Re: [Bioc-devel] Fwd: singscore problems reported in the Multiple platform build/check report for BioC 3.8
That's interesting, thank you for testing it. :)
Regards,
Ruqian
On Tue, Nov 6, 2018 at 5:01 AM Martin Morgan
wrote:
> Further to this it is helpful to ensure that you are using the correct
> version of Bioconductor and that your packages are up-to-date
>
> BiocManager::version() == "3.8"
> BiocManager::valid()
>
> Martin
>
> On 11/5/18, 12:11 PM, "Bioc-devel on behalf of Mike Smith" <
> bioc-devel-boun...@r-project.org on behalf of grimbo...@gmail.com> wrote:
>
> Hi Ruqian,
>
> I think this is a consequence of your internal data.frames have column
> names that include the minus sign i.e. "-". The code clearly tries to
> deal
> with this by wrapping them in back-ticks at certain points, but I
> think it
> doesn't do this successfully in projectScoreLandscape()
>
> First, consider this example, which I think is a simplified version of
> what
> happens in plotScoreLandscape()
>
> df <- data.frame(x = 1:10, y = 1:10)
> colnames(df) <- c("tgca-EPI","tgca-MES")
> ggplot(df, aes_string("`tgca-EPI`", "`tgca-MES`")) +
> geom_point()
>
> For me this works & produces a plot where the axis labels include the
> backticks i.e. `tgca-EPI` and `tgca-EPI`
>
> Now we rename the columns of our data.frame to include the back-ticks,
> which is what happens when plabs = c(plotObj$labels$x,
> plotObj$labels$y) is
> called within projectScoreLandscape(). We plot in the same fashion and
> get
> an error similar to what you're seeing.
>
> colnames(df) <- c("`tgca-EPI`","`tgca-MES`")
> ggplot(df, aes_string("`tgca-EPI`", "`tgca-MES`")) +
> geom_point()
>
> Error in FUN(X[[i]], ...) : object 'tgca-EPI' not found
>
> Why this behavior would change I don't know, but presumably something
> in
> one of the tidyverse packages has led to this. You should probably
> investigate more, but if this is the problem then you can modify that
> plabs
> line in projectScoreLandscape() to strip the back-ticks. However,
> perhaps a
> more robust solution is to enforce the use of "_" rather than "-" in
> column
> names, that way you don't have to worry about using back-ticks to
> quote the
> non-syntactic names.
>
> Best regards,
>
> Mike
>
> On Mon, 5 Nov 2018 at 14:21, Ruqian Lyu <
> ruqi...@student.unimelb.edu.au>
> wrote:
>
> > Hi Bioconductor,
> >
> > I received a notification email regarding the building error for our
> > package 'singscore'.
> >
> > I pull the RELEASE_3_8 branch and checked/built on my local machine,
> it was
> > successful without errors.
> >
> > The error message was within the vignette which hasn't been updated
> for
> > several months.
> >
> > Would please help with identifying the problem?
> >
> > Thanks a lot!
> >
> > Best regards,
> > Ruqian
> >
> > -- Forwarded message -
> > From:
> > Date: Fri, Nov 2, 2018 at 12:14 AM
> > Subject: singscore problems reported in the Multiple platform
> build/check
> > report for BioC 3.8
> > To:
> >
> >
> > [This is an automatically generated email. Please don't reply.]
> >
> > Hi singscore maintainer,
> >
> > According to the Multiple platform build/check report for BioC 3.8,
> > the singscore package has the following problem(s):
> >
> > o ERROR for 'R CMD build' on malbec1. See the details here:
> >
> >
> >
> https://master.bioconductor.org/checkResults/3.8/bioc-LATEST/singscore/malbec1-buildsrc.html
> >
> > Please take the time to address this by committing and pushing
> > changes to your package at git.bioconductor.org
> >
> > Notes:
> >
> > * This was the status of your package at the time this email was
> sent to
> > you.
> > Given that the online report is updated daily (in normal
> conditions)
> > you
> > could see something different when you visit the URL(s) above,
> > especially if
> > you do so several days after you received this email.
> >
> > * It is possible that the problems reported in this report are
> false
> > positives,
> > either because another package (from CRAN or Bioconductor)
> breaks your
> > package (if yours depends on it) or because of a Build System
> problem.
> > If this is the case, then you can ignore this email.
> >
> > * Please check the report again 24h after you've committed your
> changes
> > to the
> > package and make sure that all the problems have gone.
> >
> > * If you have questions about this report or need help with the
> > maintenance of your package, please use the Bioc-devel mailing
> list:
> >
> > https://bioconductor.org/help/mailing-list/
> >
> > (all package maintainers are requested to subscribe to this list)
> >
> > For immediate notification of
Re: [Bioc-devel] How would you identify a package causing a NAMESPACE issue that you don't depend on in your DESCRIPTION/NAMESPACE?
For the general problem of understanding your package dependency structure,
see http://bioconductor.org/packages/release/bioc/html/pkgDepTools.html.
On Mon, Nov 5, 2018 at 3:44 PM Martin Morgan
wrote:
>
>
> On 11/5/18, 5:11 PM, "Bioc-devel on behalf of Leonardo Collado Torres" <
> bioc-devel-boun...@r-project.org on behalf of lcoll...@jhu.edu> wrote:
>
> Hi bioc-devel,
>
> recount is getting a warning on Bioc 3.9 (devel) on macOS:
>
> * checking whether package ‘recount’ can be installed ... WARNING
> Found the following significant warnings:
> Warning: S3 method ‘xts::as.xts.data.table’ was declared in
> NAMESPACE but not found
>
> I'm not sure how to trace this since recount doesn't depend on xts. At
> least not directly. What is the best way to find which of the recount
> dependencies is triggering this NAMESPACE warning? While it's a
> warning in this case, it seems to break the installation of the GitHub
> package LieberInstitute/recount.bwtool as shown below.
