Re: [Bioc-devel] Incorrect version of package MSstatsTMT in Bioconductor 3.10
Thanks very much for the detailed explanation. That’s exactly what I did
before. Now I see the problem.
Best,
Ting
> On Oct 31, 2019, at 4:13 PM, Martin Morgan wrote:
>
> On the 3_9 branch I see
>
> commit c1382c3f7a0e3872cb66d077f9572b2b9618ecec (HEAD -> RELEASE_3_9,
> origin/RELEASE_3_9)
> Author: Ting Huang
> Date: Sat May 4 16:12:18 2019 -0400
>
>Update version bump
>
> commit 21273e6d818ed70fd258a9574700cc0f53ce0b8b
> Author: Ting Huang
> Date: Thu Aug 22 01:08:03 2019 -0400
>
>Add global normalization
>
> commit d98e5a84473f0d3d505b9cc7edeed2c169361648
> Author: Ting Huang
> Date: Sat May 4 16:12:18 2019 -0400
>
>Update version bump
>
> where it looks like there was a commit in August, and then a commit from
> earlier was re-applied. The August commit has
>
> git show 21273e6d818ed70fd258a9574700cc0f53ce0b8b
> ...
> -Version: 1.2.5
> -Date: 2019-06-18
> +Version: 1.3.7
> +Date: 2019-08-15
>
> Remember that the 3.9 branch is the 'release' branch, where the 'y' version
> of x.y.z should be even. So probably you tried to push this to the
> repository, but were told the version number was bad, so you changed it by
> re-applying the earlier commit
>
> git show c1382c3f7a0e3872cb66d077f9572b2b9618ecec
> ...
> -Version: 1.3.7
> +Version: 1.2.7
>
> So the 3.9 branch has an August commit.
>
> But remember that Bioconductor always has a current release branch, and a
> devel (master) branch. The devel (master) branch always gives rise to the
> next release. So your August commit on the 3.9 branch did not propagate to
> the 3.10 branch.
> -+-3.9. -+- 3.10
> / /
> +-+-+-+-+-+ devel / master
>
> I guess your August commit was a 'new feature' ('add global normalization')
> so should have been added to the devel (master) branch.
>
> You could re-apply the august commit to the 3.10 branch, and also to devel /
> master.
>
> Martin
>
> On 10/31/19, 3:52 PM, "Bioc-devel on behalf of Pages, Herve"
> wrote:
>
>Hi Ting,
>
>We don't roll back anything. We just take whatever is in
>https://git.bioconductor.org/packages/MSstatsTMT and build that.
>I don't see any commit from August in the RELEASE_3_10 branch there:
>
>hpages@spectre:~/sandbox/MSstatsTMT$ git status
>On branch master
>Your branch is up-to-date with 'origin/master'.
>nothing to commit, working directory clean
>hpages@spectre:~/sandbox/MSstatsTMT$ git log
>commit 8597c7bd033b5690013604317490f8cca1507185
>Author: Nitesh Turaga
>Date: Tue Oct 29 13:43:20 2019 -0400
>
> bump x.y.z version to odd y after creation of RELEASE_3_10 branch
>
>commit 10bd72b5b331be9085401ea2d294f8906bd0992d
>Author: Nitesh Turaga
>Date: Tue Oct 29 13:11:24 2019 -0400
>
> bump x.y.z version to even y prior to creation of RELEASE_3_10 branch
>
>commit f8fa7784468e4494678379c6fbe2ea86bb5a412a
>Author: Ting Huang
>Date: Sat May 4 16:12:18 2019 -0400
>
> Fix version number
>
>commit d401543723af97fb2204bd91a58677e649b391f2
>Author: Ting Huang
>Date: Sat May 4 14:36:40 2019 -0400
>
> bug fix: my bug fix
>
>commit 76d20aabeb8a2990c7ca794aea4ffb4633239c56
>Author: Ting Huang
>Date: Sat May 4 14:11:32 2019 -0400
>
> bug fix: my bug fix
>
>commit 3b5924216f9d82867696d978adb735d69f765593
>Author: Ting Huang
>Date: Sat May 4 14:09:28 2019 -0400
>
> Update version number
>
>etc...
>
>If you've committed something in August, make sure to push your changes
>to git.bioconductor.org in addition to GitHub. See our collections of
>HOWTO documents for how to do this:
>
> https://bioconductor.org/developers/how-to/git/
>
>Hope this helps.
>
>Best,
>H.
>
>
>On 10/31/19 12:31, ting huang wrote:
>> Dear Bioc-Team,
>>
>> I’m the developer of package MSstatsTMT. Today I tried to install MSstatsTMT
>> from the new released Bioconductor 3.10. But it was found that the version
>> of MSstatsTMT is rolled back.
