Address build issues - Githubissues

> devtools::check(document = T)
Updating ROMOPOmics documentation
Loading ROMOPOmics
Writing NAMESPACE
Writing NAMESPACE
Writing fetch_geo_series.Rd
Writing loadDataModel.Rd
── Building ───────────────────────────────────────────────────────────────────────────────────────── ROMOPOmics ──
Setting env vars:
● CFLAGS    : -Wall -pedantic -fdiagnostics-color=always
● CXXFLAGS  : -Wall -pedantic -fdiagnostics-color=always
● CXX11FLAGS: -Wall -pedantic -fdiagnostics-color=always
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✓  checking for file ‘/Users/nickgiangreco/GitHub/ROMOPOmics/DESCRIPTION’ ...
─  preparing ‘ROMOPOmics’: (6.4s)
✓  checking DESCRIPTION meta-information
─  installing the package to build vignettes
✓  creating vignettes (7m 54.3s)
─  checking for LF line-endings in source and make files and shell scripts (680ms)
─  checking for empty or unneeded directories
─  building ‘ROMOPOmics_0.1.0.tar.gz’

── Checking ───────────────────────────────────────────────────────────────────────────────────────── ROMOPOmics ──
Setting env vars:
● _R_CHECK_CRAN_INCOMING_REMOTE_: FALSE
● _R_CHECK_CRAN_INCOMING_       : FALSE
● _R_CHECK_FORCE_SUGGESTS_      : FALSE
● NOT_CRAN                      : true
── R CMD check ────────────────────────────────────────────────────────────────────────────────────────────────────
─  using log directory ‘/private/var/folders/00/hrw448cj27l47l_0f2lrz1rr0000gp/T/RtmpqtSf1P/ROMOPOmics.Rcheck’
─  using R version 4.0.3 (2020-10-10)
─  using platform: x86_64-apple-darwin17.0 (64-bit)
─  using session charset: UTF-8
─  using options ‘--no-manual --as-cran’
✓  checking for file ‘ROMOPOmics/DESCRIPTION’
─  checking extension type ... Package
─  this is package ‘ROMOPOmics’ version ‘0.1.0’
─  package encoding: UTF-8
✓  checking package namespace information
✓  checking package dependencies (1.2s)
✓  checking if this is a source package
✓  checking if there is a namespace
✓  checking for executable files (651ms)
✓  checking for hidden files and directories
✓  checking for portable file names ...
✓  checking for sufficient/correct file permissions
✓  checking serialization versions
✓  checking whether package ‘ROMOPOmics’ can be installed (6.8s)
✓  checking installed package size ...
✓  checking package directory ...
N  checking for future file timestamps (1.5s)
   unable to verify current time
✓  checking ‘build’ directory
✓  checking DESCRIPTION meta-information ...
N  checking top-level files
   Non-standard files/directories found at top level:
     ‘LICENSE.md’ ‘README.Rmd’
✓  checking for left-over files
✓  checking index information ...
✓  checking package subdirectories ...
✓  checking R files for non-ASCII characters ...
✓  checking R files for syntax errors ...
✓  checking whether the package can be loaded (1.8s)
✓  checking whether the package can be loaded with stated dependencies (1.6s)
✓  checking whether the package can be unloaded cleanly (1.6s)
✓  checking whether the namespace can be loaded with stated dependencies (1.6s)
✓  checking whether the namespace can be unloaded cleanly (1.8s)
✓  checking dependencies in R code (1.6s)
✓  checking S3 generic/method consistency (2.2s)
✓  checking replacement functions (1.7s)
✓  checking foreign function calls (1.6s)
N  checking R code for possible problems (7.3s)
   combineInputTables: no visible binding for global variable ‘field’
   combineInputTables: no visible binding for global variable
     ‘table_field’
   combineInputTables: no visible binding for global variable ‘required’
   combineInputTables: no visible binding for global variable ‘type’
   combineInputTables: no visible binding for global variable
     ‘description’
   combineInputTables: no visible binding for global variable
     ‘table_index’
   combineInputTables: no visible binding for global variable ‘value’
   combineInputTables: no visible binding for global variable ‘is_used’
   combineInputTables: no visible binding for global variable ‘name’
   combineInputTables: no visible global function definition for ‘:=’
   combineInputTables : <anonymous>: no visible binding for global
