Re: [Bioc-devel] BiocCheck result
- Original Message - From: Karim Mezhoud kmezh...@gmail.com To: bioc-devel@r-project.org Sent: Friday, January 2, 2015 4:22:44 AM Subject: [Bioc-devel] BiocCheck result Dear all, I have these comments and did not found solution for silencing them. 1 - What about Vignette? The message (below) is saying you need to evaluate more vignette chunks, as mentioned in the BiocCheck vignette (http://www.bioconductor.org/packages/devel/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#Interpreting_BiocCheck_output) at least 50% of vignette chunks need to be evaluated, otherwise you get this RECOMMENDation. 2 - The version is package.0.99.0.tar.gz Looks like you are running BiocCheck under Bioconductor 3.0 (the release version). You should be developing your package under the devel version of Bioconductor (currently 3.1, requires R-devel (R-3.2)). If you do that you won't see this message. 3 - In wich file can I clarify permanent objects. To avoid - I create new Environment with myGlobalEnv - new.env(parent = emptyenv()) I have many permanent objects because my package is a GUI. All these objects are useful for different functions and reduce the computing time and the multiple running of the same function. This is something that is best looked at during the package review process. 4- Indenting, Tabs and long lines were not found. As mentioned in the BiocCheck output and in the vignette, the formatting suggestions are just suggestions. Some of them are more important than others, for example, most reviewers will insist on lines shorter than 80 columns, for readability's sake. Can I submit with theses comments? You can submit, and these issues will be looked at as part of the package review process. Dan Thanks Karim $requirements character(0) $recommendations [1] Evaluate more vignette chunks. y of x.y.z version should be even in release $considerations [1] Clarifying how objects Li, A, ttCasesGenProfs, EventTime, Category, Continu, Category, ttMain, CasesStudies, curselectCases, fname.GCT, fname.CLS, ttMain, GenesDetails, CaseChoice, mSigDB_SubName, GenesDetails, lenght, ttCasesGenProfs, myGlobalEnv (used in canceR , dialogMut , dialogOptionPhenoTest, dialogOptionPhenoTest , getClinicalDataMatrix, geteSet, getGCTCLSExample, getGeneExpMatrix, getGenesClassifier, getGenesTree_MultipleCases, getGSEAlm_Diseases, getGSEAlm_Variables, getMegaProfData, getMetDataMultipleGenes, getMSigDBExample , getMSigDBExample, GSEA, GSEA.Analyze.Sets, plot_1Gene_2GenProfs, testCheckedCaseGenProf) were initialized. Maybe they are part of a data set loaded with data(), or perhaps part of an object referenced in with() or within(). [2] Shortening lines; 1227 lines (11%) are 80 characters long. [3] Replacing tabs with 4 spaces; 6 lines (0%) contain tabs. [4] Indenting lines with a multiple of 4 spaces; 1752 lines (15%) are not. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BiocCheck result
Dear Dr Dan, Thanks, With GUI package the vignette does not have chunks only for installation paragraph. Thanks Karim Ô__ c/ /'_;kmezhoud (*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ http://bioinformatics.tn/ On Fri, Jan 2, 2015 at 6:55 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Karim Mezhoud kmezh...@gmail.com To: bioc-devel@r-project.org Sent: Friday, January 2, 2015 4:22:44 AM Subject: [Bioc-devel] BiocCheck result Dear all, I have these comments and did not found solution for silencing them. 1 - What about Vignette? The message (below) is saying you need to evaluate more vignette chunks, as mentioned in the BiocCheck vignette ( http://www.bioconductor.org/packages/devel/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#Interpreting_BiocCheck_output) at least 50% of vignette chunks need to be evaluated, otherwise you get this RECOMMENDation. 2 - The version is package.0.99.0.tar.gz Looks like you are running BiocCheck under Bioconductor 3.0 (the release version). You should be developing your package under the devel version of Bioconductor (currently 3.1, requires R-devel (R-3.2)). If you do that you won't see this message. 3 - In wich file can I clarify permanent objects. To avoid - I create new Environment with myGlobalEnv - new.env(parent = emptyenv()) I have many permanent objects because my package is a GUI. All these objects are useful for different functions and reduce the computing time and the multiple running of the same function. This is something that is best looked at during the package review process. 