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On February 16, 2016 8:41:25 AM PST, Yuande Tan <tanyua...@gmail.com> wrote: >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 -- Sent from my Android device with K-9 Mail. Please excuse my brevity. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel