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.
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 54 |
| has_vignettes | 2 |
| export_help | 54 |
| has_website | TRUE |
| has_maintainer | Zhenke Wu zhenkewu@gmail.com |
| bugs_status | 0.952381 |
| size_codebase | 8407 |
| has_source_control | https://github.com/zhenkewu/baker |
| has_bug_reports_url | 1 |
| downloads_1yr | 68848 |
| reverse_dependencies | 0 |
| has_examples | 1 |
| dependencies | 18 |
| 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 | R(>= 4.3.0) | Depends |
| 2 | rjags(>= 4-6) | Imports |
| 3 | R2jags(>= 0.5) | Imports |
| 4 | lubridate(>= 1.3) | Imports |
| 5 | binom(>= 1.1) | Imports |
| 6 | coda(>= 0.16) | Imports |
| 7 | robCompositions(>= 2.0.3) | Imports |
| 8 | ggplot2(>= 1.0) | Imports |
| 9 | ggpubr(>= 0.4.0) | Imports |
| 10 | gridExtra(>= 2.0) | Imports |
| 11 | reshape2(>= 1.4) | Imports |
| 12 | mgcv(>= 1.8-6) | Imports |
| 13 | mvbutils(>= 2.7.4.1) | Imports |
| 14 | shinyFiles(>= 0.6) | Imports |
| 15 | shinydashboard(>= 0.5.1) | Imports |
| 16 | stats | Imports |
| 17 | utils | Imports |
| 18 | abind | Imports |
Package dependencies
Reverse dependencies
Overall the package has 0 reverse dependencies:
Namespace
Overall the package has 54 exported objects. 54 are documented:
assign_model beta_parms_from_quantiles TRUE TRUE beta_plot bin2dec TRUE TRUE check_dir_create clean_combine_subsites TRUE TRUE clean_perch_data combine_data_nplcm TRUE TRUE compute_logOR_single_cause delete_start_with TRUE TRUE expit extract_data_raw TRUE TRUE get_individual_data get_individual_prediction TRUE TRUE get_top_pattern H TRUE TRUE has_non_basis I2symb TRUE TRUE Imat2cat is_jags_folder TRUE TRUE is_length_all_one line2user TRUE TRUE logit logsumexp TRUE TRUE make_filename make_foldername TRUE TRUE make_list make_meas_object TRUE TRUE make_template marg_H TRUE TRUE match_cause merge_lists TRUE TRUE my_reorder nplcm TRUE TRUE nplcm_read_folder overall_uniform TRUE TRUE plot_check_common_pattern plot_check_pairwise_SLORD TRUE TRUE plot_logORmat read_meas_object TRUE TRUE rvbern s_date_Eti TRUE TRUE s_date_FPR show_dep TRUE TRUE show_individual simulate_nplcm TRUE TRUE softmax subset_data_nplcm_by_index TRUE TRUE summarize_BrS summarize_SS TRUE TRUE symb2I tsb TRUE TRUE unfactor unique_cause TRUE TRUE Examples
There are 153 help pages with examples, from 153 (100.00 %).
NEWS
The package has NEWS file and it is current.
License
The package uses .
