Re: [Bioc-devel] Resetting to previous commits
Thank you for the prompt response! I will just add more versions on top of what I have already added. Would it be correct to assume that Bioconductor will try to build the most recent version available, even though it failed builds for previous versions? Regarding the change, it was indeed a breaking change, and I thus believed that it would have been counted as a bug-fix for the release branch. All the best, Erik On 14 Aug 2019, at 17:15, Kasper Daniel Hansen mailto:kasperdanielhan...@gmail.com>> wrote: Also, it is not clear to me if this qualifies for a update to the release branch. Updates to release should be restricted to critical bug fixes (although if tidyr updates will break your package, that sounds like a critical bug fix to me) Note to others: this (again) emphasizes that we may need to "copy" a snapshot of CRAN into release. Best, Kasper On Wed, Aug 14, 2019 at 11:13 AM Kasper Daniel Hansen mailto:kasperdanielhan...@gmail.com>> wrote: You cannot revert. By pushing those updates, you released a version into the wild. It is true that as long as it doesn't build on the build servers, it would have been hard to obtain for anyone, but it is still possible through git. You need to update the version. Best, Kasper On Wed, Aug 14, 2019 at 11:05 AM Erik Fasterius mailto:erik.faster...@outlook.com>> wrote: I made some changes to my seqCAT package the last few days in order to prepare for version 1.0.0 of tidyr, which was apparently harder than I initially thought. I was also a bit too quick with pushing to Bioconductor (both the release and devel branches), and now I’ve got several updates and versions that don’t work - very stupid of me, I know. I do seem to have a working version now, though, and I finally learnt my lesson and have NOT pushed this to Bioconductor yet. Now I want to reset to the previously working versions of my package (1.6.0 for release and 1.7.2 for devel) I did try to make (temporary) hard resets and force push these to Bioconductor (as per the “reset to a previous commit” in the “abandon changes” developer section), but these did not work: all I got was errors say I cannot move from a higher version (e.g. 1.6.2) back to a lower one (1.6.0). Is there a way to bypass this? If not, I assume I’ll just have to make a new version for each branch (1.6.3 and 1.7.5, as it were) and push those, leaving several non-functional versions at Bioconductor? If at all possible I’d like to avoid this. Again, I realise these problems are because of errors on my part, and would like to know if I can solve them somehow or if I’ll just have to live with them. ___ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Best, Kasper -- Best, Kasper [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Resetting to previous commits
I made some changes to my seqCAT package the last few days in order to prepare for version 1.0.0 of tidyr, which was apparently harder than I initially thought. I was also a bit too quick with pushing to Bioconductor (both the release and devel branches), and now I’ve got several updates and versions that don’t work - very stupid of me, I know. I do seem to have a working version now, though, and I finally learnt my lesson and have NOT pushed this to Bioconductor yet. Now I want to reset to the previously working versions of my package (1.6.0 for release and 1.7.2 for devel) I did try to make (temporary) hard resets and force push these to Bioconductor (as per the “reset to a previous commit” in the “abandon changes” developer section), but these did not work: all I got was errors say I cannot move from a higher version (e.g. 1.6.2) back to a lower one (1.6.0). Is there a way to bypass this? If not, I assume I’ll just have to make a new version for each branch (1.6.3 and 1.7.5, as it were) and push those, leaving several non-functional versions at Bioconductor? If at all possible I’d like to avoid this. Again, I realise these problems are because of errors on my part, and would like to know if I can solve them somehow or if I’ll just have to live with them. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Remaining windows build error
I am still getting a Windows build error in my seqCAT package. I thought this was a problem with VariantAnnotation after an update, which also seemed to be the case after communication with Valerie Obenchain. My package was apparently not the only package affected by this, and I was told the problem was being worked on. What is the status on this? I would very much like my package to successfully build on all platforms (OS X and Linux are fine) before the deadline for the next Bioconductor release. Is there anything I can do here? Erik [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Windows-specific build error of 'seqCAT' package
