Validation Report - ddpcr@1.15.2
Context
This report is fully automated and builds on rhub/ref-image image. Documents the installation of this package on an open source R environment, focusing on:
- Installation environment description
- Testing coverage
It is limited to assess whether unit tests and documentation are present and can execute without error. An assessment would be required that the tests and documentation are meaningful.
Package ddpcr
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 126 |
| has_vignettes | 8 |
| export_help | 126 |
| has_website | TRUE |
| has_maintainer | Dean Attali daattali@gmail.com |
| bugs_status | 1 |
| has_source_control | https://github.com/daattali/ddpcr |
| has_bug_reports_url | 1 |
| downloads_1yr | 6896 |
| reverse_dependencies | 4 |
| has_examples | 0.9933333 |
| dependencies | 12 |
| license | MIT + file LICENSE |
Package general assessment: Coverage, check results, size, download the last year, reverse dependencies and number of dependencies.
Dependencies
Overall the package has these dependencies:
| package | type | |
|---|---|---|
| 1 | DT (>= 0.2) | Imports |
| 2 | dplyr (>= 0.5.0) | Imports |
| 3 | ggplot2 (>= 2.2.0) | Imports |
| 4 | lazyeval (>= 0.1.10) | Imports |
| 5 | magrittr (>= 1.5) | Imports |
| 6 | mixtools (>= 1.0.2) | Imports |
| 7 | plyr (>= 1.8.1) | Imports |
| 8 | readr (>= 0.1.0) | Imports |
| 9 | shiny (>= 0.11.0) | Imports |
| 10 | shinydisconnect | Imports |
| 11 | shinyjs (>= 0.4.0) | Imports |
| 12 | tibble | Imports |
Package dependencies
Reverse dependencies
Overall the package has 4 reverse dependencies:
CDatanet, EFAfactors, RRphylo, vMF
Namespace
Overall the package has 126 exported objects. 124 are documented:
%>% %btwn%
FALSE FALSE
analysis_complete analyze
TRUE TRUE
bind_df_ends calc_negative_freq_simple
TRUE TRUE
calculate_concentration calculate_concentration_single
TRUE TRUE
calculate_neg_freq_single calculate_negative_freqs
TRUE TRUE
capitalize cat0
TRUE TRUE
check_step classify_droplets
TRUE TRUE
classify_droplets_single classify_thresholds
TRUE TRUE
cluster cluster_name
TRUE TRUE
clusters col_to_num
TRUE TRUE
define_clusters define_params
TRUE TRUE
define_steps err_msg
TRUE TRUE
get_col get_empty_cutoff
TRUE TRUE
get_filled_border get_filled_drops
TRUE TRUE
get_outlier_cutoff get_row
TRUE TRUE
get_single_well get_wells_btwn
TRUE TRUE
has_signif_negative_cluster has_step
TRUE TRUE
is_dir is_dirty
TRUE TRUE
is_empty_plate is_file
TRUE TRUE
is_range is_well_success
TRUE TRUE
launch load_plate
TRUE TRUE
local_maxima local_minima
TRUE TRUE
lol_to_df mark_clusters
TRUE TRUE
merge_dfs_overwrite_col meta_var_name
TRUE TRUE
move_back move_front
TRUE TRUE
msg name
TRUE TRUE
name<- named_vec_to_df
TRUE TRUE
negative_name negative_name<-
TRUE TRUE
new_plate next_step
TRUE TRUE
normalize_to_rds num_to_col
TRUE TRUE
num_to_row other_dim
TRUE TRUE
params params<-
TRUE TRUE
parent_plate_type plate_data
TRUE TRUE
plate_data<- plate_meta
TRUE TRUE
plate_meta<- plate_types
TRUE TRUE
point2d positive_dim
TRUE TRUE
positive_dim_var positive_dim<-
TRUE TRUE
positive_name positive_name<-
TRUE TRUE
quiet range_list_to_vec
TRUE TRUE
range_to_endpoints range_to_seq
TRUE TRUE
reclassify_droplets reclassify_droplets_single
TRUE TRUE
remove_empty remove_failures
TRUE TRUE
remove_outliers reset
TRUE TRUE
row_to_num sample_data_dir
TRUE TRUE
sample_data_file sample_plate
TRUE TRUE
sample_results_file save_plate
TRUE TRUE
set_default_params set_thresholds
TRUE TRUE
status status<-
TRUE TRUE
step step_begin
TRUE TRUE
step_end step_name
TRUE TRUE
steps thresholds
TRUE TRUE
thresholds<- type
TRUE TRUE
unanalyzed_clusters variable_dim
TRUE TRUE
variable_dim_var variable_dim<-
TRUE TRUE
warn_msg WELL_ID_REGEX
TRUE TRUE
well_info wells_failed
TRUE TRUE
wells_mutant wells_negative
TRUE TRUE
wells_positive wells_success
TRUE TRUE
wells_used wells_wildtype
TRUE TRUE
x_threshold x_threshold<-
TRUE TRUE
x_var x_var<-
TRUE TRUE
y_threshold y_threshold<-
TRUE TRUE
y_var y_var<-
TRUE TRUE Examples
There are 149 help pages with examples, from 150 (99.33 %).
