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BioC 3.1: CHECK report for MassSpecWavelet on zin2

This page was generated on 2015-10-09 09:23:17 -0700 (Fri, 09 Oct 2015).

Package 557/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MassSpecWavelet 1.34.0
Pan Du
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/MassSpecWavelet
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MassSpecWavelet
Version: 1.34.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings MassSpecWavelet_1.34.0.tar.gz
StartedAt: 2015-10-09 03:12:22 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 03:12:53 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 31.0 seconds
RetCode: 0
Status:  OK 
CheckDir: MassSpecWavelet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings MassSpecWavelet_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/MassSpecWavelet.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MassSpecWavelet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MassSpecWavelet’ version ‘1.34.0’
* 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 ‘MassSpecWavelet’ can be installed ... [1s/1s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' call to ‘waveslim’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘waveslim’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
smoothDWT: no visible global function definition for ‘dwt’
smoothDWT: no visible global function definition for ‘modwt’
smoothDWT: no visible global function definition for ‘idwt’
smoothDWT: no visible global function definition for ‘imodwt’
* checking Rd files ... NOTE
prepare_Rd: getRidgeValue.Rd:24-26: Dropping empty section \examples
prepare_Rd: sav.gol.Rd:28-29: Dropping empty section \examples
prepare_Rd: smoothDWT.Rd:22-25: Dropping empty section \details
prepare_Rd: smoothDWT.Rd:29: Dropping empty section \references
prepare_Rd: smoothDWT.Rd:32-34: Dropping empty section \examples
* 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 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 ... [18s/19s] 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/MassSpecWavelet.Rcheck/00check.log’
for details.


MassSpecWavelet.Rcheck/00install.out:

* installing *source* package ‘MassSpecWavelet’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c convolve2.c -o convolve2.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o MassSpecWavelet.so convolve2.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/MassSpecWavelet.Rcheck/MassSpecWavelet/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 (MassSpecWavelet)

MassSpecWavelet.Rcheck/MassSpecWavelet-Ex.timings:

nameusersystemelapsed
MassSpecWavelet.package2.6870.0562.764
cwt0.5160.0240.542
extendLength0.0010.0000.001
extendNBase000
getLocalMaximumCWT0.3240.0040.344
getRidge0.2920.0000.293
identifyMajorPeaks3.1950.0123.235
localMaximum0.0520.0000.057
peakDetectionCWT4.6690.0194.756
plotLocalMax0.2320.0080.250
plotPeak2.2900.0162.335
plotRidgeList0.3530.0000.354
tuneInPeakInfo3.3290.0083.366