>>
>> My last commit to MSstatsTMT is 2019 Aug 15 and the version in Bioconductor
>> 3.9 is 1.2.7. However the new version MSstatsTMT 1.4.0 in Bioconductor 3.10
>> showed the last commit is 2019 May 4. Somehow MSstatsTMT was rolled back to
>> an old version in Bioconductor 3.10. Any clue on why this happened?
>>
>> Many thanks and best regards,
>> Ting
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=UTF1FgVr08NqiYrWipNdjYVk7sr6fhyDedfbva_FOF8=NN6x1AClUMXzcjoQSrE24IrJ63mBCMao1t6gaLBOtkQ=
>>
>
>--
>Hervé Pagès
>
>Program in Computational Biology
>Division of Public Health Sciences
>Fred Hutchinson
Re: [Bioc-devel] Incorrect version of package MSstatsTMT in Bioconductor 3.10
On the 3_9 branch I see
commit c1382c3f7a0e3872cb66d077f9572b2b9618ecec (HEAD -> RELEASE_3_9,
origin/RELEASE_3_9)
Author: Ting Huang
Date: Sat May 4 16:12:18 2019 -0400
Update version bump
commit 21273e6d818ed70fd258a9574700cc0f53ce0b8b
Author: Ting Huang
Date: Thu Aug 22 01:08:03 2019 -0400
Add global normalization
commit d98e5a84473f0d3d505b9cc7edeed2c169361648
Author: Ting Huang
Date: Sat May 4 16:12:18 2019 -0400
Update version bump
where it looks like there was a commit in August, and then a commit from
earlier was re-applied. The August commit has
git show 21273e6d818ed70fd258a9574700cc0f53ce0b8b
...
-Version: 1.2.5
-Date: 2019-06-18
+Version: 1.3.7
+Date: 2019-08-15
Remember that the 3.9 branch is the 'release' branch, where the 'y' version of
x.y.z should be even. So probably you tried to push this to the repository, but
were told the version number was bad, so you changed it by re-applying the
earlier commit
git show c1382c3f7a0e3872cb66d077f9572b2b9618ecec
...
-Version: 1.3.7
+Version: 1.2.7
So the 3.9 branch has an August commit.
But remember that Bioconductor always has a current release branch, and a devel
(master) branch. The devel (master) branch always gives rise to the next
release. So your August commit on the 3.9 branch did not propagate to the 3.10
branch.
-+-3.9. -+- 3.10
/ /
+-+-+-+-+-+ devel / master
I guess your August commit was a 'new feature' ('add global normalization') so
should have been added to the devel (master) branch.
You could re-apply the august commit to the 3.10 branch, and also to devel /
master.
Martin
On 10/31/19, 3:52 PM, "Bioc-devel on behalf of Pages, Herve"
wrote:
Hi Ting,
We don't roll back anything. We just take whatever is in
https://git.bioconductor.org/packages/MSstatsTMT and build that.
I don't see any commit from August in the RELEASE_3_10 branch there:
hpages@spectre:~/sandbox/MSstatsTMT$ git status
On branch master
Your branch is up-to-date with 'origin/master'.
nothing to commit, working directory clean
hpages@spectre:~/sandbox/MSstatsTMT$ git log
commit 8597c7bd033b5690013604317490f8cca1507185
Author: Nitesh Turaga
Date: Tue Oct 29 13:43:20 2019 -0400
bump x.y.z version to odd y after creation of RELEASE_3_10 branch
commit 10bd72b5b331be9085401ea2d294f8906bd0992d
Author: Nitesh Turaga
Date: Tue Oct 29 13:11:24 2019 -0400
bump x.y.z version to even y prior to creation of RELEASE_3_10 branch
commit f8fa7784468e4494678379c6fbe2ea86bb5a412a
Author: Ting Huang
Date: Sat May 4 16:12:18 2019 -0400
Fix version number
commit d401543723af97fb2204bd91a58677e649b391f2
Author: Ting Huang
Date: Sat May 4 14:36:40 2019 -0400
bug fix: my bug fix
commit 76d20aabeb8a2990c7ca794aea4ffb4633239c56
Author: Ting Huang
Date: Sat May 4 14:11:32 2019 -0400
bug fix: my bug fix
commit 3b5924216f9d82867696d978adb735d69f765593
Author: Ting Huang
Date: Sat May 4 14:09:28 2019 -0400
Update version number
etc...
If you've committed something in August, make sure to push your changes
to git.bioconductor.org in addition to GitHub. See our collections of
HOWTO documents for how to do this:
https://bioconductor.org/developers/how-to/git/
Hope this helps.
Best,
H.
On 10/31/19 12:31, ting huang wrote:
> Dear Bioc-Team,
>
> I’m the developer of package MSstatsTMT. Today I tried to install
MSstatsTMT from the new released Bioconductor 3.10. But it was found that the
version of MSstatsTMT is rolled back.
>
> My last commit to MSstatsTMT is 2019 Aug 15 and the version in
Bioconductor 3.9 is 1.2.7. However the new version MSstatsTMT 1.4.0 in
Bioconductor 3.10 showed the last commit is 2019 May 4. Somehow MSstatsTMT was
rolled back to an old version in Bioconductor 3.10. Any clue on why this
happened?
>
> Many thanks and best regards,
> Ting
> ___
> Bioc-devel@r-project.org mailing list
>
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=UTF1FgVr08NqiYrWipNdjYVk7sr6fhyDedfbva_FOF8=NN6x1AClUMXzcjoQSrE24IrJ63mBCMao1t6gaLBOtkQ=
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
___
Bioc-devel@r-project.org
Re: [Bioc-devel] Incorrect version of package MSstatsTMT in Bioconductor 3.10
I meant to show the history of the RELEASE_3_10 branch sorry: hpages@spectre:~/sandbox/MSstatsTMT$ git status On branch RELEASE_3_10 Your branch is up-to-date with 'origin/RELEASE_3_10'. nothing to commit, working directory clean hpages@spectre:~/sandbox/MSstatsTMT$ git log commit 10bd72b5b331be9085401ea2d294f8906bd0992d Author: Nitesh Turaga Date: Tue Oct 29 13:11:24 2019 -0400 bump x.y.z version to even y prior to creation of RELEASE_3_10 branch commit f8fa7784468e4494678379c6fbe2ea86bb5a412a Author: Ting Huang Date: Sat May 4 16:12:18 2019 -0400 Fix version number commit d401543723af97fb2204bd91a58677e649b391f2 Author: Ting Huang Date: Sat May 4 14:36:40 2019 -0400 bug fix: my bug fix commit 76d20aabeb8a2990c7ca794aea4ffb4633239c56 Author: Ting Huang Date: Sat May 4 14:11:32 2019 -0400 bug fix: my bug fix commit 3b5924216f9d82867696d978adb735d69f765593 Author: Ting Huang Date: Sat May 4 14:09:28 2019 -0400 Update version number commit 61c2cf989bbd1bc052583daa8c6da148004edcca Merge: 056fcfd 469290a Author: Ting Huang Date: Sat May 4 13:52:10 2019 -0400 etc... No commit from August either. Cheers, H. On 10/31/19 12:44, Pages, Herve wrote: > Hi Ting, > > We don't roll back anything. We just take whatever is in > https://urldefense.proofpoint.com/v2/url?u=https-3A__git.bioconductor.org_packages_MSstatsTMT=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Ay9Zu8LthDvNBc76atW9maFKlelMTjwPkrhWpFcu1Cc=FDvw-fviyhpH0XUjcISEWgzCRMZmxBpBWCHKJ8dpl50= > and build that. > I don't see any commit from August in the RELEASE_3_10 branch there: > > hpages@spectre:~/sandbox/MSstatsTMT$ git status > On branch master > Your branch is up-to-date with 'origin/master'. > nothing to commit, working directory clean > hpages@spectre:~/sandbox/MSstatsTMT$ git log > commit 8597c7bd033b5690013604317490f8cca1507185 > Author: Nitesh Turaga > Date: Tue Oct 29 13:43:20 2019 -0400 > > bump x.y.z version to odd y after creation of RELEASE_3_10 branch > > commit 10bd72b5b331be9085401ea2d294f8906bd0992d > Author: Nitesh Turaga > Date: Tue Oct 29 13:11:24 2019 -0400 > > bump x.y.z version to even y prior to creation of RELEASE_3_10 branch > > commit f8fa7784468e4494678379c6fbe2ea86bb5a412a > Author: Ting Huang > Date: Sat May 4 16:12:18 2019 -0400 > > Fix version number > > commit d401543723af97fb2204bd91a58677e649b391f2 > Author: Ting Huang > Date: Sat May 4 14:36:40 2019 -0400 > > bug fix: my bug fix > > commit 76d20aabeb8a2990c7ca794aea4ffb4633239c56 > Author: Ting Huang > Date: Sat May 4 14:11:32 2019 -0400 > > bug fix: my bug fix > > commit 3b5924216f9d82867696d978adb735d69f765593 > Author: Ting Huang > Date: Sat May 4 14:09:28 2019 -0400 > > Update version number > > etc... > > If you've committed something in August, make sure to push your changes > to git.bioconductor.org in addition to GitHub. See our collections of > HOWTO documents for how to do this: > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_developers_how-2Dto_git_=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Ay9Zu8LthDvNBc76atW9maFKlelMTjwPkrhWpFcu1Cc=n9OJdDZzGUEdu3kPDKdXAvhh0HmrPaga6kBh495OxSM= > > Hope this helps. > > Best, > H. > > > On 10/31/19 12:31, ting huang wrote: >> Dear Bioc-Team, >> >> I’m the developer of package MSstatsTMT. Today I tried to install MSstatsTMT >> from the new released Bioconductor 3.10. But it was found that the version >> of MSstatsTMT is rolled back. >> >> My last commit to MSstatsTMT is 2019 Aug 15 and the version in Bioconductor >> 3.9 is 1.2.7. However the new version MSstatsTMT 1.4.0 in Bioconductor 3.10 >> showed the last commit is 2019 May 4. Somehow MSstatsTMT was rolled back to >> an old version in Bioconductor 3.10. Any clue on why this happened? >> >> Many thanks and best regards, >> Ting >> ___ >> Bioc-devel@r-project.org mailing list >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=UTF1FgVr08NqiYrWipNdjYVk7sr6fhyDedfbva_FOF8=NN6x1AClUMXzcjoQSrE24IrJ63mBCMao1t6gaLBOtkQ= >> > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocManager::install() downgrade installed packages
If it were me I might update version
BiocManager::install(version="3.10")
...
Update xxx packages [y/n]: n
Confirm I've got the right version
BiocManager::version()
and then recover the URLs
BiocManager::repositories()
as arguments to install.packages(). It doesn't make sense to ask for
repositories(version="...") if that's not the version BiocManager knows about...
Martin
On 10/31/19, 3:54 PM, "Bioc-devel on behalf of Henrik Bengtsson"
wrote:
On Thu, Oct 31, 2019 at 11:52 AM James W. MacDonald wrote:
>
> The main goal for BiocManager is to help end users ensure that their
R/BioC installation is consistent for the version of R that they are using. So
by definition, any packages that are outside the versions for a given R/BioC
installation should be up or down-graded to make the installation valid. There
are those of us who are l33t enough to mix'n'match packages and debug errors
that may then occur. But it's probably not a good idea to make it easily hacked
by naive users, allowing them to do things that might cause problems.
>
> Anyway, I believe doing
>
> options("BIOCMANAGER_CRANCHECK_BEHAVIOR" = FALSE)
>
> will stop BiocManager::install from changing any installed CRAN packages.
And it's suitably obscure to limit that to the cool kids who can find it.
Unfortunately, this doesn't seem to make a difference. By searching
the GitHub code base it doesn't look like this option is used
anywhere:
https://github.com/search?q=org%3ABioconductor+BIOCMANAGER_CRANCHECK_BEHAVIOR=Code
My current workaround it to not use BiocManager and roll my own
'repos' settings;
> unname(getOption("repos"))
[1] "https://cloud.r-project.org;
[2] "https://bioconductor.org/packages/3.10/bioc;
[3] "https://bioconductor.org/packages/3.10/data/annotation;
[4] "https://bioconductor.org/packages/3.10/data/experiment;
[5] "https://bioconductor.org/packages/3.10/workflows;
and use good old update.packages().
Alternative wish: It would be handy if there was a
BiocManager::repositories(version = "3.10") for finding these,
especially since some of them come and go depending on Bioc version.
/Henrik
PS. I also tried setting ditto env var because it looked more like an
env var than R option name to me.
>
> On Thu, Oct 31, 2019 at 2:21 PM Henrik Bengtsson
wrote:
>>
>> (posting this here since I think it's not a support question per se)
>>
>> Hi, I just started an upgrade from Bioc 3.9 to 3.10 on my local R 3.6.1
setup:
>>
>> > BiocManager::install(version = "3.10")
>> Upgrade 73 packages to Bioconductor version '3.10'? [y/n]: y
>> Bioconductor version 3.10 (BiocManager 1.30.9), R 3.6.1 Patched
(2019-09-12
>> r77183)
>> Installing package(s) 'BiocVersion'
>> ...