NEWS
The package has NEWS file and it is current.
License
The package uses .
Installation environment
System Info
| Field | Value |
|---|---|
| Image | rhub/ref-image |
| OS | Ubuntu 24.04.1 LTS |
| Platform | x86_64-pc-linux-gnu |
| System | x86_64, linux-gnu |
| Execution Time | 2025-02-18 03:29:44 UTC |
System information. Table about the system used to check the package.
R Session Info
Information about the R environment and capabilities:
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: UTC
tzcode source: system (glibc)
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
loaded via a namespace (and not attached):
[1] riskreports_0.0.0.9003 compiler_4.4.2 fastmap_1.2.0
[4] cli_3.6.4 htmltools_0.5.8.1 yaml_2.3.10
[7] rmarkdown_2.29 knitr_1.49 jsonlite_1.8.9
[10] xfun_0.50 digest_0.6.37 rlang_1.1.5
[13] evaluate_1.0.3 Platform used:
OS.type file.sep dynlib.ext GUI endian pkgType path.sep
"unix" "/" ".so" "X11" "little" "source" ":"
r_arch
"" R’s capabilities:
jpeg png tiff tcltk X11 aqua
TRUE TRUE TRUE TRUE FALSE FALSE
http/ftp sockets libxml fifo cledit iconv
TRUE TRUE FALSE TRUE FALSE TRUE
NLS Rprof profmem cairo ICU long.double
TRUE TRUE TRUE TRUE TRUE TRUE
libcurl
TRUE External software:
zlib
"1.3"
bzlib
"1.0.8, 13-Jul-2019"
xz
"5.4.5"
libdeflate
"1.19"
PCRE
"10.42 2022-12-11"
ICU
"74.2"
TRE
"TRE 0.8.0 R_fixes (BSD)"
iconv
"glibc 2.39"
readline
"8.2"
BLAS
"/usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3" Graphics external software:
cairo cairoFT pango
"1.18.0" "" "1.52.1"
libpng jpeg libtiff
"1.6.43" "8.0" "LIBTIFF, Version 4.5.1" Numerical characteristics of the machine:
double.eps double.neg.eps double.xmin
2.220446e-16 1.110223e-16 2.225074e-308
double.xmax double.base double.digits
1.797693e+308 2.000000e+00 5.300000e+01
double.rounding double.guard double.ulp.digits
5.000000e+00 0.000000e+00 -5.200000e+01
double.neg.ulp.digits double.exponent double.min.exp
-5.300000e+01 1.100000e+01 -1.022000e+03
double.max.exp integer.max sizeof.long
1.024000e+03 2.147484e+09 8.000000e+00
sizeof.longlong sizeof.longdouble sizeof.pointer
8.000000e+00 1.600000e+01 8.000000e+00
sizeof.time_t longdouble.eps longdouble.neg.eps
8.000000e+00 1.084202e-19 5.421011e-20
longdouble.digits longdouble.rounding longdouble.guard
6.400000e+01 5.000000e+00 0.000000e+00
longdouble.ulp.digits longdouble.neg.ulp.digits longdouble.exponent
-6.300000e+01 -6.400000e+01 1.500000e+01
longdouble.min.exp longdouble.max.exp
-1.638200e+04 1.638400e+04 Random number generation process:
[1] "Mersenne-Twister" "Inversion" "Rejection" Information about the environment
Environmental and options variables affect how package checks and software in it might behave. Here is the environmental variables when running this report
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PHARMAPKGS_EXCLUDED_METRICS
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TZ UTC
USER runner
VCPKG_INSTALLATION_ROOT
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$bitmapType
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$browser
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$callr.condition_handler_cli_message
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<bytecode: 0x55f41dc67910>
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