Re: [Bioc-devel] [EXTERNAL] Deeptarget package
Dear Trinh and Martin, thanks for the update and for the suggestions how to deal in such situation. Best regards Kristian -- Kristian Ullrich, Ph.D. Max Planck Institute For Evolutionary Biology Scientific IT group Department of Evolutionary Genetics August Thienemann Str. 2 24306 Plön Germany +49 4522 763 313 ullr...@evolbio.mpg.de “Ich weiß, allen tut's leid. Jeder muss gucken, wo er bleibt. Dein Lohn, so gut wie nichts. Nichts, was du tust, fällt ins Gewicht.” (Die traurigen Hummer; Moritz Krämer) -- CONFIDENTIALITY NOTICE: The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential and/or privileged information and may be legally protected from disclosure. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited. > On 8. Jul 2024, at 23:23, Nguyen, Trinh (NIH/NCI) [C] > wrote: > > Dear Dr. Kristian, > > We consulted with experts at our NIH/NCI here and per their suggestion, we > have added the following paragraph to the description and document of > Workflow Demonstration as below: > “The user of this package is required to agree to the terms and conditions of > DepMap portal (https://depmap.org/portal/ <https://depmap.org/portal/>). > Some of these terms and conditions are problematic for U.S. Federal > Government employees, and they should consult their technology transfer > office/legal office before agreeing to such terms and conditions” > > Best, > > Trinh > > From: Kristian Ullrich <mailto:ullr...@evolbio.mpg.de>> > Date: Tuesday, June 25, 2024 at 1:45 AM > To: Nguyen, Trinh (NIH/NCI) [C] <mailto:tinh.ngu...@nih.gov>> > Cc: Laurent Gatto <mailto:laurent.ga...@uclouvain.be>>, Kern, Lori > mailto:lori.sheph...@roswellpark.org>>, > bioc-devel@r-project.org <mailto:bioc-devel@r-project.org> > mailto:bioc-devel@r-project.org>> > Subject: Re: [EXTERNAL] [Bioc-devel] Deeptarget package > > Dear Nguyen, > > Thank you for your response. > > I am just a bit puzzled, and no other developer has answered so far. > > E.g. in the description of the depmap package it says: > > "This data is distributed under the Creative Commons license (Attribution 4.0 > International (CC BY 4.0))." > > Anyhow if you visit the original source database it comes with the Terms and > conditions that one need to agree and it says specifically: > > "Governing Law > The terms and conditions herein shall be construed, governed, interpreted, > and applied in accordance with the internal laws of the Commonwealth of > Massachusetts, U.S.A. Furthermore, by accessing, downloading, or using the > Database, You consent to the personal jurisdiction of, and venue in, the > state and federal courts within Massachusetts with respect to Your download > or use of the Database." > So if it comes to law, it does not matter, that you just use a subset of the > original data or that you just get it from another source, since the > statement is kind of very clear. > > I do not see any kind of agreement in the depmap package nor a "warning" > statement, like "by using this package you agree on the following terms …" > > So how to deal correctly (legally and code-wise) in this situation? > > Best regards > > -- > Kristian Ullrich, Ph.D. > Max Planck Institute > For Evolutionary Biology > > Scientific IT group > Department of Evolutionary Genetics > August Thienemann Str. 2 > 24306 Plön > Germany > +49 4522 763 313 > ullr...@evolbio.mpg.de <mailto:ullr...@evolbio.mpg.de> > > “Ich weiß, allen tut's leid. Jeder muss gucken, wo er bleibt. Dein Lohn, so > gut wie nichts. Nichts, was du tust, fällt ins Gewicht.” (Die traurigen > Hummer; Moritz Krämer) > > -- > CONFIDENTIALITY NOTICE: > The contents of this email message and any attachments are intended solely > for the addressee(s) and may contain confidential and/or privileged > information and may be legally protected from disclosure. If you are not the > intended recipient, you are hereby notified that any use, dissemination, > copying, or storage of this message or its attachments is strictly prohibited. > > > On 12. Jun 2024, at 15:53, Nguyen, Trinh (NIH/NCI) [C] <mailto:tinh.ngu...@nih.gov>> wrote: > > Dear Kristian, > > This is very important question. Thanks for checking in. The manuscript is > under review, and I believe that we already agreed and followed to Depmap’s > policies. The input data we used in this package here contains only a subset > o
Re: [Bioc-devel] [EXTERNAL] Deeptarget package
Dear Nguyen, Thank you for your response. I am just a bit puzzled, and no other developer has answered so far. E.g. in the description of the depmap package it says: "This data is distributed under the Creative Commons license (Attribution 4.0 International (CC BY 4.0))." Anyhow if you visit the original source database it comes with the Terms and conditions that one need to agree and it says specifically: "Governing Law The terms and conditions herein shall be construed, governed, interpreted, and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A. Furthermore, by accessing, downloading, or using the Database, You consent to the personal jurisdiction of, and venue in, the state and federal courts within Massachusetts with respect to Your download or use of the Database." So if it comes to law, it does not matter, that you just use a subset of the original data or that you just get it from another source, since the statement is kind of very clear. I do not see any kind of agreement in the depmap package nor a "warning" statement, like "by using this package you agree on the following terms …" So how to deal correctly (legally and code-wise) in this situation? Best regards -- Kristian Ullrich, Ph.D. Max Planck Institute For Evolutionary Biology Scientific IT group Department of Evolutionary Genetics August Thienemann Str. 2 24306 Plön Germany +49 4522 763 313 ullr...@evolbio.mpg.de “Ich weiß, allen tut's leid. Jeder muss gucken, wo er bleibt. Dein Lohn, so gut wie nichts. Nichts, was du tust, fällt ins Gewicht.” (Die traurigen Hummer; Moritz Krämer) -- CONFIDENTIALITY NOTICE: The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential and/or privileged information and may be legally protected from disclosure. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited. > On 12. Jun 2024, at 15:53, Nguyen, Trinh (NIH/NCI) [C] > wrote: > > Dear Kristian, > > This is very important question. Thanks for checking in. The manuscript is > under review, and I believe that we already agreed and followed to Depmap’s > policies. The input data we used in this package here contains only a subset > of the data we used in the manuscript, and it is for demonstration how the > package works. In addition to this, Deeptarget does have a function to pull > out the data from Depmap and it is called Depmap2DeepTarget. I think this is > where your concern is coming from. This function we incorporated the Depmap > package from @Laurent Gatto <mailto:laurent.ga...@uclouvain.be> which allows > users to download data from depmap.org <http://depmap.org/>. Therefore, I > would love to leave this for @Laurent Gatto > <mailto:laurent.ga...@uclouvain.be> to chime in to address your concern. > > Thanks, > > Trinh > > From: Kristian Ullrich > Date: Wednesday, June 12, 2024 at 2:42 AM > To: Nguyen, Trinh (NIH/NCI) [C] > Cc: Kern, Lori , bioc-devel@r-project.org > > Subject: [EXTERNAL] Re: [Bioc-devel] Deeptarget package > > Dear Nguyen, > > I have a question related to the data that you use and I just bring it up > here since I would also like to ask the bioconductor developers, how this can > be handled properly. > > The depmap.org <http://depmap.org/> portal has a clear "Terms and Condition" > statement that you need to agree on if one uses any of the data that is > provided by the portal. (See below) So one need to click a "I agree" button > to stick to their policies. > > How have you managed that a user of your package first send this agreement to > the depmap.org <http://depmap.org/> portal once the user uses data from the > portal? > > Thank you in anticipation > > Best regards > > Kristian > > Here is their policy: > > " > Terms and Conditions > > By using this site, you agree to our terms and conditions below. > > Overview of Terms > > These Terms of Use reflect the Broad Institute’s commitment to Open Science > through its mission to provide freely available online services, databases > and software relating to data contributed from life science experiments to > the largest possible community. They impose no additional constraints on the > use of the contributed data than those provided by the original data owners. > The data made available on this website were generated for research purposes > and are not intended for clinical use. > The original data may be subject to rights claimed by third parties, > including but not limi
Re: [Bioc-devel] Deeptarget package
ued, governed, interpreted, and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A. Furthermore, by accessing, downloading, or using the Database, You consent to the personal jurisdiction of, and venue in, the state and federal courts within Massachusetts with respect to Your download or use of the Database. Privacy See our privacy policy here <https://depmap.org/portal/privacy/>. " -- Kristian Ullrich, Ph.D. Max Planck Institute For Evolutionary Biology Scientific IT group Department of Evolutionary Genetics August Thienemann Str. 2 24306 Plön Germany +49 4522 763 313 ullr...@evolbio.mpg.de “Ich weiß, allen tut's leid. Jeder muss gucken, wo er bleibt. Dein Lohn, so gut wie nichts. Nichts, was du tust, fällt ins Gewicht.” (Die traurigen Hummer; Moritz Krämer) -- CONFIDENTIALITY NOTICE: The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential and/or privileged information and may be legally protected from disclosure. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited. > On 11. Jun 2024, at 20:04, Nguyen, Trinh (NIH/NCI) [C] via Bioc-devel > wrote: > > Thank You! > > Trinh > > From: Kern, Lori > Date: Tuesday, June 11, 2024 at 12:19 PM > To: bioc-devel@r-project.org , Nguyen, Trinh > (NIH/NCI) [C] > Subject: [EXTERNAL] Re: Deeptarget package > Two things: > > > 1. The package was accepted on Friday. Currently our software builds are > only building twice a week Tue and Fri. You can see the schedule of all the > different builds at https://bioconductor.org/checkResults/. Eventually devel > Bioc will go back to daily builds but there are some configurations we are > currently working on. Once the package builds/checks cleanly on the daily > builder it will then be available (likely later today) > > > 1. Your package will only be available in Bioc devel 3.19 until the fall > release as newly accepted package are placed until devel until a full release > announcement. > > > > 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 Nguyen, > Trinh (NIH/NCI) [C] via Bioc-devel > Sent: Tuesday, June 11, 2024 12:10 PM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] Deeptarget package > > Dear Bioconductor team, > > Deeptarget package has been accepted. However, when I installed it has error > of �package �DeepTarget� is not available for Bioconductor version '3.18'� > > Could you please give me some guidance? > > Thanks, > > Trinh > > >[[alternative HTML version deleted]] > > 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. > CAUTION: This email originated from outside of the organization. Do not click > links or open attachments unless you recognize the sender and are confident > the content is safe. > > > [[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] nebbiolo1 - build report
Hi,
I just got an email from bbs:
Hi MSA2dist maintainer,
According to the Multiple platform build/check report for BioC 3.19,
the MSA2dist package has the following problem(s):
o ERROR for 'R CMD INSTALL' on nebbiolo1. See the details here:
https://bioconductor.org/checkResults/3.19/bioc-LATEST/MSA2dist/nebbiolo1-install.html
<https://bioconductor.org/checkResults/3.19/bioc-LATEST/MSA2dist/nebbiolo1-install.html>
o ERROR for 'R CMD build' on nebbiolo1. See the details here:
https://bioconductor.org/checkResults/3.19/bioc-LATEST/MSA2dist/nebbiolo1-buildsrc.html
<https://bioconductor.org/checkResults/3.19/bioc-LATEST/MSA2dist/nebbiolo1-buildsrc.html>
However, if I check the the page, there are no ERROR listed:
Report page was generated:
This page was generated on 2024-04-23 11:37:19 -0400 (Tue, 23 Apr 2024).
Should I just wait or where I can find the mentioned ERROR?
Best regards
Kristian
--
Kristian Ullrich, Ph.D.
Max Planck Institute
For Evolutionary Biology
Scientific IT group
Department of Evolutionary Genetics
August Thienemann Str. 2
24306 Plön
Germany
+49 4522 763 313
ullr...@evolbio.mpg.de
“Ich weiß, allen tut's leid. Jeder muss gucken, wo er bleibt. Dein Lohn, so gut
wie nichts. Nichts, was du tust, fällt ins Gewicht.” (Die traurigen Hummer;
Moritz Krämer)
--
CONFIDENTIALITY NOTICE:\ The contents of this email mess...{{dropped:11}}
___
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Re: [Bioc-devel] Build issue on nebbiolo2 for DEWSeq
Dear Sudeep, Have you tried to use the R basic pipe "|>" instead of the magrittr pipe? If you use it directly in your R function you could add in the corresponding function the following line: @importFrom magrittr %>% Best regards Kristian -- Kristian Ullrich, Ph.D. Max Planck Institute For Evolutionary Biology Scientific IT group Department of Evolutionary Genetics August Thienemann Str. 2 24306 Plön Germany +49 4522 763 313 ullr...@evolbio.mpg.de “Und was wir, was wir haben wollen, es liegt vor uns. Und was wir, was wir haben wollen, es gehört uns, gehört uns nicht.” (Aliens; Die Höchste Eisenbahn) -- CONFIDENTIALITY NOTICE: The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential and/or privileged information and may be legally protected from disclosure. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited. > On 15. Nov 2023, at 08:23, Biohentze wrote: > > Dear all, > > We are facing build issue on nebbiolo2 on our vignette for the package > DEWSeq. The issue is that we use magittr pipe (%>%) in the vignette and the > issue occurs only on the linux machine. > Checks, builds and installation completes successfully on windows and mac. > Here is the complete build report: > https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/DEWSeq/nebbiolo2-checksrc.html > > Could you please look into it ? > > Thank you in advance, > Sudeep. > > [[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
