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cinf log file (check_x86_64_linux)

Sun Dec 24 18:25:10 2017: Checking package cinf (SVN revision 28) ...
* using log directory ‘/srv/rf/building/build_2017-12-24-18-24/RF_PKG_CHECK/PKGS/cinf.Rcheck’
* using R version 3.4.3 Patched (2017-12-23 r73953)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘cinf/DESCRIPTION’ ... OK
* this is package ‘cinf’ version ‘0.0-19’
* checking CRAN incoming feasibility ...Warning: /srv/rf/building/build_2017-12-24-18-24/RF_PKG_CHECK/PKGS/cinf.Rcheck/00_pkg_src/cinf/man/add_mol_attribs.Rd:7: unexpected section header '\format'
Warning: /srv/rf/building/build_2017-12-24-18-24/RF_PKG_CHECK/PKGS/cinf.Rcheck/00_pkg_src/cinf/man/connect.Rd:7: unexpected section header '\format'
Warning: /srv/rf/building/build_2017-12-24-18-24/RF_PKG_CHECK/PKGS/cinf.Rcheck/00_pkg_src/cinf/man/elem.Rd:7: unexpected section header '\format'
Warning: /srv/rf/building/build_2017-12-24-18-24/RF_PKG_CHECK/PKGS/cinf.Rcheck/00_pkg_src/cinf/man/add_mol_attribs.Rd:7: unexpected section header '\format'
Warning: /srv/rf/building/build_2017-12-24-18-24/RF_PKG_CHECK/PKGS/cinf.Rcheck/00_pkg_src/cinf/man/connect.Rd:7: unexpected section header '\format'
Warning: /srv/rf/building/build_2017-12-24-18-24/RF_PKG_CHECK/PKGS/cinf.Rcheck/00_pkg_src/cinf/man/elem.Rd:7: unexpected section header '\format'
 NOTE
Maintainer: ‘Igor Baskin ’

New submission

The Title field should be in title case, current version then in title case:
‘Basic tools for chemoinformatics’
‘Basic Tools for Chemoinformatics’

The Description field should not start with the package name,
  'This package' or similar.
* 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cinf’ can be installed ... [1s/1s] WARNING
Found the following significant warnings:
  Warning: /srv/rf/building/build_2017-12-24-18-24/RF_PKG_CHECK/PKGS/cinf.Rcheck/00_pkg_src/cinf/man/add_mol_attribs.Rd:7: unexpected section header '\format'
  Warning: /srv/rf/building/build_2017-12-24-18-24/RF_PKG_CHECK/PKGS/cinf.Rcheck/00_pkg_src/cinf/man/connect.Rd:7: unexpected section header '\format'
  Warning: /srv/rf/building/build_2017-12-24-18-24/RF_PKG_CHECK/PKGS/cinf.Rcheck/00_pkg_src/cinf/man/elem.Rd:7: unexpected section header '\format'
See ‘/srv/rf/building/build_2017-12-24-18-24/RF_PKG_CHECK/PKGS/cinf.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package 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 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 ... [8s/8s] WARNING
Found an obsolete/platform-specific call in the following function:
  ‘inv_free_wilson’
Found the defunct/removed function:
  ‘real’

In addition to the above warning(s), found the following notes:

add_impl_hydr: no visible global function definition for ‘data’
add_impl_hydr: no visible binding for global variable ‘PT’
calc_ss: no visible global function definition for ‘var’
connect: no visible global function definition for ‘data’
connect: no visible binding for global variable ‘PT’
inv_free_wilson: no visible global function definition for ‘real’
inv_free_wilson: no visible global function definition for ‘qnorm’
inv_free_wilson: no visible global function definition for ‘dnorm’
inv_free_wilson: no visible global function definition for ‘plot’
mlr: no visible global function definition for ‘lm’
mlr: no visible global function definition for ‘step’
mlr: no visible global function definition for ‘fitted.values’
mlr: no visible global function definition for ‘residuals’
plot_mlr_model: no visible global function definition for
  ‘fitted.values’
plot_mlr_model: no visible global function definition for ‘residuals’
plot_regr: no visible global function definition for ‘plot’
plot_regr: no visible global function definition for ‘abline’
plot_regr: no visible global function definition for ‘title’
predict_free_wilson_mlr: no visible global function definition for
  ‘predict’
predict_table_free_wilson_mlr: no visible global function definition
  for ‘predict’
regr_param: no visible global function definition for ‘var’
rm_low_var: no visible global function definition for ‘var’
test_free_wilson: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  PT abline data dnorm fitted.values lm plot predict qnorm read.table
  real residuals step title var
Consider adding
  importFrom("graphics", "abline", "plot", "title")
  importFrom("stats", "dnorm", "fitted.values", "lm", "predict", "qnorm",
             "residuals", "step", "var")
  importFrom("utils", "data", "read.table")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘cinf/R/cinf-descr-connect.R’:
  data(PT)
File ‘cinf/R/cinf-hydrogens.R’:
  data(PT)
See section ‘Good practice’ in ‘?data’.
* checking Rd files ... WARNING
prepare_Rd: add_mol_attribs.Rd:7: unexpected section header '\format'
prepare_Rd: calc_accuracy.Rd:18-19: Dropping empty section \examples
prepare_Rd: calc_balaccuracy.Rd:18-19: Dropping empty section \examples
prepare_Rd: calc_f1.Rd:18-19: Dropping empty section \examples
prepare_Rd: calc_kappa.Rd:18-19: Dropping empty section \examples
prepare_Rd: calc_matcorcoef.Rd:18-19: Dropping empty section \examples
prepare_Rd: calc_precision.Rd:18-19: Dropping empty section \examples
prepare_Rd: calc_recall.Rd:18-19: Dropping empty section \examples
prepare_Rd: calc_sensitivity.Rd:18-19: Dropping empty section \examples
prepare_Rd: calc_specificity.Rd:18-19: Dropping empty section \examples
prepare_Rd: connect.Rd:7: unexpected section header '\format'
prepare_Rd: elem.Rd:7: unexpected section header '\format'
prepare_Rd: extract_new.Rd:15: Dropping empty section \value
prepare_Rd: extract_new.Rd:16-17: Dropping empty section \examples
find_substr_isomorph.Rd: non-ASCII input and no declared encoding
prepare_Rd: full_design.Rd:15-16: Dropping empty section \examples
prepare_Rd: inv_free_wilson.Rd:18-19: Dropping empty section \examples
prepare_Rd: make_freq_table.Rd:16-17: Dropping empty section \examples
prepare_Rd: predict_free_wilson_mlr.Rd:17-18: Dropping empty section \examples
prepare_Rd: predict_table_free_wilson_mlr.Rd:16-17: Dropping empty section \examples
prepare_Rd: sample_subst.Rd:16-17: Dropping empty section \examples
problem found in ‘find_substr_isomorph.Rd’
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘calc_ss’ ‘mdb_delete_metal’ ‘mlr’ ‘mol_delete_metal’
  ‘plot_mlr_model’ ‘plot_regr’ ‘regr_param’ ‘rm_low_var’
  ‘test_free_wilson’
Undocumented data sets:
  ‘free-wilson-boehm’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 examples ... [3s/3s] OK
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 2 NOTEs
See
  ‘/srv/rf/building/build_2017-12-24-18-24/RF_PKG_CHECK/PKGS/cinf.Rcheck/00check.log’
for details.


Run time: 33.46 seconds.