Hi, Valerie! Thanks for looking into the problem! I hope it’ll work out. Erik On 16 Mar 2019, at 22:51, Valerie Obenchain mailto:obenchain.vale...@gene.com>> wrote: It doesn't look like it was the patch - the error is still there. I'll look in to this some more. Valerie On Fri, Mar 15, 2019 at 11:10 AM Valerie Obenchain mailto:obenc...@gene.com>> wrote: Hi Erik, I think the problem was introduced in a contributed patch applied to VariantAnnotation in devel. I've reverted the patch and expect VariantAnnotation (and downstream packages) to clear up on Windows with tomorrow's builds. Valerie On Thu, Mar 7, 2019 at 4:10 AM Erik Fasterius mailto:erik.faster...@outlook.com>> wrote: Hi, My seqCAT package recently broke building on the Windows platform, which I assume has to do with changes to the VariantAnnotation package (upon which seqCAT depends). The error (which comes during the creation of the vignette) looks like this: Quitting from lines 102-112 (seqCAT.Rmd) Error: processing vignette 'seqCAT.Rmd' failed with diagnostics: invalid class "VCFHeader" object: 1: 'info(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description invalid class "VCFHeader" object: 2: 'geno(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description --- failed re-building 'seqCAT.Rmd' It builds and completes all checks successfully on all other platforms, though. I have no experience with Windows, so I don’t really know how to even start debugging this issue (I’m working on OS X). Given that other platforms are working fine I’m thinking (hoping) that this is some incompatibility with recent changes to VariantAnnotation (or its dependencies) and the Windows platform, but I have no clue if this is the case. Does anybody have any idea as to what is the issue here, or have any tips regarding to be debug something on a different platform than the one you are using yourself? Erik [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Windows-specific build error of 'seqCAT' package
Hi, My seqCAT package recently broke building on the Windows platform, which I assume has to do with changes to the VariantAnnotation package (upon which seqCAT depends). The error (which comes during the creation of the vignette) looks like this: Quitting from lines 102-112 (seqCAT.Rmd) Error: processing vignette 'seqCAT.Rmd' failed with diagnostics: invalid class "VCFHeader" object: 1: 'info(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description invalid class "VCFHeader" object: 2: 'geno(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description --- failed re-building 'seqCAT.Rmd' It builds and completes all checks successfully on all other platforms, though. I have no experience with Windows, so I don’t really know how to even start debugging this issue (I’m working on OS X). Given that other platforms are working fine I’m thinking (hoping) that this is some incompatibility with recent changes to VariantAnnotation (or its dependencies) and the Windows platform, but I have no clue if this is the case. Does anybody have any idea as to what is the issue here, or have any tips regarding to be debug something on a different platform than the one you are using yourself? Erik [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] scanVCF: _DNAencode(): invalid DNAString input character: '1'
Thanks for the update, Valerie! And thanks for asking the question that I also
had in mind, Kevin. I’ll follow the GitHub issue and retry once the change has
been reverted.
Erik
On 10 Jan 2019, at 03:13, Obenchain, Valerie
mailto:valerie.obench...@roswellpark.org>>
wrote:
On 1/9/19 8:36 AM, Kevin RUE wrote:
Thanks for the update Valerie.
Needless to say, I ran R CMD check locally yesterday, and it crashed
with the same issue.
Naive question, without looking into the original issue: is it purely a
programming issue, or is there a chance that our (seqCAT and TVTB) VCF
files need to be updated to match any kind of new standard?
I don't think it's related to the vcf standard but more with handling
buffer overflow gracefully under different circumstances.
Valerie
Best,
Kevin
On Wed, Jan 9, 2019 at 3:49 PM Obenchain, Valerie
mailto:valerie.obench...@roswellpark.org>
<mailto:valerie.obench...@roswellpark.org>> wrote:
The problem is related to a change I made to handle buffer overflow:
https://github.com/Bioconductor/VariantAnnotation/issues/19
This clearly doesn't work for all cases, thanks for reporting the
problems with seqCAT and TVTB. I've reverted the change so your
packages
will build and will re-think the fix.
Valerie
On 1/8/19 10:45 AM, Kevin RUE wrote:
Hi all,
Same kind of error for my TVTB package
(https://master.bioconductor.org/checkResults/3.8/bioc-LATEST/TVTB/malbec1-checksrc.html).
I'll run R CMD check locally ASAP to see whether I need to update
TVTB
or if it's something upstream.
Best,
Kevin
On Tue, Jan 8, 2019 at 5:05 PM Obenchain, Valerie
mailto:valerie.obench...@roswellpark.org>
<mailto:valerie.obench...@roswellpark.org>
<mailto:valerie.obench...@roswellpark.org
<mailto:valerie.obench...@roswellpark.org>>> wrote:
Hi Erik,
There have been a few changes to VariantAnnotation lately.
I'll take a
look at seqCAT and get back to you.
