build report for tokay1 shows:
>>  >
>>  > Loading required package: ontologyIndex
>>  > Invalid Parameter - /figure-html
>>  > Warning in shell(paste(c(cmd, args), collapse = " ")) :
>>  >    'convert "BiocOncoTK_files/figure-html/lkgbm-1.png" -trim
>>  > "BiocOncoTK_files/figure-html/lkgbm-1.png"' execution failed with
>>  > error code 4
>>  > Invalid Parameter - /figure-html
>>  >
>>  > The figure code is introduced with ```{r
>> lkgbm,fig=TRUE,message=FALSE}
>>  > ... the 'convert' process is not requested by me
>>  >
>>  > Is the fig=TRUE problematic for windows?  It seems unnecessary.
>>
>> Not sure what's going on. A few observations:
>>
>> a) About 500 software packages use fig=TRUE.
>>
>> b) The convert warning is just a warning. The actual error in the case
>> of BiocOncoTK is:
>>
>>     Error: processing vignette 'BiocOncoTK.Rmd' failed with diagnostics:
>> argument is of length zero
>>
>>     Note that the ndexr vignette also fails with this error on tokay1
>> only but it doesn't have the convert warning (this vignette does not
>> use
>> 'fig' at all). So it's not clear to me that the "argument is of length
>> zero" error is related to the convert warning.
>>
>> c) The devel build report shows the convert warning for 4 other
>> packages
>> (CAGEfightR, CATALYST, CTDquerier, specL) but each of them actually
>> fails with a different error message:
>>
>>     CAGEfightR:
>>       colData(object1) not identical to colData(object2)
>>
>>     CATALYST:
>>       no slot of name "reducedDims" for this object of class "daFrame"
>>
>>     CTDquerier:
>>       bfcadd() failed; see warnings()
>>
>>     specL:
>>       pandoc.exe: Out of memory
>>
>>     These errors don't seem related to the convert warning either.
>>
>> So I'm wondering: could it be that the convert warning is actually
>> common but we generally don't see it because 'R CMD build' doesn't
>> report warnings? And that we just happen to see the warning when 'R CMD
>> build' fails to build a vignette.
>>
>> We'll investigate more.
>>
>> H.
>>
>>
>>  >
>>  > On Tue, Sep 10, 2019 at 11:35 AM Christian Mertes
>> mailto:mer...@in.tum.de>> wrote:
>>  >
>>  >> Thanks a lot for the info! So from my understanding we dont use any
>>  >> trimming or editing function from ImageMagick directly. I think
>> this is
>>  >> rather knitr based since we just include png files in the vignette.
>>  >>
>>  >> I guess it was an hickup since now the error is gone over night.
>>  >>
>>  >> Best regards,
>>  >>
>>  >> Christian
>>  >>
>>  >> On 9/9/19 4:34 PM, Kasper Daniel Hansen wrote:
>>  >>> You don't declare any systems requirements for ImageMagick
>> (doing so
>>  >>> will probably not solve your problem, but you really should).
>>  >>>
>>  >>> Alternatively you could look into using the tools provided by the
>>  >>> magick package, which wraps ImageMagick.
>>  >>>
>>  >>> But it looks like you're editing PNG files for your vignette. I
>> would
>>  >>> really recommend not doing so. It introduces a system
>> dependency which
>>  >>> is just going to increase headaches on your end, for (perhaps)
>> no real
>>  >>> tangible benefits. If you're trimming PNGs, you should be able to
>>  >>> achieve the same effect when using the png device(s) in R, and that
>>  >>> will make everything more portable anyway.
>>  >>>
>>  >>> On Mon, Sep 9, 2019 at 9:42 AM Christian Mertes
>> mailto:mer...@in.tum.de>
>>  >>> >> wrot

Re: [Bioc-devel] Failing to build vignette because of problems with ImageMagick

[Pages, Herve]

New to me too. But it seems that knitr suggests magick, which itself has

   SystemRequirements: ImageMagick++: ImageMagick-c++-devel (rpm) or 
libmagick++-dev (deb)

Don't know when this knitr dep on magick was introduced tough... Bummer!

H.