>
> Can you reproduce this warning when you load recount in a new session? If
> so, you can
>
> options(warn = 2) # make them errors
> trace(registerS3methods, tracer = quote(print(package)))
> library(recount)
>
> which will print out each package as it is loaded, the last being printed
> is the culprit.
>
> This failed a problem for me, but on the builder I see
>
> Tracing registerS3methods(nsInfo$S3methods, package, env) on entry
> [1] "data.table"
> Error: package or namespace load failed for ‘recount’:
> (converted from warning) S3 method ‘xts::as.xts.data.table’ was declared
> in NAMESPACE but not found
>
> The builder has
>
> > packageVersion("xts")
> [1] ‘0.11.1’
>
> whereas I have 0.11.2. The reason is because my R installs xts from source
> where the most recent version is 0.11.2, whereas the builder plays like
> most mac users and installs built binaries. The last mac binary available
> is 0.11.1, as summarized here:
>
> https://cran.r-project.org/web/packages/xts/index.html
>
> where the Published date is 2018-11-05 (today!) and where the binaries are
> 0.11.1 but source is 0.11.2.
>
> A further complexity is that there are NO MAC BINARIES for R-devel so
> basically the build machine is stuck with this situation until the mac
> binaries become available... when binaries become available would be a
> question for the R-sig-mac mailing list, though likely it has been asked /
> answered there before...
>
> Martin
>
> Anyhow, I might just wait a while as was recommended in another thread
> https://stat.ethz.ch/pipermail/bioc-devel/2018-November/014263.html.
> I'm assuming that there are no recount.bwtool R 3.6 macOS users :P
> Though it's worrisome if a package can't depend on recount right now
> on R 3.6 / Bioc 3.9.
>
> Thanks,
> Leo
>
> Main links:
>
> *
> https://bioconductor.org/checkResults/3.9/bioc-LATEST/recount/merida2-checksrc.html
> * https://github.com/leekgroup/recount
> * https://github.com/LieberInstitute/recount.bwtool
>
> Full info:
>
> > library('devtools')
> > install_github('LieberInstitute/recount.bwtool')
> Downloading GitHub repo LieberInstitute/recount.bwtool@master
> Skipping 28 packages ahead of CRAN: AnnotationDbi, Biobase,
> BiocGenerics, BiocParallel, biomaRt, Biostrings, BSgenome,
> DelayedArray, derfinder, derfinderHelper, GenomeInfoDb,
> GenomeInfoDbData, GenomicAlignments, GenomicFeatures, GenomicFiles,
> GenomicRanges, GEOquery, IRanges, limma, qvalue, recount, Rsamtools,
> rtracklayer, S4Vectors, SummarizedExperiment, VariantAnnotation,
> XVector, zlibbioc
> ✔ checking for file
>
> ‘/private/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T/Rtmp8Ho5Vh/remotes85e95180016e/LieberInstitute-recount.bwtool-0de3145/DESCRIPTION’
> (350ms)
> ─ preparing ‘recount.bwtool’:
> ✔ checking DESCRIPTION meta-information ...
> ─ checking for LF line-endings in source and make files and shell
> scripts
> ─ checking for empty or unneeded directories
> ─ building ‘recount.bwtool_0.99.29.tar.gz’
>
> Loading required package: colorout
> * installing *source* package ‘recount.bwtool’ ...
> ** R
> ** inst
> ** byte-compile and prepare package for lazy loading
> Error: package or namespace load failed for ‘recount’:
> (converted from warning) S3 method ‘xts::as.xts.data.table’ was
> declared in NAMESPACE but not found
> Error : package ‘recount’ could not be loaded
> ERROR: lazy loading failed for package ‘recount.bwtool’
> * removing
> ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/recount.bwtool’
> Error in i.p(...) :
> (converted from warning) installation of package
>
> ‘/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//Rtmp8Ho5Vh/file85e92ade068f/recount.bwtool_0.99.29.tar.gz’
> had non-zero exit status
> > traceback()
> 20: doWithOneRestart(return(expr), restart)
Re: [Bioc-devel] How would you identify a package causing a NAMESPACE issue that you don't depend on in your DESCRIPTION/NAMESPACE?
On 11/5/18, 5:11 PM, "Bioc-devel on behalf of Leonardo Collado Torres"
wrote:
Hi bioc-devel,
recount is getting a warning on Bioc 3.9 (devel) on macOS:
* checking whether package ‘recount’ can be installed ... WARNING
Found the following significant warnings:
Warning: S3 method ‘xts::as.xts.data.table’ was declared in
NAMESPACE but not found
I'm not sure how to trace this since recount doesn't depend on xts. At
least not directly. What is the best way to find which of the recount
dependencies is triggering this NAMESPACE warning? While it's a
warning in this case, it seems to break the installation of the GitHub
package LieberInstitute/recount.bwtool as shown below.
Can you reproduce this warning when you load recount in a new session? If so,
you can
options(warn = 2) # make them errors
trace(registerS3methods, tracer = quote(print(package)))
library(recount)
which will print out each package as it is loaded, the last being printed is
the culprit.
