R Development Page

batman log file (check_x86_64_linux)

Fri Jan 26 07:45:19 2018: Checking package batman (SVN revision 408) ...
Additional arguments to R CMD check: --no-examples --no-tests --no-vignettes
* using log directory ‘/srv/rf/building/build_2018-01-26-07-44/RF_PKG_CHECK/PKGS/batman.Rcheck’
* using R version 3.4.3 Patched (2018-01-25 r74161)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-examples --no-tests --no-vignettes --as-cran’
* checking for file ‘batman/DESCRIPTION’ ... OK
* this is package ‘batman’ version ‘1.2.1.11’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Jie Hao ’

New maintainer:
  Jie Hao 
Old maintainer(s):
  Oliver Keyes 

Uses the superseded packages: ‘doSNOW’, ‘snow’

No package encoding and non-ASCII characters in the following R files:
  R/batman.R
    174:     # modified as suggested by Dr Gonalo Correia

The Title field should be in title case, current version then in title case:
‘Bayesian AuTomated Metabolite Analyser for NMR spectra’
‘Bayesian AuTomated Metabolite Analyser for NMR Spectra’

The Description field should not start with the package name,
  'This package' or similar.

Size of tarball: 7310097 bytes
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... NOTE
Found the following non-portable file path:
  batman/src/boostLib/boost/numeric/odeint/stepper/generation/generation_runge_kutta_cash_karp54_classic.hpp

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘batman’ can be installed ... [234s/236s] OK
* checking installed package size ... NOTE
  installed size is 15.2Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs     11.2Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘LICENSE_1_0.txt’
* 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 loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [16s/16s] NOTE
Found an obsolete/platform-specific call in the following functions:
  ‘plotBatmanFit’ ‘plotBatmanFitHR’ ‘plotBatmanFitStack’
  ‘plotChemShiftDist’ ‘plotDiagnosticScatter’ ‘plotMetaFit’
  ‘plotRelCon’ ‘plotShift’
Found the platform-specific device:
  ‘x11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
plotBatmanFit: no visible global function definition for ‘rainbow’
plotBatmanFit: no visible global function definition for ‘pdf’
plotBatmanFit: no visible global function definition for ‘x11’
plotBatmanFit: no visible global function definition for ‘par’
plotBatmanFit: no visible global function definition for ‘plot’
plotBatmanFit: no visible global function definition for ‘box’
plotBatmanFit: no visible global function definition for ‘axis’
plotBatmanFit: no visible global function definition for ‘lines’
plotBatmanFit: no visible global function definition for ‘legend’
plotBatmanFit: no visible global function definition for ‘dev.off’
plotBatmanFit: no visible global function definition for ‘dev.copy2pdf’
plotBatmanFit: no visible binding for global variable ‘x11’
plotBatmanFitHR: no visible global function definition for ‘rainbow’
plotBatmanFitHR: no visible global function definition for ‘pdf’
plotBatmanFitHR: no visible global function definition for ‘x11’
plotBatmanFitHR: no visible global function definition for ‘plot’
plotBatmanFitHR: no visible global function definition for ‘points’
plotBatmanFitHR: no visible global function definition for ‘lines’
plotBatmanFitHR: no visible global function definition for ‘legend’
plotBatmanFitHR: no visible global function definition for ‘dev.off’
plotBatmanFitHR: no visible global function definition for
  ‘dev.copy2pdf’
plotBatmanFitHR: no visible binding for global variable ‘x11’
plotBatmanFitStack: no visible global function definition for ‘rainbow’
plotBatmanFitStack: no visible global function definition for ‘pdf’
plotBatmanFitStack: no visible global function definition for ‘x11’
plotBatmanFitStack: no visible global function definition for ‘plot’
plotBatmanFitStack: no visible global function definition for ‘lines’
plotBatmanFitStack: no visible global function definition for ‘box’
plotBatmanFitStack: no visible global function definition for ‘axis’
plotBatmanFitStack: no visible global function definition for ‘legend’
plotBatmanFitStack: no visible global function definition for ‘dev.off’
plotBatmanFitStack: no visible global function definition for
  ‘dev.copy2pdf’
plotBatmanFitStack: no visible binding for global variable ‘x11’
plotChemShiftDist: no visible global function definition for ‘pdf’
plotChemShiftDist: no visible global function definition for ‘x11’
plotChemShiftDist: no visible global function definition for ‘par’
plotChemShiftDist: no visible global function definition for ‘hist’
plotChemShiftDist: no visible global function definition for ‘dev.off’
plotChemShiftDist: no visible global function definition for
  ‘dev.copy2pdf’
plotChemShiftDist: no visible binding for global variable ‘x11’
plotDiagnosticScatter: no visible global function definition for ‘pdf’
plotDiagnosticScatter: no visible global function definition for ‘x11’
plotDiagnosticScatter: no visible global function definition for ‘par’
plotDiagnosticScatter: no visible global function definition for ‘plot’
plotDiagnosticScatter: no visible global function definition for ‘text’
plotDiagnosticScatter: no visible global function definition for
  ‘points’
plotDiagnosticScatter: no visible global function definition for
  ‘legend’
plotDiagnosticScatter: no visible global function definition for ‘box’
plotDiagnosticScatter: no visible global function definition for
  ‘dev.off’
plotDiagnosticScatter: no visible global function definition for
  ‘dev.copy2pdf’
plotDiagnosticScatter: no visible binding for global variable ‘x11’
plotMetaFit: no visible global function definition for ‘pdf’
plotMetaFit: no visible global function definition for ‘x11’
plotMetaFit: no visible global function definition for ‘par’
plotMetaFit: no visible binding for global variable ‘quantile’
plotMetaFit: no visible global function definition for ‘plot’
plotMetaFit: no visible global function definition for ‘lines’
plotMetaFit: no visible global function definition for ‘legend’
plotMetaFit: no visible global function definition for ‘dev.off’
plotMetaFit: no visible global function definition for ‘dev.copy2pdf’
plotMetaFit: no visible binding for global variable ‘x11’
plotRelCon: no visible global function definition for ‘pdf’
plotRelCon: no visible global function definition for ‘x11’
plotRelCon: no visible global function definition for ‘par’
plotRelCon: no visible global function definition for ‘hist’
plotRelCon: no visible global function definition for ‘quantile’
plotRelCon: no visible global function definition for ‘abline’
plotRelCon: no visible global function definition for ‘legend’
plotRelCon: no visible global function definition for ‘title’
plotRelCon: no visible global function definition for ‘dev.off’
plotRelCon: no visible global function definition for ‘dev.copy2pdf’
plotRelCon: no visible binding for global variable ‘x11’
plotRelCon: no visible global function definition for ‘boxplot’
plotRelCon: no visible global function definition for ‘axis’
plotShift: no visible global function definition for ‘pdf’
plotShift: no visible global function definition for ‘x11’
plotShift: no visible global function definition for ‘par’
plotShift: no visible global function definition for ‘hist’
plotShift: no visible global function definition for ‘lines’
plotShift: no visible global function definition for ‘density’
plotShift: no visible global function definition for ‘quantile’
plotShift: no visible global function definition for ‘abline’
plotShift: no visible global function definition for ‘legend’
plotShift: no visible global function definition for ‘box’
plotShift: no visible global function definition for ‘title’
plotShift: no visible global function definition for ‘boxplot’
plotShift: no visible global function definition for ‘axis’
plotShift: no visible global function definition for ‘dev.off’
plotShift: no visible global function definition for ‘dev.copy2pdf’
plotShift: no visible binding for global variable ‘x11’
readBatmanOutput: no visible global function definition for ‘quantile’
readBruker: no visible global function definition for ‘approx’
Undefined global functions or variables:
  abline approx axis box boxplot density dev.copy2pdf dev.off hist
  legend lines par pdf plot points quantile rainbow text title x11
Consider adding
  importFrom("grDevices", "dev.copy2pdf", "dev.off", "pdf", "rainbow",
             "x11")
  importFrom("graphics", "abline", "axis", "box", "boxplot", "hist",
             "legend", "lines", "par", "plot", "points", "text", "title")
  importFrom("stats", "approx", "density", "quantile")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'batman.Rd':
  \examples lines wider than 100 characters:
     ## time used for burnin is 76 seconds.                                                                         

