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CHECK report for IPPD on malbec1

This page was generated on 2018-04-12 13:09:18 -0400 (Thu, 12 Apr 2018).

Package 711/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IPPD 1.26.0
Martin Slawski
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/IPPD
Branch: RELEASE_3_6
Last Commit: 9caa36a
Last Changed Date: 2017-10-30 12:39:31 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: IPPD
Version: 1.26.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings IPPD_1.26.0.tar.gz
StartedAt: 2018-04-12 00:29:39 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:30:51 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 72.5 seconds
RetCode: 0
Status:  OK 
CheckDir: IPPD.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings IPPD_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/IPPD.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IPPD/DESCRIPTION’ ... OK
* this is package ‘IPPD’ version ‘1.26.0’
* 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 ‘IPPD’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  GPL (version 2 or later)
Standardizable: TRUE
Standardized license specification:
  GPL (>= 2)
* 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' calls to packages already attached by Depends:
  ‘MASS’ ‘Matrix’ ‘bitops’
  Please remove these calls from your code.
Package in Depends field not imported from: ‘bitops’
  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
analyzeLCMS: no visible global function definition for ‘read.table’
base64decode: no visible global function definition for ‘bitOr’
base64decode: no visible global function definition for ‘bitShiftL’
base64decode: no visible global function definition for ‘bitShiftR’
base64decode: no visible global function definition for ‘bitAnd’
getPeaklist,numeric-numeric: no visible global function definition for
  ‘data’
getPeaklist,numeric-numeric: no visible binding for global variable
  ‘tableaveragine’
threshold,peaklist: no visible binding for global variable ‘peaklist’
visualize,modelfit-missing-missing: no visible global function
  definition for ‘lines’
visualize,modelfit-missing-missing: no visible global function
  definition for ‘par’
visualize,peaklist-numeric-numeric: no visible global function
  definition for ‘layout’
visualize,peaklist-numeric-numeric: no visible global function
  definition for ‘lines’
visualize,peaklist-numeric-numeric: no visible global function
  definition for ‘matlines’
Undefined global functions or variables:
  bitAnd bitOr bitShiftL bitShiftR data layout lines matlines par
  peaklist read.table tableaveragine
Consider adding
  importFrom("graphics", "layout", "lines", "matlines", "par")
  importFrom("utils", "data", "read.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: analyzeLCMS.Rd:50: Dropping empty section \examples
prepare_Rd: read.mzXML.Rd:21: Dropping empty section \examples
prepare_Rd: sweepline.Rd:40: 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
getPeaklist 21.36   0.14   21.53
* 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-3.6-bioc/meat/IPPD.Rcheck/00check.log’
for details.



Installation output

IPPD.Rcheck/00install.out

* installing *source* package ‘IPPD’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_IPPD.c -o R_init_IPPD.o
R_init_IPPD.c:17:40: warning: missing braces around initializer [-Wmissing-braces]
 static const R_CMethodDef cmethods[] = {
                                        ^
R_init_IPPD.c:17:40: note: (near initialization for ‘cmethods’)
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o IPPD.so R_init_IPPD.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/IPPD.Rcheck/IPPD/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 (IPPD)

Tests output


Example timings

IPPD.Rcheck/IPPD-Ex.timings

nameusersystemelapsed
fitModelParameters3.7920.0203.813
getPeaklist21.36 0.1421.53
myo5000.0520.0000.053
toyspectrum0.1400.0040.147