Dear all: Today I resubmit the revised version of MBttest with fix error occurring in building windows. Right now I received message from SinglePackageBuilder BioC-Submit. It said one or more warnings in build. I checked the History Biocond Single Builder, the warnings list in morelia and moscato2 check column But I really did not find the warnings in morelia and moscato2 checking recordings.
Any guys can help me how to fix the problem with hided warnings? *I copied them here:* Bioconductor Single Package Builder - Build History Snapshot Date: URL: https://tracker.bioconductor.org/file7025/MBttest_0.99.0.tar.gz Last Changed Rev: / Revision: Last Changed Date: HostnameOS /ArchBUILDCHECKBUILD BINPOST-PROCESSING zin2 Linux (Ubuntu 14.04.2 LTS)/x86_64 OK <http://bioconductor.org/spb_reports/MBttest_0.99.0_buildreport_20160216092641.html#zin2_buildsrc_anchor> <http://bioconductor.org/spb_reports/MBttest_0.99.0_buildreport_20160216092641.html#zin2_check_anchor> skipped <http://bioconductor.org/spb_reports/MBttest_0.99.0_buildreport_20160216092641.html#zin2_buildbin_anchor> OK <http://bioconductor.org/spb_reports/MBttest_0.99.0_buildreport_20160216092641.html#zin2_anchor> morelia Mac OS X Mavericks (10.9.5)/x86_64 OK <http://bioconductor.org/spb_reports/MBttest_0.99.0_buildreport_20160216092641.html#morelia_buildsrc_anchor> WARNINGS <http://bioconductor.org/spb_reports/MBttest_0.99.0_buildreport_20160216092641.html#morelia_check_anchor> OK <http://bioconductor.org/spb_reports/MBttest_0.99.0_buildreport_20160216092641.html#morelia_buildbin_anchor> OK <http://bioconductor.org/spb_reports/MBttest_0.99.0_buildreport_20160216092641.html#morelia_anchor> moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit)/x64 OK <http://bioconductor.org/spb_reports/MBttest_0.99.0_buildreport_20160216092641.html#moscato2_buildsrc_anchor> WARNINGS <http://bioconductor.org/spb_reports/MBttest_0.99.0_buildreport_20160216092641.html#moscato2_check_anchor> OK <http://bioconductor.org/spb_reports/MBttest_0.99.0_buildreport_20160216092641.html#moscato2_buildbin_anchor> OK <http://bioconductor.org/spb_reports/MBttest_0.99.0_buildreport_20160216092641.html#moscato2_anchor> ------------------------------ zin2 Summary morelia CHECK output [top] <http://bioconductor.org/spb_reports/MBttest_0.99.0_buildreport_20160216092641.html#top> * using log directory /Users/pkgbuild/packagebuilder/workers/jobs/MBttest_20160216062110/MBttest.Rcheck * using R Under development (unstable) (2016-01-24 r69993) * using platform: x86_64-apple-darwin13.4.0 (64-bit) * using session charset: UTF-8 * using option --no-vignettes * checking for file MBttest/DESCRIPTION ... OK * checking extension type ... Package * this is package MBttest version 0.99.0 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package MBttest can be installed ... [1s/1s] 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 ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of data directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under inst/doc ... OK * checking installed files from inst/doc ... OK * checking files in vignettes ... OK * checking examples ... [12s/13s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in inst/doc ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK * This is BiocCheck, version 1.7.2. * BiocCheck is a work in progress. Output and severity of issues may change. * Installing package... * Checking for version number mismatch... * Checking if other packages can import this one... * Checking to see if we understand object initialization.... * CONSIDER: Clarifying how objects pt, heat.colors, heat.colors, hclust, as.dist, cor (used in mbetattest, myheatmap, myheatmap, oddratio, simulat, smbetattest) were initialized. Maybe they are part of a data set loaded with data(), or perhaps part of an object referenced in with() or within(). * Checking vignette directory... * This is a software package, checking vignette directories... # of chunks: 20, # of eval=FALSE: 0 (0%) * Checking version number... * Checking new package version number... * Checking version number validity... * Checking R Version dependency... * RECOMMENDED: Update R version dependency from 3.2.0 to 3.3. * Checking biocViews... * Checking that biocViews are present... * Checking that biocViews come from the same category... * Checking biocViews validity... * Checking for recommended biocViews... * Checking build system compatibility... * Checking for blank lines in DESCRIPTION... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches dir/tarball name... * Checking for Version field... * Checking for valid maintainer... * Checking unit tests... * CONSIDER: Adding unit tests. We strongly encourage them. See http://www.bioconductor.org/developers/how-to/unitTesting-guidelines/. * Checking native routine registration... * Checking for deprecated package usage... * Checking parsed R code in R directory, examples, vignettes... * Checking for direct slot access... * Checking for T... * Checking for F... * Checking for browser()... * Checking for <<-... * Checking for library/require of MBttest... * Checking DESCRIPTION/NAMESPACE consistency... * Checking function lengths............................... The longest function is 171 lines long The longest 5 functions are: simulat() (R/simulat.R, line 1): 171 lines betaparametVP() (R/betaparametVP.R, line 1): 156 lines myheatmap() (R/myheatmap.R, line 1): 70 lines mbetattest() (R/mbetattest.R, line 1): 60 lines smbetattest() (R/smbetattest.R, line 1): 50 lines * Checking man pages... * Checking exported objects have runnable examples... * Checking package NEWS... * Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vignette source... * CONSIDER: Shortening lines; 129 lines (6%) are > 80 characters long. * CONSIDER: Replacing tabs with 4 spaces; 509 lines (25%) contain tabs. * CONSIDER: Indenting lines with a multiple of 4 spaces; 173 lines (8%) are not. See http://bioconductor.org/developers/how-to/coding-style/ * Checking for canned comments in man pages... * Checking if package already exists in CRAN... * Checking if new package already exists in Bioconductor... * Checking for bioc-devel mailing list subscription... * Maintainer is subscribed to bioc-devel! * Checking for support site registration... * Maintainer is registered at support site! Summary: REQUIRED count: 0 RECOMMENDED count: 1 CONSIDERATION count: 5 For detailed information about these checks, see the BiocCheck vignette, available athttp://bioconductor.org/packages/3.3/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output moscato2 CHECK output [top] <http://bioconductor.org/spb_reports/MBttest_0.99.0_buildreport_20160216092641.html#top> Installing package prior to check... install for i386 * installing *source* package 'MBttest' ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded install for x64 * installing *source* package 'MBttest' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'MBttest' as MBttest_0.99.0.zip * DONE (MBttest) * using log directory 'E:/packagebuilder/workers/jobs/MBttest_20160216062110/MBttest.Rcheck' * using R Under development (unstable) (2015-12-15 r69777) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'MBttest/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'MBttest' version '0.99.0' * checking package namespace information ... OK * checking package dependencies ... OK * 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 'MBttest' 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking for missing documentation entries ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking Rd \usage sections ... OK * checking for unstated dependencies in examples ... ** running examples for arch 'i386' ... OK * checking Rd contents ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking data for ASCII and uncompressed saves ... OK Examples with CPU or elapsed time > 5s user system elapsed mbetattest 11.53 0.01 11.55 myheatmap 6.62 0.11 6.74 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed mbetattest 11.03 0.02 11.05 myheatmap 7.25 0.05 7.30 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK * This is BiocCheck, version 1.7.2. * BiocCheck is a work in progress. Output and severity of issues may change. * Installing package... * Checking for version