[Bioc-devel] BiocGenerics attaches when methods package is imported

Tue Feb 16 17:41:25 CET 2016

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]]