Re: [Bioc-devel] TADCompare, permissions denied
Thank you, solved. Another reminder that Docker containers don't have access to the ~/.ssh folder. Pushing from the local terminal after debugging in a container helps. Thanks, Mikhail On Wed, Feb 28, 2024 at 8:42 AM Kern, Lori wrote: > Everything looks correct on our configuration. You might need to add a > new ssh key to your BiocCredentials account. Or since there are multiple > keys on your account already, explicitly state the correct ssh key you > would like to use . > > > Lori Shepherd - Kern > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ------ > *From:* Bioc-devel on behalf of > Mikhail Dozmorov > *Sent:* Wednesday, February 28, 2024 8:36 AM > *To:* bioc-devel > *Subject:* [Bioc-devel] TADCompare, permissions denied > > I'm trying to push fixes for > > https://secure-web.cisco.com/1gTfFROxVBHZNIvNeHURcWxcDfldi3nsGs93V7hourmSWcnlL0k0cSLr_WO7fNoy78PEpV7edyoPDutmeTWRR6NYRBzNMRUi5DyN6tJTlu2C88HP4EfAj8UKHXIY9hsgcWgJf-rKfXc3DJJV-Oaqwzd3IDmchipQfFgOVHyAiGZMj2dmHBviUcN5aq4Bf5fnUfbp5fgDGQVXsMnN5GAuKqJaSbVeGypdoDLbqi_516zxe3M3axM6tINOkFCryo_vQ3ElgwoRGw3y3xkyCqjz1pvO-8ZkrW3h31QhX5S_9cR2lAiAfqBenSaWrBE24QOTb/https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.19%2Fbioc-LATEST%2FTADCompare%2Fnebbiolo1-buildsrc.html > git remote -v > biocg...@git.bioconductor.org:packages/TADCompare.git (fetch) > biocg...@git.bioconductor.org:packages/TADCompare.git (push) > > E.g., for git fetch --all, I'm getting > g...@git.bioconductor.org: Permission denied (publickey). > fatal: Could not read from remote repository. > > Please make sure you have the correct access rights > and the repository exists. > > Please, help > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > > https://secure-web.cisco.com/1zrnrjAuLh2883VT60Lg6sFcNRLWoedOXZxaVjzZh04ngw2Jst-kTU76L-TiOZpjhSwZwnQY7g2C4pZbmpGXkmyA8geudnab5jp-JPo1NJLDJVVuBZeB7-bV086eqHvGCzAdAEUv8b9v0l_lbtpsAoVODtqXJtJOuQclP8JdQzzZ1sFu8pD_VY8mXl_GweS2Y-ZxbKPuyR3sUD_vrBKw5koLWLqm8N_b8hWVh4J7tLg1C-XlHlb-hpj446L7H4BeNs-rbDTeVYkhkWcmCLrrwbNgAy4tovNjI4ltF5rz1-W2nYNL34ANi6QbnsEWbg-xy/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-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. > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] TADCompare, permissions denied
I'm trying to push fixes for https://master.bioconductor.org/checkResults/3.19/bioc-LATEST/TADCompare/nebbiolo1-buildsrc.html. git remote -v biocg...@git.bioconductor.org:packages/TADCompare.git (fetch) biocg...@git.bioconductor.org:packages/TADCompare.git (push) E.g., for git fetch --all, I'm getting g...@git.bioconductor.org: Permission denied (publickey). fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists. Please, help [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] CTCF annotation package's vignette not updating
Thank you, Lori. My understanding, a version bump for a data package won't trigger rebuild, but this branching process will. I'm still confused how to version data package updates (e.g., vignettes). Any attempt to bump version results in "Error: Illegal version bump" when pushing. Changes without version bump can be pushed. And, will probably be propagated by the manual branching process. Here is another example when the old vignette results in error when used in 3.16, but the new one is not showing up https://bioconductor.org/checkResults/3.16/data-annotation-LATEST/excluderanges/. I'll wait, hopefully this branching process will resolve these issues. It'll be great to