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update dev from main #52

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merged 3 commits into from
Nov 24, 2024
+3,634 −170
Merged

update dev from main #52

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5bc3fea
remove cran submission file
e-kotov Sep 13, 2024
49ab665
update why-rJavaEnv article
e-kotov Sep 26, 2024
1de37c0
fix readme link to vignette
e-kotov Nov 12, 2024
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3 changes: 0 additions & 3 deletions CRAN-SUBMISSION
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This file was deleted.

2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -135,7 +135,7 @@ environment variables in the current session and does not copy or link

More details are in the vignette [Multiple `Java` environments in one
project with `targets` and
`callr`](https://www.ekotov.pro/rJavaEnv/articles/multiple-java-with-targets-callr.qmd).
`callr`](https://www.ekotov.pro/rJavaEnv/articles/multiple-java-with-targets-callr.html).

## Cleanup

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2 changes: 1 addition & 1 deletion README.qmd
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Expand Up @@ -107,7 +107,7 @@ rJavaEnv::use_java("21")

This acts exactly like `java_quick_install()`, but only sets the environment variables in the current session and does not copy or link `Java` binaries into the project directory.

More details are in the vignette [Multiple `Java` environments in one project with `targets` and `callr`](https://www.ekotov.pro/rJavaEnv/articles/multiple-java-with-targets-callr.qmd).
More details are in the vignette [Multiple `Java` environments in one project with `targets` and `callr`](https://www.ekotov.pro/rJavaEnv/articles/multiple-java-with-targets-callr.html).

## Cleanup

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5 changes: 4 additions & 1 deletion vignettes/data-for-vignettes/data_table_dlstats.csv
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Expand Up @@ -124,4 +124,7 @@ start;end;downloads;package
2024-03-01;2024-03-31;845520;data.table
2024-04-01;2024-04-30;886330;data.table
2024-05-01;2024-05-31;846726;data.table
2024-06-01;2024-06-26;550578;data.table
2024-06-01;2024-06-30;677560;data.table
2024-07-01;2024-07-31;698441;data.table
2024-08-01;2024-08-31;749291;data.table
2024-09-01;2024-09-26;729796;data.table
2 changes: 1 addition & 1 deletion vignettes/data-for-vignettes/get-data-for-vignettes.R
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Expand Up @@ -8,7 +8,7 @@ rm(package_list)

dlstats::set_cran_start_year(2014)

rJava_dependants <- devtools::revdep("rJava", dependencies = c("Imports", "Depends"), bioconductor = FALSE)
rJava_dependants <- devtools::revdep("rJava", dependencies = c("Imports", "Depends"), bioconductor = TRUE)

rJava_dlstats <- dlstats::cran_stats("rJava", use_cache = FALSE)
rJava_dependants_dlstats_cran <- dlstats::cran_stats(rJava_dependants, use_cache = FALSE)
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5 changes: 4 additions & 1 deletion vignettes/data-for-vignettes/ggplot2_dlstats.csv
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Expand Up @@ -124,4 +124,7 @@ start;end;downloads;package
2024-03-01;2024-03-31;2469492;ggplot2
2024-04-01;2024-04-30;1932736;ggplot2
2024-05-01;2024-05-31;1891742;ggplot2
2024-06-01;2024-06-26;1302455;ggplot2
2024-06-01;2024-06-30;1599144;ggplot2
2024-07-01;2024-07-31;1536478;ggplot2
2024-08-01;2024-08-31;1458005;ggplot2
2024-09-01;2024-09-26;1329676;ggplot2
80 changes: 41 additions & 39 deletions vignettes/data-for-vignettes/produce-graphs-for-why-rJavaEnv.R
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Expand Up @@ -11,7 +11,7 @@ rJava_dependants_dlstats_bioc <- readr::read_csv2("vignettes/data-for-vignettes/
data_table_dlstats <- readr::read_csv2("vignettes/data-for-vignettes/data_table_dlstats.csv")
ggplot2_dlstats <- readr::read_csv2("vignettes/data-for-vignettes/ggplot2_dlstats.csv")