This failed a problem for me, but on the builder I see
Tracing registerS3methods(nsInfo$S3methods, package, env) on entry
[1] "data.table"
Error: package or namespace load failed for ‘recount’:
(converted from warning) S3 method ‘xts::as.xts.data.table’ was declared in
NAMESPACE but not found
The builder has
> packageVersion("xts")
[1] ‘0.11.1’
whereas I have 0.11.2. The reason is because my R installs xts from source
where the most recent version is 0.11.2, whereas the builder plays like most
mac users and installs built binaries. The last mac binary available is 0.11.1,
as summarized here:
https://cran.r-project.org/web/packages/xts/index.html
where the Published date is 2018-11-05 (today!) and where the binaries are
0.11.1 but source is 0.11.2.
A further complexity is that there are NO MAC BINARIES for R-devel so basically
the build machine is stuck with this situation until the mac binaries become
available... when binaries become available would be a question for the
R-sig-mac mailing list, though likely it has been asked / answered there
before...
Martin
Anyhow, I might just wait a while as was recommended in another thread
https://stat.ethz.ch/pipermail/bioc-devel/2018-November/014263.html.
I'm assuming that there are no recount.bwtool R 3.6 macOS users :P
Though it's worrisome if a package can't depend on recount right now
on R 3.6 / Bioc 3.9.
Thanks,
Leo
Main links:
*
https://bioconductor.org/checkResults/3.9/bioc-LATEST/recount/merida2-checksrc.html
* https://github.com/leekgroup/recount
* https://github.com/LieberInstitute/recount.bwtool
Full info:
> library('devtools')
> install_github('LieberInstitute/recount.bwtool')
Downloading GitHub repo LieberInstitute/recount.bwtool@master
Skipping 28 packages ahead of CRAN: AnnotationDbi, Biobase,
BiocGenerics, BiocParallel, biomaRt, Biostrings, BSgenome,
DelayedArray, derfinder, derfinderHelper, GenomeInfoDb,
GenomeInfoDbData, GenomicAlignments, GenomicFeatures, GenomicFiles,
GenomicRanges, GEOquery, IRanges, limma, qvalue, recount, Rsamtools,
rtracklayer, S4Vectors, SummarizedExperiment, VariantAnnotation,
XVector, zlibbioc
✔ checking for file
‘/private/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T/Rtmp8Ho5Vh/remotes85e95180016e/LieberInstitute-recount.bwtool-0de3145/DESCRIPTION’
(350ms)
─ preparing ‘recount.bwtool’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘recount.bwtool_0.99.29.tar.gz’
Loading required package: colorout
* installing *source* package ‘recount.bwtool’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘recount’:
(converted from warning) S3 method ‘xts::as.xts.data.table’ was
declared in NAMESPACE but not found
Error : package ‘recount’ could not be loaded
ERROR: lazy loading failed for package ‘recount.bwtool’
* removing
‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/recount.bwtool’
Error in i.p(...) :
(converted from warning) installation of package
‘/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//Rtmp8Ho5Vh/file85e92ade068f/recount.bwtool_0.99.29.tar.gz’
had non-zero exit status
> traceback()
20: doWithOneRestart(return(expr), restart)
19: withOneRestart(expr, restarts[[1L]])
18: withRestarts({
.Internal(.signalCondition(simpleWarning(msg, call), msg,
call))
.Internal(.dfltWarn(msg, call))
}, muffleWarning = function() NULL)
17: .signalSimpleWarning("installation of package
‘/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//Rtmp8Ho5Vh/file85e92ade068f/recount.bwtool_0.99.29.tar.gz’
Re: [Bioc-devel] Request upstream pull --force of sanitized master branch
Thanks for fixing this Nitesh and Sam!
I wrote that R check and forgot that it depended on the Gencode url. I
had to fix this too for recount
https://github.com/leekgroup/recount/commit/056e81c326143e3748b452988ac15a6bed3b035e.
Best,
Leo
On Mon, Nov 5, 2018 at 3:14 PM Turaga, Nitesh
wrote:
>
> Hi Sam,
>
> I fixed the RELEASE_3_8 branch as well. There was a minor discrepancy in the
> commit history for RELEASE_3_8 though, (which I fixed in
> git.bioconductor.org/packages/bumphunter) so you should resync RELEASE_3_8 in
> rafalab/bumphunter.
>
> The commit history on rafalab/bumphunter:RELEASE_3_8 looks like this,
>
> 7437f04 Apply interval bugfix to sanitized master branch
> a58c60a bump x.y.z versions to odd y after creation of RELEASE_3_8
> branch
> 3d4f308 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
>
> The commit showing "bump x.y.z versions to odd y after creation of
> RELEASE_3_8 branch” should not be in the RELEASE_3_8 branch. The version
> number in the RELEASE_3_8 branch should have an “even” Y, in the X.Y.Z
> version numbering scheme.
>
> After fixing your RELEASE_3_8 branch now looks like this,
>
> 96fd715 Bump version after cherry-picking bug fix,
> ac34111 Apply interval bugfix to sanitized master branch
> 3d4f308 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
>
> Please sync your RELEASE_3_8 branch on GitHub as well. “bumphunter" should
> now build on RELEASE_3_8 if the fix works.
>
> NOTE: After a push is made it can take up to 48 hours for it to
> appear on the build report and landing pages - i.e. we do one pull,
> build, check, propagate in 24 hours - so if your commit was after the pull
> for the day it wont be until the following day
>
>
> Best,
>
> Nitesh
>
>
> > On Nov 5, 2018, at 2:56 PM, Samuela Pollack
> > wrote:
> >
> > Hi Nitesh,
> >
> > I have fixed the commit history for rafalab/bumphunter RELEASE_3_8 branch,
> > and request synchronization with Bioconductor RELEASE_3_8. We need this,
> > because bumphunter is not building on RELEASE_3_8, due to an obsolete URL
> > in one of the tests.
> >
> > thanks,
> >
> > - Sam
> >
> >
> > On 11/5/18 7:56 AM, Turaga, Nitesh wrote:
> >> External Email - Use Caution
> >>
> >> Hi Sam,
> >>
> >> I have updated your “master” branch on git.bioconductor.com to reflect
> >> what you have on GitHub, at https://github.com/rafalab/bumphunter. You
> >> will not get the duplicate commit error when you push to the master branch
> >> anymore.
> >>
> >> However, RELEASE_3_8 still has duplicate commits in the history. You could
> >> follow the same procedure as you did for the master branch, and
> >> de-duplicate the commit history for RELEASE_3_8. You should invest time in
> >> this only if you think there will be any changes made to the release
> >> branch. If not, then this is not an issue. If you do choose to follow
> >> through with RELEASE_3_8 as well, please reply to this thread when you
> >> have made the de-duplication changes and added the branch to your GitHub
> >> repository.
> >>
> >> Best regards,
> >>
> >> Nitesh
> >>
> >>> On Nov 2, 2018, at 5:09 PM, Samuela Pollack
> >>> wrote:
> >>>
> >>> Dear Bioconductor,
> >>>
> >>> I believe I have removed all duplicate commits from the bumphunter
> >>> package. The main branch in rafalab/bumphunter incorporates the new
> >>> commit history. It passes 'library(devtools); build("."); install();
> >>> check("."); BiocCheck(".")'
> >>>
> >>> I am contacting you in accordance with item 6 of the instructions at this
> >>> URL:
> >>> http://bioconductor.org/developers/how-to/git/resolve-duplicate-commits/
> >>>
> >>> - Sam
> >>>
> >>> ___
> >>> Bioc-devel@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.
> ___
> Bioc-devel@r-project.org mailing list
[Bioc-devel] RFC: Bioc repository for single-version packages
This is a continuation of the discussion at
https://support.bioconductor.org/p/114814/#114824
Where Wolfgang asks about "creating a corner in the Bioconductor package
ecosystem for packages that are only ever supposed to build and check with a
single release"
I think this would be quite challenging to implement correctly, for instance
ensuring that the user of an appropriate version of R can easily install the
intended dependencies, and what exactly it means for a package to be restricted
to a single release, e.g., CRAN packages are updated without versioned releases
[I mean, a user of Bioc 3.7 will get the current version of the CRAN package,
not the version that was available at the (beginning or end) of the 3.7
release], so presumably the idea is that there is a snapshot of package
versions that one requires. This part sounds as much like a job for packrat /
switchr etc. Maybe 'our' job is to ensure that the appropriate information is
discoverable?
I took as an example the defunct package BioMedR. Our friend google
("Bioconductor BioMedR") took me to the last-known-good landing page (initially
by way of a mirror in Japan...). The DOI on the (bioconductor.org version) of
that page took me to the 'Removed packages' (
https://bioconductor.org/about/removed-packages/ ) page, which again points to
the last-known-good page. Likewise https://bioconductor.org/packages/BioMedR .
The 'In bioc since' tag on the 'last-known-good' page allowed me to find the
version of Bioconductor where the package was introduced. With some work I can
find the AMI (https://bioconductor.org/help/bioconductor-cloud-ami/ ) and
docker images (https://hub.docker.com/r/bioconductor/release_base2/tags/ ) for
that release of Bioconductor; neither of these would be sufficient for
reproducibility (I could get relevant Bioconductor package versions simply
installing the package from our archive via BiocInstaller / BiocManager, but R
packages would be more challenging). The package has a (impressively
extensive!) vignette, but the vignette does not include sessionInfo() so one
has to do considerable extra work to find the relevant packages. Again maybe
packrat / switchr help with this...
I think 'incoming' versions of such packages would go through the usual review
process, in an attempt to hue to some sort of overall Bioconductor standard of
quality; the return on this investment would be limited by the short intended
shelf-life of the package. These packages often have unique considerations,
too, e.g., 'large' data and long build times, maintainer concerns about when
the package is released relative to publication, etc. Also of interest would be
commitment to the actual data storage and transfer costs and to the management
costs of this type of package, coupled with appropriate consideration on scope
of the repository (not just the Bioconductor cognoscenti, presumably) and
advertising of availability e.g., via
https://www.nature.com/sdata/policies/repositories .
Contemplating this type of package repository suggests a number of small items
that provide 'cosmetic' improvements to the current situation (e.g., the
removed-packages page could be organized in a tabular fashion to include from /
to versions); a more meaningful attempt would probably require efforts to
embrace packrat / switchr to avoid reinventing the reproducibility wheel, as
well as commitment to reviewing and managing these packages for their long-term
contribution. These are certainly noble goals and align with Bioconductor's
emphasis on reproducibility; is this something that rises to the level of
securing separate funding?
Martin
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] How would you identify a package causing a NAMESPACE issue that you don't depend on in your DESCRIPTION/NAMESPACE?
Hi bioc-devel,
recount is getting a warning on Bioc 3.9 (devel) on macOS:
* checking whether package ‘recount’ can be installed ... WARNING
Found the following significant warnings:
Warning: S3 method ‘xts::as.xts.data.table’ was declared in
NAMESPACE but not found
I'm not sure how to trace this since recount doesn't depend on xts. At
least not directly. What is the best way to find which of the recount
dependencies is triggering this NAMESPACE warning? While it's a
warning in this case, it seems to break the installation of the GitHub
package LieberInstitute/recount.bwtool as shown below.
Anyhow, I might just wait a while as was recommended in another thread
https://stat.ethz.ch/pipermail/bioc-devel/2018-November/014263.html.
I'm assuming that there are no recount.bwtool R 3.6 macOS users :P
Though it's worrisome if a package can't depend on recount right now
on R 3.6 / Bioc 3.9.
Thanks,
Leo
Main links:
*
https://bioconductor.org/checkResults/3.9/bioc-LATEST/recount/merida2-checksrc.html
* https://github.com/leekgroup/recount
* https://github.com/LieberInstitute/recount.bwtool
Full info:
> library('devtools')
> install_github('LieberInstitute/recount.bwtool')
Downloading GitHub repo LieberInstitute/recount.bwtool@master
Skipping 28 packages ahead of CRAN: AnnotationDbi, Biobase,
BiocGenerics, BiocParallel, biomaRt, Biostrings, BSgenome,
DelayedArray, derfinder, derfinderHelper, GenomeInfoDb,
GenomeInfoDbData, GenomicAlignments, GenomicFeatures, GenomicFiles,
GenomicRanges, GEOquery, IRanges, limma, qvalue, recount, Rsamtools,
rtracklayer, S4Vectors, SummarizedExperiment, VariantAnnotation,
XVector, zlibbioc
✔ checking for file
‘/private/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T/Rtmp8Ho5Vh/remotes85e95180016e/LieberInstitute-recount.bwtool-0de3145/DESCRIPTION’
(350ms)
─ preparing ‘recount.bwtool’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘recount.bwtool_0.99.29.tar.gz’
Loading required package: colorout
* installing *source* package ‘recount.bwtool’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘recount’:
(converted from warning) S3 method ‘xts::as.xts.data.table’ was
declared in NAMESPACE but not found
Error : package ‘recount’ could not be loaded
ERROR: lazy loading failed for package ‘recount.bwtool’
* removing
‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/recount.bwtool’
Error in i.p(...) :
(converted from warning) installation of package
‘/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//Rtmp8Ho5Vh/file85e92ade068f/recount.bwtool_0.99.29.tar.gz’
had non-zero exit status
> traceback()
20: doWithOneRestart(return(expr), restart)
19: withOneRestart(expr, restarts[[1L]])
18: withRestarts({
.Internal(.signalCondition(simpleWarning(msg, call), msg,
call))
.Internal(.dfltWarn(msg, call))
}, muffleWarning = function() NULL)
17: .signalSimpleWarning("installation of package
‘/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//Rtmp8Ho5Vh/file85e92ade068f/recount.bwtool_0.99.29.tar.gz’
had non-zero exit status",
base::quote(i.p(...)))
16: warning(gettextf("installation of package %s had non-zero exit status",
sQuote(update[i, 1L])), domain = NA)
15: i.p(...)
14: force(code)
13: force(code)
12: with_envvar(c(R_PROFILE_USER = temp_rprofile), {
force(code)
})
11: with_rprofile_user("options(warn = 2)", i.p(...))
10: force(code)
9: with_options(list(warn = 2), with_rprofile_user("options(warn = 2)",
i.p(...)))
8: force(code)
7: with_envvar(c(R_LIBS = lib, R_LIBS_USER = lib, R_LIBS_SITE = lib),
if (should_error_for_warnings()) {
with_options(list(warn = 2), with_rprofile_user("options(warn = 2)",
i.p(...)))
} else {
i.p(...)
})
6: safe_install_packages(pkgdir, repos = NULL, quiet = quiet, type = "source",
...)
5: install(source, dependencies = dependencies, upgrade = upgrade,
force = force, quiet = quiet, build = build, build_opts = build_opts,
repos = repos, type = type, ...)
4: FUN(X[[i]], ...)
3: vapply(remotes, install_remote, ..., FUN.VALUE = character(1))
2: install_remotes(remotes, auth_token = auth_token, host = host,
dependencies = dependencies, upgrade = upgrade, force = force,
quiet = quiet, build = build, build_opts = build_opts, repos = repos,
type = type, ...)
1: install_github("LieberInstitute/recount.bwtool")
> library('recount')
Warning message:
S3 method ‘xts::as.xts.data.table’ was declared in NAMESPACE but not found
> options(width = 120)
> sessioninfo::session_info()
─ Session info
───
setting value
version R Under development (unstable) (2018-11-02 r75540)
os macOS Mojave
Re: [Bioc-devel] Fwd: singscore problems reported in the Multiple platform build/check report for BioC 3.8
Further to this it is helpful to ensure that you are using the correct version
of Bioconductor and that your packages are up-to-date
BiocManager::version() == "3.8"
BiocManager::valid()
Martin
On 11/5/18, 12:11 PM, "Bioc-devel on behalf of Mike Smith"
wrote:
Hi Ruqian,
I think this is a consequence of your internal data.frames have column
names that include the minus sign i.e. "-". The code clearly tries to deal
with this by wrapping them in back-ticks at certain points, but I think it
doesn't do this successfully in projectScoreLandscape()
First, consider this example, which I think is a simplified version of what
happens in plotScoreLandscape()
df <- data.frame(x = 1:10, y = 1:10)
colnames(df) <- c("tgca-EPI","tgca-MES")
ggplot(df, aes_string("`tgca-EPI`", "`tgca-MES`")) +
geom_point()
For me this works & produces a plot where the axis labels include the
backticks i.e. `tgca-EPI` and `tgca-EPI`
Now we rename the columns of our data.frame to include the back-ticks,
which is what happens when plabs = c(plotObj$labels$x, plotObj$labels$y) is
called within projectScoreLandscape(). We plot in the same fashion and get
an error similar to what you're seeing.
colnames(df) <- c("`tgca-EPI`","`tgca-MES`")
ggplot(df, aes_string("`tgca-EPI`", "`tgca-MES`")) +
geom_point()
Error in FUN(X[[i]], ...) : object 'tgca-EPI' not found
Why this behavior would change I don't know, but presumably something in
one of the tidyverse packages has led to this. You should probably
investigate more, but if this is the problem then you can modify that plabs
line in projectScoreLandscape() to strip the back-ticks. However, perhaps a
more robust solution is to enforce the use of "_" rather than "-" in column
names, that way you don't have to worry about using back-ticks to quote the
non-syntactic names.