On 9/11/19 06:13, Kasper Daniel Hansen wrote:
> Yeah, does this imply that the render operation uses (or tries to use) 
> ImageMagick? That's news to me, but I am not following this closely.
> 
> On Wed, Sep 11, 2019 at 5:21 AM Pages, Herve  > wrote:
> 
> On 9/11/19 00:50, Vincent Carey wrote:
>  > I seem to be running into a similar problem with BiocOncoTK on
> windows
>  >
>  > The build report for tokay1 shows:
>  >
>  > Loading required package: ontologyIndex
>  > Invalid Parameter - /figure-html
>  > Warning in shell(paste(c(cmd, args), collapse = " ")) :
>  >    'convert "BiocOncoTK_files/figure-html/lkgbm-1.png" -trim
>  > "BiocOncoTK_files/figure-html/lkgbm-1.png"' execution failed with
>  > error code 4
>  > Invalid Parameter - /figure-html
>  >
>  > The figure code is introduced with ```{r
> lkgbm,fig=TRUE,message=FALSE}
>  > ... the 'convert' process is not requested by me
>  >
>  > Is the fig=TRUE problematic for windows?  It seems unnecessary.
> 
> Not sure what's going on. A few observations:
> 
> a) About 500 software packages use fig=TRUE.
> 
> b) The convert warning is just a warning. The actual error in the case
> of BiocOncoTK is:
> 
>     Error: processing vignette 'BiocOncoTK.Rmd' failed with diagnostics:
> argument is of length zero
> 
>     Note that the ndexr vignette also fails with this error on tokay1
> only but it doesn't have the convert warning (this vignette does not
> use
> 'fig' at all). So it's not clear to me that the "argument is of length
> zero" error is related to the convert warning.
> 
> c) The devel build report shows the convert warning for 4 other
> packages
> (CAGEfightR, CATALYST, CTDquerier, specL) but each of them actually
> fails with a different error message:
> 
>     CAGEfightR:
>       colData(object1) not identical to colData(object2)
> 
>     CATALYST:
>       no slot of name "reducedDims" for this object of class "daFrame"
> 
>     CTDquerier:
>       bfcadd() failed; see warnings()
> 
>     specL:
>       pandoc.exe: Out of memory
> 
>     These errors don't seem related to the convert warning either.
> 
> So I'm wondering: could it be that the convert warning is actually
> common but we generally don't see it because 'R CMD build' doesn't
> report warnings? And that we just happen to see the warning when 'R CMD
> build' fails to build a vignette.
> 
> We'll investigate more.
> 
> H.
> 
> 
>  >
>  > On Tue, Sep 10, 2019 at 11:35 AM Christian Mertes
> mailto:mer...@in.tum.de>> wrote:
>  >
>  >> Thanks a lot for the info! So from my understanding we dont use any
>  >> trimming or editing function from ImageMagick directly. I think
> this is
>  >> rather knitr based since we just include png files in the vignette.
>  >>
>  >> I guess it was an hickup since now the error is gone over night.
>  >>
>  >> Best regards,
>  >>
>  >> Christian
>  >>
>  >> On 9/9/19 4:34 PM, Kasper Daniel Hansen wrote:
>  >>> You don't declare any systems requirements for ImageMagick
> (doing so
>  >>> will probably not solve your problem, but you really should).
>  >>>
>  >>> Alternatively you could look into using the tools provided by the
>  >>> magick package, which wraps ImageMagick.
>  >>>
>  >>> But it looks like you're editing PNG files for your vignette. I
> would
>  >>> really recommend not doing so. It introduces a system
> dependency which
>  >>> is just going to increase headaches on your end, for (perhaps)
> no real
>  >>> tangible benefits. If you're trimming PNGs, you should be able to
>  >>> achieve the same effect when using the png device(s) in R, and that
>  >>> will make everything more portable anyway.
>  >>>
>  >>> On Mon, Sep 9, 2019 at 9:42 AM Christian Mertes
> mailto:mer...@in.tum.de>
>  >>> >> wrote:
>  >>>
>  >>>      Dear BioC team,
>  >>>
>  >>>      I just noticed that our package is failing on the
> bioconductor build
>  >>>      system during the build of the vignette on Windows and on
> MacOS
>  >>>      platforms.
>  >>>
>  >>>      From the error I would guess its a problem with the
> installation
>  >>>      of the
>  >>>      ImageMagick package. Please correct me if Im wrong.
>  >>>
>  >>>      It goes through on travis and appveyor. Any suggestions?
>  >>>
>  >>>      Here are some links to the build logs:
>  >>>
> 

Re: [Bioc-devel] Failing to build vignette because of problems with ImageMagick

[Kasper Daniel Hansen]

Yeah, does this imply that the render operation uses (or tries to use)
ImageMagick? That's news to me, but I am not following this closely.