cutoff_date <- "2024-05-31"
cutoff_date <- "2024-09-26"

rj_and_rj_dep_total_down <- rJava_dependants_dlstats_cran |>
rbind(rJava_dlstats) |>
Expand Down Expand Up @@ -69,15 +69,21 @@ rJavaPopularity_GTable <- ggplot_gtable(ggplot_build(p_rJavaPopularity))
rJavaPopularity_GTable$layout$clip[rJavaPopularity_GTable$layout$name == "panel"] <- "off"

# Draw the plot
p_rJavaPopularity_filepath <- "vignettes/media/images/rJavaPopularity.png"
if ( ! file.exists(p_rJavaPopularity_filepath) ) {
dir.create(dirname(p_rJavaPopularity_filepath), recursive = TRUE)
png(p_rJavaPopularity_filepath, width = 12, height = 6, units = "in", res = 300)
grid::grid.draw(rJavaPopularity_GTable)
dev.off()
}
p_rJavaPopularity_filepath <- "vignettes/media/images/rJavaPopularity.svg"
dir.create(dirname(p_rJavaPopularity_filepath), recursive = TRUE)
svg(p_rJavaPopularity_filepath, width = 12, height = 6)
grid::grid.draw(rJavaPopularity_GTable)
dev.off()

# resmush::resmush_file(p_rJavaPopularity_filepath, overwrite = TRUE)

p_rJavaPopularity_filepath_pdf <- "vignettes/media/images/rJavaPopularity.pdf"
dir.create(dirname(p_rJavaPopularity_filepath_pdf), recursive = TRUE)
cairo_pdf(p_rJavaPopularity_filepath_pdf, width = 12, height = 6)
grid::grid.draw(rJavaPopularity_GTable)
dev.off()


resmush::resmush_file(p_rJavaPopularity_filepath, overwrite = TRUE)



Expand All @@ -97,22 +103,21 @@ p_rJavaDepIndivAll <- rJava_dependants_dlstats_cran |>
color = "Package")

# Draw the plot
p_rJavaDepIndivAll_filepath <- "vignettes/media/images/rJavaDepIndivAll.png"
if ( ! file.exists(p_rJavaDepIndivAll_filepath) ) {
dir.create(dirname(p_rJavaDepIndivAll_filepath), recursive = TRUE)
png(p_rJavaDepIndivAll_filepath, width = 12, height = 6, units = "in", res = 300)
grid::grid.draw(p_rJavaDepIndivAll)
dev.off()
}
p_rJavaDepIndivAll_filepath <- "vignettes/media/images/rJavaDepIndivAll.svg"
dir.create(dirname(p_rJavaDepIndivAll_filepath), recursive = TRUE)
svg(p_rJavaDepIndivAll_filepath, width = 12, height = 6)
grid::grid.draw(p_rJavaDepIndivAll)
dev.off()


resmush::resmush_file(p_rJavaDepIndivAll_filepath, overwrite = TRUE)
# resmush::resmush_file(p_rJavaDepIndivAll_filepath, overwrite = TRUE)

# top 20 rJava-dependent packages without xlsx -----------------------------------------

p_rJavaDepIndivFiltered <- rJava_dependants_dlstats_cran |>
filter(! package %in% c("xlsx", "xlsxjars") ) |>
filter(! grepl("jars$", package)) |>
filter(end >= "2023-05-01") |>
filter(end >= "2023-09-26") |>
group_by(package) |>
summarise(downloads = sum(downloads, na.rm = T), .groups = "drop") |>
arrange(desc(downloads)) |>
Expand All @@ -128,27 +133,25 @@ p_rJavaDepIndivFiltered <- rJava_dependants_dlstats_cran |>
# gghighlight(max(downloads), max_highlight = 6L) +
theme_pubclean(base_size = 18) +
labs(title = "Top rJava-based Package Downloads",
subtitle = "Over the Last Year (May 2023 - May 2024)",
subtitle = "Over the Last Year (September 2023 - September 2024)",
x = "Total dowloads",
y = "")

# Draw the plot
# Draw the plot
p_rJavaDepIndivFiltered_filepath <- "vignettes/media/images/rJavaDepIndivFiltered.png"
if ( ! file.exists(p_rJavaDepIndivFiltered_filepath) ) {
dir.create(dirname(p_rJavaDepIndivFiltered_filepath), recursive = TRUE)
png(p_rJavaDepIndivFiltered_filepath, width = 12, height = 6, units = "in", res = 300)
grid::grid.draw(p_rJavaDepIndivFiltered)
dev.off()
}
p_rJavaDepIndivFiltered_filepath <- "vignettes/media/images/rJavaDepIndivFiltered.svg"
dir.create(dirname(p_rJavaDepIndivFiltered_filepath), recursive = TRUE)
svg(p_rJavaDepIndivFiltered_filepath, width = 12, height = 6)
grid::grid.draw(p_rJavaDepIndivFiltered)
dev.off()


resmush::resmush_file(p_rJavaDepIndivFiltered_filepath, overwrite = TRUE)
# resmush::resmush_file(p_rJavaDepIndivFiltered_filepath, overwrite = TRUE)

# top 20 rJava-dependent packages with xlsx -----------------------------------------

p_rJavaDepIndivFilteredXslx <- rJava_dependants_dlstats_cran |>
filter(! grepl("jars$", package)) |>
filter(end >= "2023-05-01") |>
filter(end >= "2023-09-26") |>
group_by(package) |>
summarise(downloads = sum(downloads, na.rm = T), .groups = "drop") |>
arrange(desc(downloads)) |>
Expand All @@ -164,18 +167,17 @@ p_rJavaDepIndivFilteredXslx <- rJava_dependants_dlstats_cran |>
# gghighlight(max(downloads), max_highlight = 6L) +
theme_pubclean(base_size = 18) +
labs(title = "Top rJava-based Package Downloads",
subtitle = "Over the Last Year (May 2023 - May 2024)",
subtitle = "Over the Last Year (September 2023 - September 2024)",
x = "Total dowloads",
y = "")


# Draw the plot
# Draw the plot
p_rJavaDepIndivFilteredXslx_filepath <- "vignettes/media/images/rJavaDepIndivFilteredXslx.png"
if ( ! file.exists(p_rJavaDepIndivFilteredXslx_filepath) ) {
dir.create(dirname(p_rJavaDepIndivFilteredXslx_filepath), recursive = TRUE)
png(p_rJavaDepIndivFilteredXslx_filepath, width = 12, height = 6, units = "in", res = 300)
grid::grid.draw(p_rJavaDepIndivFilteredXslx)
dev.off()
}
p_rJavaDepIndivFilteredXslx_filepath <- "vignettes/media/images/rJavaDepIndivFilteredXslx.svg"
dir.create(dirname(p_rJavaDepIndivFilteredXslx_filepath), recursive = TRUE)
svg(p_rJavaDepIndivFilteredXslx_filepath, width = 12, height = 6)
grid::grid.draw(p_rJavaDepIndivFilteredXslx)
dev.off()