number mismatch... * Checking if other packages can import this one... * Checking to see if we understand object initialization.... * CONSIDER: Clarifying how objects 'pt, heat.colors, heat.colors, hclust, as.dist, cor' (used in mbetattest, myheatmap, myheatmap, oddratio, simulat, smbetattest) were initialized. Maybe they are part of a data set loaded with data(), or perhaps part of an object referenced in with() or within(). * Checking vignette directory... * This is a software package, checking vignette directories... # of chunks: 20, # of eval=FALSE: 0 (0%) * Checking version number... * Checking new package version number... * Checking version number validity... * Checking R Version dependency... * RECOMMENDED: Update R version dependency from 3.2.0 to 3.3. * Checking biocViews... * Checking that biocViews are present... * Checking that biocViews come from the same category... * Checking biocViews validity... * Checking for recommended biocViews... * Checking build system compatibility... * Checking for blank lines in DESCRIPTION... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches dir/tarball name... * Checking for Version field... * Checking for valid maintainer... * Checking unit tests... * CONSIDER: Adding unit tests. We strongly encourage them. See http://www.bioconductor.org/developers/how-to/unitTesting-guidelines/. * Checking native routine registration... * Checking for deprecated package usage... * Checking parsed R code in R directory, examples, vignettes... * Checking for direct slot access... * Checking for T... * Checking for F... * Checking for browser()... * Checking for <<-... * Checking for library/require of MBttest... * Checking DESCRIPTION/NAMESPACE consistency... * Checking function lengths............................... The longest function is 171 lines long The longest 5 functions are: simulat() (R/simulat.R, line 1): 171 lines betaparametVP() (R/betaparametVP.R, line 1): 156 lines myheatmap() (R/myheatmap.R, line 1): 70 lines mbetattest() (R/mbetattest.R, line 1): 60 lines smbetattest() (R/smbetattest.R, line 1): 50 lines * Checking man pages... * Checking exported objects have runnable examples... * Checking package NEWS... * Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vignette source... * CONSIDER: Shortening lines; 129 lines (6%) are > 80 characters long. * CONSIDER: Replacing tabs with 4 spaces; 509 lines (25%) contain tabs. * CONSIDER: Indenting lines with a multiple of 4 spaces; 173 lines (8%) are not. See http://bioconductor.org/developers/how-to/coding-style/ * Checking for canned comments in man pages... * Checking if package already exists in CRAN... * Checking if new package already exists in Bioconductor... * Checking for support site registration... * Maintainer is registered at support site! Summary: REQUIRED count: 0 RECOMMENDED count: 1 CONSIDERATION count: 5 For detailed information about these checks, see the BiocCheck vignette, available athttp://bioconductor.org/packages/3.3/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output On Tue, Feb 16, 2016 at 6:46 AM, Andreas Kapouranis < kapouranis.andr...@gmail.com> wrote: > Hi Michael, > > Thanks for the suggestion. When I depend my package on GenomicRanges the > warning is now gone. > > Regards, > Andreas > > ---------------------------------------------------------- > Chantriolnt - Andreas Kapourani > PhD Candidate in Data Science, > School of Informatics, > University of Edinburgh > > e-mail : c.a.kapour...@sms.ed.ac.uk <c.a.kapour...@sms.ed.ac.uk> > : kapouranis.andr...@gmail.com > > On Tue, Feb 16, 2016 at 11:28 AM, Michael Lawrence < > lawrence.mich...@gene.com> wrote: > > > If you are expecting the user to manipulate that granges then you should > > depend on GenomicRanges. > > > > I guess R is loading the data to check the docs. When the methods > > namespace is loaded, it conveniently attaches the package defining the > > class. > > On Feb 16, 2016 3:48 AM, "Andreas Kapouranis" < > > kapouranis.andr...