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 | 2025-02-14 07:40:40 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-gnuRunning under: Ubuntu 24.04.1 LTSMatrix products: defaultBLAS: /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 3.12.0locale: [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: UTCtzcode 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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/usr/local/share/edge_driverEDITOR viGECKOWEBDRIVER /usr/local/share/gecko_driverGHCUP_INSTALL_BASE_PREFIX /usr/localGITHUB_ACTION __runGITHUB_ACTION_REF GITHUB_ACTION_REPOSITORY GITHUB_ACTIONS trueGITHUB_ACTOR GotfridGITHUB_ACTOR_ID 8464262GITHUB_API_URL https://api.github.comGITHUB_BASE_REF GITHUB_ENV /home/runner/work/_temp/_runner_file_commands/set_env_a74ce9d3-fe61-4935-aabd-1f14f9ce8080GITHUB_EVENT_NAME workflow_dispatchGITHUB_EVENT_PATH /home/runner/work/_temp/_github_workflow/event.jsonGITHUB_GRAPHQL_URL https://api.github.com/graphqlGITHUB_HEAD_REF GITHUB_JOB mainGITHUB_OUTPUT /home/runner/work/_temp/_runner_file_commands/set_output_a74ce9d3-fe61-4935-aabd-1f14f9ce8080GITHUB_PATH /home/runner/work/_temp/_runner_file_commands/add_path_a74ce9d3-fe61-4935-aabd-1f14f9ce8080GITHUB_REF refs/heads/mainGITHUB_REF_NAME mainGITHUB_REF_PROTECTED falseGITHUB_REF_TYPE branchGITHUB_REPOSITORY pharmaR/pharmapkgsGITHUB_REPOSITORY_ID 798326913GITHUB_REPOSITORY_OWNER pharmaRGITHUB_REPOSITORY_OWNER_ID 42115094GITHUB_RETENTION_DAYS 90GITHUB_RUN_ATTEMPT 1GITHUB_RUN_ID 13324244226GITHUB_RUN_NUMBER 87GITHUB_SERVER_URL https://github.comGITHUB_SHA 8610147c702e3ad4252323a87f6fad53534f1b0aGITHUB_STATE /home/runner/work/_temp/_runner_file_commands/save_state_a74ce9d3-fe61-4935-aabd-1f14f9ce8080GITHUB_STEP_SUMMARY /home/runner/work/_temp/_runner_file_commands/step_summary_a74ce9d3-fe61-4935-aabd-1f14f9ce8080GITHUB_TRIGGERING_ACTOR GotfridGITHUB_WORKFLOW Update package repositoriesGITHUB_WORKFLOW_REF pharmaR/pharmapkgs/.github/workflows/update-repos.yml@refs/heads/mainGITHUB_WORKFLOW_SHA 8610147c702e3ad4252323a87f6fad53534f1b0aGITHUB_WORKSPACE /home/runner/work/pharmapkgs/pharmapkgsGOROOT_1_21_X64 /opt/hostedtoolcache/go/1.21.13/x64GOROOT_1_22_X64 /opt/hostedtoolcache/go/1.22.12/x64GOROOT_1_23_X64 /opt/hostedtoolcache/go/1.23.6/x64GRADLE_HOME /usr/share/gradle-8.12.1HOME /home/runnerHOMEBREW_CLEANUP_PERIODIC_FULL_DAYS 3650HOMEBREW_NO_AUTO_UPDATE 1ImageOS ubuntu24ImageVersion 20250209.1.0INVOCATION_ID 61e3901631f74f2a9dcc6462ffec2653JAVA_HOME /usr/lib/jvm/temurin-17-jdk-amd64JAVA_HOME_11_X64 /usr/lib/jvm/temurin-11-jdk-amd64JAVA_HOME_17_X64 /usr/lib/jvm/temurin-17-jdk-amd64JAVA_HOME_21_X64 /usr/lib/jvm/temurin-21-jdk-amd64JAVA_HOME_8_X64 /usr/lib/jvm/temurin-8-jdk-amd64JOURNAL_STREAM 8:6015LANG C.UTF-8LD_LIBRARY_PATH /opt/R/4.4.2/lib/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/temurin-17-jdk-amd64/lib/server:/opt/R/4.4.2/lib/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/temurin-17-jdk-amd64/lib/serverLN_S ln -sLOGGER_LOG_LEVEL DEBUGMAKE makeMEMORY_PRESSURE_WATCH /sys/fs/cgroup/system.slice/runner-provisioner.service/memory.pressureMEMORY_PRESSURE_WRITE c29tZSAyMDAwMDAgMjAwMDAwMAA=NOT_CRAN trueNVM_DIR /home/runner/.nvmPAGER /usr/bin/pagerPATH 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