Re: [Bioc-devel] check returns error on multiple dependent functions
The collate field in the description file might help. It will control the order in which files are loaded I would imagine this would also alter the order examples are run in but I can not say with 100% certainty. Zach On 6/27/17 4:19 PM, Arman Sh wrote: I’m developing a package in which there are multiple functions that are dependent to each other. I have saved the functions in separate R files. When I run functions in correct order, I can easily get the output, but cmd check returns error. How can I prevent the error? Best regards, Arman ==> devtools::check() Updating cbaf documentation Loading cbaf Loading required package: cgdsr Loading required package: xlsxjars Loading required package: rJava Loading required package: xlsx Loading required package: gplots Attaching package: 'gplots' The following object is masked from 'package:stats': lowess Loading required package: RColorBrewer Loading required package: rafalib Loading required package: Biobase Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:rJava': anyDuplicated, duplicated, sort, unique The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': anyDuplicated, append, as.data.frame, cbind, colMeans, colnames, colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: genefilter Setting env vars -- CFLAGS : -Wall -pedantic CXXFLAGS: -Wall -pedantic Building cbaf - "C:/PROGRA~1/R/R-34~1.0/bin/x64/R" --no-site-file --no-environ --no-save \ --no-restore --quiet CMD build "Z:\cbaf\Source code\cbaf" --no-resave-data \ --no-manual * checking for file 'Z:\cbaf\Source code\cbaf/DESCRIPTION' ... OK * preparing 'cbaf': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... OK * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building 'cbaf_0.99.0.tar.gz' Setting env vars -- _R_CHECK_CRAN_INCOMING_ : FALSE _R_CHECK_FORCE_SUGGESTS_: FALSE Checking cbaf - "C:/PROGRA~1/R/R-34~1.0/bin/x64/R" --no-site-file --no-environ --no-save \ --no-restore --quiet CMD check \ "C:\Users\Arman\AppData\Local\Temp\RtmpoZ2dZa/cbaf_0.99.0.tar.gz" --as-cran \ --timings --no-manual * using log directory 'Z:/cbaf/Source code/cbaf.Rcheck' * using R version 3.4.0 (2017-04-21) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using options '--no-manual --as-cran' * checking for file 'cbaf/DESCRIPTION' ... OK * this is package 'cbaf' version '0.99.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'cgdsr' 'xlsxjars' 'xlsx' 'gplots' 'RColorBrewer' 'rafalib' 'Biobase' 'genefilter' Adding so many packages to the search path is excessive and importing selectively is preferable. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'cbaf' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... O
Re: [Bioc-devel] check returns error on multiple dependent functions
On 06/27/2017 05:19 PM, Arman Sh wrote: I’m developing a package in which there are multiple functions that are dependent to each other. I have saved the functions in separate R files. When I run functions in correct order, I can easily get the output, but cmd check returns error. How can I prevent the error? Clean up the simple stuff first * checking package dependencies ... NOTE Depends: includes the non-default packages: 'cgdsr' 'xlsxjars' 'xlsx' 'gplots' 'RColorBrewer' 'rafalib' 'Biobase' 'genefilter' Adding so many packages to the search path is excessive and importing selectively is preferable. only include packages that the end-user would need to invoke in the Depends: field, otherwise use Imports: * checking R code for possible problems ... NOTE ... Undefined global functions or variables: Stop colorRampPalette dev.off head i median na.omit png setTxtProgressBar simplifiction.cuttoff txtProgressBar Consider adding importFrom("grDevices", "colorRampPalette", "dev.off", "png") importFrom("stats", "median", "na.omit") importFrom("utils", "head", "setTxtProgressBar", "txtProgressBar") to your NAMESPACE file. do as the instructions say and add the suggested statements to the NAMESPACE file. * checking Rd line widths ... NOTE Rd file 'heatmapOutput.Rd': \usage lines wider than 90 characters: heatmapOutput(submissionName, shortenStudyNames = TRUE, genelimit = "none", resolution = 600, RowCex = 0.8, ColCex = 0.8, heatmapMargines = c(10,10), angleForYaxisNames = 45, heatmapColor = "RdBu", reverseColor = TRUE, wrap the lines to 90 characters max (80 is the norm, for easy reading in a plain terminal). Your problem though likely comes from these Found the following assignments to the global environment: File 'cbaf/R/cbaf-automatedStatistics.R': assign(paste("Pa.PrData.", submissionName, sep = ""), newParameters, envir = globalenv()) ... It is VERY BAD PRACTICE to assign variables to the global environment, for exactly the reason you experience in your code -- the successful execution of your functions depends in a very precise and fragile way on the order in which they are called. Make sure your functions are true 'functions' that rely ONLY on the input values and symbols defined or imported into the package. One possible approach is to return the parameter values as an object (e.g., an S4 class) that is then required for input into other functions. Martin Best regards, Arman ==> devtools::check() Updating cbaf documentation Loading cbaf Loading required package: cgdsr Loading required package: xlsxjars Loading required package: rJava Loading required package: xlsx Loading required package: gplots Attaching package: 'gplots' The following object is masked from 'package:stats': lowess Loading required package: RColorBrewer Loading required package: rafalib Loading required package: Biobase Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:rJava': anyDuplicated, duplicated, sort, unique The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': anyDuplicated, append, as.data.frame, cbind, colMeans, colnames, colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: genefilter Setting env vars -- CFLAGS : -Wall -pedantic CXXFLAGS: -Wall -pedantic Building cbaf - "C:/PROGRA~1/R/R-34~1.0/bin/x64/R" --no-site-file --no-environ --no-save \ --no-restore --quiet CMD build "Z:\cbaf\Source code\cbaf" --no-resave-data \ --no-manual * checking for file 'Z:\cbaf\Source code\cbaf/DESCRIPTION' ... OK * preparing 'cbaf': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... OK * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building 'cbaf_0.99.0.tar.gz' Setting env vars --
