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BioC 3.2: CHECK report for methylPipe on zin1

This page was generated on 2016-04-23 10:14:04 -0700 (Sat, 23 Apr 2016).

Package 635/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylPipe 1.4.5
Kamal Kishore
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/methylPipe
Last Changed Rev: 114854 / Revision: 116712
Last Changed Date: 2016-03-16 08:50:48 -0700 (Wed, 16 Mar 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: methylPipe
Version: 1.4.5
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings methylPipe_1.4.5.tar.gz
StartedAt: 2016-04-23 02:48:52 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 02:54:13 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 321.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: methylPipe.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings methylPipe_1.4.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/methylPipe.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methylPipe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methylPipe’ version ‘1.4.5’
* 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 ‘methylPipe’ can be installed ... [25s/25s] 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 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
findDMR,BSdataSet: no visible global function definition for
  ‘stopCluster’
findPMDs,BSdata : PMDchr: no visible global function definition for
  ‘segmentPMDs’
methstats,BSdataSet: no visible global function definition for
  ‘stopCluster’
show,BSdata: no visible global function definition for ‘organism’
show,BSdataSet: no visible global function definition for ‘organism’
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [36s/97s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
findDMR  0.384  0.392  18.807
findPMDs 0.118  0.058  14.280
* 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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/methylPipe.Rcheck/00check.log’
for details.


methylPipe.Rcheck/00install.out:

* installing *source* package ‘methylPipe’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_methylPipe.c -o R_init_methylPipe.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c binning.c -o binning.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o methylPipe.so R_init_methylPipe.o binning.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/methylPipe.Rcheck/methylPipe/libs
** R
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (methylPipe)

methylPipe.Rcheck/methylPipe-Ex.timings:

nameusersystemelapsed
BSdata-class0.1660.0040.171
BSdataSet-class0.1320.0000.133
BSprepare0.0010.0000.000
GEcollection-class1.7610.0161.778
GElist-class0.0340.0000.034
chiCombP0.0010.0000.001
consolidateDMRs0.0980.0000.098
extractBinGRanges0.0250.0000.024
findDMR 0.384 0.39218.807
findPMDs 0.118 0.05814.280
getCpos0.1360.0120.155
getCposDensity0.1330.0000.144
mCsmoothing0.3450.0040.348
mapBSdata2GRanges1.5140.0511.567