> 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