@gmail.com> wrote: > > > >> Hi Michael, > >> > >> Thanks for the reply. > >> > >> I created a minimal reproducible package with the issue. As it seems the > >> warning comes because I have a 'data' folder where I have stored some > >> example data, and one of the data is stored in GRanges format. > >> If I delete the GRanges example data and keep any other data, I get no > >> warning. > >> > >> So the issue is only when I import the 'methods' package and I have data > >> locally stored as GRanges objects in the 'data' folder. > >> > >> You can download and install the simple example package by typing: > >> > >> devtools::install_github("andreaskapou/simplePackage") > >> > >> > >> Or you can see the code in the following link, which just contains a > >> simple function to call the methods::is() function and create a GRanges > >> object. > >> https://github.com/andreaskapou/simplePackage > >> > >> Thanks, > >> Andreas > >> > >> ---------------------------------------------------------- > >> Chantriolnt - Andreas Kapourani > >> PhD Candidate in Data Science, > >> School of Informatics, > >> University of Edinburgh > >> > >> e-mail : c.a.kapour...@sms.ed.ac.uk <c.a.kapour...@sms.ed.ac.uk> > >> : kapouranis.andr...@gmail.com > >> > >> On Mon, Feb 15, 2016 at 4:22 PM, Michael Lawrence < > >> lawrence.mich...@gene.com> wrote: > >> > >>> It would be helpful to have a reproducible example, i.e., your actual > >>> package or a skeleton of it that reproduces the issue. Btw, you might > >>> be able to debug this behavior by: > >>> > >>> debug(tools::undoc) > >>> tools::undoc(dir=yourPackageDir) > >>> > >>> > >>> > >>> On Mon, Feb 15, 2016 at 7:52 AM, Andreas Kapouranis > >>> <kapouranis.andr...@gmail.com> wrote: > >>> > Hi, > >>> > > >>> > I am developing a package for Bioconductor, and I have a weird issue > >>> when > >>> > importing the 'methods' package. Before I add the 'methods' package > in > >>> > Imoprts in the DESCRIPTION file, I pass the CMD check without any > >>> warnings. > >>> > > >>> > However, when I add the 'methods' package in the Imports field, I > get a > >>> > warning during CMD check. (I need the methods package since I use the > >>> > methods::is() function, and if I call it just as is(), when running > the > >>> > package from Rscript will fail since by default it does not load the > >>> > 'methods' package.) > >>> > > >>> > I read a similar issue here: > >>> > https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008193.html > >>> > and I updated all my packages from Bioconductor including IRanges and > >>> > GenomicRanges. > >>> > > >>> > This is the warning that I get, which is exactly the same as the > >>> previous > >>> > issue in Bioc-Devel, and I understand that for some reason the > >>> BiocGenerics > >>> > is attached only when the 'methods' package is imported. > >>> > > >>> > * checking for missing documentation entries ... WARNING > >>> > > >>> > 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:stats’: > >>> > > >>> > IQR, mad, xtabs > >>> > > >>> > The following objects are masked from ‘package:base’: > >>> > > >>> > Filter, Find, Map, Position, Reduce, anyDuplicated, append, > >>> > as.data.frame, as.vector, cbind, colnames, do.call, duplicated, > >>> > eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, > >>> > lengths, mapply, match, mget, order, paste, pmax, pmax.int, > pmin, > >>> > pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, > >>> > tapply, union, unique, unlist, unsplit > >>> > > >>> > All user-level objects in a package should have documentation > entries. > >>> > See chapter ‘Writing R documentation files’ in the ‘Writing R > >>> > Extensions’ manual. > >>> > > >>> > > >>> > > >>> > My DESCRIPTION file when I add the 'methods' package is the > following: > >>> > ... > >>> > Depends: R (>= 3.2.0) > >>> > LazyData: TRUE > >>> > RoxygenNote: 5.0.1 > >>> > Imports: GenomicRanges, > >>> > IRanges, > >>> > assertthat, > >>> > S4Vectors, > >>> > graphics, > >>> > data.table, > >>> > methods > >>> > Suggests: knitr, > >>> > rmarkdown, > >>> > testthat > >>> > VignetteBuilder: knitr > >>> > > >>> > > >>> > > >>> > Regards, > >>> > Andreas > >>> > > >>> > [[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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
