Multiple platform build/check report for BioC 3.8 - CHECK report for IPPD on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:IPPD.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings IPPD_1.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/IPPD.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.30.0’
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
getPeaklist 22.2  0.072  22.326
* 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/IPPD.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL IPPD
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘IPPD’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-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’)
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o IPPD.so R_init_IPPD.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/IPPD/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (IPPD)

name	user	system	elapsed
fitModelParameters	2.128	0.016	2.142
getPeaklist	22.200	0.072	22.326
myo500	0.084	0.004	0.090
toyspectrum	0.196	0.008	0.204

CHECK report for IPPD on malbec1

Summary

Command output

Installation output

Tests output

Example timings