[Bioc-devel] Accepted packages can't find each other and fail build
Shepherd, Lori
Lori.Shepherd at RoswellPark.org
Fri Nov 3 12:52:27 CET 2017
The data package and software package are in Bioc 3.6 not Bioc 3.5. You will need to update BiocInstaller in order to have access to the packages.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Sokratis Kariotis <s.kariotis at sheffield.ac.uk>
Sent: Friday, November 3, 2017 7:04:08 AM
To: Hervé Pagès
Cc: Shepherd, Lori; bioc-devel
Subject: Re: [Bioc-devel] Accepted packages can't find each other and fail build
Hey all,
I can see the landing pages for both packages now (pcxn and pcxnData) but as I try to install them using:
source("https://bioconductor.org/biocLite.R")
biocLite("pcxnData")
I get the following:
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.0 (2017-04-21).
Installing package(s) ‘pcxnData’
Warning message:
package ‘pcxnData’ is not available (for R version 3.4.0)
The same happens with the pcxn package but other unrelated packages seem to install fine.
Regards,
Sokratis
On 1 November 2017 at 22:25, Hervé Pagès <hpages at fredhutch.org<mailto:hpages at fredhutch.org>> wrote:
FYI today's data-experiment builds completed and pcxnData is
green:
https://bioconductor.org/checkResults/3.6/data-experiment-LATEST/pcxnData/
and propagated:
https://bioconductor.org/packages/3.6/data/experiment/html/pcxnData.html
Now the next step is that the software builds will be able
to install pcxnData on tokay1 (Windows) and veracruz1 (Mac)
from the public data-experiment repo so the results for
pcxn should get cleared tomorrow:
https://bioconductor.org/checkResults/3.6/bioc-LATEST/pcxn/
It's a long (and admittedly confusing) ping-pong game between the
software and data-expriment builds ;-)
Thanks for your patience,
H.
On 11/01/2017 08:21 AM, Hervé Pagès wrote:
Hi Sokratis,
Not sure why but it seems that for some reason the build machines
didn't manage to install pcxn so far. Until only now. I went on
build machine malbec1 to check whether it managed to install pcxn,
and it seems that it did:
> "pcxn" %in% rownames(installed.packages())
[1] TRUE
According to the log, it looks like this is the 1st time that it
gets installed on malbec1 (the data experiment builds just started
today and did the installation).
So, if everything goes as expected, pcxnData should build successfully
today and pcxnData should propagate (granted of course that it also
passes CHECK). The build/check report for data-experiment packages
should update today around 5pm EST. It will take about 1 hour after
the report is updated for pcxnData to propagate to the public repo
and for its landing page to show up.
Sorry for the inconvenience,
H.
On 11/01/2017 01:36 AM, Sokratis Kariotis wrote:
Hey all,
After the release I can see the release page of the pcxn package but not
pcxnData package. In the build page it says it cannot find the pcxn
package and fails.
Regards,
Sokratis
On 31 October 2017 at 16:33, Shepherd, Lori
<Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at roswellpark.org> <mailto:Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at roswellpark.org>>>
wrote:
It should be the same and you should be able to see the RELEASE_3_6
branch
git fetch --all
git branch -a
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
------------------------------------------------------------------------
*From:* Sokratis Kariotis <s.kariotis at sheffield.ac.uk<mailto:s.kariotis at sheffield.ac.uk>
<mailto:s.kariotis at sheffield.ac.uk<mailto:s.kariotis at sheffield.ac.uk>>>
*Sent:* Tuesday, October 31, 2017 11:20:39 AM
*To:* Shepherd, Lori
*Cc:* Hervé Pagès; Obenchain, Valerie; bioc-devel
*Subject:* Re: [Bioc-devel] Accepted packages can't find each other
and fail build
Does the same hold for the pcxnData package? I can't see the
RELEASE_3_6 as in pcxn.
-Sokratis
On 31 October 2017 at 11:38, Shepherd, Lori
<Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at roswellpark.org>
<mailto:Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at roswellpark.org>>> wrote:
The latest version bump change you made to 0.99.27 was yesterday
Oct 30 right before we said to stop committing so we could make
the release branch. That change did make it into both the
RELEASE_3_6 and the master branch and should appear in the next
build report for both versions.
Note: It can take 12-24 hours to see version bumps and changes
on the build report. The daily builders runs once per day to
build all the packages; while a version bump is absolutely
required, it is not built instantaneously on a version bump.