Best regards,
Mike
On Mon, 5 Nov 2018 at 14:21, Ruqian Lyu
wrote:
> Hi Bioconductor,
>
> I received a notification email regarding the building error for our
> package 'singscore'.
>
> I pull the RELEASE_3_8 branch and checked/built on my local machine, it
was
> successful without errors.
>
> The error message was within the vignette which hasn't been updated for
> several months.
>
> Would please help with identifying the problem?
>
> Thanks a lot!
>
> Best regards,
> Ruqian
>
> -- Forwarded message -
> From:
> Date: Fri, Nov 2, 2018 at 12:14 AM
> Subject: singscore problems reported in the Multiple platform build/check
> report for BioC 3.8
> To:
>
>
> [This is an automatically generated email. Please don't reply.]
>
> Hi singscore maintainer,
>
> According to the Multiple platform build/check report for BioC 3.8,
> the singscore package has the following problem(s):
>
> o ERROR for 'R CMD build' on malbec1. See the details here:
>
>
>
https://master.bioconductor.org/checkResults/3.8/bioc-LATEST/singscore/malbec1-buildsrc.html
>
> Please take the time to address this by committing and pushing
> changes to your package at git.bioconductor.org
>
> Notes:
>
> * This was the status of your package at the time this email was sent to
> you.
> Given that the online report is updated daily (in normal conditions)
> you
> could see something different when you visit the URL(s) above,
> especially if
> you do so several days after you received this email.
>
> * It is possible that the problems reported in this report are false
> positives,
> either because another package (from CRAN or Bioconductor) breaks your
> package (if yours depends on it) or because of a Build System problem.
> If this is the case, then you can ignore this email.
>
> * Please check the report again 24h after you've committed your changes
> to the
> package and make sure that all the problems have gone.
>
> * If you have questions about this report or need help with the
> maintenance of your package, please use the Bioc-devel mailing list:
>
> https://bioconductor.org/help/mailing-list/
>
> (all package maintainers are requested to subscribe to this list)
>
> For immediate notification of package build status, please
> subscribe to your package's RSS feed. Information is at:
>
> https://bioconductor.org/developers/rss-feeds/
>
> Thanks for contributing to the Bioconductor project!
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
Re: [Bioc-devel] Request upstream pull --force of sanitized master branch
Hi Sam,
I fixed the RELEASE_3_8 branch as well. There was a minor discrepancy in the
commit history for RELEASE_3_8 though, (which I fixed in
git.bioconductor.org/packages/bumphunter) so you should resync RELEASE_3_8 in
rafalab/bumphunter.
The commit history on rafalab/bumphunter:RELEASE_3_8 looks like this,
7437f04 Apply interval bugfix to sanitized master branch
a58c60a bump x.y.z versions to odd y after creation of RELEASE_3_8
branch
3d4f308 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
The commit showing "bump x.y.z versions to odd y after creation of RELEASE_3_8
branch” should not be in the RELEASE_3_8 branch. The version number in the
RELEASE_3_8 branch should have an “even” Y, in the X.Y.Z version numbering
scheme.
After fixing your RELEASE_3_8 branch now looks like this,
96fd715 Bump version after cherry-picking bug fix,
ac34111 Apply interval bugfix to sanitized master branch
3d4f308 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
Please sync your RELEASE_3_8 branch on GitHub as well. “bumphunter" should now
build on RELEASE_3_8 if the fix works.
NOTE: After a push is made it can take up to 48 hours for it to
appear on the build report and landing pages - i.e. we do one pull,
build, check, propagate in 24 hours - so if your commit was after the pull
for the day it wont be until the following day
Best,
Nitesh
> On Nov 5, 2018, at 2:56 PM, Samuela Pollack
> wrote:
>
> Hi Nitesh,
>
> I have fixed the commit history for rafalab/bumphunter RELEASE_3_8 branch,
> and request synchronization with Bioconductor RELEASE_3_8. We need this,
> because bumphunter is not building on RELEASE_3_8, due to an obsolete URL in
> one of the tests.
>
> thanks,
>
> - Sam
>
>
> On 11/5/18 7:56 AM, Turaga, Nitesh wrote:
>> External Email - Use Caution
>>
>> Hi Sam,
>>
>> I have updated your “master” branch on git.bioconductor.com to reflect what
>> you have on GitHub, at https://github.com/rafalab/bumphunter. You will not
>> get the duplicate commit error when you push to the master branch anymore.
>>
>> However, RELEASE_3_8 still has duplicate commits in the history. You could
>> follow the same procedure as you did for the master branch, and de-duplicate
>> the commit history for RELEASE_3_8. You should invest time in this only if
>> you think there will be any changes made to the release branch. If not, then
>> this is not an issue. If you do choose to follow through with RELEASE_3_8 as
>> well, please reply to this thread when you have made the de-duplication
>> changes and added the branch to your GitHub repository.
>>
>> Best regards,
>>
>> Nitesh
>>
>>> On Nov 2, 2018, at 5:09 PM, Samuela Pollack
>>> wrote:
>>>
>>> Dear Bioconductor,
>>>
>>> I believe I have removed all duplicate commits from the bumphunter package.
>>> The main branch in rafalab/bumphunter incorporates the new commit history.
>>> It passes 'library(devtools); build("."); install(); check(".");
>>> BiocCheck(".")'
>>>
>>> I am contacting you in accordance with item 6 of the instructions at this
>>> URL:
>>> http://bioconductor.org/developers/how-to/git/resolve-duplicate-commits/
>>>
>>> - Sam
>>>
>>> ___
>>> Bioc-devel@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.
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Re: [Bioc-devel] Request upstream pull --force of sanitized master branch
Hi Nitesh,
I have fixed the commit history for rafalab/bumphunter RELEASE_3_8
branch, and request synchronization with Bioconductor RELEASE_3_8. We
need this, because bumphunter is not building on RELEASE_3_8, due to an
obsolete URL in one of the tests.
thanks,
- Sam
On 11/5/18 7:56 AM, Turaga, Nitesh wrote:
External Email - Use Caution
Hi Sam,
I have updated your “master” branch on git.bioconductor.com to reflect what you
have on GitHub, at https://github.com/rafalab/bumphunter. You will not get the
duplicate commit error when you push to the master branch anymore.
However, RELEASE_3_8 still has duplicate commits in the history. You could
follow the same procedure as you did for the master branch, and de-duplicate
the commit history for RELEASE_3_8. You should invest time in this only if you
think there will be any changes made to the release branch. If not, then this
is not an issue. If you do choose to follow through with RELEASE_3_8 as well,
please reply to this thread when you have made the de-duplication changes and
added the branch to your GitHub repository.
Best regards,
Nitesh
On Nov 2, 2018, at 5:09 PM, Samuela Pollack wrote:
Dear Bioconductor,
I believe I have removed all duplicate commits from the bumphunter package. The main branch in
rafalab/bumphunter incorporates the new commit history. It passes 'library(devtools); build(".");
install(); check("."); BiocCheck(".")'
I am contacting you in accordance with item 6 of the instructions at this URL:
http://bioconductor.org/developers/how-to/git/resolve-duplicate-commits/
- Sam
___
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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.
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Re: [Bioc-devel] Fwd: singscore problems reported in the Multiple platform build/check report for BioC 3.8
Hi Ruqian,
I think this is a consequence of your internal data.frames have column
names that include the minus sign i.e. "-". The code clearly tries to deal
with this by wrapping them in back-ticks at certain points, but I think it
doesn't do this successfully in projectScoreLandscape()
First, consider this example, which I think is a simplified version of what
happens in plotScoreLandscape()
df <- data.frame(x = 1:10, y = 1:10)
colnames(df) <- c("tgca-EPI","tgca-MES")
ggplot(df, aes_string("`tgca-EPI`", "`tgca-MES`")) +
geom_point()
For me this works & produces a plot where the axis labels include the
backticks i.e. `tgca-EPI` and `tgca-EPI`
Now we rename the columns of our data.frame to include the back-ticks,
which is what happens when plabs = c(plotObj$labels$x, plotObj$labels$y) is
called within projectScoreLandscape(). We plot in the same fashion and get
an error similar to what you're seeing.
colnames(df) <- c("`tgca-EPI`","`tgca-MES`")
ggplot(df, aes_string("`tgca-EPI`", "`tgca-MES`")) +
geom_point()
Error in FUN(X[[i]], ...) : object 'tgca-EPI' not found
Why this behavior would change I don't know, but presumably something in
one of the tidyverse packages has led to this. You should probably
investigate more, but if this is the problem then you can modify that plabs
line in projectScoreLandscape() to strip the back-ticks. However, perhaps a
more robust solution is to enforce the use of "_" rather than "-" in column
names, that way you don't have to worry about using back-ticks to quote the
non-syntactic names.
Best regards,
Mike
On Mon, 5 Nov 2018 at 14:21, Ruqian Lyu
wrote:
> Hi Bioconductor,
>
> I received a notification email regarding the building error for our
> package 'singscore'.
>
> I pull the RELEASE_3_8 branch and checked/built on my local machine, it was
> successful without errors.
>
> The error message was within the vignette which hasn't been updated for
> several months.
>
> Would please help with identifying the problem?
>
> Thanks a lot!
>
> Best regards,
> Ruqian
>
> -- Forwarded message -
> From:
> Date: Fri, Nov 2, 2018 at 12:14 AM
> Subject: singscore problems reported in the Multiple platform build/check
> report for BioC 3.8
> To:
>
>
> [This is an automatically generated email. Please don't reply.]
>
> Hi singscore maintainer,
>
> According to the Multiple platform build/check report for BioC 3.8,
> the singscore package has the following problem(s):
>
> o ERROR for 'R CMD build' on malbec1. See the details here:
>
>
> https://master.bioconductor.org/checkResults/3.8/bioc-LATEST/singscore/malbec1-buildsrc.html
>
> Please take the time to address this by committing and pushing
> changes to your package at git.bioconductor.org
>
> Notes:
>
> * This was the status of your package at the time this email was sent to
> you.
> Given that the online report is updated daily (in normal conditions)
> you
> could see something different when you visit the URL(s) above,
> especially if
> you do so several days after you received this email.
>
> * It is possible that the problems reported in this report are false
> positives,
> either because another package (from CRAN or Bioconductor) breaks your
> package (if yours depends on it) or because of a Build System problem.
> If this is the case, then you can ignore this email.
>
> * Please check the report again 24h after you've committed your changes
> to the
> package and make sure that all the problems have gone.
>
> * If you have questions about this report or need help with the
> maintenance of your package, please use the Bioc-devel mailing list:
>
> https://bioconductor.org/help/mailing-list/
>
> (all package maintainers are requested to subscribe to this list)
>
> For immediate notification of package build status, please
> subscribe to your package's RSS feed. Information is at:
>
> https://bioconductor.org/developers/rss-feeds/
>
> Thanks for contributing to the Bioconductor project!
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
[[alternative HTML version deleted]]
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[Bioc-devel] Initial list of deprecated packages for 3.9
The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. The list will be updated monthly. The current list of deprecated packages for Bioc 3.9 is as follows: Maintainer requested deprecation: Software: flowQ Unresponsive/not-maintained packages: Software: ProCoNA Experiment Data Package: PGPC We will be sending emails out to packages that have been broken across all platforms for an extended period of time, and therefore are now broken in Bioconductor Release 3.8 and Bioconductor Devel 3.9, as those are packages that are up for immediate deprecation if not corrected in a timely fashion. Thank you Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 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. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] No curatedMetagenomicData build triggered
Thanks Val. Indeed, the release version built yesterday, but there still hasn't been a build on devel since Thursday. On Sat, Nov 3, 2018 at 10:12 PM Obenchain, Valerie < valerie.obench...@roswellpark.org> wrote: > Hi Levi, > > We've had one experimental data build since the release, posted on Nov > 1. Data experiment packages build on Tues, Thurs and Sun. Release should > continue to follow this schedule. > > The devel builds are taking a very long time to complete and overlapping > each other which means less dependable builds. Please see this post: > > https://stat.ethz.ch/pipermail/bioc-devel/2018-November/014281.html > > Valerie > > On 11/3/18 7:08 AM, Levi Waldron wrote: > > I remember now (I think) that experimental data packages are built on > > Wednesday and *Saturday* nights - in which case I’ll just check again > > tomorrow morning. > > > > On Sat, Nov 3, 2018 at 8:59 AM Levi Waldron > > > wrote: > > > >> curatedMetagenomicData hasn't built yet on the new release or devel. I > >> believe this was originally because the required ExperimentHub database > >> update occurred after the last curatedMetagenomicData version bump, but > >> since I bumped the version on Thursday it still hasn't built. Can you > >> advise? > >> > > > > 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. > -- Levi Waldron http://www.waldronlab.io Associate Professor of BiostatisticsCUNY School of Public Health US: +1 646-364-9616 Skype: levi.waldron [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Fwd: singscore problems reported in the Multiple platform build/check report for BioC 3.8
Hi Bioconductor, I received a notification email regarding the building error for our package 'singscore'. I pull the RELEASE_3_8 branch and checked/built on my local machine, it was successful without errors. The error message was within the vignette which hasn't been updated for several months. Would please help with identifying the problem? Thanks a lot! Best regards, Ruqian -- Forwarded message - From: Date: Fri, Nov 2, 2018 at 12:14 AM Subject: singscore problems reported in the Multiple platform build/check report for BioC 3.8 To: [This is an automatically generated email. Please don't reply.] Hi singscore maintainer, According to the Multiple platform build/check report for BioC 3.8, the singscore package has the following problem(s): o ERROR for 'R CMD build' on malbec1. See the details here: https://master.bioconductor.org/checkResults/3.8/bioc-LATEST/singscore/malbec1-buildsrc.html Please take the time to address this by committing and pushing changes to your package at git.bioconductor.org Notes: * This was the status of your package at the time this email was sent to you. Given that the online report is updated daily (in normal conditions) you could see something different when you visit the URL(s) above, especially if you do so several days after you received this email. * It is possible that the problems reported in this report are false positives, either because another package (from CRAN or Bioconductor) breaks your package (if yours depends on it) or because of a Build System problem. If this is the case, then you can ignore this email. * Please check the report again 24h after you've committed your changes to the package and make sure that all the problems have gone. * If you have questions about this report or need help with the maintenance of your package, please use the Bioc-devel mailing list: https://bioconductor.org/help/mailing-list/ (all package maintainers are requested to subscribe to this list) For immediate notification of package build status, please subscribe to your package's RSS feed. Information is at: https://bioconductor.org/developers/rss-feeds/ Thanks for contributing to the Bioconductor project! [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Request upstream pull --force of sanitized master branch
Hi Sam,
I have updated your “master” branch on git.bioconductor.com to reflect what you
have on GitHub, at https://github.com/rafalab/bumphunter. You will not get the
duplicate commit error when you push to the master branch anymore.
However, RELEASE_3_8 still has duplicate commits in the history. You could
follow the same procedure as you did for the master branch, and de-duplicate
the commit history for RELEASE_3_8. You should invest time in this only if you
think there will be any changes made to the release branch. If not, then this
is not an issue. If you do choose to follow through with RELEASE_3_8 as well,
please reply to this thread when you have made the de-duplication changes and
added the branch to your GitHub repository.
Best regards,
Nitesh
> On Nov 2, 2018, at 5:09 PM, Samuela Pollack
> wrote:
>
> Dear Bioconductor,
>
> I believe I have removed all duplicate commits from the bumphunter package.
> The main branch in rafalab/bumphunter incorporates the new commit history. It
> passes 'library(devtools); build("."); install(); check("."); BiocCheck(".")'
>
> I am contacting you in accordance with item 6 of the instructions at this
> URL: http://bioconductor.org/developers/how-to/git/resolve-duplicate-commits/
>
> - Sam
>
> ___
> Bioc-devel@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.
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