On Wed, Sep 11, 2019 at 5:21 AM Pages, Herve  wrote:

> On 9/11/19 00:50, Vincent Carey wrote:
> > I seem to be running into a similar problem with BiocOncoTK on windows
> >
> > The build report for tokay1 shows:
> >
> > Loading required package: ontologyIndex
> > Invalid Parameter - /figure-html
> > Warning in shell(paste(c(cmd, args), collapse = " ")) :
> >'convert "BiocOncoTK_files/figure-html/lkgbm-1.png" -trim
> > "BiocOncoTK_files/figure-html/lkgbm-1.png"' execution failed with
> > error code 4
> > Invalid Parameter - /figure-html
> >
> > The figure code is introduced with ```{r lkgbm,fig=TRUE,message=FALSE}
> > ... the 'convert' process is not requested by me
> >
> > Is the fig=TRUE problematic for windows?  It seems unnecessary.
>
> Not sure what's going on. A few observations:
>
> a) About 500 software packages use fig=TRUE.
>
> b) The convert warning is just a warning. The actual error in the case
> of BiocOncoTK is:
>
>Error: processing vignette 'BiocOncoTK.Rmd' failed with diagnostics:
> argument is of length zero
>
>Note that the ndexr vignette also fails with this error on tokay1
> only but it doesn't have the convert warning (this vignette does not use
> 'fig' at all). So it's not clear to me that the "argument is of length
> zero" error is related to the convert warning.
>
> c) The devel build report shows the convert warning for 4 other packages
> (CAGEfightR, CATALYST, CTDquerier, specL) but each of them actually
> fails with a different error message:
>
>CAGEfightR:
>  colData(object1) not identical to colData(object2)
>
>CATALYST:
>  no slot of name "reducedDims" for this object of class "daFrame"
>
>CTDquerier:
>  bfcadd() failed; see warnings()
>
>specL:
>  pandoc.exe: Out of memory
>
>These errors don't seem related to the convert warning either.
>
> So I'm wondering: could it be that the convert warning is actually
> common but we generally don't see it because 'R CMD build' doesn't
> report warnings? And that we just happen to see the warning when 'R CMD
> build' fails to build a vignette.
>
> We'll investigate more.
>
> H.
>
>
> >
> > On Tue, Sep 10, 2019 at 11:35 AM Christian Mertes 
> wrote:
> >
> >> Thanks a lot for the info! So from my understanding we dont use any
> >> trimming or editing function from ImageMagick directly. I think this is
> >> rather knitr based since we just include png files in the vignette.
> >>
> >> I guess it was an hickup since now the error is gone over night.
> >>
> >> Best regards,
> >>
> >> Christian
> >>
> >> On 9/9/19 4:34 PM, Kasper Daniel Hansen wrote:
> >>> You don't declare any systems requirements for ImageMagick (doing so
> >>> will probably not solve your problem, but you really should).
> >>>
> >>> Alternatively you could look into using the tools provided by the
> >>> magick package, which wraps ImageMagick.
> >>>
> >>> But it looks like you're editing PNG files for your vignette. I would
> >>> really recommend not doing so. It introduces a system dependency which
> >>> is just going to increase headaches on your end, for (perhaps) no real
> >>> tangible benefits. If you're trimming PNGs, you should be able to
> >>> achieve the same effect when using the png device(s) in R, and that
> >>> will make everything more portable anyway.
> >>>
> >>> On Mon, Sep 9, 2019 at 9:42 AM Christian Mertes  >>> > wrote:
> >>>
> >>>  Dear BioC team,
> >>>
> >>>  I just noticed that our package is failing on the bioconductor
> build
> >>>  system during the build of the vignette on Windows and on MacOS
> >>>  platforms.
> >>>
> >>>  From the error I would guess its a problem with the installation
> >>>  of the
> >>>  ImageMagick package. Please correct me if Im wrong.
> >>>
> >>>  It goes through on travis and appveyor. Any suggestions?
> >>>
> >>>  Here are some links to the build logs:
> >>>
> >>>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.riken.jp_checkResults_3.9_bioc-2DLATEST_OUTRIDER_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=EwnHWfrov-A-kbkOeSotrFEWVXwIUuSJog3NysTJUnE&s=NA7UQNLz8lFT9bIMHiFka2iUJDarMgfT0uW36-nO9og&e=
> >>>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__travis-2Dci.org_gagneurlab_OUTRIDER&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=EwnHWfrov-A-kbkOeSotrFEWVXwIUuSJog3NysTJUnE&s=lf9cL5c-plgiqIP3Hx6Eht_Ataw3bG3x3rP7gi79flg&e=
> >>>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__ci.appveyor.com_project_c-2Dmertes_OUTRIDER&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=EwnHWfrov-A-kbkOeSotrFEWVXwIUuSJog3NysTJUnE&s=l-gS-eeyNnK7JCEdHKIUQifQoI40TZZXQox80MniKEA&e=
> >>>
> >>>  Best,
> >>>
> >>>  Christian
> >>>
> >>>  PS: the error mess