[Bioc-devel] check returns error on multiple dependent functions
I’m developing a package in which there are multiple functions that are dependent to each other. I have saved the functions in separate R files. When I run functions in correct order, I can easily get the output, but cmd check returns error. How can I prevent the error? Best regards, Arman ==> devtools::check() Updating cbaf documentation Loading cbaf Loading required package: cgdsr Loading required package: xlsxjars Loading required package: rJava Loading required package: xlsx Loading required package: gplots Attaching package: 'gplots' The following object is masked from 'package:stats': lowess Loading required package: RColorBrewer Loading required package: rafalib Loading required package: Biobase Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:rJava': anyDuplicated, duplicated, sort, unique The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': anyDuplicated, append, as.data.frame, cbind, colMeans, colnames, colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: genefilter Setting env vars -- CFLAGS : -Wall -pedantic CXXFLAGS: -Wall -pedantic Building cbaf - "C:/PROGRA~1/R/R-34~1.0/bin/x64/R" --no-site-file --no-environ --no-save \ --no-restore --quiet CMD build "Z:\cbaf\Source code\cbaf" --no-resave-data \ --no-manual * checking for file 'Z:\cbaf\Source code\cbaf/DESCRIPTION' ... OK * preparing 'cbaf': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... OK * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building 'cbaf_0.99.0.tar.gz' Setting env vars -- _R_CHECK_CRAN_INCOMING_ : FALSE _R_CHECK_FORCE_SUGGESTS_: FALSE Checking cbaf - "C:/PROGRA~1/R/R-34~1.0/bin/x64/R" --no-site-file --no-environ --no-save \ --no-restore --quiet CMD check \ "C:\Users\Arman\AppData\Local\Temp\RtmpoZ2dZa/cbaf_0.99.0.tar.gz" --as-cran \ --timings --no-manual * using log directory 'Z:/cbaf/Source code/cbaf.Rcheck' * using R version 3.4.0 (2017-04-21) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using options '--no-manual --as-cran' * checking for file 'cbaf/DESCRIPTION' ... OK * this is package 'cbaf' version '0.99.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'cgdsr' 'xlsxjars' 'xlsx' 'gplots' 'RColorBrewer' 'rafalib' 'Biobase' 'genefilter' Adding so many packages to the search path is excessive and importing selectively is preferable. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'cbaf' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ..
[Bioc-devel] warning on href
I got this warning when I perform CRAN check on my package * checking Rd files ... WARNING gmtGene2Cat.Rd:27-28: First argument to \href must be verbatim URL problem found in ‘gmtGene2Cat.Rd’ Here is my code for this Rd @details This function reads a gene set file in \href{ https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29}{GMT format}, and returns a list with its name being a gene id, and each element of ... I did not get this warning when I perform BiocCheck on my package. Does anyone has an idea on how to fix this? Thank you, Aimin [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Deprecating a class
Hi Carlos, Deprecating the constructors should be enough if you don't expect that your users have serialized instances of the class around (i.e. objects that they saved to disk with save() or saveRDS()). It's actually impossible to know whether your users have done this or not but they would typically do this only if these objects take a long time to compute or if the typical workflow that you present in your vignette encourages this. If it's the case then the situation is a little bit more complicated: - You would need to provide a coercion method from this class to the replacement class. - You would also need to put a deprecation warning in all the methods defined on this class (this includes validity and show methods if you've defined them, and also coercion methods *to* this class. The deprecation warning would typically explain how to coerce the deprecated object to the new replacement class. Hope this helps, H. On 06/27/2017 01:50 AM, Carlos Ruiz wrote: Hi Bioc developers, A year ago, we introduced a class in my package MEAL to manage methylation data. After some Bioc releases, we realised that we don't really need this class and that it is better to reuse other Bioc classes to facilitate package usability. Is there any protocol to deprecate a class? There is only a guide to deprecate functions and methods. For the new release, I was thinking on deprecating the constructors of my class, while keeping the methods. Is that OK? Bests, -- 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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Bioconductor stats
