Hello, Not sure what to make of this error with building the vingette by bioconductor. The figures are all there. Did something change with knitr? Thank you. Zach ############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ERSSA ### ############################################################################## ############################################################################## * checking for file ?ERSSA/DESCRIPTION? ... OK * preparing ?ERSSA?: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ?ERSSA.Rmd? using rmarkdown Quitting from lines 45-46 (ERSSA.Rmd) Error: processing vignette 'ERSSA.Rmd' failed with diagnostics: Magick: unable to open image `/tmp/Rtmp9aQlKg/Rbuild6d1427846a56/ERSSA/vignettes/ERSSA_files/figure-html/unnamed-chunk-2-1.png': No such file or directory @ error/blob.c/OpenBlob/2701 --- failed re-building ?ERSSA.Rmd? SUMMARY: processing the following file failed: ?ERSSA.Rmd? Error: Vignette re-building failed. Execution halted
[Bioc-devel] Error unable to find image
6 messages · Zach Shao, Martin Morgan, Leonardo Collado Torres +1 more
This seems to be a problem with a recent change to knitr https://github.com/Bioconductor/BiocStyle/issues/71 https://github.com/yihui/knitr/issues/1797 Please follow these issues; it looks like it is fixed in the github repository, but needs to be made available in CRAN for this to be fixed on our build systems. Martin ?On 1/20/20, 12:00 PM, "Bioc-devel on behalf of Zach Shao" <bioc-devel-bounces at r-project.org on behalf of zach.shao at gmail.com> wrote: Hello, Not sure what to make of this error with building the vingette by bioconductor. The figures are all there. Did something change with knitr? Thank you. Zach ############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ERSSA ### ############################################################################## ############################################################################## * checking for file ?ERSSA/DESCRIPTION? ... OK * preparing ?ERSSA?: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ?ERSSA.Rmd? using rmarkdown Quitting from lines 45-46 (ERSSA.Rmd) Error: processing vignette 'ERSSA.Rmd' failed with diagnostics: Magick: unable to open image `/tmp/Rtmp9aQlKg/Rbuild6d1427846a56/ERSSA/vignettes/ERSSA_files/figure-html/unnamed-chunk-2-1.png': No such file or directory @ error/blob.c/OpenBlob/2701 --- failed re-building ?ERSSA.Rmd? SUMMARY: processing the following file failed: ?ERSSA.Rmd? Error: Vignette re-building failed. Execution halted _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
1 day later
Hi, Thanks for the links! Should we wait for the knitr fix to be available through CRAN or edit our DESCRIPTION files to force the Bioc machines to install `knitr` from GitHub? Best, Leo On Mon, Jan 20, 2020 at 12:11 PM Martin Morgan <mtmorgan.bioc at gmail.com> wrote:
This seems to be a problem with a recent change to knitr https://github.com/Bioconductor/BiocStyle/issues/71 https://github.com/yihui/knitr/issues/1797 Please follow these issues; it looks like it is fixed in the github repository, but needs to be made available in CRAN for this to be fixed on our build systems. Martin ?On 1/20/20, 12:00 PM, "Bioc-devel on behalf of Zach Shao" < bioc-devel-bounces at r-project.org on behalf of zach.shao at gmail.com> wrote: Hello, Not sure what to make of this error with building the vingette by bioconductor. The figures are all there. Did something change with knitr? Thank you. Zach ############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ERSSA ### ############################################################################## ############################################################################## * checking for file ?ERSSA/DESCRIPTION? ... OK * preparing ?ERSSA?: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ?ERSSA.Rmd? using rmarkdown Quitting from lines 45-46 (ERSSA.Rmd) Error: processing vignette 'ERSSA.Rmd' failed with diagnostics: Magick: unable to open image `/tmp/Rtmp9aQlKg/Rbuild6d1427846a56/ERSSA/vignettes/ERSSA_files/figure-html/unnamed-chunk-2-1.png': No such file or directory @ error/blob.c/OpenBlob/2701 --- failed re-building ?ERSSA.Rmd? SUMMARY: processing the following file failed: ?ERSSA.Rmd? Error: Vignette re-building failed. Execution halted [[alternative HTML version deleted]]
_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________
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Wait for knitr to be available on CRAN. The builders do not respect remotes to github repos. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Leonardo Collado Torres <lcolladotor at gmail.com>
Sent: Tuesday, January 21, 2020 1:19 PM
To: Martin Morgan <mtmorgan.bioc at gmail.com>
Cc: Zach Shao <zach.shao at gmail.com>; bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Error unable to find image
Sent: Tuesday, January 21, 2020 1:19 PM
To: Martin Morgan <mtmorgan.bioc at gmail.com>
Cc: Zach Shao <zach.shao at gmail.com>; bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Error unable to find image
Hi, Thanks for the links! Should we wait for the knitr fix to be available through CRAN or edit our DESCRIPTION files to force the Bioc machines to install `knitr` from GitHub? Best, Leo On Mon, Jan 20, 2020 at 12:11 PM Martin Morgan <mtmorgan.bioc at gmail.com> wrote: > This seems to be a problem with a recent change to knitr > > https://github.com/Bioconductor/BiocStyle/issues/71 > https://github.com/yihui/knitr/issues/1797 > > Please follow these issues; it looks like it is fixed in the github > repository, but needs to be made available in CRAN for this to be fixed on > our build systems. > > Martin > > ?On 1/20/20, 12:00 PM, "Bioc-devel on behalf of Zach Shao" < > bioc-devel-bounces at r-project.org on behalf of zach.shao at gmail.com> wrote: > > Hello, > > Not sure what to make of this error > > with building the vingette by bioconductor. > > The figures are all there. > > Did something change with knitr? > > Thank you. > > > Zach > > > ############################################################################## > > ############################################################################## > ### > ### Running command: > ### > ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD build > --keep-empty-dirs --no-resave-data ERSSA > ### > > ############################################################################## > > ############################################################################## > > > * checking for file ?ERSSA/DESCRIPTION? ... OK > * preparing ?ERSSA?: > * checking DESCRIPTION meta-information ... OK > * installing the package to build vignettes > * creating vignettes ... ERROR > --- re-building ?ERSSA.Rmd? using rmarkdown > Quitting from lines 45-46 (ERSSA.Rmd) > Error: processing vignette 'ERSSA.Rmd' failed with diagnostics: > Magick: unable to open image > > `/tmp/Rtmp9aQlKg/Rbuild6d1427846a56/ERSSA/vignettes/ERSSA_files/figure-html/unnamed-chunk-2-1.png': > No such file or directory @ error/blob.c/OpenBlob/2701 > --- failed re-building ?ERSSA.Rmd? > > SUMMARY: processing the following file failed: > ?ERSSA.Rmd? > > Error: Vignette re-building failed. > Execution halted > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > _______________________________________________ > 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.
Will do, thanks Lori! Best, Leo On Tue, Jan 21, 2020 at 1:24 PM Shepherd, Lori <
Lori.Shepherd at roswellpark.org> wrote:
Wait for knitr to be available on CRAN. The builders do not respect remotes to github repos. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ------------------------------ *From:* Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Leonardo Collado Torres <lcolladotor at gmail.com> *Sent:* Tuesday, January 21, 2020 1:19 PM *To:* Martin Morgan <mtmorgan.bioc at gmail.com> *Cc:* Zach Shao <zach.shao at gmail.com>; bioc-devel at r-project.org < bioc-devel at r-project.org> *Subject:* Re: [Bioc-devel] Error unable to find image Hi, Thanks for the links! Should we wait for the knitr fix to be available through CRAN or edit our DESCRIPTION files to force the Bioc machines to install `knitr` from GitHub? Best, Leo On Mon, Jan 20, 2020 at 12:11 PM Martin Morgan <mtmorgan.bioc at gmail.com> wrote:
This seems to be a problem with a recent change to knitr https://github.com/Bioconductor/BiocStyle/issues/71 https://github.com/yihui/knitr/issues/1797 Please follow these issues; it looks like it is fixed in the github repository, but needs to be made available in CRAN for this to be fixed
on
our build systems. Martin ?On 1/20/20, 12:00 PM, "Bioc-devel on behalf of Zach Shao" < bioc-devel-bounces at r-project.org on behalf of zach.shao at gmail.com>
wrote:
Hello,
Not sure what to make of this error
with building the vingette by bioconductor.
The figures are all there.
Did something change with knitr?
Thank you.
Zach
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD build
--keep-empty-dirs --no-resave-data ERSSA
###
##############################################################################
##############################################################################
* checking for file ?ERSSA/DESCRIPTION? ... OK
* preparing ?ERSSA?:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ?ERSSA.Rmd? using rmarkdown
Quitting from lines 45-46 (ERSSA.Rmd)
Error: processing vignette 'ERSSA.Rmd' failed with diagnostics:
Magick: unable to open image
`/tmp/Rtmp9aQlKg/Rbuild6d1427846a56/ERSSA/vignettes/ERSSA_files/figure-html/unnamed-chunk-2-1.png':
No such file or directory @ error/blob.c/OpenBlob/2701
--- failed re-building ?ERSSA.Rmd?