     variable ‘.’
   composite_geo_table: no visible binding for global variable ‘detail’
   composite_geo_table : <anonymous>: no visible binding for global
     variable ‘gse_geo_accession’
   composite_geo_table: no visible binding for global variable ‘.’
   expand_entry_columns: no visible binding for global variable ‘.’
   fetch_geo_datasets: no visible binding for global variable ‘is’
   fetch_geo_datasets: no visible binding for global variable ‘.’
   fetch_geo_series: no visible binding for global variable ‘.’
   getDBTables: no visible global function definition for
     ‘getTableDependencies’
   getDependencies: no visible binding for global variable ‘table_index’
   getDependencies: no visible binding for global variable ‘field’
   metadata_mask: no visible binding for global variable ‘value’
   metadata_mask: no visible global function definition for ‘na.exclude’
   metadata_mask: no visible binding for global variable
     ‘examples_from_data’
   metadata_mask: no visible binding for global variable ‘name’
   metadata_mask: no visible binding for global variable ‘alias’
   metadata_mask: no visible binding for global variable ‘field’
   metadata_mask: no visible binding for global variable ‘field_idx’
   parse_gds_coldata: no visible binding for global variable ‘desc_name’
   parse_gds_coldata: no visible binding for global variable ‘desc_value’
   parse_geo_metadata: no visible global function definition for ‘as’
   parse_geo_metadata: no visible binding for global variable ‘V1’
   parse_geo_metadata: no visible global function definition for ‘head’
   parse_geo_metadata: no visible binding for global variable ‘text’
   parse_geo_metadata: no visible global function definition for ‘is’
   parse_geo_text_results: no visible binding for global variable
     ‘data_dir’
   parse_gse_metadata: no visible global function definition for
     ‘abstract’
   parse_gse_metadata: no visible global function definition for ‘pData’
   parse_gse_metadata: no visible binding for global variable
     ‘geo_accession’
   parse_gse_metadata: no visible binding for global variable ‘detail’
   parse_gse_metadata: no visible binding for global variable ‘channel’
   parse_gse_metadata: no visible binding for global variable ‘value’
   parse_gse_metadata: no visible binding for global variable ‘.’
   parse_gse_metadata: no visible binding for global variable ‘name’
   parse_metadata: no visible global function definition for ‘is’
   readInputFile: no visible binding for global variable ‘.’
   readInputFile: no visible binding for global variable ‘table_index’
   Undefined global functions or variables:
     . := V1 abstract alias as channel data_dir desc_name desc_value
     description detail examples_from_data field field_idx geo_accession
     getTableDependencies gse_geo_accession head is is_used na.exclude
     name pData required table_field table_index text type value
   Consider adding
     importFrom("graphics", "text")
     importFrom("methods", "as", "is")
     importFrom("stats", "alias", "na.exclude")
     importFrom("utils", "head")
   to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
   contains 'methods').
✓  checking Rd files ...
✓  checking Rd metadata ...
✓  checking Rd line widths ...
✓  checking Rd cross-references ...
✓  checking for missing documentation entries (1.8s)
✓  checking for code/documentation mismatches (4.7s)
✓  checking Rd \usage sections (2.4s)
✓  checking Rd contents ...
✓  checking for unstated dependencies in examples ...
✓  checking installed files from ‘inst/doc’ ...
✓  checking files in ‘vignettes’ ...
─  checking examples ... NONE
✓  checking for unstated dependencies in ‘tests’ ...
─  checking tests ...
✓  Running ‘testthat.R’ (2s)
✓  checking for unstated dependencies in vignettes (2.3s)
✓  checking package vignettes in ‘inst/doc’ ...
✓  checking re-building of vignette outputs (8m 30s)
✓  checking for non-standard things in the check directory
✓  checking for detritus in the temp directory

   See
     ‘/private/var/folders/00/hrw448cj27l47l_0f2lrz1rr0000gp/T/RtmpqtSf1P/ROMOPOmics.Rcheck/00check.log’
   for details.

