Closed hyunhwan-jeong closed 3 years ago
0 errors, 0 warnings, and 3 notes now.
> checking installed package size ... NOTE
I am not sure I can decrease the size.
> checking R code for possible problems ... NOTE
The problems are related with https://cran.r-project.org/web/packages/dplyr/vignettes/programming.html
> checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘phangorn’
The SO page would be a solution to the problem: https://stackoverflow.com/questions/9899943/is-it-possible-to-use-non-imported-packages-in-a-package-vignette
── R CMD check results ────────────────────────────────────── TraceQC 0.1.0 ────
Duration: 4m 48.6s
> checking installed package size ... NOTE
installed size is 7.9Mb
sub-directories of 1Mb or more:
extdata 7.0Mb
> checking R code for possible problems ... NOTE
build_character_table: no visible binding for global variable ‘type’
build_character_table: no visible binding for global variable
‘target_seq’
build_character_table: no visible binding for global variable ‘start’
build_character_table: no visible binding for global variable
‘mutate_to’
build_character_table: no visible binding for global variable
‘mutationID’
build_character_table: no visible binding for global variable
‘sequenceID’
circular_chordgram: no visible binding for global variable ‘region’
circular_chordgram: no visible binding for global variable ‘start’
circular_chordgram: no visible binding for global variable ‘end’
circular_histogram: no visible binding for global variable ‘region’
circular_histogram: no visible binding for global variable ‘start’
circular_histogram: no visible binding for global variable ‘end’
create_TraceQC_object: no visible global function definition for
‘setNames’
create_TraceQC_object: no visible binding for global variable ‘start’
create_TraceQC_object: no visible binding for global variable ‘end’
create_TraceQC_object: no visible binding for global variable ‘region’
find_position: no visible binding for global variable ‘end’
find_position: no visible binding for global variable ‘start’
find_position: no visible binding for global variable ‘type’
find_position: no visible binding for global variable ‘tmp’
find_position: no visible binding for global variable ‘align’
find_position: no visible binding for global variable ‘mutate_to’
generate_qc_report: no visible global function definition for
‘browseURL’
lorenz_curve: no visible binding for global variable ‘target_seq’
lorenz_curve: no visible binding for global variable ‘x’
lorenz_curve: no visible binding for global variable ‘y’
lorenz_curve: no visible binding for global variable ‘cs’
mutation_type: no visible binding for global variable ‘type’
mutation_type: no visible binding for global variable ‘start’
mutation_type: no visible binding for global variable ‘mutate_to’
mutation_type: no visible binding for global variable ‘length_category’
mutation_type: no visible binding for global variable ‘ymax’
mutation_type: no visible binding for global variable ‘ymin’
mutation_type: no visible binding for global variable ‘labelPosition’
mutation_type: no visible binding for global variable ‘label’
num_mutation_histogram: no visible binding for global variable
‘target_seq’
num_mutation_histogram: no visible binding for global variable
‘num_mutation’
plot_construct: no visible binding for global variable ‘x’
plot_construct: no visible binding for global variable ‘y’
plot_construct: no visible binding for global variable ‘text’
plot_construct: no visible binding for global variable ‘region’
plot_deletion_hotspot: no visible binding for global variable ‘type’
plot_deletion_hotspot: no visible binding for global variable ‘start’
plot_insertion_hotspot: no visible binding for global variable ‘type’
plot_insertion_hotspot: no visible binding for global variable ‘start’
plot_point_mutation_hotspot: no visible binding for global variable
‘type’
plot_point_mutation_hotspot: no visible binding for global variable
‘start’
plot_point_mutation_hotspot: no visible binding for global variable
‘mutate_to’
plot_score_distribution: no visible binding for global variable ‘score’
plot_score_distribution: no visible binding for global variable
‘..density..’
seq_to_character: no visible binding for global variable ‘target_seq’
seq_to_character: no visible binding for global variable ‘target_ref’
sequence_alignment: no visible global function definition for
‘alignment’
Undefined global functions or variables:
..density.. align alignment browseURL cs end label labelPosition
length_category mutate_to mutationID num_mutation region score
sequenceID setNames start target_ref target_seq text tmp type x y
ymax ymin
Consider adding
importFrom("graphics", "text")
importFrom("stats", "end", "setNames", "start")
importFrom("utils", "browseURL")
to your NAMESPACE file.
> checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘phangorn’
0 errors ✓ | 0 warnings ✓ | 3 notes x
No more checking for unstated dependencies in vignettes
by 66f995c65626bda1e7b2c217252bd7d34afeafff.
all the issues have been resolved. Ready to go.
Current status
Duration: 2m 16.9s
> checking whether package ‘TraceQC’ can be installed ... WARNING
See below...
> checking package dependencies ... NOTE
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
> checking R code for possible problems ... NOTE
find_position: no visible binding for global variable ‘alignment_score’
find_position: no visible binding for global variable ‘type’
find_position: no visible binding for global variable ‘start’
find_position: no visible binding for global variable ‘mutate_to’
seq_to_character: no visible binding for global variable ‘target_seq’
seq_to_character: no visible binding for global variable ‘target_ref’
seq_to_character: no visible binding for global variable ‘score’
Undefined global functions or variables:
alignment_score mutate_to score start target_ref target_seq type
Consider adding
importFrom("stats", "start")
to your NAMESPACE file.
> checking Rd files ... NOTE
prepare_Rd: table_to_phyDat.Rd:12-14: Dropping empty section \value
0 errors ✓ | 1 warning x | 3 notes x
Error: R CMD check found WARNINGs
Execution halted
Exited with status 1.
It is a current status of the package check, we need to fix it.