Please be sure to pull from upstream before making further
changes as we have bumped the versions in both the release and
devel versions of packages for the release.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
------------------------------------------------------------------------
*From:* Sokratis Kariotis <s.kariotis at sheffield.ac.uk<mailto:s.kariotis at sheffield.ac.uk>
<mailto:s.kariotis at sheffield.ac.uk<mailto:s.kariotis at sheffield.ac.uk>>>
*Sent:* Tuesday, October 31, 2017 5:21:21 AM
*To:* Hervé Pagès
*Cc:* Obenchain, Valerie; Shepherd, Lori; bioc-devel
*Subject:* Re: [Bioc-devel] Accepted packages can't find each
other and fail build
Hi all,
There was an error in the pcxn package (and pcxnData as a resut
of not finding pcxn since it didnt build) which I fixed
yesterday morning, but it doesnt seem to accept my changes as
the version in the build report is not the last one I created
but the erroneous one (2 days ago). I checked the upstream of my
package and it has my latest changes.
Regards,
Sokratis
On 27 October 2017 at 16:57, Hervé Pagès <hpages at fredhutch.org<mailto:hpages at fredhutch.org>
<mailto:hpages at fredhutch.org<mailto:hpages at fredhutch.org>>> wrote:
Hi guys,
On 10/27/2017 05:50 AM, Obenchain, Valerie wrote:
Hi Sokratis,
I added the .BBSoptions file to pcxn when it should have
been added to pcxnData. The .BBSoptions file should be
put in the package that 'Suggests' (not 'Depends') on
the other. In this case it's pcxnData that needs the
.BBSoptions. Sorry for the mix up, this has been fixed.
The data package should install with today's builds and
be clean on the Saturday report. The software package
should then install with the Saturday builds and be
clean on the Sunday report.
This is what should happen:
- pcxnData should install with today's data-exp builds
(they
started this morning) but vignette will still fail
(pcxn still
missing)
- pcxn won't install (will be back to NotNeeded) but
should pass
build/check and propagate on Saturday afternoon
- on Sunday morning, the data exp builds will find pcxn
**on line**
(because now it propagated) so will be able to install
it so
vignette will finally build and the package will
propagate
Thanks for taking care of this,
H.
Valerie
On 10/26/2017 04:26 AM, Shepherd, Lori wrote:
We have already taken care of this on our end and you
shouldn't need to do anything else. As always changes
reflected may take a few days to reflect in the build
reports.
The solution is to add a .BBSoptions file with
ForceInstall: TRUE to the software package. Since there
is a circular dependency this will force install the
software package even though there will be ERRORs
because of the missing data package. On the next build
of the data packages, the data package will then
successfully build finding the software package. Then
following, the software package will also build finding
the data package.
Cheers,
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Bioc-devel <bioc-devel-bounces at r-project.org<mailto:bioc-devel-bounces at r-project.org>
<mailto:bioc-devel-bounces at r-project.org<mailto:bioc-devel-bounces at r-project.org>>><mailto:bioc-devel-bounces at r-project.org<mailto:bioc-devel-bounces at r-project.org>
<mailto:bioc-devel-bounces at r-project.org<mailto:bioc-devel-bounces at r-project.org>>> on behalf of
Sokratis Kariotis <s.kariotis at sheffield.ac.uk<mailto:s.kariotis at sheffield.ac.uk>
<mailto:s.kariotis at sheffield.ac.uk<mailto:s.kariotis at sheffield.ac.uk>>><mailto:s.kariotis at sheffield.ac.uk<mailto:s.kariotis at sheffield.ac.uk>
<mailto:s.kariotis at sheffield.ac.uk<mailto:s.kariotis at sheffield.ac.uk>>>
Sent: Thursday, October 26, 2017 4:02:53 AM
To: bioc-devel
Subject: [Bioc-devel] Accepted packages can't find each
other and fail build
Hey all,
I created 2 packages that got accepted (pcxn and
pcxnData) where pcxn
depends on the data coming from pcxnData. However, in
the vignettes of
pcxnData I am using library(pcxn) to demonstrate what
can you do with the
data. As a result both packages fail building in BioC
3.6 as they can't
find each other. In a previous pair of packages I am
maintaining (pathprint
and pathprintGEOData) I could use the first library in
the data package
vignette and building was fine. Is it necessary to
remove library(pcxn)
from pcxnData to get them build? Thanks in advance!
