Dear Bioc team, I?m the mantainer of the DaMiRseq package. About a week ago, the BUILD ended up in ERROR in the stable release (3.6). The error occurs in each platform during the creation of the vignette. Here the Build/Check report: http://bioconductor.org/checkResults/release/bioc-LATEST/DaMiRseq/ In addition, I noted that the devel release fails, as well; however, here the reason seems to be different: http://bioconductor.org/checkResults/devel/bioc-LATEST/DaMiRseq/ Actually, I didn?t push any changes since the last new Bioc release. Can errors in dependencies be the reason of this BUILD failure? What could I do to solve these issues? Thanks in advance, Mattia
[Bioc-devel] DaMiRseq in ERROR in the stable release
5 messages · Mattia Chiesa, Shepherd, Lori, Martin Morgan
It is quite possible that it could be because of a dependent package. Unfortunately the only way to tell would be to see if any of those packages are producing a similar ERROR on the build report or to investigate your code to see where and how this ERROR is occurring. It is possible that it is a bug in one of the dependencies' code or that it is an intended change that your package would now need to adjust for but you need to better understand where it is coming from. Normally we hope that the release stays fairly stable and only bug fixes are pushed to code in that branch; the devel branch is intended to implement changes to give other maintainers a chance to adapt (or point out bugs to correct). 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> on behalf of Mattia Chiesa <mattia.chiesa at hotmail.it>
Sent: Monday, November 20, 2017 6:12:45 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] DaMiRseq in ERROR in the stable release
Sent: Monday, November 20, 2017 6:12:45 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] DaMiRseq in ERROR in the stable release
Dear Bioc team, I?m the mantainer of the DaMiRseq package. About a week ago, the BUILD ended up in ERROR in the stable release (3.6). The error occurs in each platform during the creation of the vignette. Here the Build/Check report: http://bioconductor.org/checkResults/release/bioc-LATEST/DaMiRseq/ In addition, I noted that the devel release fails, as well; however, here the reason seems to be different: http://bioconductor.org/checkResults/devel/bioc-LATEST/DaMiRseq/ Actually, I didn?t push any changes since the last new Bioc release. Can errors in dependencies be the reason of this BUILD failure? What could I do to solve these issues? Thanks in advance, Mattia [[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.
On 11/20/2017 08:54 AM, Shepherd, Lori wrote:
It is quite possible that it could be because of a dependent package. Unfortunately the only way to tell would be to see if any of those packages are producing a similar ERROR on the build report or to investigate your code to see where and how this ERROR is occurring.
Another place to start is to simply reproduce the error on your own system. Usually this requires running the version of R and Bioconductor on the build system (noted at the top of the multi-platform build / check report page), and making sure that dependencies are current, e.g., by BiocInstaller::biocValid(). For vignettes, it can be helpful to 'Stangle' them and step through the R code chunks in the resulting file R CMD Stangle DaMiRseq.Rnw Martin
It is possible that it is a bug in one of the dependencies' code or that it is an intended change that your package would now need to adjust for but you need to better understand where it is coming from. Normally we hope that the release stays fairly stable and only bug fixes are pushed to code in that branch; the devel branch is intended to implement changes to give other maintainers a chance to adapt (or point out bugs to correct). 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> on behalf of Mattia Chiesa <mattia.chiesa at hotmail.it> Sent: Monday, November 20, 2017 6:12:45 AM To: bioc-devel at r-project.org Subject: [Bioc-devel] DaMiRseq in ERROR in the stable release Dear Bioc team, I?m the mantainer of the DaMiRseq package. About a week ago, the BUILD ended up in ERROR in the stable release (3.6). The error occurs in each platform during the creation of the vignette. Here the Build/Check report: http://bioconductor.org/checkResults/release/bioc-LATEST/DaMiRseq/ In addition, I noted that the devel release fails, as well; however, here the reason seems to be different: http://bioconductor.org/checkResults/devel/bioc-LATEST/DaMiRseq/ Actually, I didn?t push any changes since the last new Bioc release. Can errors in dependencies be the reason of this BUILD failure? What could I do to solve these issues? Thanks in advance, Mattia [[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. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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2 days later
Dear all, we looked at the traceback(): 7: array(STATS, dims[perm]) 6: aperm(array(STATS, dims[perm]), order(perm)) 5: sweep(WW[, 1:opt.comp], 2, Q2TT, "*") 4: apply(sweep(WW[, 1:opt.comp], 2, Q2TT, "*"), 1, sum) 3: VIP(pls.fit, opt.comp = opt.comp) 2: bve_pls(df$class, as.matrix(data), ncomp = num_PC, VIP.threshold = th.VIP) 1: DaMiR.FSelect(data_clean<http://data_clean.mx>, df = df, th.corr = 0.6) and it seems that the problem is the forth point (apply(sweep(WW[, 1:opt.comp], 2, Q2TT, "*"), 1, sum) when opt.comp = 1. ?In this case, WW is a object with NULL dimensions (it is not a matrix anymore), which gives problems to 'sweep()' function (it needs a matrix with at least 1 column). We have already advised the authors and suggested them a possible solution (i.e. WW[, 1:opt.comp, drop=FALSE]) that can fix this bug. Notably, this happens only with 'plsVarSel version = 0.9.2' (released on November 11th ,2017 !!!), which embeds the modified "filter.R" source code, but not with the previous ones. For this reason, in the meantime, we would modify the DESCRIPTION file (both in devel and RELEASE 3_6), forcing the usage of 'plsVarSel version = 0.9.1'. Mattia
Da: Martin Morgan <martin.morgan at roswellpark.org>
Inviato: luned? 20 novembre 2017 15:48 A: Shepherd, Lori; Mattia Chiesa; bioc-devel at r-project.org Oggetto: Re: [Bioc-devel] DaMiRseq in ERROR in the stable release On 11/20/2017 08:54 AM, Shepherd, Lori wrote: > It is quite possible that it could be because of a dependent package. Unfortunately the only way to tell would be to see if any of those packages are producing a similar ERROR on the build report or to investigate your code to see where and how this ERROR is occurring. Another place to start is to simply reproduce the error on your own system. Usually this requires running the version of R and Bioconductor on the build system (noted at the top of the multi-platform build / check report page), and making sure that dependencies are current, e.g., by BiocInstaller::biocValid(). For vignettes, it can be helpful to 'Stangle' them and step through the R code chunks in the resulting file R CMD Stangle DaMiRseq.Rnw Martin > > > It is possible that it is a bug in one of the dependencies' code or that it is an intended change that your package would now need to adjust for but you need to better understand where it is coming from. > > > Normally we hope that the release stays fairly stable and only bug fixes are pushed to code in that branch; the devel branch is intended to implement changes to give other maintainers a chance to adapt (or point out bugs to correct). > > > 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> on behalf of Mattia Chiesa <mattia.chiesa at hotmail.it> > Sent: Monday, November 20, 2017 6:12:45 AM > To: bioc-devel at r-project.org > Subject: [Bioc-devel] DaMiRseq in ERROR in the stable release > > Dear Bioc team, > I?m the mantainer of the DaMiRseq package. About a week ago, the BUILD ended up in ERROR in the stable release (3.6). > The error occurs in each platform during the creation of the vignette. > Here the Build/Check report: > http://bioconductor.org/checkResults/release/bioc-LATEST/DaMiRseq/ > In addition, I noted that the devel release fails, as well; however, here the reason seems to be different: > http://bioconductor.org/checkResults/devel/bioc-LATEST/DaMiRseq/ > Actually, I didn?t push any changes since the last new Bioc release. > Can errors in dependencies be the reason of this BUILD failure? > What could I do to solve these issues? > Thanks in advance, > Mattia > > > [[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. > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > 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.
On 11/22/2017 09:51 AM, Mattia Chiesa wrote:
Dear all, we looked at the traceback(): 7: array(STATS, dims[perm]) 6: aperm(array(STATS, dims[perm]), order(perm)) 5: sweep(WW[, 1:opt.comp], 2, Q2TT, "*") 4: apply(sweep(WW[, 1:opt.comp], 2, Q2TT, "*"), 1, sum) 3: VIP(pls.fit, opt.comp = opt.comp) 2: bve_pls(df$class, as.matrix(data), ncomp = num_PC, VIP.threshold = th.VIP) 1: DaMiR.FSelect(data_clean <http://data_clean.mx>, df = df, th.corr = 0.6) and it seems that the problem is the forth point (apply(sweep(WW[, 1:opt.comp], 2, Q2TT, "*"), 1, sum) when*opt.comp = 1*. ?In this case, WW is a object with NULL dimensions (it is not a matrix anymore), which gives problems to 'sweep()' function (it needs a matrix with at least 1 column). We have already advised the authors and suggested them a possible solution (i.e. WW[, 1:opt.comp, drop=FALSE]) that can fix this bug. Notably, this happens only with 'plsVarSel? version = 0.9.2' (released on November 11th ,2017 !!!), which embeds the modified "filter.R" source code, but not with the previous ones. For this reason,? in the meantime, we would modify the DESCRIPTION file (both in devel and RELEASE 3_6), forcing the usage of 'plsVarSel version = 0.9.1'.
Since this version is not available in the main CRAN repository, your package will simply fail because the specified version cannot be loaded. The best solution is simply to wait for the authors to fix the bug. Note also that 1:opt.comp causes problems, much like omitting drop=FALSE, when opt.comp == 0 and it is always better to use seq_len() (or its compatriot seq_along()). > 1:opt.comp [1] 1 0 > seq_len(opt.comp) integer(0) Martin
Mattia ------------------------------------------------------------------------ *Da:* Martin Morgan <martin.morgan at roswellpark.org> *Inviato:* luned? 20 novembre 2017 15:48 *A:* Shepherd, Lori; Mattia Chiesa; bioc-devel at r-project.org *Oggetto:* Re: [Bioc-devel] DaMiRseq in ERROR in the stable release On 11/20/2017 08:54 AM, Shepherd, Lori wrote:
It is quite possible that it could be because of a dependent package.? Unfortunately the only way to tell would be to see if any of those packages are producing a similar ERROR on the build report or to investigate your code to see where and how this ERROR is occurring.
Another place to start is to simply reproduce the error on your own system. Usually this requires running the version of R and Bioconductor on the build system (noted at the top of the multi-platform build / check report page), and making sure that dependencies are current, e.g., by BiocInstaller::biocValid(). For vignettes, it can be helpful to 'Stangle' them and step through the R code chunks in the resulting file ?? R CMD Stangle DaMiRseq.Rnw Martin
It is possible that it is a bug in one of the dependencies' code or that it is an intended change that your package would now need to adjust for but you need to better understand where it is coming from. Normally we hope that the release stays fairly stable and only bug fixes are pushed to code in that branch; the devel branch is intended to implement changes to give other maintainers a chance to adapt (or point out bugs to correct). 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> on behalf of Mattia Chiesa <mattia.chiesa at hotmail.it> Sent: Monday, November 20, 2017 6:12:45 AM To: bioc-devel at r-project.org Subject: [Bioc-devel] DaMiRseq in ERROR in the stable release Dear Bioc team, I?m the mantainer of the DaMiRseq package. About a week ago, the BUILD ended up in ERROR in the stable release (3.6). The error occurs in each platform during the creation of the vignette. Here the Build/Check report: http://bioconductor.org/checkResults/release/bioc-LATEST/DaMiRseq/ In addition, I noted that the devel release fails, as well; however, here the reason seems to be different: http://bioconductor.org/checkResults/devel/bioc-LATEST/DaMiRseq/ Actually, I didn?t push any changes since the last new Bioc release. Can errors in dependencies be the reason of this BUILD failure? What could I do to solve these issues? Thanks in advance, Mattia ????????? [[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.
??????? [[alternative HTML version deleted]]
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