Re: [Bioc-devel] SBGNview package build error: data package not available. (SBGNview.data not in build/check results)
Got it! Thank you all for the information!
On Tue, Jun 25, 2019 at 10:24 AM Pages, Herve wrote:
> Also please note that data experiment packages are on a different
> report (and SBGNview.data is in it):
>
>https://bioconductor.org/checkResults/3.10/data-experiment-LATEST/
>
> As Lori said it can take a few build cycles before SBGNview.data gets
> installed on all the build machines.
>
> H.
>
> On 6/25/19 05:14, Shepherd, Lori wrote:
> > Data packages are built Sunday, Tuesday, and Thursday. It can sometimes
> take a full week for the experiment package to build and the software
> package to pick up on it. Please be patient and if it still can't find it
> by next week please let us know and we will investigate further.
> >
> >
> > Lori Shepherd
> >
> > Bioconductor Core Team
> >
> > Roswell Park Cancer Institute
> >
> > Department of Biostatistics & Bioinformatics
> >
> > Elm & Carlton Streets
> >
> > Buffalo, New York 14263
> >
> >
> > From: Bioc-devel on behalf of dong
> xiaoxi
> > Sent: Sunday, June 23, 2019 1:00:55 PM
> > To: bioc-devel@r-project.org
> > Subject: [Bioc-devel] SBGNview package build error: data package not
> available. (SBGNview.data not in build/check results)
> >
> > Dear Bioconductor team,
> >
> > I'm checking the 'checkResults' of a recently accepted package
> 'SBGNview'.
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_3.10_bioc-2DLATEST_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-6k1qazDmtdnPp75PIf_bEXdVRIZd3tWtvhHKDXkdDo=INvtI5jnfX7jcxOXjHqxTfODGozRG9jkW8yjr_R3ONQ=
> > The result shows error because the data package it depends on
> > ('SBGNview.data') is 'not available'. Also 'SBGNview.data' is not in the
> > 'checkResults' page. Can I do something to fix this? Thanks!
> >
> >
> > Best,
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-6k1qazDmtdnPp75PIf_bEXdVRIZd3tWtvhHKDXkdDo=ckNz41rDHG57AZ7s8LneA_-6u5b4ngofPBHllVUOYQE=
> >
> >
> > 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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-6k1qazDmtdnPp75PIf_bEXdVRIZd3tWtvhHKDXkdDo=ckNz41rDHG57AZ7s8LneA_-6u5b4ngofPBHllVUOYQE=
> >
>
> --
> 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
>
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Re: [Bioc-devel] SBGNview package build error: data package not available. (SBGNview.data not in build/check results)
Also please note that data experiment packages are on a different
report (and SBGNview.data is in it):
https://bioconductor.org/checkResults/3.10/data-experiment-LATEST/
As Lori said it can take a few build cycles before SBGNview.data gets
installed on all the build machines.
H.
On 6/25/19 05:14, Shepherd, Lori wrote:
> Data packages are built Sunday, Tuesday, and Thursday. It can sometimes take
> a full week for the experiment package to build and the software package to
> pick up on it. Please be patient and if it still can't find it by next week
> please let us know and we will investigate further.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
>
> From: Bioc-devel on behalf of dong xiaoxi
>
> Sent: Sunday, June 23, 2019 1:00:55 PM
> To: bioc-devel@r-project.org
> Subject: [Bioc-devel] SBGNview package build error: data package not
> available. (SBGNview.data not in build/check results)
>
> Dear Bioconductor team,
>
> I'm checking the 'checkResults' of a recently accepted package 'SBGNview'.
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_3.10_bioc-2DLATEST_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-6k1qazDmtdnPp75PIf_bEXdVRIZd3tWtvhHKDXkdDo=INvtI5jnfX7jcxOXjHqxTfODGozRG9jkW8yjr_R3ONQ=
> The result shows error because the data package it depends on
> ('SBGNview.data') is 'not available'. Also 'SBGNview.data' is not in the
> 'checkResults' page. Can I do something to fix this? Thanks!
>
>
> Best,
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-6k1qazDmtdnPp75PIf_bEXdVRIZd3tWtvhHKDXkdDo=ckNz41rDHG57AZ7s8LneA_-6u5b4ngofPBHllVUOYQE=
>
>
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-6k1qazDmtdnPp75PIf_bEXdVRIZd3tWtvhHKDXkdDo=ckNz41rDHG57AZ7s8LneA_-6u5b4ngofPBHllVUOYQE=
>
--
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
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Re: [Bioc-devel] Error No internet connection using 'localHub=TRUE' during FlowSorted.CordBloodCombined.450k package installation
There are system environment variables that can be set that
ExperimentHub/AnnotationHub will grab automatically from the environment.
