Multiple platform build/check report for BioC 3.6 - CHECK report for IPPD on tokay1

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### Running command:
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###   rm -rf IPPD.buildbin-libdir IPPD.Rcheck && mkdir IPPD.buildbin-libdir IPPD.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IPPD.buildbin-libdir IPPD_1.26.0.tar.gz >IPPD.Rcheck\00install.out 2>&1 && cp IPPD.Rcheck\00install.out IPPD-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=IPPD.buildbin-libdir --install="check:IPPD-install.out" --force-multiarch --no-vignettes --timings IPPD_1.26.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/IPPD.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 loading without being on the library search path ... 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/IPPD.buildbin-libdir/IPPD/libs/i386/IPPD.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
getPeaklist        29.20   2.06   31.26
fitModelParameters  7.95   0.03    7.99
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
getPeaklist 27.87    1.7   29.59
* 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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/IPPD.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'IPPD' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_IPPD.c -o R_init_IPPD.o
R_init_IPPD.c:29:1: warning: missing braces around initializer [-Wmissing-braces]
 };
 ^
R_init_IPPD.c:29:1: warning: (near initialization for 'cmethods[10]') [-Wmissing-braces]
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o IPPD.dll tmp.def R_init_IPPD.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/IPPD.buildbin-libdir/IPPD/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'IPPD'
    finding HTML links ... done
    IPPD-package                            html  
    analyzeLCMS                             html  
    fitModelParameters                      html  
    getPeaklist                             html  
    internals                               html  
    modelfit-class                          html  
    myo500                                  html  
    peaklist-class                          html  
    read.mzXML                              html  
    sweepline                               html  
    toyspectrum                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'IPPD' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_IPPD.c -o R_init_IPPD.o
R_init_IPPD.c:29:1: warning: missing braces around initializer [-Wmissing-braces]
 };
 ^
R_init_IPPD.c:29:1: warning: (near initialization for 'cmethods[10]') [-Wmissing-braces]
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o IPPD.dll tmp.def R_init_IPPD.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/IPPD.buildbin-libdir/IPPD/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IPPD' as IPPD_1.26.0.zip
* DONE (IPPD)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for IPPD on tokay1

Summary

Command output

Installation output

Tests output

Example timings