Closed scanopm closed 5 years ago
Hi @scanopm
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: GladiaTOX
Type: Package
biocViews:
Software,
WorkflowStep,
Normalization,
Preprocessing
Title: R Package for Processing High Content Screening data
Version: 0.99.0
Author: Vincenzo Belcastro [aut, cre],
Dayne L Filer <dayne.filer@gmail.com> [aut],
Stephane Cano [aut]
Maintainer: PMP S.A. R Support <DL.RSupport@pmi.com>
Description: GladiaTOX is an open-source solution for HCS data processing and reporting that expands the toxcast pipeline package.
License: GPL-2, file COPYING, file LICENSE
Depends:
R (>= 3.2.0),
data.table (>= 1.9.4)
Imports:
DBI,
RMySQL,
RSQLite,
numDeriv,
RColorBrewer,
parallel,
stats,
methods,
graphics,
grDevices,
xtable,
tools,
brew,
stringr,
RJSONIO,
ggplot2,
ggrepel,
tidyr,
utils
LazyData: TRUE
VignetteBuilder: knitr
Suggests:
roxygen2,
knitr,
rmarkdown,
testthat
NeedsCompilation: no
RoxygenNote: 5.0.1
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Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Received a valid push; starting a build. Commits are:
793d158 Bump version
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Received a valid push; starting a build. Commits are:
4f511e2 bump version
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Dear Team,
I get an error message while my package is BiocChecked:
Error in SweaveParseOptions(chunkopts, drobj$options, driver$checkopts) : parse error or empty option in <%= paste0("m4id", pcid) %>,fig=true,strip.white=true,echo=false,height=7,width=12 Calls: ... lapply -> FUN -> Stangle -> Sweave -> SweaveParseOptions Execution halted
http://bioconductor.org/spb_reports/GladiaTOX_buildreport_20181112095459.html#tokay1_check_anchor
I believe that the issue is that the code (paste0("m4id", pcid)) is not evaluated (only syntax check), and the Sweave parses reject it. I’m not sure how to cope with this situation.
Best, Vincenzo
From: bioc-issue-bot [mailto:notifications@github.com] Sent: 12 November 2018 15:55 To: Bioconductor/Contributions Contributions@noreply.github.com Cc: Belcastro, Vincenzo (contracted) Vincenzo.Belcastro@contracted.pmi.com; Manual manual@noreply.github.com Subject: Re: [Bioconductor/Contributions] New Package Submission: GladiaTOX (#932)
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build reporthttp://bioconductor.org/spb_reports/GladiaTOX_buildreport_20181112095459.html for more details.
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/Bioconductor/Contributions/issues/932#issuecomment-437910453, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AkvW6_rg-3nrQL3Eldi8FKqxH9IOxUgRks5uuYvFgaJpZM4YWziT.
If this is a false positive please ignore the error. Please clean up the other parts of the build report, e.g., the undefined global symbols, so it is clear what the remaining issues are.
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Received a valid push; starting a build. Commits are:
67a9400 Version bump: 0.99.5
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Received a valid push; starting a build. Commits are:
450b15b version 0.99.6; R>=3.5
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
I was able to overcome the Sweave issue. New the package builds with no ERRORS/WARNINGS.
About the “undefined symbols”: those are data.table column names, unquoted as expected by data.table.
Best, Vincenzo
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build reporthttp://bioconductor.org/spb_reports/GladiaTOX_buildreport_20181113032607.html for more details. —
From: Martin Morgan [mailto:notifications@github.com] Sent: 12 November 2018 16:46 To: Bioconductor/Contributions Contributions@noreply.github.com Cc: Belcastro, Vincenzo (contracted) Vincenzo.Belcastro@contracted.pmi.com; Manual manual@noreply.github.com Subject: Re: [Bioconductor/Contributions] New Package Submission: GladiaTOX (#932)
If this is a false positive please ignore the error. Please clean up the other parts of the build report, e.g., the undefined global symbols, so it is clear what the remaining issues are.
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/Bioconductor/Contributions/issues/932#issuecomment-437928872, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AkvW6zficCEUGSa39JIyYxBqghcJBmUbks5uuZfLgaJpZM4YWziT.
See ?globalVariables
to see how to suppress these messages; it is in the long run better to suppress these messages and have an obviously clean build report than to have a build report filled with false positives.