If a computer has the system environment variable EXPERIMENT_HUB_PROXY
(ANNOTATION_HUB_PROXY) the hubs recognize these and set them automatically
rather than having to call the constructor with the proxy. The User that is
operating through a proxy should set these values on their machine.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Bioc-devel on behalf of Lucas A. Salas
Diaz
Sent: Monday, June 24, 2019 3:19:09 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Error No internet connection using 'localHub=TRUE' during
FlowSorted.CordBloodCombined.450k package installation
Hi,
One of the users of our FlowSorted.CordBloodCombined.450k package contacted me
for advice about an issue during installation using either Bioconductor 3.9 and
3.10. The issue appears when trying to access the ExperimentHub and dealing
with a proxy. A similar error was previously reported by Tim Triche and lead to
an interesting discussion with the Bioconductor group:
https://support.bioconductor.org/p/111958/
However, in this case the problem appears during the .onLoad instead of during
the .onAttach. I was not able to reproduce the problem locally. Thus, I believe
this is a problem that I should solve for future users.
Do you have any advice on how to solve this problem from the
BiocManager::install or from the FlowSorted.CordBloodCombined.450k:::.onLoad?
Your advice will be really appreciated.
Lucas
Below a fragment of the issue and potential problematic areas:
> library(BiocManager)
�
> BiocManager::install("FlowSorted.CordBloodCombined.450k")
Bioconductor version 3.10 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing package(s) 'FlowSorted.CordBloodCombined.450k'
trying URL
'https://bioconductor.org/packages/3.10/data/experiment/src/contrib/FlowSorted.CordBloodCombined.450k_1.1.0.tar.gz'
Content type 'application/x-gzip' length 57511 bytes (56 KB)
==
downloaded 56 KB
* installing *source* package �FlowSorted.CordBloodCombined.450k� ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package �FlowSorted.CordBloodCombined.450k�
finding HTML links ... done
FlowSorted.CordBloodCombined.450K html
FlowSorted.CordBloodCombined.450k.compTable
html
IDOLOptimizedCpGsCordBlood html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No internet connection using 'localHub=TRUE'
snapshotDate(): 2019-06-20
Error: package or namespace load failed for �FlowSorted.CordBloodCombined.450k�:
.onLoad failed in loadNamespace() for 'FlowSorted.CordBloodCombined.450k',
details:
call: FUN(X[[i]], ...)
error: �FlowSorted.CordBloodCombined.450k� not found in ExperimentHub
Error: loading failed
Execution halted
ERROR: loading failed
* removing
�/usr/local/apps/R/3.6/site-library_3.6.0/FlowSorted.CordBloodCombined.450k�
* restoring previous
�/usr/local/apps/R/3.6/site-library_3.6.0/FlowSorted.CordBloodCombined.450k�
The .onLoad here calls to createHubAccessors:
> FlowSorted.CordBloodCombined.450k:::.onLoad
function (libname = find.package("FlowSorted.CordBloodCombined.450k"),
pkgname = "FlowSorted.CordBloodCombined.450k")
{
fl <- system.file("extdata", "metadata.csv",
package = pkgname)
titles <- read.csv(fl, stringsAsFactors = FALSE)$Title
createHubAccessors(pkgname, titles)
}
In the meantime they were able to access the database using the following
commands:
> library(ExperimentHub)
�
> hub <- ExperimentHub(proxy=Sys.getenv("http_proxy"))
Cannot determine internet connection.
If you experience connection issues consider using 'localHub=TRUE'
snapshotDate(): 2019-06-20
> query(hub, "FlowSorted.CordBloodCombined.450k")
ExperimentHub with 1 record
# snapshotDate(): 2019-06-20
# names(): EH2256
# package(): FlowSorted.CordBloodCombined.450k
# $dataprovider: Bioconductor, Bioconductor, GEO, karnanilab
# $species: Homo sapiens
# $rdataclass: RGChannelSet
# $rdatadateadded: 2019-01-25
# $title: FlowSorted.CordBloodCombined.450k
# $description: The FlowSorted.CordBloodCombined.450k package contains data ...
# $taxonomyid: 9606
# $genome: hg19
# $sourcetype: tar.gz
# $sourceurl: https://bit.ly/2UaTNSi, https://bit.ly/2RQ1nVF, https://bit.ly...
# $sourcesize: NA
# $tags: c("ExperimentData", "Homo_sapiens_Data", "Tissue",
# "MicroarrayData", "Genome", "TissueMicroarrayData",
# "MethylationArrayData", "ExperimentHub")
# retrieve record with 'object[["EH2256"]]'
His sessionInfo
>
Re: [Bioc-devel] SBGNview package build error: data package not available. (SBGNview.data not in build/check results)
Data packages are built Sunday, Tuesday, and Thursday. It can sometimes take a
full week for the experiment package to build and the software package to pick
up on it. Please be patient and if it still can't find it by next week please
let us know and we will investigate further.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Bioc-devel on behalf of dong xiaoxi
Sent: Sunday, June 23, 2019 1:00:55 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] SBGNview package build error: data package not available.
(SBGNview.data not in build/check results)
Dear Bioconductor team,
I'm checking the 'checkResults' of a recently accepted package 'SBGNview'.
https://bioconductor.org/checkResults/3.10/bioc-LATEST/
The result shows error because the data package it depends on
('SBGNview.data') is 'not available'. Also 'SBGNview.data' is not in the
'checkResults' page. Can I do something to fix this? Thanks!
Best,
[[alternative HTML version deleted]]
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Re: [Bioc-devel] Fwd: banocc problems reported in the Multiple platform build/check report for BioC 3.9
The error reported by the build system is reproducible on my mac running R
CMD check on
banocc_1.8.0.tar.gz
The check error is pretty terse. I turned your vignette into
an R script using knitr::purl and ran into
> compiled_banocc_model <- rstan::stan_model(model_code =
banocc::banocc_model)
DIAGNOSTIC(S) FROM PARSER:
Info: integer division implicitly rounds to integer. Found int division: (P
* (P - 1)) / 2
Positive values rounded down, negative values rounded up or down in
platform-dependent way.
*Error in compileCode(f, code, language = language, verbose = verbose) : *
* Compilation ERROR, function(s)/method(s) not created! In file included
from file15ef4c04043e.cpp:8:*
*In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:*
*In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math.hpp:4:*
*In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:*
*In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:5:*
*In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/rev/core/build_vari_array.hpp:4:*
*In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:*
*In file included from
/Library/Frameworks/R.framework/Versions/3.6/Resources/l*
*In addition: Warning message:*
*In system(cmd, intern = !verbose) :*
* running command '/Library/Frameworks/R.framework/Resources/bin/R CMD
SHLIB file15ef4c04043e.cpp 2> file15ef4c04043e.cpp.err.txt' had status 1*
Selection:
I don't know how to interpret this as I don't make much use of rstan.
Even though you have not changed anything in this version of banocc,
other software that you rely on may be changing ... perhaps
https://github.com/stan-dev/rstan/issues/666 is relevant?
On Mon, Jun 24, 2019 at 10:27 PM George Weingart
wrote:
> Hello !
>
> I am receiving these messages.
>
> We haven't changed anything in the package and all of a sudden we are
> getting errors to the effect that the "vignette build failed" "because a
> connect error"
>
> I do not know what causes the error (Since we haven't changed anything in
> the package) and how to recreate it.
>
> Can you assist solving the issue ?
>
> Thanks!
>
> George Weingart PhD
> Huttenhower Lab
> Harvard School of Pubilc Health
>
>
>
> -- Forwarded message -
> From:
> Date: Mon, Jun 24, 2019 at 11:36 AM
> Subject: banocc problems reported in the Multiple platform build/check
> report for BioC 3.9
> To:
>
>
> [This is an automatically generated email. Please don't reply.]
>
> Hi banocc maintainer,
>
> According to the Multiple platform build/check report for BioC 3.9,
> the banocc package has the following problem(s):
>
> o ERROR for 'R CMD build' on malbec2. See the details here:
>
>
> https://master.bioconductor.org/checkResults/3.9/bioc-LATEST/banocc/malbec2-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!
>
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>
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[Bioc-devel] package test failing due to CSAW
Hi All The check of my package is failing locally due to the error in "csaw::scaledAverage" function. Untill version 3.9, I used to pass a DGElist object to this function call as follows: /dat.y <- csaw::asDGEList(data, assay = assay.data)//# create DGElist from SE object //dat.y <- edgeR::estimateCommonDisp(dat.y)//# estimate dispersion / /data.ab <- csaw::scaledAverage(dat.y, scale = 1, prior.count = 1) # get scaled average / Now in version 3.10 I get the following error: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘assay’ for signature ‘"DGEList", "character"’ Is CSAW not accepting DGElist anymore? How shall I replace this function call here? Thanks, Vivek [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