Re: [Bioc-devel] Failing to build vignette because of problems with ImageMagick

[Pages, Herve]

On 9/11/19 00:50, Vincent Carey wrote:
> I seem to be running into a similar problem with BiocOncoTK on windows
> 
> The build report for tokay1 shows:
> 
> Loading required package: ontologyIndex
> Invalid Parameter - /figure-html
> Warning in shell(paste(c(cmd, args), collapse = " ")) :
>'convert "BiocOncoTK_files/figure-html/lkgbm-1.png" -trim
> "BiocOncoTK_files/figure-html/lkgbm-1.png"' execution failed with
> error code 4
> Invalid Parameter - /figure-html
> 
> The figure code is introduced with ```{r lkgbm,fig=TRUE,message=FALSE}
> ... the 'convert' process is not requested by me
> 
> Is the fig=TRUE problematic for windows?  It seems unnecessary.

Not sure what's going on. A few observations:

a) About 500 software packages use fig=TRUE.

b) The convert warning is just a warning. The actual error in the case 
of BiocOncoTK is:

   Error: processing vignette 'BiocOncoTK.Rmd' failed with diagnostics:
argument is of length zero

   Note that the ndexr vignette also fails with this error on tokay1 
only but it doesn't have the convert warning (this vignette does not use 
'fig' at all). So it's not clear to me that the "argument is of length 
zero" error is related to the convert warning.

c) The devel build report shows the convert warning for 4 other packages 
(CAGEfightR, CATALYST, CTDquerier, specL) but each of them actually 
fails with a different error message:

   CAGEfightR:
 colData(object1) not identical to colData(object2)

   CATALYST:
 no slot of name "reducedDims" for this object of class "daFrame"

   CTDquerier:
 bfcadd() failed; see warnings()

   specL:
 pandoc.exe: Out of memory

   These errors don't seem related to the convert warning either.

So I'm wondering: could it be that the convert warning is actually 
common but we generally don't see it because 'R CMD build' doesn't 
report warnings? And that we just happen to see the warning when 'R CMD 
build' fails to build a vignette.

We'll investigate more.

H.


