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CHECK report for methylPipe on tokay1

This page was generated on 2019-04-13 11:24:14 -0400 (Sat, 13 Apr 2019).

Package 942/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylPipe 1.16.0
Kamal Kishore
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/methylPipe
Branch: RELEASE_3_8
Last Commit: 0cc3f02
Last Changed Date: 2018-10-30 11:41:55 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: methylPipe
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methylPipe.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings methylPipe_1.16.0.tar.gz
StartedAt: 2019-04-13 03:45:38 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:55:48 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 609.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: methylPipe.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methylPipe.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings methylPipe_1.16.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/methylPipe.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'methylPipe/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'methylPipe' version '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 whether package 'methylPipe' 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
* 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 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 ... NOTE
BSprepare : binomTestMulti: no visible global function definition for
  'binom.test'
BSprepare : binomTestMulti : pVfun: no visible global function
  definition for 'binom.test'
BSprepare : binomTestMulti: no visible global function definition for
  'p.adjust'
chiCombP: no visible global function definition for 'pchisq'
consolidateDMRs: no visible global function definition for 'p.adjust'
plotMeth: no visible global function definition for 'rainbow'
process.hmc: no visible global function definition for 'write.table'
findDMR,BSdataSet : DMRchr: no visible global function definition for
  'kruskal.test'
findDMR,BSdataSet : DMRchr: no visible global function definition for
  'wilcox.test'
findDMR,BSdataSet: no visible global function definition for
  'stopCluster'
findPMDs,BSdata : PMDchr: no visible global function definition for
  'segmentPMDs'
mCsmoothing,BSdata: no visible global function definition for
  'smooth.spline'
mCsmoothing,BSdata: no visible global function definition for 'box'
mCsmoothing,BSdata: no visible global function definition for 'axis'
mCsmoothing,BSdata: no visible global function definition for 'mtext'
methstats,BSdataSet: no visible global function definition for
  'stopCluster'
methstats,BSdataSet : panel.cor: no visible global function definition
  for 'par'
methstats,BSdataSet : panel.cor: no visible global function definition
  for 'cor.test'
methstats,BSdataSet : panel.cor: no visible global function definition
  for 'text'
methstats,BSdataSet : panel.smooth: no visible global function
  definition for 'points'
methstats,BSdataSet : panel.smooth: no visible global function
  definition for 'lines'
methstats,BSdataSet : panel.hist: no visible global function definition
  for 'par'
methstats,BSdataSet : panel.hist: no visible global function definition
  for 'hist'
methstats,BSdataSet : panel.hist: no visible global function definition
  for 'rect'
methstats,BSdataSet: no visible global function definition for 'pairs'
methstats,BSdataSet: no visible global function definition for 'dist'
methstats,BSdataSet: no visible global function definition for 'hclust'
methstats,BSdataSet: no visible global function definition for
  'dev.new'
methstats,BSdataSet: no visible global function definition for 'plot'
show,BSdata: no visible global function definition for 'organism'
show,BSdataSet: no visible global function definition for 'organism'
Undefined global functions or variables:
  axis binom.test box cor.test dev.new dist hclust hist kruskal.test
  lines mtext organism p.adjust pairs par pchisq plot points rainbow
  rect segmentPMDs smooth.spline stopCluster text wilcox.test
  write.table
Consider adding
  importFrom("grDevices", "dev.new", "rainbow")
  importFrom("graphics", "axis", "box", "hist", "lines", "mtext",
             "pairs", "par", "plot", "points", "rect", "text")
  importFrom("stats", "binom.test", "cor.test", "dist", "hclust",
             "kruskal.test", "p.adjust", "pchisq", "smooth.spline",
             "wilcox.test")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'BSdataSet,ANY,ANY,ANY'
  generic '[' and siglist 'GElist,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/methylPipe/libs/i386/methylPipe.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpmckn04', resetting
Examples with CPU or elapsed time > 5s
           user system elapsed
plotMeth  22.34   0.56   36.99
findDMR    0.80   2.55   23.12
methstats  1.23   0.44   15.09
findPMDs   0.10   0.31   16.20
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpeIIbPZ', resetting
Examples with CPU or elapsed time > 5s
           user system elapsed
plotMeth  21.75   0.35   33.03
findDMR    0.58   3.65   24.16
methstats  0.99   0.25   18.56
findPMDs   0.09   0.21   17.55
* 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: 3 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/methylPipe.Rcheck/00check.log'
for details.



Installation output

methylPipe.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/methylPipe_1.16.0.tar.gz && rm -rf methylPipe.buildbin-libdir && mkdir methylPipe.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methylPipe.buildbin-libdir methylPipe_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL methylPipe_1.16.0.zip && rm methylPipe_1.16.0.tar.gz methylPipe_1.16.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  389k  100  389k    0     0  13.6M      0 --:--:-- --:--:-- --:--:-- 15.8M

install for i386

* installing *source* package 'methylPipe' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_methylPipe.c -o R_init_methylPipe.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c binning.c -o binning.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o methylPipe.dll tmp.def R_init_methylPipe.o binning.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/methylPipe.buildbin-libdir/methylPipe/libs/i386
** R
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'methylPipe'
    finding HTML links ... done
    BSdata-class                            html  
    finding level-2 HTML links ... done

    BSdataSet-class                         html  
    BSprepare                               html  
    GEcollection-class                      html  
    GElist-class                            html  
    chiCombP                                html  
    consolidateDMRs                         html  
    extractBinGRanges                       html  
    findDMR                                 html  
    findPMDs                                html  
    getCpos                                 html  
    getCposDensity                          html  
    mCsmoothing                             html  
    mapBSdata2GRanges                       html  
    meth.call                               html  
    methstats                               html  
    methylPipe-package                      html  
    plotMeth                                html  
    pool.reads                              html  
    process.hmc                             html  
    profileDNAmetBin                        html  
    splitChrs                               html  
    tabixdata2GR                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'methylPipe' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_methylPipe.c -o R_init_methylPipe.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c binning.c -o binning.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o methylPipe.dll tmp.def R_init_methylPipe.o binning.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/methylPipe.buildbin-libdir/methylPipe/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methylPipe' as methylPipe_1.16.0.zip
* DONE (methylPipe)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'methylPipe' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

methylPipe.Rcheck/examples_i386/methylPipe-Ex.timings

nameusersystemelapsed
BSdata-class0.160.000.17
BSdataSet-class0.110.000.12
BSprepare000
GEcollection-class2.670.162.83
GElist-class0.050.010.06
chiCombP000
consolidateDMRs0.170.000.17
extractBinGRanges0.000.020.02
findDMR 0.80 2.5523.12
findPMDs 0.10 0.3116.20
getCpos0.070.030.11
getCposDensity0.080.010.10
mCsmoothing0.220.110.40
mapBSdata2GRanges0.550.250.80
methstats 1.23 0.4415.09
plotMeth22.34 0.5636.99
pool.reads000
process.hmc000
profileDNAmetBin1.050.051.10

methylPipe.Rcheck/examples_x64/methylPipe-Ex.timings

nameusersystemelapsed
BSdata-class0.190.010.20
BSdataSet-class0.140.000.15
BSprepare000
GEcollection-class2.340.062.41
GElist-class0.030.000.03
chiCombP000
consolidateDMRs0.140.000.14
extractBinGRanges0.020.000.01
findDMR 0.58 3.6524.16
findPMDs 0.09 0.2117.55
getCpos0.130.020.14
getCposDensity0.120.020.14
mCsmoothing0.280.000.29
mapBSdata2GRanges0.890.000.89
methstats 0.99 0.2518.56
plotMeth21.75 0.3533.03
pool.reads000
process.hmc000
profileDNAmetBin1.290.081.36