Cheers
--
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ
<https://urldefense.proofpoint.com/v2/url?u=https-3A__maps.google.com_-3Fq-3D385a-2BGlossop-2BRd-2C-2BSheffield-2C-2BS10-2B2HQ-26entry-3Dgmail-26source-3Dg&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=uyIFjpL7wep4FyufJhLYsoBHxnLP8tcCArZLZdua1MY&s=4qo8KXmEZAYrs1orxWWzZrYuQLlLsLtq57YxqhFOyb0&e=>
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org>
<mailto:Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org>><mailto:Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org>
<mailto:Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org>>> mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FlPSgWYPpq5eZzzBTZvEIOmMB-UUoVXl-H0Ds6o-8QI&s=o2C7x5uPOBDM04QgZwXutO5Ss-V-ZqiQSgw3JctMdgs&e=
<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FlPSgWYPpq5eZzzBTZvEIOmMB-UUoVXl-H0Ds6o-8QI&s=o2C7x5uPOBDM04QgZwXutO5Ss-V-ZqiQSgw3JctMdgs&e=>
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 at r-project.org<mailto:Bioc-devel at r-project.org>
<mailto:Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org>><mailto:Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org>
<mailto:Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org>>> mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FlPSgWYPpq5eZzzBTZvEIOmMB-UUoVXl-H0Ds6o-8QI&s=o2C7x5uPOBDM04QgZwXutO5Ss-V-ZqiQSgw3JctMdgs&e=
<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FlPSgWYPpq5eZzzBTZvEIOmMB-UUoVXl-H0Ds6o-8QI&s=o2C7x5uPOBDM04QgZwXutO5Ss-V-ZqiQSgw3JctMdgs&e=>
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 at r-project.org<mailto:Bioc-devel at r-project.org>
<mailto:Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org>> mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FlPSgWYPpq5eZzzBTZvEIOmMB-UUoVXl-H0Ds6o-8QI&s=o2C7x5uPOBDM04QgZwXutO5Ss-V-ZqiQSgw3JctMdgs&e=
<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FlPSgWYPpq5eZzzBTZvEIOmMB-UUoVXl-H0Ds6o-8QI&s=o2C7x5uPOBDM04QgZwXutO5Ss-V-ZqiQSgw3JctMdgs&e=>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N
<https://urldefense.proofpoint.com/v2/url?u=https-3A__maps.google.com_-3Fq-3D1100-2BFairview-2BAve.-2BN-26entry-3Dgmail-26source-3Dg&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=uyIFjpL7wep4FyufJhLYsoBHxnLP8tcCArZLZdua1MY&s=dchTsUqdQMAnLluyGzpxyuxQ1PEFqkvuibVSfgh5w2Y&e=>,
M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fredhutch.org<mailto:hpages at fredhutch.org> <mailto:hpages at fredhutch.org<mailto:hpages at fredhutch.org>>
Phone: (206) 667-5791<tel:%28206%29%20667-5791> <tel:%28206%29%20667-5791>
Fax: (206) 667-1319<tel:%28206%29%20667-1319> <tel:%28206%29%20667-1319>
_______________________________________________
Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> <mailto:Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org>>
mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zSoaByKtFW_c5CWf0Fc98NkhxwypZpujFQp0ZN5jwOI&s=D8I8ZrFeeBUFenF3KnBb2_mVP4mvvQpK-H2Pwm0Z-mk&e=
<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=uyIFjpL7wep4FyufJhLYsoBHxnLP8tcCArZLZdua1MY&s=JPlDv116uLNLKB7qugE7ScZnpehEnLXnL-ALP5aiD0Q&e=>
--
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ
<https://urldefense.proofpoint.com/v2/url?u=https-3A__maps.google.com_-3Fq-3D385a-2BGlossop-2BRd-2C-2BSheffield-2C-2BS10-2B2HQ-26entry-3Dgmail-26source-3Dg&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=uyIFjpL7wep4FyufJhLYsoBHxnLP8tcCArZLZdua1MY&s=4qo8KXmEZAYrs1orxWWzZrYuQLlLsLtq57YxqhFOyb0&e=>
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.
--
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ
<https://urldefense.proofpoint.com/v2/url?u=https-3A__maps.google.com_-3Fq-3D385a-2BGlossop-2BRd-2C-2BSheffield-2C-2BS10-2B2HQ-26entry-3Dgmail-26source-3Dg&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=uyIFjpL7wep4FyufJhLYsoBHxnLP8tcCArZLZdua1MY&s=4qo8KXmEZAYrs1orxWWzZrYuQLlLsLtq57YxqhFOyb0&e=>
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.
--
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ
--
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: hpages at fredhutch.org<mailto:hpages at fredhutch.org>
Phone: (206) 667-5791<tel:%28206%29%20667-5791>
Fax: (206) 667-1319<tel:%28206%29%20667-1319>
--
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ
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]]
More information about the Bioc-devel
mailing list