> 
> On Tue, Sep 10, 2019 at 11:35 AM Christian Mertes  wrote:
> 
>> Thanks a lot for the info! So from my understanding we dont use any
>> trimming or editing function from ImageMagick directly. I think this is
>> rather knitr based since we just include png files in the vignette.
>>
>> I guess it was an hickup since now the error is gone over night.
>>
>> Best regards,
>>
>> Christian
>>
>> On 9/9/19 4:34 PM, Kasper Daniel Hansen wrote:
>>> You don't declare any systems requirements for ImageMagick (doing so
>>> will probably not solve your problem, but you really should).
>>>
>>> Alternatively you could look into using the tools provided by the
>>> magick package, which wraps ImageMagick.
>>>
>>> But it looks like you're editing PNG files for your vignette. I would
>>> really recommend not doing so. It introduces a system dependency which
>>> is just going to increase headaches on your end, for (perhaps) no real
>>> tangible benefits. If you're trimming PNGs, you should be able to
>>> achieve the same effect when using the png device(s) in R, and that
>>> will make everything more portable anyway.
>>>
>>> On Mon, Sep 9, 2019 at 9:42 AM Christian Mertes >> > wrote:
>>>
>>>  Dear BioC team,
>>>
>>>  I just noticed that our package is failing on the bioconductor build
>>>  system during the build of the vignette on Windows and on MacOS
>>>  platforms.
>>>
>>>  From the error I would guess its a problem with the installation
>>>  of the
>>>  ImageMagick package. Please correct me if Im wrong.
>>>
>>>  It goes through on travis and appveyor. Any suggestions?
>>>
>>>  Here are some links to the build logs:
>>>
>>>  
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.riken.jp_checkResults_3.9_bioc-2DLATEST_OUTRIDER_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=EwnHWfrov-A-kbkOeSotrFEWVXwIUuSJog3NysTJUnE&s=NA7UQNLz8lFT9bIMHiFka2iUJDarMgfT0uW36-nO9og&e=
>>>  
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__travis-2Dci.org_gagneurlab_OUTRIDER&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=EwnHWfrov-A-kbkOeSotrFEWVXwIUuSJog3NysTJUnE&s=lf9cL5c-plgiqIP3Hx6Eht_Ataw3bG3x3rP7gi79flg&e=
>>>  
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__ci.appveyor.com_project_c-2Dmertes_OUTRIDER&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=EwnHWfrov-A-kbkOeSotrFEWVXwIUuSJog3NysTJUnE&s=l-gS-eeyNnK7JCEdHKIUQifQoI40TZZXQox80MniKEA&e=
>>>
>>>  Best,
>>>
>>>  Christian
>>>
>>>  PS: the error message on the bioc build system:
>>>
>>>
>>   
>> ##
>>>
>>   
>> ##
>>>  ###
>>>  ### Running command:
>>>  ###
>>>  ###   chmod a+r OUTRIDER -R &&
>>>  C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD b

Re: [Bioc-devel] Failing to build vignette because of problems with ImageMagick

[Vincent Carey]

I seem to be running into a similar problem with BiocOncoTK on windows

The build report for tokay1 shows:

Loading required package: ontologyIndex
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "BiocOncoTK_files/figure-html/lkgbm-1.png" -trim
"BiocOncoTK_files/figure-html/lkgbm-1.png"' execution failed with
error code 4
Invalid Parameter - /figure-html

The figure code is introduced with ```{r lkgbm,fig=TRUE,message=FALSE}
... the 'convert' process is not requested by me

Is the fig=TRUE problematic for windows?  It seems unnecessary.


On Tue, Sep 10, 2019 at 11:35 AM Christian Mertes  wrote:

> Thanks a lot for the info! So from my understanding we dont use any
> trimming or editing function from ImageMagick directly. I think this is
> rather knitr based since we just include png files in the vignette.
>
> I guess it was an hickup since now the error is gone over night.
>
> Best regards,
>
> Christian
>
> On 9/9/19 4:34 PM, Kasper Daniel Hansen wrote:
> > You don't declare any systems requirements for ImageMagick (doing so
> > will probably not solve your problem, but you really should).
> >
> > Alternatively you could look into using the tools provided by the
> > magick package, which wraps ImageMagick.
> >
> > But it looks like you're editing PNG files for your vignette. I would
> > really recommend not doing so. It introduces a system dependency which
> > is just going to increase headaches on your end, for (perhaps) no real
> > tangible benefits. If you're trimming PNGs, you should be able to
> > achieve the same effect when using the png device(s) in R, and that
> > will make everything more portable anyway.
> >
> > On Mon, Sep 9, 2019 at 9:42 AM Christian Mertes  > > wrote:
> >
> > Dear BioC team,
> >
> > I just noticed that our package is failing on the bioconductor build
> > system during the build of the vignette on Windows and on MacOS
> > platforms.
> >
> > From the error I would guess its a problem with the installation
> > of the
> > ImageMagick package. Please correct me if Im wrong.
> >
> > It goes through on travis and appveyor. Any suggestions?
> >
> > Here are some links to the build logs:
> >
> > http://bioconductor.riken.jp/checkResults/3.9/bioc-LATEST/OUTRIDER/
> > https://travis-ci.org/gagneurlab/OUTRIDER
> > https://ci.appveyor.com/project/c-mertes/OUTRIDER
> >
> > Best,
> >
> > Christian
> >
> > PS: the error message on the bioc build system:
> >
> >
>  
> ##
> >
>  
> ##
> > ###
> > ### Running command:
> > ###
> > ###   chmod a+r OUTRIDER -R &&
> > C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build
> > --keep-empty-dirs --no-resave-data OUTRIDER
> > ###
> >
>  
> ##
> >
>  
> ##
> >
> >
> > * checking for file 'OUTRIDER/DESCRIPTION' ... OK
> > * preparing 'OUTRIDER':
> > * checking DESCRIPTION meta-information ... OK
> > * cleaning src
> > * installing the package to build vignettes
> > * creating vignettes ... ERROR
> > --- re-building 'OUTRIDER.Rnw' using knitr
> > Invalid Parameter - /deVsOutlier-1.png"
> > Warning in shell(paste(c(cmd, args), collapse = " ")) :
> >   'convert "figure/deVsOutlier-1.png" -trim
> > "figure/deVsOutlier-1.png"' execution failed with error code 4
> > 229 genes did not passed the filter due to zero counts. This is
> > 22.9% of the genes.
> > Sat Sep 07 01:16:53 2019: SizeFactor estimation ...
> > Sat Sep 07 01:16:53 2019: Controlling for confounders ...
> > Using estimated q with: 23
> > Sat Sep 07 01:16:53 2019: Using the autoencoder implementation for
> > controlling.
> > Sat Sep 07 01:17:52 2019: Used the autoencoder implementation for
> > controlling.
> > Sat Sep 07 01:17:52 2019: P-value calculation ...
> > Sat Sep 07 01:17:52 2019: Zscore calculation ...
> > Invalid Parameter - /quick_guide-1.png"
> > Warning in shell(paste(c(cmd, args), collapse = " ")) :
> >   'convert "figure/quick_guide-1.png" -trim
> > "figure/quick_guide-1.png"' execution failed with error code 4
> > Quitting from lines 222-232 (OUTRIDER.Rnw)
> > Error: processing vignette 'OUTRIDER.Rnw' failed with diagnostics:
> > no lines available in input
> > --- failed re-building 'OUTRIDER.Rnw'
> >
> > SUMMARY: processing the following file failed:
> >   'OUTRIDER.Rnw'
> >
> > Error: Vignette re-building failed.
> > Execution halted
> >
> > --
> >
> > Christian Mertes
> > PhD Student / Lab Administrator
> > Gagneur lab
> >
> > Computational Genomics
> > I12 

Re: [Bioc-devel] Failing to build vignette because of problems with ImageMagick

[Christian Mertes]

Thanks a lot for the info! So from my understanding we dont use any
trimming or editing function from ImageMagick directly. I think this is
rather knitr based since we just include png files in the vignette.

I guess it was an hickup since now the error is gone over night.

Best regards,

Christian

On 9/9/19 4:34 PM, Kasper Daniel Hansen wrote:
> You don't declare any systems requirements for ImageMagick (doing so
> will probably not solve your problem, but you really should).
>
> Alternatively you could look into using the tools provided by the
> magick package, which wraps ImageMagick.
>
> But it looks like you're editing PNG files for your vignette. I would
> really recommend not doing so. It introduces a system dependency which
> is just going to increase headaches on your end, for (perhaps) no real
> tangible benefits. If you're trimming PNGs, you should be able to
> achieve the same effect when using the png device(s) in R, and that
> will make everything more portable anyway.
>
> On Mon, Sep 9, 2019 at 9:42 AM Christian Mertes  > wrote:
>
> Dear BioC team,
>
> I just noticed that our package is failing on the bioconductor build
> system during the build of the vignette on Windows and on MacOS
> platforms.
>
> From the error I would guess its a problem with the installation
> of the
> ImageMagick package. Please correct me if Im wrong.
>
> It goes through on travis and appveyor. Any suggestions?
>
> Here are some links to the build logs:
>
> http://bioconductor.riken.jp/checkResults/3.9/bioc-LATEST/OUTRIDER/
> https://travis-ci.org/gagneurlab/OUTRIDER
> https://ci.appveyor.com/project/c-mertes/OUTRIDER
>
> Best,
>
> Christian
>
> PS: the error message on the bioc build system:
>
> 
> ##
> 
> ##
> ###
> ### Running command:
> ###
> ###   chmod a+r OUTRIDER -R &&
> C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build
> --keep-empty-dirs --no-resave-data OUTRIDER
> ###
> 
> ##
> 
> ##
>
>
> * checking for file 'OUTRIDER/DESCRIPTION' ... OK
> * preparing 'OUTRIDER':
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> * installing the package to build vignettes
> * creating vignettes ... ERROR
> --- re-building 'OUTRIDER.Rnw' using knitr
> Invalid Parameter - /deVsOutlier-1.png"
> Warning in shell(paste(c(cmd, args), collapse = " ")) :
>   'convert "figure/deVsOutlier-1.png" -trim
> "figure/deVsOutlier-1.png"' execution failed with error code 4
> 229 genes did not passed the filter due to zero counts. This is
> 22.9% of the genes.
> Sat Sep 07 01:16:53 2019: SizeFactor estimation ...
> Sat Sep 07 01:16:53 2019: Controlling for confounders ...
> Using estimated q with: 23
> Sat Sep 07 01:16:53 2019: Using the autoencoder implementation for
> controlling.
> Sat Sep 07 01:17:52 2019: Used the autoencoder implementation for
> controlling.
> Sat Sep 07 01:17:52 2019: P-value calculation ...
> Sat Sep 07 01:17:52 2019: Zscore calculation ...
> Invalid Parameter - /quick_guide-1.png"
> Warning in shell(paste(c(cmd, args), collapse = " ")) :
>   'convert "figure/quick_guide-1.png" -trim
> "figure/quick_guide-1.png"' execution failed with error code 4
> Quitting from lines 222-232 (OUTRIDER.Rnw)
> Error: processing vignette 'OUTRIDER.Rnw' failed with diagnostics:
> no lines available in input
> --- failed re-building 'OUTRIDER.Rnw'
>
> SUMMARY: processing the following file failed:
>   'OUTRIDER.Rnw'
>
> Error: Vignette re-building failed.
> Execution halted
>
> -- 
>
> Christian Mertes
> PhD Student / Lab Administrator
> Gagneur lab
>
> Computational Genomics
> I12 - Bioinformatics Department
> Technical University Munich
> Boltzmannstr. 3
> 85748 Garching, Germany
>
> Mail: mer...@in.tum.de 
> Phone: +49-89-289-19416
> http://gagneurlab.in.tum.de
>
>
>         [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org  mailing
> list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> -- 
> Best,
> Kasper

-- 

Christian Mertes
PhD Student / Lab Administrator
Gagneur lab
 
Computational Genomics
I12 - Bioinformatics Department
Technical University Munich
Boltzmannstr. 3
85748 Garching, Germany

Mail: mer...@in.tum.de
Phone: +49-89-289-19416
http://gagneurlab.in.tum.de


[[alternative HTML version deleted]]

___

Re: [Bioc-devel] Failing to build vignette because of problems with ImageMagick

[Kasper Daniel Hansen]

You don't declare any systems requirements for ImageMagick (doing so will
probably not solve your problem, but you really should).

Alternatively you could look into using the tools provided by the magick
package, which wraps ImageMagick.

But it looks like you're editing PNG files for your vignette. I would
really recommend not doing so. It introduces a system dependency which is
just going to increase headaches on your end, for (perhaps) no real
tangible benefits. If you're trimming PNGs, you should be able to achieve
the same effect when using the png device(s) in R, and that will make
everything more portable anyway.

On Mon, Sep 9, 2019 at 9:42 AM Christian Mertes  wrote:

> Dear BioC team,
>
> I just noticed that our package is failing on the bioconductor build
> system during the build of the vignette on Windows and on MacOS platforms.
>
> From the error I would guess its a problem with the installation of the
> ImageMagick package. Please correct me if Im wrong.
>
> It goes through on travis and appveyor. Any suggestions?
>
> Here are some links to the build logs:
>
> http://bioconductor.riken.jp/checkResults/3.9/bioc-LATEST/OUTRIDER/
> https://travis-ci.org/gagneurlab/OUTRIDER
> https://ci.appveyor.com/project/c-mertes/OUTRIDER
>
> Best,
>
> Christian
>
> PS: the error message on the bioc build system:
>
>
> ##
>
> ##
> ###
> ### Running command:
> ###
> ###   chmod a+r OUTRIDER -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe
> CMD build --keep-empty-dirs --no-resave-data OUTRIDER
> ###
>
> ##
>
> ##
>
>
> * checking for file 'OUTRIDER/DESCRIPTION' ... OK
> * preparing 'OUTRIDER':
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> * installing the package to build vignettes
> * creating vignettes ... ERROR
> --- re-building 'OUTRIDER.Rnw' using knitr
> Invalid Parameter - /deVsOutlier-1.png"
> Warning in shell(paste(c(cmd, args), collapse = " ")) :
>   'convert "figure/deVsOutlier-1.png" -trim "figure/deVsOutlier-1.png"'
> execution failed with error code 4
> 229 genes did not passed the filter due to zero counts. This is 22.9% of
> the genes.
> Sat Sep 07 01:16:53 2019: SizeFactor estimation ...
> Sat Sep 07 01:16:53 2019: Controlling for confounders ...
> Using estimated q with: 23
> Sat Sep 07 01:16:53 2019: Using the autoencoder implementation for
> controlling.
> Sat Sep 07 01:17:52 2019: Used the autoencoder implementation for
> controlling.
> Sat Sep 07 01:17:52 2019: P-value calculation ...
> Sat Sep 07 01:17:52 2019: Zscore calculation ...
> Invalid Parameter - /quick_guide-1.png"
> Warning in shell(paste(c(cmd, args), collapse = " ")) :
>   'convert "figure/quick_guide-1.png" -trim "figure/quick_guide-1.png"'
> execution failed with error code 4
> Quitting from lines 222-232 (OUTRIDER.Rnw)
> Error: processing vignette 'OUTRIDER.Rnw' failed with diagnostics:
> no lines available in input
> --- failed re-building 'OUTRIDER.Rnw'
>
> SUMMARY: processing the following file failed:
>   'OUTRIDER.Rnw'
>
> Error: Vignette re-building failed.
> Execution halted
>
> --
>
> Christian Mertes
> PhD Student / Lab Administrator
> Gagneur lab
>
> Computational Genomics
> I12 - Bioinformatics Department
> Technical University Munich
> Boltzmannstr. 3
> 85748 Garching, Germany
>
> Mail: mer...@in.tum.de
> Phone: +49-89-289-19416
> http://gagneurlab.in.tum.de
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
Best,
Kasper

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[Bioc-devel] Failing to build vignette because of problems with ImageMagick

[Christian Mertes]

Dear BioC team,

I just noticed that our package is failing on the bioconductor build
system during the build of the vignette on Windows and on MacOS platforms.

>From the error I would guess its a problem with the installation of the
ImageMagick package. Please correct me if Im wrong.

It goes through on travis and appveyor. Any suggestions?

Here are some links to the build logs:

http://bioconductor.riken.jp/checkResults/3.9/bioc-LATEST/OUTRIDER/
https://travis-ci.org/gagneurlab/OUTRIDER
https://ci.appveyor.com/project/c-mertes/OUTRIDER

Best,

Christian

PS: the error message on the bioc build system:

##
##
###
### Running command:
###
###   chmod a+r OUTRIDER -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD 
build --keep-empty-dirs --no-resave-data OUTRIDER
###
##
##


* checking for file 'OUTRIDER/DESCRIPTION' ... OK
* preparing 'OUTRIDER':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'OUTRIDER.Rnw' using knitr
Invalid Parameter - /deVsOutlier-1.png"
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "figure/deVsOutlier-1.png" -trim "figure/deVsOutlier-1.png"' 
execution failed with error code 4
229 genes did not passed the filter due to zero counts. This is 22.9% of the 
genes.
Sat Sep 07 01:16:53 2019: SizeFactor estimation ...
Sat Sep 07 01:16:53 2019: Controlling for confounders ...
Using estimated q with: 23
Sat Sep 07 01:16:53 2019: Using the autoencoder implementation for controlling.
Sat Sep 07 01:17:52 2019: Used the autoencoder implementation for controlling.
Sat Sep 07 01:17:52 2019: P-value calculation ...
Sat Sep 07 01:17:52 2019: Zscore calculation ...
Invalid Parameter - /quick_guide-1.png"
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "figure/quick_guide-1.png" -trim "figure/quick_guide-1.png"' 
execution failed with error code 4
Quitting from lines 222-232 (OUTRIDER.Rnw) 
Error: processing vignette 'OUTRIDER.Rnw' failed with diagnostics:
no lines available in input
--- failed re-building 'OUTRIDER.Rnw'

SUMMARY: processing the following file failed:
  'OUTRIDER.Rnw'

Error: Vignette re-building failed.
Execution halted

-- 

Christian Mertes
PhD Student / Lab Administrator
Gagneur lab

Computational Genomics
I12 - Bioinformatics Department
Technical University Munich
Boltzmannstr. 3
85748 Garching, Germany

Mail: mer...@in.tum.de
Phone: +49-89-289-19416
http://gagneurlab.in.tum.de


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