On Tue, Jun 27, 2017 at 7:34 AM, Lluís Revilla wrote: > Hi, > > I have been looking at the stats of Bioconductor, and I would like to know > more about how are they calculated. > > Do these stats account for the mirror sites? Are there any stats of the > usage of mirrors? > Mirrors are not counted. > > I found some packages that for the same month they have downloads in two > categories. For instance AnnotationDbi has some downloads as experimental > data package: > http://bioconductor.org/packages/stats/data-experiment/AnnotationDbi/ > while > most of the downloads are in the software category (The right one). It > seems that near 500 packages have downloads in two categories. > I'm not sure on this one. > > The "Nb of distinct IPs" if I understand correctly is for each package and > month. So if the same IP downloads again the package is listed as a new IP, > isn't it? I assume that if mirrors are counted either no one downloads the > same packages from different mirrors in the same IP or that these > information is shared across mirrors for these stats. > Again, mirrors are not included. I think the distinct IPs are reset per month for the monthly stats. > > Regards, > > Lluís > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Sean Davis, MD, PhD Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda, MD 20892 https://seandavi.github.io/ https://twitter.com/seandavis12 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Bioconductor stats
Hi, I have been looking at the stats of Bioconductor, and I would like to know more about how are they calculated. Do these stats account for the mirror sites? Are there any stats of the usage of mirrors? I found some packages that for the same month they have downloads in two categories. For instance AnnotationDbi has some downloads as experimental data package: http://bioconductor.org/packages/stats/data-experiment/AnnotationDbi/ while most of the downloads are in the software category (The right one). It seems that near 500 packages have downloads in two categories. The "Nb of distinct IPs" if I understand correctly is for each package and month. So if the same IP downloads again the package is listed as a new IP, isn't it? I assume that if mirrors are counted either no one downloads the same packages from different mirrors in the same IP or that these information is shared across mirrors for these stats. Regards, Lluís [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Deprecating a class
Hi Bioc developers, A year ago, we introduced a class in my package MEAL to manage methylation data. After some Bioc releases, we realised that we don't really need this class and that it is better to reuse other Bioc classes to facilitate package usability. Is there any protocol to deprecate a class? There is only a guide to deprecate functions and methods. For the new release, I was thinking on deprecating the constructors of my class, while keeping the methods. Is that OK? Bests, -- Carlos Ruiz PhD Student ISGlobal Barcelona Institute for Global Health - Campus MAR Barcelona Biomedical Research Park (PRBB) (office 001) Doctor Aiguader, 88 08003 Barcelona, Spain Tel. +34 93 214 7309 carlos.r...@isglobal.org www.isglobal.org We are pleased to tell you that after three years of a strategic alliance between ISGlobal and CREAL, both institutions have merged. The resulting institution, which retains the ISGlobal name, will build upon the existing areas of excellence to become a world-class player in research, education and innovation in Global Health. More info at: http://ow.ly/krQd301Nj3w This message is intended exclusively for its addressee and may contain information that is CONFIDENTIAL and protected by professional privilege. If you are not the intended recipient you are hereby notified that any dissemination, copy or disclosure of this communication is strictly prohibited by law. If this message has been received in error, please immediately notify us via e-mail and delete it. DATA PROTECTION. We inform you that your personal data, including your e-mail address and data included in your email correspondence, are included in the ISGlobal Foundation files. Your personal data will be used for the purpose of contacting you and sending information on the activities of the above foundations. You can exercise your rights of access, rectification, cancellation and opposition by contacting the following address: l...@isglobal.org. ISGlobal Privacy Policy at www.isglobal.org. -- This message is intended exclusively for its addressee and may contain information that is CONFIDENTIAL and protected by professional privilege. If you are not the intended recipient you are hereby notified that any dissemination, copy or disclosure of this communication is strictly prohibited by law. If this message has been received in error, please immediately notify us via e-mail and delete it. DATA PROTECTION. We inform you that your personal data, including your e-mail address and data included in your email correspondence, are included in the ISGlobal Foundation files. Your personal data will be used for the purpose of contacting you and sending information on the activities of the above foundations. You can exercise your rights of access, rectification, cancellation and opposition by contacting the following address: l...@isglobal.org. ISGlobal Privacy Policy at www.isglobal.org. - CONFIDENCIALIDAD. Este mensaje y sus anexos se dirigen exclusivamente a su destinatario y puede contener información confidencial, por lo que la utilización, divulgación y/o copia sin autorización está prohibida por la legislación vigente. Si ha recibido este mensaje por error, le rogamos lo comunique inmediatamente por esta misma vía y proceda a su destrucción. PROTECCIÓN DE DATOS. Sus datos de carácter personal utilizados en este envío, incluida su dirección de e-mail, forman parte de ficheros de titularidad de la Fundación ISGlobal para cualquier finalidades de contacto, relación institucional y/o envío de información sobre sus actividades. Los datos que usted nos pueda facilitar contestando este correo quedarán incorporados en los correspondientes ficheros, autorizando el uso de su dirección de e-mail para las finalidades citadas. Puede ejercer los derechos de acceso, rectificación, cancelación y oposición dirigiéndose a l...@isglobal.org . Política de privacidad en www.isglobal.org. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel