[Bioc-devel] BiocGenerics attaches when methods package is imported
Dan Tenenbaum
dtenenba at fredhutch.org
Tue Feb 16 18:11:39 CET 2016
I have answered your email in the tracker, twice. Please do not reply all to random threads on bioc-devel.
On February 16, 2016 8:41:25 AM PST, Yuande Tan <tanyuande at 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.andreas at 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.kapourani at sms.ed.ac.uk <c.a.kapourani at sms.ed.ac.uk>
>> : kapouranis.andreas at gmail.com
>>
>> On Tue, Feb 16, 2016 at 11:28 AM, Michael Lawrence <
>> lawrence.michael at 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.andreas at 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.kapourani at sms.ed.ac.uk <c.a.kapourani at sms.ed.ac.uk>
>> >> : kapouranis.andreas at gmail.com
>> >>
>> >> On Mon, Feb 15, 2016 at 4:22 PM, Michael Lawrence <
>> >> lawrence.michael at 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.andreas at 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 at r-project.org mailing list
>> >>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >>>
>> >>
>> >>
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
> [[alternative HTML version deleted]]
>
>_______________________________________________
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>https://stat.ethz.ch/mailman/listinfo/bioc-devel
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