clarify in the documentation. Thanks again, Mikhail On Mon, Nov 14, 2022 at 7:19 AM Kern, Lori wrote: > Annotation packages are slightly different - we don't automatically bump > the versions of annotations at release as it implies annotations were > updated when most of the time they are not. > > We also have not reimplemented the auto process of git hosted annotations > as we have to branch the annotations as part of the release process. Due to > the large number of packages that could be affected, we normally wait a > week or so to branch to allow the other release updates to settle. > > We plan to do this branching process today or tomorrow. After that time, > changes pushed to the git hosted annotation packages will be reflected in > weekly reports. > > I'm very sorry for the confusion and delay. > > > > Lori Shepherd - Kern > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > -- > *From:* Mikhail Dozmorov > *Sent:* Friday, November 11, 2022 10:30 AM > *To:* bioc-devel ; Kern, Lori > > *Subject:* Re: [Bioc-devel] CTCF annotation package's vignette not > updating > > It must be very simple, but I'm still unable to trigger the build - > confused by version numbering. CTCF had version 0.99.5 in BioC 3.15, > https://bioconductor.org/packages/3.15/data/annotation/html/CTCF.html > <https://secure-web.cisco.com/11SfcSGs4ZZwaIIwBqVkHeQD6vQ8L-EJ5yHoT-kyvApm8alpLidSDiL4dpxaUEApgk359bfZjYIJnfJLV-c_YbnCzFkDwEEpVMv6lst_Oxdsa4EMp0-K2yXrzvHIsOQaKsAyjLVjMdRcUfPlooUlkpbtPGeGk81FwgdAtctb74YrUyO7x7tlC-7vQPLXX1SGXV99macucJ99MPrxbBMmmBpvSvdEsQudyWeteavNitEWej_yK4apKO5Ot2oi1j32naCXToK9HKsA-DjZQFUK1lpOr2x1NohQhZTn2ukhmsqMLF-M0s4K6rOU_zvBVXtZc/https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.15%2Fdata%2Fannotation%2Fhtml%2FCTCF.html>. > According to guidelines > https://contributions.bioconductor.org/versionnum.html > <https://secure-web.cisco.com/1Ji55I99uGIxLYNCvStQt1WLoOMNm3ZlCvvBpZT093MnuWH5JDV98LX-tjZCKkauABSUs-PUD1bJlS7SIA5ANgYIKfmqqlTnUiQJsPANwECE0UjzRHeGoIwZu6-NluMMVycKpTGWO0wepCTpSBd99AdwzoFofsPvkSDj1ZxARHX4o1RQ1Wa-_cvUpW4l3CZwIu1b_Qy2W9mWOeSUODPqZCg1mNzVUnWZhy_vpuxp5oQkGvnXhBHt1LRrVhbr4fUR6pgnkYtuFn-N0ufZ_zLR2AoRdqYVNMZNLZ0EazjAX2Qj2rJqMIuLVrDdQC8ynzAFR/https%3A%2F%2Fcontributions.bioconductor.org%2Fversionnum.html>, > its version should be 1.0.0 in the next release, 3.16. But it shows 0.99.9, > https://bioconductor.org/packages/release/data/annotation/html/CTCF.html > <https://secure-web.cisco.com/1-HAas6uKczMa97dum6aDLNdzsZnXMYuveFVQxWaxDoh9rvacjeTs3WMAt0O-eooA8Q7FqZn9iArd1OukmW3s91CU0iBR52XyqSRfCUtGeJbBX7uVq2jyBBXnaAXhmCTwlyhs86eAyt3a0VjEgCmIh2VN1_EmtOvLuLAOmsq_h1IHeTluYvlnIdeaZJ2-eTf-39PvyLmko3WIhjQx1tMFS0J8TJUHZp0q83bFllBFnVJb-cTOPHxc_FXC1qc2xtJ8sSi-T3G0QqzGZVd6jROteWJoI-mo7RBbkqDpmqcsDvVWJ0nGqYl8Z4ywmNAyb63w/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fdata%2Fannotation%2Fhtml%2FCTCF.html>. > Incrementing "the z" part has no effect, even after waiting for Wednesday's > report update. Other attempts like setting the version to 1.0.0 fail with > "remote: Error: Illegal version bump" when pushing to the "RELEASE_3_16" > branch. Which version number should I set to trigger the build? > > Thanks, > Mikhail > > On Mon, Oct 31, 2022 at 7:22 AM Kern, Lori > wrote: > > Please remember that once accepted the packages are only built and > propagated on a particular schedule and not on demand. Annotation packages > that are in git are updated once a week. The schedule of the builds of > different packages can be found: > > http://bioconductor.org/checkResults/ > <http://secure-web.cisco.com/1cfqN3qMzaLQA1lWYolkIbhsv9WGMpsY66OEXdCIPzSd1yNFbBP6GSHrkzH7a9yKpkLvDUgpLeoHt_xuDF1W8xb-NbGK05m_bZCoi13PBtWmot0DSpYuEF0PxvfawZShy7WegFieevp6sGsT50v99SlhnhoufX6iwmLZdEpJxaUeuLZiDzDdzzuZQQipr73iDYOuHbMudvWrZiLm72n9kCzo73oAgvq42bBuYOVQ7GEgJIU9Z0jeK1EcWFF6WYcvDQzQ1-y4HY4nFhD_dkLC3zXUlQ4ElQR8EwtgBUhfHH1NRuEqg-Q64ozC7mMgJdHA_/http%3A%2F%2Fbioco
Re: [Bioc-devel] CTCF annotation package's vignette not updating
It must be very simple, but I'm still unable to trigger the build -
confused by version numbering. CTCF had version 0.99.5 in BioC 3.15,
https://bioconductor.org/packages/3.15/data/annotation/html/CTCF.html.
According to guidelines
https://contributions.bioconductor.org/versionnum.html, its version should
be 1.0.0 in the next release, 3.16. But it shows 0.99.9,
https://bioconductor.org/packages/release/data/annotation/html/CTCF.html.
Incrementing "the z" part has no effect, even after waiting for Wednesday's
report update. Other attempts like setting the version to 1.0.0 fail with
"remote: Error: Illegal version bump" when pushing to the "RELEASE_3_16"
branch. Which version number should I set to trigger the build?
Thanks,
Mikhail
On Mon, Oct 31, 2022 at 7:22 AM Kern, Lori
wrote:
> Please remember that once accepted the packages are only built and
> propagated on a particular schedule and not on demand. Annotation packages
> that are in git are updated once a week. The schedule of the builds of
> different packages can be found:
>
> http://bioconductor.org/checkResults/
>
> Vince is also correct. You will still be able to update 3.16 but after
> tomorrow it would have to be done on the RELEASE_3_16 branch and master
> (3.17) branch.
>
> Cheers,
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> ------
> *From:* Bioc-devel on behalf of
> Vincent Carey
> *Sent:* Sunday, October 30, 2022 9:13 PM
> *To:* Mikhail Dozmorov
> *Cc:* bioc-devel
> *Subject:* Re: [Bioc-devel] CTCF annotation package's vignette not
> updating
>
> Maybe I am wrong Mikhail but I think you have about 6 months to enhance the
> documentation of your package in 3.16.
>
> On Sun, Oct 30, 2022 at 7:54 PM Mikhail Dozmorov <
> mikhail.dozmo...@gmail.com>
> wrote:
>
> > Hello,
> > I'm trying to update documentation for the
> >
> https://secure-web.cisco.com/1p7VBteo2CRqcBZV-zNncaSH__4Q_rsUE7Tn2Jkq-yeqpCers_iPa5A4EytZziK_btn-kss-FCaAzY0CSPldbZubwnGgPQgU04BMpStqnTNklfw-_ddCnIOgtYwUAN6qdYRlypSYHUwSyBtC6gWj1hXZNcs55UpZ06-GtOnl0Lj9HrD_1VTmnUwEd5Q4iw4n-1jo6Z_u2Mfz-XXVjbbdRDbyVRbcybt2rJuElNK_pBimikAbulhNN-cB7Qi-FU22CPGSd2aflxOQ9NbzZ8zsTw5vmru5HNLzAizCcaBesTCiYcIgbNaEhmmQR4MHK060c/https%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2Fdata%2Fannotation%2Fhtml%2FCTCF.html
> > package so it can be shown in the 3.16 release. Pushed to bioc master
> > twice, with version bump. But the build is not triggered
> >
> https://secure-web.cisco.com/1sBV614NyVTESrurr0us0eF9hlgOxwbnKgjdZcAZHH3VbS8lsHGGEBUiZTaHOxgv8Fv2pVah4r-j1Roi7k0KRBrVF6DeQMeM43DlY5Ua4ovtWWhIWA6iy2CLp7SCH2VMVeL2h_jHVb8hOvDVA37A4Uz7QjD_tb7UWK5L4pemedIxxWDpoCQzaueRv4O-fjjz2gB4eqI8IrXNibaWEXrT0F0K7-QcTFZLpSsVP1OFHSCZKQw1rIA2vOjMSxZqEZlftwz_3SW507U8Z6rxaklHUWNOrX_SQK8F4x20XwQctLWVDW9RO2o2_pHumKAErweRB/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.16%2Fdata-annotation-LATEST%2FCTCF%2F
> > It
> > may be due to the 3.16 release schedule or something very simple, but I'm
> > trying to meet the October 31 1:30 pm EST deadline and running out of
> ideas
> > what to do to update the package.
> > Thanks,
> > Mikhail
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> >
> https://secure-web.cisco.com/1mueWKL3AMBjbkUJbDAqpWGLMWD-5Jsb_WUCt5eZZyzaY9qAg0iypSVjgckFNG0n3vlDSi5njIeMnl3aDgga-H4koSxK-E0Om-GewGInXGSWP8lQROFryCUI29Rds3DBhKrKKIyGrWI_3ZIHJynixzUzhU1pMpa3Kz1NIcEoCMvGXPfHCmBCCQa2A011_wb7rqUXGvevN9fYOBQBj6ILBcyBWfDAw2MA6GG9UOVa8tkotsOI4wWiZ8zkNj5lTx16Qa0KFb4JI1dvPyjye-WtMQBXCfFAOSKEGkHVjZJYJN3WP36NiiuDr7A0jY9JYfu5R/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
> >
>
> --
> The information in this e-mail is intended only for th...{{dropped:25}}
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[Bioc-devel] CTCF annotation package's vignette not updating
Hello, I'm trying to update documentation for the https://bioconductor.org/packages/devel/data/annotation/html/CTCF.html package so it can be shown in the 3.16 release. Pushed to bioc master twice, with version bump. But the build is not triggered https://bioconductor.org/checkResults/3.16/data-annotation-LATEST/CTCF/. It may be due to the 3.16 release schedule or something very simple, but I'm trying to meet the October 31 1:30 pm EST deadline and running out of ideas what to do to update the package. Thanks, Mikhail [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Maintainer change
Thank you, Nitesh, it worked. Best, Mikhail --- Mikhail Dozmorov, Ph.D. Department of Biostatistics, VCU On Mon, Jul 19, 2021 at 12:36 PM Nitesh Turaga wrote: > Hi Mikhail, > > You now have access to both packages. > > Please remove the previous maintainer in the DESCRIPTION file and add > yourself as the new maintainer. > > Best, > > Nitesh > > Nitesh Turaga > Scientist II, Department of Data Science, > Bioconductor Core Team Member > Dana Farber Cancer Institute > > > On Jul 18, 2021, at 8:48 PM, Mikhail Dozmorov < > mikhail.dozmo...@gmail.com> wrote: > > > > Please, add me, Mikhail Dozmorov, as a maintainer of the > > https://bioconductor.org/packages/preciseTAD/ and > > https://bioconductor.org/packages/preciseTADhub/ packages. The current > > maintainer cannot be reached. > > > > Thanks, > > Mikhail > > > > --- > > Mikhail Dozmorov, Ph.D. > > Department of Biostatistics, VCU > > > > [[alternative HTML version deleted]] > > > > ___ > > 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] Maintainer change
Please, add me, Mikhail Dozmorov, as a maintainer of the https://bioconductor.org/packages/preciseTAD/ and https://bioconductor.org/packages/preciseTADhub/ packages. The current maintainer cannot be reached. Thanks, Mikhail --- Mikhail Dozmorov, Ph.D. Department of Biostatistics, VCU [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] CTCF AnnotationHub package
I'm submitting the CTCF AnnotationHub package, https://github.com/mdozmorov/CTCF, with the coordinates of predicted CTCF binding sites as GRanges. The package builds on all OSs, passes AnnotationHubData:::makeAnnotationHubMetadata(). It has been submitted to the tracker, but was immediately closed https://github.com/Bioconductor/Contributions/issues/2108. Please, advise what to do next and how to upload the data to AWS S3? Thanks, Mikhail --- Mikhail Dozmorov, Ph.D. Department of Biostatistics, VCU E-mail: mdozmo...@vcu.edu [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Maintainer for preciseTAD
Hi, I noted our package https://bioconductor.org/packages/preciseTAD/ shows build error. This is because https://CRAN.R-project.org/package=DMwR was removed. Please, add me as a maintainer to the preciseTAD repo. Spiro should remain a maintainer, but he is getting harder to reach after graduation. Thanks, Mikhail --- Mikhail Dozmorov, Ph.D. Department of Biostatistics, VCU E-mail: mdozmo...@vcu.edu Phone: 804-827-2055 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Co-maintainer for SpectralTAD and TADCompare
Thank you, Nitesh. Currently, SpectralTAD and TADCompare packages are failing to build due to PRIMME package, the main dependence, has been removed from CRAN. The developers seem to address it, https://github.com/primme/primme/issues/38, but it may take a while for it to reappear. We are looking for options. If we need to do anything immediately for the failing packages, please, let know. Thanks, Mikhail On Mon, Oct 19, 2020 at 11:06 PM Nitesh Turaga wrote: > Hi Mikhail, > > You should have access to your packages now. > > Best, > > Nitesh > > On Oct 19, 2020, at 3:13 PM, Mikhail Dozmorov > wrote: > > Hello, > Would it be possible to add me as a co-maintainer to two packages? > https://bioconductor.org/packages/SpectralTAD/ > https://bioconductor.org/packages/TADCompare/ > > It'll be best if both Kellen, the current maintainer, and I will have push > access. > > Thanks, > Mikhail > > [[alternative HTML version deleted]] > > ___ > 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] Co-maintainer for SpectralTAD and TADCompare
Hello, Would it be possible to add me as a co-maintainer to two packages? https://bioconductor.org/packages/SpectralTAD/ https://bioconductor.org/packages/TADCompare/ It'll be best if both Kellen, the current maintainer, and I will have push access. Thanks, Mikhail [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] non-conformable arrays
I see it now and didn't catch because ran md5sum on the same folder. Not sure how the two repositories diverged. Will synchronize back, that should solve the problem. Thank you. Mikhail On Sun, Aug 9, 2020 at 7:10 AM Vincent Carey wrote: > > > On Sun, Aug 9, 2020 at 6:57 AM Mikhail Dozmorov < > mikhail.dozmo...@gmail.com> wrote: > >> Thanks, Vincent. If I clone the Bioconductor version >> from g...@git.bioconductor.org:packages/HiCcompare, it builds >> without errors. The version from >> https://github.com/dozmorovlab/HiCcompare.git, which supposed to be >> identical, errors as before - rcmdcheck::rcmdcheck() throws the same >> > > "supposed to be identical" but no -- I checked out the one you mention > above, reproduced the error you report with R CMD *build* but > note that the versions in DESCRIPTION are different, and, for example > > stvjc@stvjc-XPS-13-9300:~/BIOC_SOURCES/MIK/HiCcompare/R$ diff > hic_compare.R ~/BIOC_SOURCES/HiCcompare/R/hic_compare.R > 99c99 > < A.min <- ceiling(mean(A_q10)) > --- > > A.min <- mean(A_q10) %>% ceiling() > > perhaps there is a branch in your lab repo that needs to be checked out? > > > > Error: processing vignette 'HiCcompare-vignette.Rmd' failed with > diagnostics: >> >> non-conformable arrays >> But the vignette builds using the "Knit" button. >> >> I still don't understand what is going on. The MD5 sums for files in both >> repositories are identical, except some in .git folder. I'll use the >> Bioconductor version and we don't need to dig more since this version >> works. Still, very strange situation. >> >> Thanks again, >> Mikhail >> >> On Sat, Aug 8, 2020 at 7:12 AM Vincent Carey >> wrote: >> >>> Hi Mikhail -- I cannot reproduce your problem. I think I need more >>> details as to how >>> your error is triggered. Using rcmdcheck::rcmdcheck within R as shown >>> in this transcript, >>> on the built tar.gz from the current git checkout master branch, I have >>> >>> ── R CMD check results ── HiCcompare >>> 1.11.0 >>> Duration: 3m 11.5s >>> >>> ❯ checking installed package size ... NOTE >>> installed size is 6.2Mb >>> sub-directories of 1Mb or more: >>> data 5.6Mb >>> >>> ❯ checking R code for possible problems ... NOTE >>> .adjust_pval : : no visible binding for global variable >>> ‘p.adj’ >>> .adjust_pval : : no visible binding for global variable >>> ‘p.value’ >>> .adjust_pval: no visible binding for global variable ‘p.value’ >>> .adjust_pval: no visible binding for global variable ‘p.adj’ >>> .calc.diff.thresh: no visible global function definition for ‘sd’ >>> .calc.pval: no visible binding for global variable ‘D’ >>> .calc.pval: no visible binding for global variable ‘p.value’ >>> .calc.pval: no visible binding for global variable ‘p.adj’ >>> .calc.pval: no visible binding for global variable ‘adj.M’ >>> .calc.pval: no visible binding for global variable ‘fold.change’ >>> .calc.pval: no visible binding for global variable ‘adj.IF2’ >>> .calc.pval: no visible binding for global variable ‘adj.IF1’ >>> .calc_z2: no visible global function definition for ‘sd’ >>> .calc_z2: no visible binding for global variable ‘Z’ >>> .calc_z2: no visible global function definition for ‘pnorm’ >>> .calc_z2: no visible binding for global variable ‘p.value’ >>> .loess.matrix: no visible binding for global variable ‘adj.IF1’ >>> .loess.matrix: no visible binding for global variable ‘IF1’ >>> .loess.matrix: no visible binding for global variable ‘adj.IF2’ >>> .loess.matrix: no visible binding for global variable ‘IF2’ >>> .loess.matrix: no visible binding for global variable ‘adj.M’ >>> .loess.matrix: no visible binding for global variable ‘A’ >>> .sim.mat: no visible global function definition for ‘head’ >>> .split_cent: no visible binding for global variable >>> ‘centromere_locations’ >>> .split_cent: no visible binding for global variable ‘start1’ >>> .split_cent: no visible binding for global variable ‘start2’ >>> .split_cent: no visible binding for global variable ‘chr1’ >>> .split_cent: no visible binding for global variable ‘chr2’ >>> MA_norm: no visible binding for global variable ‘D’ >>> MA_norm: no visible binding for global variable ‘M’ >>> MA_norm: n
Re: [Bioc-devel] non-conformable arrays
‘bias.slope’
> hic_simulate: no visible global function definition for ‘na.omit’
> hicpro2bedpe: no visible binding for global variable ‘chr1’
> hicpro2bedpe: no visible binding for global variable ‘chr2’
> manhattan_plot: no visible binding for global variable ‘bp’
> manhattan_plot: no visible binding for global variable ‘count’
> sim.other.methods: no visible binding for global variable ‘adj.IF1’
> sim.other.methods: no visible binding for global variable ‘IF1’
> sim.other.methods: no visible binding for global variable ‘adj.IF2’
> sim.other.methods: no visible binding for global variable ‘IF2’
> sim.other.methods: no visible binding for global variable ‘adj.M’
> sim.other.methods: no visible binding for global variable ‘M’
> sim.other.methods: no visible global function definition for ‘na.omit’
> sim_matrix: no visible binding for global variable ‘bias.slope’
> total_sum: no visible binding for global variable ‘IF2’
> total_sum: no visible binding for global variable ‘M’
> total_sum: no visible binding for global variable ‘IF1’
> total_sum: no visible binding for global variable ‘chr1’
> volcano: no visible binding for global variable ‘A’
> volcano: no visible binding for global variable ‘adj.IF1’
> volcano: no visible binding for global variable ‘adj.IF2’
> volcano: no visible binding for global variable ‘p.value’
> volcano: no visible binding for global variable ‘D’
> Undefined global functions or variables:
> A D IF IF1 IF2 M Z adj.IF1 adj.IF2 adj.M axis bias.slope bp
> centromere_locations chr1 chr2 count fold.change head i j na.omit
> p.adj p.value pnorm region1 region2 sd start1 start2
> Consider adding
> importFrom("graphics", "axis")
> importFrom("stats", "D", "na.omit", "pnorm", "sd")
> importFrom("utils", "head")
> to your NAMESPACE file.
>
> 0 errors ✔ | 0 warnings ✔ | 2 notes ✖
> > sessionInfo()
> R version 4.0.2 Patched (2020-07-19 r78892)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 20.04 LTS (fossa-melisa X20)
>
> Matrix products: default
> BLAS: /home/stvjc/R-4-0-dist/lib/R/lib/libRblas.so
> LAPACK: /home/stvjc/R-4-0-dist/lib/R/lib/libRlapack.so
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] rcmdcheck_1.3.3
>
> loaded via a namespace (and not attached):
> [1] ps_1.3.3 fansi_0.4.1 prettyunits_1.1.1 withr_2.2.0
>
> [5] digest_0.6.25 crayon_1.3.4 rprojroot_1.3-2
> assertthat_0.2.1
> [9] R6_2.4.1 backports_1.1.8 cli_2.0.2 callr_3.4.3
>
> [13] desc_1.2.0tools_4.0.2 glue_1.4.1compiler_4.0.2
>
> [17] processx_3.4.3xopen_1.0.0 pkgbuild_1.1.0
> >
>
> On Fri, Aug 7, 2020 at 7:08 PM Mikhail Dozmorov <
> mikhail.dozmo...@gmail.com> wrote:
>
>> Dear Bioconductor team,
>>
>> I am trying to update a package we developed, HiCcompare.
>> https://bioconductor.org/packages/HiCcompare/. The package has been
>> successfully submitted previously. However, now `R CMD check` throws an
>> error:
>> E> Quitting from lines 426-427 (HiCcompare-vignette.Rmd)
>> E> Error: processing vignette 'HiCcompare-vignette.Rmd' failed with
>> diagnostics:
>> E> non-conformable arrays
>> E> --- failed re-building ‘HiCcompare-vignette.Rmd’
>>
>> Yet, If I knit the vignette manually, it builds. If I execute the code
>> manually, it works. If I install the package from Bioconductor, it also
>> works.
>>
>> I'm working with this package using
>> bioconductor/bioconductor_docker:devel.
>> But the strange behavior - vignette knits manually but fails in CMD check
>> -
>> persists both in Docker container and on local R installation.
>>
>> Please advise, where to troubleshoot next.
>> Thanks,
>> Mikhail
>>
>> ---
>> Mikhail Dozmorov, Ph.D., Blick scholar
>> Associate Professor, Department of Biostatistics
>> Affiliate, Department of Pathology
>> Virginia Commonwealth University
>> OCS #738, 830 E. Main St, RVA, 23298
>> E-mail: mikhail.dozmo...@vcuhealth.org
>> Phone: 804-827-2055
>> https://medschool.vcu.edu/expertise/detail.html?id=mdozmorov
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
> The information in this e-mail is intended only for th...{{dropped:16}}
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] non-conformable arrays
Dear Bioconductor team, I am trying to update a package we developed, HiCcompare. https://bioconductor.org/packages/HiCcompare/. The package has been successfully submitted previously. However, now `R CMD check` throws an error: E> Quitting from lines 426-427 (HiCcompare-vignette.Rmd) E> Error: processing vignette 'HiCcompare-vignette.Rmd' failed with diagnostics: E> non-conformable arrays E> --- failed re-building ‘HiCcompare-vignette.Rmd’ Yet, If I knit the vignette manually, it builds. If I execute the code manually, it works. If I install the package from Bioconductor, it also works. I'm working with this package using bioconductor/bioconductor_docker:devel. But the strange behavior - vignette knits manually but fails in CMD check - persists both in Docker container and on local R installation. Please advise, where to troubleshoot next. Thanks, Mikhail --- Mikhail Dozmorov, Ph.D., Blick scholar Associate Professor, Department of Biostatistics Affiliate, Department of Pathology Virginia Commonwealth University OCS #738, 830 E. Main St, RVA, 23298 E-mail: mikhail.dozmo...@vcuhealth.org Phone: 804-827-2055 https://medschool.vcu.edu/expertise/detail.html?id=mdozmorov [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