SUMMARY: processing the following file failed:
?ERSSA.Rmd?
Error: Vignette re-building failed.
Execution halted
[[alternative HTML version deleted]]
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Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________
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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.
We have actually decided to upload the current github version on the builders manually while we wait for it to get into CRAN so that you can all hopefully get clean builds. The release builders were updated yesterday and the devel builders are being updated now. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: Leonardo Collado Torres <lcolladotor at gmail.com>
Sent: Tuesday, January 21, 2020 3:08 PM
To: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
Cc: Martin Morgan <mtmorgan.bioc at gmail.com>; Zach Shao <zach.shao at gmail.com>; bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Error unable to find image
Sent: Tuesday, January 21, 2020 3:08 PM
To: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
Cc: Martin Morgan <mtmorgan.bioc at gmail.com>; Zach Shao <zach.shao at gmail.com>; bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Error unable to find image
Will do, thanks Lori! Best, Leo On Tue, Jan 21, 2020 at 1:24 PM Shepherd, Lori <Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at roswellpark.org>> wrote: Wait for knitr to be available on CRAN. The builders do not respect remotes to github repos. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Bioc-devel <bioc-devel-bounces at r-project.org<mailto:bioc-devel-bounces at r-project.org>> on behalf of Leonardo Collado Torres <lcolladotor at gmail.com<mailto:lcolladotor at gmail.com>> Sent: Tuesday, January 21, 2020 1:19 PM To: Martin Morgan <mtmorgan.bioc at gmail.com<mailto:mtmorgan.bioc at gmail.com>> Cc: Zach Shao <zach.shao at gmail.com<mailto:zach.shao at gmail.com>>; bioc-devel at r-project.org<mailto:bioc-devel at r-project.org> <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>> Subject: Re: [Bioc-devel] Error unable to find image Hi, Thanks for the links! Should we wait for the knitr fix to be available through CRAN or edit our DESCRIPTION files to force the Bioc machines to install `knitr` from GitHub? Best, Leo On Mon, Jan 20, 2020 at 12:11 PM Martin Morgan <mtmorgan.bioc at gmail.com<mailto:mtmorgan.bioc at gmail.com>> wrote: > This seems to be a problem with a recent change to knitr > > https://github.com/Bioconductor/BiocStyle/issues/71 > https://github.com/yihui/knitr/issues/1797 > > Please follow these issues; it looks like it is fixed in the github > repository, but needs to be made available in CRAN for this to be fixed on > our build systems. > > Martin > > ?On 1/20/20, 12:00 PM, "Bioc-devel on behalf of Zach Shao" < > bioc-devel-bounces at r-project.org<mailto:bioc-devel-bounces at r-project.org> on behalf of zach.shao at gmail.com<mailto:zach.shao at gmail.com>> wrote: > > Hello, > > Not sure what to make of this error > > with building the vingette by bioconductor. > > The figures are all there. > > Did something change with knitr? > > Thank you. > > > Zach > > > ############################################################################## > > ############################################################################## > ### > ### Running command: > ### > ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD build > --keep-empty-dirs --no-resave-data ERSSA > ### > > ############################################################################## > > ############################################################################## > > > * checking for file ?ERSSA/DESCRIPTION? ... OK > * preparing ?ERSSA?: > * checking DESCRIPTION meta-information ... OK > * installing the package to build vignettes > * creating vignettes ... ERROR > --- re-building ?ERSSA.Rmd? using rmarkdown > Quitting from lines 45-46 (ERSSA.Rmd) > Error: processing vignette 'ERSSA.Rmd' failed with diagnostics: > Magick: unable to open image > > `/tmp/Rtmp9aQlKg/Rbuild6d1427846a56/ERSSA/vignettes/ERSSA_files/figure-html/unnamed-chunk-2-1.png': > No such file or directory @ error/blob.c/OpenBlob/2701 > --- failed re-building ?ERSSA.Rmd? > > SUMMARY: processing the following file failed: > ?ERSSA.Rmd? > > Error: Vignette re-building failed. > Execution halted > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > _______________________________________________ > 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<mailto: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 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.