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
Received a valid push; starting a build. Commits are:
cd1929d version bump
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "ABNORMAL". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Received a valid push; starting a build. Commits are:
7f2cf2e version bump
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "ABNORMAL". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Received a valid push; starting a build. Commits are:
658ca53 version bump
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "ABNORMAL". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "skipped, ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
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Received a valid push; starting a build. Commits are:
7212112 version bump
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "skipped, ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
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Received a valid push; starting a build. Commits are:
ae1400c version bump
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS, skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Received a valid push; starting a build. Commits are:
e64e1e9 version bump
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Dear BioC team,
The package submission resulted in an ERROR on the new building system you recently deployed (I had no ERRORS on the previous one). The ERROR only appear on OS building/check. I’m not sure if that is a package issue or the “merida2” is missing some component.
Best, Vincenzo
From: bioc-issue-bot [mailto:notifications@github.com] Sent: 19 November 2018 09:25 To: Bioconductor/Contributions Contributions@noreply.github.com Cc: Belcastro, Vincenzo (contracted) Vincenzo.Belcastro@contracted.pmi.com; Manual manual@noreply.github.com Subject: Re: [Bioconductor/Contributions] New Package Submission: GladiaTOX (#932)
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build reporthttp://bioconductor.org/spb_reports/GladiaTOX_buildreport_20181119032439.html for more details.
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/Bioconductor/Contributions/issues/932#issuecomment-439808514, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AkvW63mgBSitcpCMUG0igr5MzkMAkzZmks5uwmrKgaJpZM4YWziT.
Hello @vbelcastPM,
Thank you for bringing this to our attention. Our team is looking into the issue and we will let you know when it is resolved.
Kayla Morrell
Received a valid push; starting a build. Commits are:
c1dfb78 version bump
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "skipped, ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Dear Kayla,
Is there any news about the issue below? It is preventing us to move forward with the publication of the package.
Best, Vincenzo
From: Kayla-Morrell [mailto:notifications@github.com] Sent: 21 November 2018 15:27 To: Bioconductor/Contributions Contributions@noreply.github.com Cc: Belcastro, Vincenzo (contracted) Vincenzo.Belcastro@contracted.pmi.com; Mention mention@noreply.github.com Subject: Re: [Bioconductor/Contributions] New Package Submission: GladiaTOX (#932)
Hello @vbelcastPMhttps://github.com/vbelcastPM,
Thank you for bringing this to our attention. Our team is looking into the issue and we will let you know when it is resolved.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/Bioconductor/Contributions/issues/932#issuecomment-440679829, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AkvW68L50iyK6iYwIrpDedeN849XVgRmks5uxWKxgaJpZM4YWziT.
Received a valid push; starting a build. Commits are:
a1afef8 version bump
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Hello Vincenzo,
We are still looking into the issue in regard to the merida2 build. Please work on the error for the malbec2 platform. In the mean time I have begun working on the review of your package so we can get it ready for acceptance. Please be on the look out for my comments soon.
Thank you. Kayla
Received a valid push; starting a build. Commits are:
d1d1d00 version bump
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "skipped, ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Received a valid push; starting a build. Commits are:
6f8171f ncore detection changed - version bump
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "skipped, ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Thank you for the update.
About the error. It builds nicely on my side. Is it possible you have issues with the parallel package? It is like is not able to detect the number of cores…and cannot fork.
Best, Vincenzo
From: Kayla-Morrell [mailto:notifications@github.com] Sent: 12 December 2018 18:28 To: Bioconductor/Contributions Contributions@noreply.github.com Cc: Belcastro, Vincenzo (contracted) Vincenzo.Belcastro@contracted.pmi.com; Mention mention@noreply.github.com Subject: Re: [Bioconductor/Contributions] New Package Submission: GladiaTOX (#932)
Hello Vincenzo,
We are still looking into the issue in regard to the merida2 build. Please work on the error for the malbec2 platform. In the mean time I have begun working on the review of your package so we can get it ready for acceptance. Please be on the look out for my comments soon.
Thank you. Kayla
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/Bioconductor/Contributions/issues/932#issuecomment-446672466, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AkvW6z2wXBeLF1qvR5c-u96c8xLwcJJ6ks5u4TyrgaJpZM4YWziT.
When running code in examples and vignettes try setting ncores to 2. Right now it seems the package is using the default with is max cores (or detectcores() - 1).
Repository: https://github.com/philipmorrisintl/GladiaTOX
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