4- Indenting, Tabs and long lines were not found. As mentioned in the BiocCheck output and in the vignette, the formatting suggestions are just suggestions. Some of them are more important than others, for example, most reviewers will insist on lines shorter than 80 columns, for readability's sake. Can I submit with theses comments? You can submit, and these issues will be looked at as part of the package review process. Dan Thanks Karim $requirements character(0) $recommendations [1] Evaluate more vignette chunks. y of x.y.z version should be even in release $considerations [1] Clarifying how objects Li, A, ttCasesGenProfs, EventTime, Category, Continu, Category, ttMain, CasesStudies, curselectCases, fname.GCT, fname.CLS, ttMain, GenesDetails, CaseChoice, mSigDB_SubName, GenesDetails, lenght, ttCasesGenProfs, myGlobalEnv (used in canceR , dialogMut , dialogOptionPhenoTest, dialogOptionPhenoTest , getClinicalDataMatrix, geteSet, getGCTCLSExample, getGeneExpMatrix, getGenesClassifier, getGenesTree_MultipleCases, getGSEAlm_Diseases, getGSEAlm_Variables, getMegaProfData, getMetDataMultipleGenes, getMSigDBExample , getMSigDBExample, GSEA, GSEA.Analyze.Sets, plot_1Gene_2GenProfs, testCheckedCaseGenProf) were initialized. Maybe they are part of a data set loaded with data(), or perhaps part of an object referenced in with() or within(). [2] Shortening lines; 1227 lines (11%) are 80 characters long. [3] Replacing tabs with 4 spaces; 6 lines (0%) contain tabs. [4] Indenting lines with a multiple of 4 spaces; 1752 lines (15%) are not. [[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
Re: [Bioc-devel] BiocCheck result
- Original Message - From: Karim Mezhoud kmezh...@gmail.com To: Dan Tenenbaum dtene...@fredhutch.org Cc: bioc-devel@r-project.org Sent: Friday, January 2, 2015 12:15:31 PM Subject: Re: [Bioc-devel] BiocCheck result Dear Dr Dan, Thanks, With GUI package the vignette does not have chunks only for installation paragraph. I'm not sure what you mean here, but I think you should just submit the package and these issues will be discussed during the review process. Don't worry if your package does not pass BiocCheck the first time. We're here to help you through these things. Thanks, Dan Thanks Karim Ô__ c/ /'_;kmezhoud (*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ http://bioinformatics.tn/ On Fri, Jan 2, 2015 at 6:55 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Karim Mezhoud kmezh...@gmail.com To: bioc-devel@r-project.org Sent: Friday, January 2, 2015 4:22:44 AM Subject: [Bioc-devel] BiocCheck result Dear all, I have these comments and did not found solution for silencing them. 1 - What about Vignette? The message (below) is saying you need to evaluate more vignette chunks, as mentioned in the BiocCheck vignette ( http://www.bioconductor.org/packages/devel/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#Interpreting_BiocCheck_output ) at least 50% of vignette chunks need to be evaluated, otherwise you get this RECOMMENDation. 2 - The version is package.0.99.0.tar.gz Looks like you are running BiocCheck under Bioconductor 3.0 (the release version). You should be developing your package under the devel version of Bioconductor (currently 3.1, requires R-devel (R-3.2)). If you do that you won't see this message. 3 - In wich file can I clarify permanent objects. To avoid - I create new Environment with myGlobalEnv - new.env(parent = emptyenv()) I have many permanent objects because my package is a GUI. All these objects are useful for different functions and reduce the computing time and the multiple running of the same function. This is something that is best looked at during the package review process. 4- Indenting, Tabs and long lines were not found. As mentioned in the BiocCheck output and in the vignette, the formatting suggestions are just suggestions. Some of them are more important than others, for example, most reviewers will insist on lines shorter than 80 columns, for readability's sake. Can I submit with theses comments? You can submit, and these issues will be looked at as part of the package review process. Dan Thanks Karim $requirements character(0) $recommendations [1] Evaluate more vignette chunks. y of x.y.z version should be even in release $considerations [1] Clarifying how objects Li, A, ttCasesGenProfs, EventTime, Category, Continu, Category, ttMain, CasesStudies, curselectCases, fname.GCT, fname.CLS, ttMain, GenesDetails, CaseChoice, mSigDB_SubName, GenesDetails, lenght, ttCasesGenProfs, myGlobalEnv (used in canceR , dialogMut , dialogOptionPhenoTest, dialogOptionPhenoTest , getClinicalDataMatrix, geteSet, getGCTCLSExample, getGeneExpMatrix, getGenesClassifier, getGenesTree_MultipleCases, getGSEAlm_Diseases, getGSEAlm_Variables, getMegaProfData, getMetDataMultipleGenes, getMSigDBExample , getMSigDBExample, GSEA, GSEA.Analyze.Sets, plot_1Gene_2GenProfs, testCheckedCaseGenProf) were initialized. Maybe they are part of a data set loaded with data(), or perhaps part of an object referenced in with() or within(). [2] Shortening lines; 1227 lines (11%) are 80 characters long. [3] Replacing tabs with 4 spaces; 6 lines (0%) contain tabs. [4] Indenting lines with a multiple of 4 spaces; 1752 lines (15%) are not. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