>> Installing package(s) 'base64enc', 'future', 'future.callr', 'listenv',
>> 'matrixStats', 'munsell', 'png', 'profmem', 'R.oo', 'rcmdcheck',
'scales',
>> 'affxparser', 'affy', 'affyio', 'AffymetrixDataTestFiles', 'annotate',
>> 'AnnotationDbi', 'AnnotationForge', 'aroma.light', 'Biobase',
'BiocCheck',
>> 'BiocGenerics', 'BiocParallel', 'BiocStyle', 'BiocVersion',
'biocViews',
>> 'Biostrings', 'BSgenome', 'CGHbase', 'CGHcall', 'cytolib',
'DelayedArray',
>> 'DNAcopy', 'edgeR', 'flowCore', 'flowViz', 'genefilter',
'GenomeInfoDb',
>> 'GenomeInfoDbData', 'GenomicAlignments', 'GenomicRanges', 'GO.db',
'graph',
>> 'GSEABase', 'IlluminaDataTestFiles', 'illuminaio', 'impute', 'IRanges',
>> 'limma', 'marray', 'ncdfFlow', 'oligo', 'oligoClasses', 'org.Hs.eg.db',
>> 'pdInfoBuilder', 'preprocessCore', 'QDNAseq', 'QDNAseq.hg19',
'QDNAseq.mm10',
>> 'RBGL', 'Rgraphviz', 'Rhdf5lib', 'Rhtslib', 'RProtoBufLib',
'Rsamtools',
>> 'rtracklayer', 'S4Vectors', 'ShortRead', 'STROMA4',
'SummarizedExperiment',
>> 'XVector', 'zlibbioc'
>> trying URL
'https://cloud.r-project.org/src/contrib/base64enc_0.1-3.tar.gz'
>> Content type 'application/x-gzip' length 7833 bytes
>> ==
>> downloaded 7833 bytes
>>
>> trying URL 'https://cloud.r-project.org/src/contrib/future_1.14.0.tar.gz'
>> Content type 'application/x-gzip' length 294967 bytes (288 KB)
>> ==
>> downloaded 288 KB
>> ...
>>
>> It surprised me that BiocManager::install() will _downgrade_ to CRAN(*)
>> package versions, even if you have newer versions installed. For
>> instance, I've got base64enc 0.1.4 from
>> http://www.rforge.net/base64enc/, my own development version of future
>> 1.14.0-9000, and so on. Note that the prompt says nothing about
>> downgrading. Is this really wanted and is there a way to avoid this?
>>
>> (*) Will this also downgrade Bioc developers' Bioc
Re: [Bioc-devel] BiocManager::install() downgrade installed packages
On Thu, Oct 31, 2019 at 11:52 AM James W. MacDonald wrote:
>
> The main goal for BiocManager is to help end users ensure that their R/BioC
> installation is consistent for the version of R that they are using. So by
> definition, any packages that are outside the versions for a given R/BioC
> installation should be up or down-graded to make the installation valid.
> There are those of us who are l33t enough to mix'n'match packages and debug
> errors that may then occur. But it's probably not a good idea to make it
> easily hacked by naive users, allowing them to do things that might cause
> problems.
>
> Anyway, I believe doing
>
> options("BIOCMANAGER_CRANCHECK_BEHAVIOR" = FALSE)
>
> will stop BiocManager::install from changing any installed CRAN packages. And
> it's suitably obscure to limit that to the cool kids who can find it.
Unfortunately, this doesn't seem to make a difference. By searching
the GitHub code base it doesn't look like this option is used
anywhere:
https://github.com/search?q=org%3ABioconductor+BIOCMANAGER_CRANCHECK_BEHAVIOR=Code
My current workaround it to not use BiocManager and roll my own
'repos' settings;
> unname(getOption("repos"))
[1] "https://cloud.r-project.org;
[2] "https://bioconductor.org/packages/3.10/bioc;
[3] "https://bioconductor.org/packages/3.10/data/annotation;
[4] "https://bioconductor.org/packages/3.10/data/experiment;
[5] "https://bioconductor.org/packages/3.10/workflows;
and use good old update.packages().
Alternative wish: It would be handy if there was a
BiocManager::repositories(version = "3.10") for finding these,
especially since some of them come and go depending on Bioc version.
/Henrik
PS. I also tried setting ditto env var because it looked more like an
env var than R option name to me.
>
> On Thu, Oct 31, 2019 at 2:21 PM Henrik Bengtsson
> wrote:
>>
>> (posting this here since I think it's not a support question per se)
>>
>> Hi, I just started an upgrade from Bioc 3.9 to 3.10 on my local R 3.6.1
>> setup:
>>
>> > BiocManager::install(version = "3.10")
>> Upgrade 73 packages to Bioconductor version '3.10'? [y/n]: y
>> Bioconductor version 3.10 (BiocManager 1.30.9), R 3.6.1 Patched (2019-09-12
>> r77183)
>> Installing package(s) 'BiocVersion'
>> ...
>> Installing package(s) 'base64enc', 'future', 'future.callr', 'listenv',
>> 'matrixStats', 'munsell', 'png', 'profmem', 'R.oo', 'rcmdcheck', 'scales',
>> 'affxparser', 'affy', 'affyio', 'AffymetrixDataTestFiles', 'annotate',
>> 'AnnotationDbi', 'AnnotationForge', 'aroma.light', 'Biobase', 'BiocCheck',
>> 'BiocGenerics', 'BiocParallel', 'BiocStyle', 'BiocVersion', 'biocViews',
>> 'Biostrings', 'BSgenome', 'CGHbase', 'CGHcall', 'cytolib', 'DelayedArray',
>> 'DNAcopy', 'edgeR', 'flowCore', 'flowViz', 'genefilter', 'GenomeInfoDb',
>> 'GenomeInfoDbData', 'GenomicAlignments', 'GenomicRanges', 'GO.db', 'graph',
>> 'GSEABase', 'IlluminaDataTestFiles', 'illuminaio', 'impute', 'IRanges',
>> 'limma', 'marray', 'ncdfFlow', 'oligo', 'oligoClasses', 'org.Hs.eg.db',
>> 'pdInfoBuilder', 'preprocessCore', 'QDNAseq', 'QDNAseq.hg19',
>> 'QDNAseq.mm10',
>> 'RBGL', 'Rgraphviz', 'Rhdf5lib', 'Rhtslib', 'RProtoBufLib', 'Rsamtools',
>> 'rtracklayer', 'S4Vectors', 'ShortRead', 'STROMA4', 'SummarizedExperiment',
>> 'XVector', 'zlibbioc'
>> trying URL 'https://cloud.r-project.org/src/contrib/base64enc_0.1-3.tar.gz'
>> Content type 'application/x-gzip' length 7833 bytes
>> ==
>> downloaded 7833 bytes
>>
>> trying URL 'https://cloud.r-project.org/src/contrib/future_1.14.0.tar.gz'
>> Content type 'application/x-gzip' length 294967 bytes (288 KB)
>> ==
>> downloaded 288 KB
>> ...
>>
>> It surprised me that BiocManager::install() will _downgrade_ to CRAN(*)
>> package versions, even if you have newer versions installed. For
>> instance, I've got base64enc 0.1.4 from
>> http://www.rforge.net/base64enc/, my own development version of future
>> 1.14.0-9000, and so on. Note that the prompt says nothing about
>> downgrading. Is this really wanted and is there a way to avoid this?
>>
>> (*) Will this also downgrade Bioc developers' Bioc packages?
>>
>> Thanks,
>>
>> Henrik
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Incorrect version of package MSstatsTMT in Bioconductor 3.10
Hi Ting, We don't roll back anything. We just take whatever is in https://git.bioconductor.org/packages/MSstatsTMT and build that. I don't see any commit from August in the RELEASE_3_10 branch there: hpages@spectre:~/sandbox/MSstatsTMT$ git status On branch master Your branch is up-to-date with 'origin/master'. nothing to commit, working directory clean hpages@spectre:~/sandbox/MSstatsTMT$ git log commit 8597c7bd033b5690013604317490f8cca1507185 Author: Nitesh Turaga Date: Tue Oct 29 13:43:20 2019 -0400 bump x.y.z version to odd y after creation of RELEASE_3_10 branch commit 10bd72b5b331be9085401ea2d294f8906bd0992d Author: Nitesh Turaga Date: Tue Oct 29 13:11:24 2019 -0400 bump x.y.z version to even y prior to creation of RELEASE_3_10 branch commit f8fa7784468e4494678379c6fbe2ea86bb5a412a Author: Ting Huang Date: Sat May 4 16:12:18 2019 -0400 Fix version number commit d401543723af97fb2204bd91a58677e649b391f2 Author: Ting Huang Date: Sat May 4 14:36:40 2019 -0400 bug fix: my bug fix commit 76d20aabeb8a2990c7ca794aea4ffb4633239c56 Author: Ting Huang Date: Sat May 4 14:11:32 2019 -0400 bug fix: my bug fix commit 3b5924216f9d82867696d978adb735d69f765593 Author: Ting Huang Date: Sat May 4 14:09:28 2019 -0400 Update version number etc... If you've committed something in August, make sure to push your changes to git.bioconductor.org in addition to GitHub. See our collections of HOWTO documents for how to do this: https://bioconductor.org/developers/how-to/git/ Hope this helps. Best, H. On 10/31/19 12:31, ting huang wrote: > Dear Bioc-Team, > > I’m the developer of package MSstatsTMT. Today I tried to install MSstatsTMT > from the new released Bioconductor 3.10. But it was found that the version of > MSstatsTMT is rolled back. > > My last commit to MSstatsTMT is 2019 Aug 15 and the version in Bioconductor > 3.9 is 1.2.7. However the new version MSstatsTMT 1.4.0 in Bioconductor 3.10 > showed the last commit is 2019 May 4. Somehow MSstatsTMT was rolled back to > an old version in Bioconductor 3.10. Any clue on why this happened? > > Many thanks and best regards, > Ting > ___ > Bioc-devel@r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=UTF1FgVr08NqiYrWipNdjYVk7sr6fhyDedfbva_FOF8=NN6x1AClUMXzcjoQSrE24IrJ63mBCMao1t6gaLBOtkQ= > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] package cliqueMS missing from BioC 3.10 and BioC 3.11
Sorry, this should be included in the builds tonight for release tomorrow. I'll update the release announcement when the package becomes available. Martin On 10/31/19, 3:09 PM, "Bioc-devel on behalf of Oriol Senan Campos" wrote: Dear list members, First of all congratulations to the Bioconductor Team for another release!. I am the maintainer of package cliqueMS. It was accepted inside the deadlines for release 3.10 of Bioconductor. https://github.com/Bioconductor/Contributions/issues/1244 Without errors or warnings. I only had to remove some *tgz files from my github repository (that were not used in the R package, but were bigger than 5 Mb). I only see the package at the bioconductor git server https://git.bioconductor.org/ But I cannot see it in the release check page https://bioconductor.org/checkResults/3.10/bioc-LATEST/ or in the devel https://bioconductor.org/checkResults/3.11/bioc-LATEST/ In addition the package webpage is showing an error: https://bioconductor.org/packages/release/bioc/html/cliqueMS.html If anyone can help me to fix this I really would appreciate. Greetings, Oriol Senan ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Incorrect version of package MSstatsTMT in Bioconductor 3.10
Dear Bioc-Team, I’m the developer of package MSstatsTMT. Today I tried to install MSstatsTMT from the new released Bioconductor 3.10. But it was found that the version of MSstatsTMT is rolled back. My last commit to MSstatsTMT is 2019 Aug 15 and the version in Bioconductor 3.9 is 1.2.7. However the new version MSstatsTMT 1.4.0 in Bioconductor 3.10 showed the last commit is 2019 May 4. Somehow MSstatsTMT was rolled back to an old version in Bioconductor 3.10. Any clue on why this happened? Many thanks and best regards, Ting ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocManager::install() downgrade installed packages
The main goal for BiocManager is to help end users ensure that their R/BioC
installation is consistent for the version of R that they are using. So by
definition, any packages that are outside the versions for a given R/BioC
installation should be up or down-graded to make the installation valid.
There are those of us who are l33t enough to mix'n'match packages and debug
errors that may then occur. But it's probably not a good idea to make it
easily hacked by naive users, allowing them to do things that might cause
problems.
Anyway, I believe doing
options("BIOCMANAGER_CRANCHECK_BEHAVIOR" = FALSE)
will stop BiocManager::install from changing any installed CRAN packages.
And it's suitably obscure to limit that to the cool kids who can find it.
On Thu, Oct 31, 2019 at 2:21 PM Henrik Bengtsson
wrote:
> (posting this here since I think it's not a support question per se)
>
> Hi, I just started an upgrade from Bioc 3.9 to 3.10 on my local R 3.6.1
> setup:
>
> > BiocManager::install(version = "3.10")
> Upgrade 73 packages to Bioconductor version '3.10'? [y/n]: y
> Bioconductor version 3.10 (BiocManager 1.30.9), R 3.6.1 Patched (2019-09-12
> r77183)
> Installing package(s) 'BiocVersion'
> ...
> Installing package(s) 'base64enc', 'future', 'future.callr', 'listenv',
> 'matrixStats', 'munsell', 'png', 'profmem', 'R.oo', 'rcmdcheck',
> 'scales',
> 'affxparser', 'affy', 'affyio', 'AffymetrixDataTestFiles', 'annotate',
> 'AnnotationDbi', 'AnnotationForge', 'aroma.light', 'Biobase',
> 'BiocCheck',
> 'BiocGenerics', 'BiocParallel', 'BiocStyle', 'BiocVersion', 'biocViews',
> 'Biostrings', 'BSgenome', 'CGHbase', 'CGHcall', 'cytolib',
> 'DelayedArray',
> 'DNAcopy', 'edgeR', 'flowCore', 'flowViz', 'genefilter', 'GenomeInfoDb',
> 'GenomeInfoDbData', 'GenomicAlignments', 'GenomicRanges', 'GO.db',
> 'graph',
> 'GSEABase', 'IlluminaDataTestFiles', 'illuminaio', 'impute', 'IRanges',
> 'limma', 'marray', 'ncdfFlow', 'oligo', 'oligoClasses', 'org.Hs.eg.db',
> 'pdInfoBuilder', 'preprocessCore', 'QDNAseq', 'QDNAseq.hg19',
> 'QDNAseq.mm10',
> 'RBGL', 'Rgraphviz', 'Rhdf5lib', 'Rhtslib', 'RProtoBufLib', 'Rsamtools',
> 'rtracklayer', 'S4Vectors', 'ShortRead', 'STROMA4',
> 'SummarizedExperiment',
> 'XVector', 'zlibbioc'
> trying URL 'https://cloud.r-project.org/src/contrib/base64enc_0.1-3.tar.gz
> '
> Content type 'application/x-gzip' length 7833 bytes
> ==
> downloaded 7833 bytes
>
> trying URL 'https://cloud.r-project.org/src/contrib/future_1.14.0.tar.gz'
> Content type 'application/x-gzip' length 294967 bytes (288 KB)
> ==
> downloaded 288 KB
> ...
>
> It surprised me that BiocManager::install() will _downgrade_ to CRAN(*)
> package versions, even if you have newer versions installed. For
> instance, I've got base64enc 0.1.4 from
> http://www.rforge.net/base64enc/, my own development version of future
> 1.14.0-9000, and so on. Note that the prompt says nothing about
> downgrading. Is this really wanted and is there a way to avoid this?
>
> (*) Will this also downgrade Bioc developers' Bioc packages?
>
> Thanks,
>
> Henrik
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
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[Bioc-devel] BiocManager::install() downgrade installed packages
(posting this here since I think it's not a support question per se) Hi, I just started an upgrade from Bioc 3.9 to 3.10 on my local R 3.6.1 setup: > BiocManager::install(version = "3.10") Upgrade 73 packages to Bioconductor version '3.10'? [y/n]: y Bioconductor version 3.10 (BiocManager 1.30.9), R 3.6.1 Patched (2019-09-12 r77183) Installing package(s) 'BiocVersion' ... Installing package(s) 'base64enc', 'future', 'future.callr', 'listenv', 'matrixStats', 'munsell', 'png', 'profmem', 'R.oo', 'rcmdcheck', 'scales', 'affxparser', 'affy', 'affyio', 'AffymetrixDataTestFiles', 'annotate', 'AnnotationDbi', 'AnnotationForge', 'aroma.light', 'Biobase', 'BiocCheck', 'BiocGenerics', 'BiocParallel', 'BiocStyle', 'BiocVersion', 'biocViews', 'Biostrings', 'BSgenome', 'CGHbase', 'CGHcall', 'cytolib', 'DelayedArray', 'DNAcopy', 'edgeR', 'flowCore', 'flowViz', 'genefilter', 'GenomeInfoDb', 'GenomeInfoDbData', 'GenomicAlignments', 'GenomicRanges', 'GO.db', 'graph', 'GSEABase', 'IlluminaDataTestFiles', 'illuminaio', 'impute', 'IRanges', 'limma', 'marray', 'ncdfFlow', 'oligo', 'oligoClasses', 'org.Hs.eg.db', 'pdInfoBuilder', 'preprocessCore', 'QDNAseq', 'QDNAseq.hg19', 'QDNAseq.mm10', 'RBGL', 'Rgraphviz', 'Rhdf5lib', 'Rhtslib', 'RProtoBufLib', 'Rsamtools', 'rtracklayer', 'S4Vectors', 'ShortRead', 'STROMA4', 'SummarizedExperiment', 'XVector', 'zlibbioc' trying URL 'https://cloud.r-project.org/src/contrib/base64enc_0.1-3.tar.gz' Content type 'application/x-gzip' length 7833 bytes == downloaded 7833 bytes trying URL 'https://cloud.r-project.org/src/contrib/future_1.14.0.tar.gz' Content type 'application/x-gzip' length 294967 bytes (288 KB) == downloaded 288 KB ... It surprised me that BiocManager::install() will _downgrade_ to CRAN(*) package versions, even if you have newer versions installed. For instance, I've got base64enc 0.1.4 from http://www.rforge.net/base64enc/, my own development version of future 1.14.0-9000, and so on. Note that the prompt says nothing about downgrading. Is this really wanted and is there a way to avoid this? (*) Will this also downgrade Bioc developers' Bioc packages? Thanks, Henrik ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Bioconductor 3.10 is released!!
Huge kudos to the team for another successful release. Sean On Wed, Oct 30, 2019 at 4:54 PM Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > Thanks to all developers and community members for contributing to the > project! > > Please see the full release announcement: > >https://www.bioconductor.org/news/bioc_3_10_release/ > > The Bioconductor Team > > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > 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 > -- Sean Davis, MD, PhD Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda, MD 20892 https://seandavi.github.io/ https://twitter.com/seandavis12 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
