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BioC 2.13: CHECK report for seqCNA on zin1

This page was generated on 2014-04-05 09:48:42 -0700 (Sat, 05 Apr 2014).

Package 650/750HostnameOS / ArchBUILDCHECKBUILD BIN
seqCNA 1.2.0
David Mosen-Ansorena
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/seqCNA
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: seqCNA
Version: 1.2.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings seqCNA_1.2.0.tar.gz
StartedAt: 2014-04-05 03:53:53 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 03:54:55 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 62.1 seconds
RetCode: 0
Status:  OK 
CheckDir: seqCNA.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/seqCNA.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqCNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqCNA’ version ‘1.2.0’
* 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 ‘seqCNA’ can be installed ... [4s/5s] 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 ... NOTE
Packages in Depends field not imported from:
  ‘GLAD’ ‘adehabitatLT’ ‘doSNOW’ ‘methods’ ‘seqCNA.annot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/home/biocbuild/bbs-2.13-bioc/meat/seqCNA.Rcheck/seqCNA/libs/seqCNA.so’:
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Object: ‘seqCNA.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘seqCNA.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [4s/31s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotCNProfile   1.004  0.024   6.545
applyThresholds 0.524  0.044   5.831
writeCNProfile  0.392  0.032   5.688
runGLAD         0.344  0.028   5.598
* 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/seqCNA.Rcheck/00check.log’
for details.

seqCNA.Rcheck/00install.out:

* installing *source* package ‘seqCNA’ ...
** libs
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c seqCNA.cpp -o seqCNA.o
g++ -shared -L/usr/local/lib -o seqCNA.so seqCNA.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/seqCNA.Rcheck/seqCNA/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (seqCNA)

seqCNA.Rcheck/seqCNA-Ex.timings:

nameusersystemelapsed
SeqCNAInfo-class0.0440.0000.042
applyFilters0.2120.0121.625
applyThresholds0.5240.0445.831
plotCNProfile1.0040.0246.545
readSeqsumm0.0520.0000.051
runGLAD0.3440.0285.598
runSeqnorm0.3880.0244.207
runSeqsumm0.0120.0000.013
seqsumm_HCC11430.0320.0000.033
writeCNProfile0.3920.0325.688