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'saveBruker2Txt':
saveBruker2Txt
  Code: function(BrukerDataDir, saveFileName, sep = "\t")
  Docs: function(BrukerDataDir)
  Argument names in code not in docs:
    saveFileName sep

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'saveBruker2Txt':
  ‘saveFileName’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... WARNING
File ‘batman/libs/batman.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Objects: ‘sample_eta_theta_beta_block.o’, ‘sample_log_fwhh.o’,
      ‘sample_log_fwhh_re.o’, ‘sample_pos.o’,
      ‘sample_pos_theta_block.o’, ‘write_results_all.o’,
      ‘yeast_analysis_Rw.o’
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Object: ‘read_multiplet_data.o’
  Found ‘exit’, possibly from ‘exit’ (C)
    Objects: ‘read_dat_chemshift.o’, ‘read_datf.o’,
      ‘read_multiplet_data.o’, ‘read_txt_batmanoptions.o’,
      ‘read_txtf.o’, ‘sample_eta_theta_beta_block.o’,
      ‘sample_log_fwhh.o’, ‘sample_log_fwhh_re.o’, ‘sample_pos.o’,
      ‘sample_pos_theta_block.o’, ‘sample_truncated_normal_gen.o’,
      ‘write_results_all.o’, ‘yeast_analysis_Rw.o’
  Found ‘printf’, possibly from ‘printf’ (C)
    Objects: ‘read_dat_chemshift.o’, ‘read_datf.o’,
      ‘read_txt_batmanoptions.o’, ‘read_txtf.o’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Objects: ‘read_multiplet_data.o’, ‘sample_truncated_normal_gen.o’,
      ‘yeast_analysis_Rw.o’
File ‘batman/libs/batman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... WARNING
  ‘gs+qpdf’ made some significant size reductions:
     compacted ‘batman_doc.pdf’ from 763Kb to 254Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 6 NOTEs
See
  ‘/srv/rf/building/build_2018-01-26-07-44/RF_PKG_CHECK/PKGS/batman.Rcheck/00check.log’
for details.


Run time: 298.74 seconds.