Valerie
On 1/8/19 6:07 AM, Erik Fasterius wrote:
> I recently started to get a weird error when building the
vignette to my seqCAT package, related to a VCF file I use as
example data. The error itself looks like this:
>
> scanVcf: _DNAencode(): invalid DNAString input character: '1'
(byte value 49) path: (...)/seqCAT/extdata/example.vcf.gz
>
> I can also reproduce the error by a simple
`VariantAnnotation::readVCF()` call. It has worked fine until the
latest devel-updates of other Bioconductor packages, so I
assumed it
was some new change that caused the error, but I cannot find
anything in the NEWS seemingly related to this. I also tried to
troubleshoot by manually inspecting my file, and it seems
that the
ANN field is the culprit; I can read the VCF if I remove the
entirety of the INFO column. I cannot, however, seem to
locate the
erroneous data itself.
>
> Does anybody have any idea what causes this?
>
> [[alternative HTML version deleted]]
>
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[Bioc-devel] scanVCF: _DNAencode(): invalid DNAString input character: '1'
I recently started to get a weird error when building the vignette to my seqCAT package, related to a VCF file I use as example data. The error itself looks like this: scanVcf: _DNAencode(): invalid DNAString input character: '1' (byte value 49) path: (...)/seqCAT/extdata/example.vcf.gz I can also reproduce the error by a simple `VariantAnnotation::readVCF()` call. It has worked fine until the latest devel-updates of other Bioconductor packages, so I assumed it was some new change that caused the error, but I cannot find anything in the NEWS seemingly related to this. I also tried to troubleshoot by manually inspecting my file, and it seems that the ANN field is the culprit; I can read the VCF if I remove the entirety of the INFO column. I cannot, however, seem to locate the erroneous data itself. Does anybody have any idea what causes this? [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Travis CI errors for BiocManager
Ah, okey! Very good to know, thank you! Is there a way I can keep track of
this, to see when it gets fixed?
Erik
> On 3 Jan 2019, at 14:00, Martin Morgan wrote:
>
> This seems to be a regression in R-devel, and has been reported.
>
> Previously (at least svn r75833, I think)
>
> df <- data.frame(vers= package_version("1.2"))
> rbind(df, df)$vers
>
> returned
>
> [1] '1.2' '1.2'
>
> now (r75945) we have
>
>> rbind(df, df)$vers
> [[1]]
> [1] 1 2
>
> [[2]]
> [1] 1 2
>
> Martin
>
> On 1/3/19, 5:25 AM, "Bioc-devel on behalf of Erik Fasterius"
>
> wrote:
>
>Hi,
>
>I’m currently updating my package `seqCAT` with some new code, and I
> always run it through Travis CI before pushing changes to Bioconductor. The
> last build errors with the following message:
>
>Updating HTML index of packages in '.Library'
>Making 'packages.html' ... done
>Error: invalid version specification ‘c(3, 9)’
>Execution halted
>The command "eval Rscript -e 'if (!requireNamespace("BiocManager",
> quietly=TRUE)) install.packages("BiocManager");if (TRUE)
> BiocManager::install(version = "devel");cat(append = TRUE, file =
> "~/.Rprofile.site<http://Rprofile.site>", "options(repos =
> BiocManager::repositories());")' " failed.
>
>This happens even though both `devtools::check()` and `BiocCheck()`
> completes without errors, like normal. I have never had this error before,
> and it started with the most recent change I did: `n()` to `dplyr::n()` in a
> single line of code (to account for the upcoming changes to the `dplyr`
> package), so I don’t believe the code itself is to blame.
>
>Does anybody know what the problem is here?
>Thanks in advance!
>Erik
>
> [[alternative HTML version deleted]]
>
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[Bioc-devel] Travis CI errors for BiocManager
Hi,
I’m currently updating my package `seqCAT` with some new code, and I always run
it through Travis CI before pushing changes to Bioconductor. The last build
errors with the following message:
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Error: invalid version specification ‘c(3, 9)’
Execution halted
The command "eval Rscript -e 'if (!requireNamespace("BiocManager",
quietly=TRUE)) install.packages("BiocManager");if (TRUE)
BiocManager::install(version = "devel");cat(append = TRUE, file =
"~/.Rprofile.site", "options(repos =
BiocManager::repositories());")' " failed.
This happens even though both `devtools::check()` and `BiocCheck()` completes
without errors, like normal. I have never had this error before, and it started
with the most recent change I did: `n()` to `dplyr::n()` in a single line of
code (to account for the upcoming changes to the `dplyr` package), so I don’t
believe the code itself is to blame.
Does anybody know what the problem is here?
Thanks in advance!
Erik
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