── R CMD check results ────────────────────────────────────────────────────────────────────── ROMOPOmics 0.1.0 ────
Duration: 9m 17.5s

> checking for future file timestamps ... NOTE
  unable to verify current time

> checking top-level files ... NOTE
  Non-standard files/directories found at top level:
    ‘LICENSE.md’ ‘README.Rmd’

> checking R code for possible problems ... NOTE
  combineInputTables: no visible binding for global variable ‘field’
  combineInputTables: no visible binding for global variable
    ‘table_field’
  combineInputTables: no visible binding for global variable ‘required’
  combineInputTables: no visible binding for global variable ‘type’
  combineInputTables: no visible binding for global variable
    ‘description’
  combineInputTables: no visible binding for global variable
    ‘table_index’
  combineInputTables: no visible binding for global variable ‘value’
  combineInputTables: no visible binding for global variable ‘is_used’
  combineInputTables: no visible binding for global variable ‘name’
  combineInputTables: no visible global function definition for ‘:=’
  combineInputTables : <anonymous>: no visible binding for global
    variable ‘.’
  composite_geo_table: no visible binding for global variable ‘detail’
  composite_geo_table : <anonymous>: no visible binding for global
    variable ‘gse_geo_accession’
  composite_geo_table: no visible binding for global variable ‘.’
  expand_entry_columns: no visible binding for global variable ‘.’
  fetch_geo_datasets: no visible binding for global variable ‘is’
  fetch_geo_datasets: no visible binding for global variable ‘.’
  fetch_geo_series: no visible binding for global variable ‘.’
  getDBTables: no visible global function definition for
    ‘getTableDependencies’
  getDependencies: no visible binding for global variable ‘table_index’
  getDependencies: no visible binding for global variable ‘field’
  metadata_mask: no visible binding for global variable ‘value’
  metadata_mask: no visible global function definition for ‘na.exclude’
  metadata_mask: no visible binding for global variable
    ‘examples_from_data’
  metadata_mask: no visible binding for global variable ‘name’
  metadata_mask: no visible binding for global variable ‘alias’
  metadata_mask: no visible binding for global variable ‘field’
  metadata_mask: no visible binding for global variable ‘field_idx’
  parse_gds_coldata: no visible binding for global variable ‘desc_name’
  parse_gds_coldata: no visible binding for global variable ‘desc_value’
  parse_geo_metadata: no visible global function definition for ‘as’
  parse_geo_metadata: no visible binding for global variable ‘V1’
  parse_geo_metadata: no visible global function definition for ‘head’
  parse_geo_metadata: no visible binding for global variable ‘text’
  parse_geo_metadata: no visible global function definition for ‘is’
  parse_geo_text_results: no visible binding for global variable
    ‘data_dir’
  parse_gse_metadata: no visible global function definition for
    ‘abstract’
  parse_gse_metadata: no visible global function definition for ‘pData’
  parse_gse_metadata: no visible binding for global variable
    ‘geo_accession’
  parse_gse_metadata: no visible binding for global variable ‘detail’
  parse_gse_metadata: no visible binding for global variable ‘channel’
  parse_gse_metadata: no visible binding for global variable ‘value’
  parse_gse_metadata: no visible binding for global variable ‘.’
  parse_gse_metadata: no visible binding for global variable ‘name’
  parse_metadata: no visible global function definition for ‘is’
  readInputFile: no visible binding for global variable ‘.’
  readInputFile: no visible binding for global variable ‘table_index’
  Undefined global functions or variables:
    . := V1 abstract alias as channel data_dir desc_name desc_value
    description detail examples_from_data field field_idx geo_accession
    getTableDependencies gse_geo_accession head is is_used na.exclude
    name pData required table_field table_index text type value
  Consider adding
    importFrom("graphics", "text")
    importFrom("methods", "as", "is")
    importFrom("stats", "alias", "na.exclude")
    importFrom("utils", "head")
  to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
  contains 'methods').

0 errors ✓ | 0 warnings ✓ | 3 notes x
AndrewC160 / ROMOPOmics

Address build issues #16