resmush::resmush_file(p_rJavaDepIndivFiltered_filepath, overwrite = TRUE)
# resmush::resmush_file(p_rJavaDepIndivFiltered_filepath, overwrite = TRUE)
70 changes: 56 additions & 14 deletions vignettes/data-for-vignettes/rJava_dependants_dlstats_bioc.csv
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Expand Up @@ -115,7 +115,10 @@ start;end;Nb_of_distinct_IPs;Nb_of_downloads;package
2024-03-01;2024-03-31;87;133;BridgeDbR
2024-04-01;2024-04-30;132;414;BridgeDbR
2024-05-01;2024-05-31;115;421;BridgeDbR
2024-06-01;2024-06-26;69;590;BridgeDbR
2024-06-01;2024-06-30;81;616;BridgeDbR
2024-07-01;2024-07-31;77;157;BridgeDbR
2024-08-01;2024-08-31;92;162;BridgeDbR
2024-09-01;2024-09-26;150;232;BridgeDbR
2016-04-01;2016-04-30;8;12;CHRONOS
2016-05-01;2016-05-31;73;99;CHRONOS
2016-06-01;2016-06-30;88;128;CHRONOS
Expand Down Expand Up @@ -214,7 +217,10 @@ start;end;Nb_of_distinct_IPs;Nb_of_downloads;package
2024-03-01;2024-03-31;96;156;CHRONOS
2024-04-01;2024-04-30;119;412;CHRONOS
2024-05-01;2024-05-31;91;404;CHRONOS
2024-06-01;2024-06-26;45;564;CHRONOS
2024-06-01;2024-06-30;56;591;CHRONOS
2024-07-01;2024-07-31;127;229;CHRONOS
2024-08-01;2024-08-31;97;179;CHRONOS
2024-09-01;2024-09-26;128;236;CHRONOS
2019-09-01;2019-09-30;1;1;debCAM
2019-10-01;2019-10-31;5;12;debCAM
2019-11-01;2019-11-30;17;58;debCAM
Expand Down Expand Up @@ -272,7 +278,10 @@ start;end;Nb_of_distinct_IPs;Nb_of_downloads;package
2024-03-01;2024-03-31;81;184;debCAM
2024-04-01;2024-04-30;83;422;debCAM
2024-05-01;2024-05-31;98;476;debCAM
2024-06-01;2024-06-26;58;669;debCAM
2024-06-01;2024-06-30;68;716;debCAM
2024-07-01;2024-07-31;71;286;debCAM
2024-08-01;2024-08-31;77;259;debCAM
2024-09-01;2024-09-26;144;368;debCAM
2017-10-01;2017-10-31;2;2;esATAC
2017-11-01;2017-11-30;51;113;esATAC
2017-12-01;2017-12-31;70;126;esATAC
Expand Down Expand Up @@ -353,7 +362,10 @@ start;end;Nb_of_distinct_IPs;Nb_of_downloads;package
2024-03-01;2024-03-31;173;270;esATAC
2024-04-01;2024-04-30;209;508;esATAC
2024-05-01;2024-05-31;122;480;esATAC
2024-06-01;2024-06-26;71;611;esATAC
2024-06-01;2024-06-30;85;644;esATAC
2024-07-01;2024-07-31;61;182;esATAC
2024-08-01;2024-08-31;109;190;esATAC
2024-09-01;2024-09-26;176;317;esATAC
2022-04-01;2022-04-30;22;25;fastreeR
2022-05-01;2022-05-31;51;69;fastreeR
2022-06-01;2022-06-30;34;44;fastreeR
Expand All @@ -380,7 +392,10 @@ start;end;Nb_of_distinct_IPs;Nb_of_downloads;package
2024-03-01;2024-03-31;86;130;fastreeR
2024-04-01;2024-04-30;110;390;fastreeR
2024-05-01;2024-05-31;128;459;fastreeR
2024-06-01;2024-06-26;65;572;fastreeR
2024-06-01;2024-06-30;78;604;fastreeR
2024-07-01;2024-07-31;89;188;fastreeR
2024-08-01;2024-08-31;95;185;fastreeR
2024-09-01;2024-09-26;108;183;fastreeR
2022-10-01;2022-10-31;1;1;metabinR
2022-11-01;2022-11-30;46;61;metabinR
2022-12-01;2022-12-31;24;36;metabinR
Expand All @@ -401,7 +416,10 @@ start;end;Nb_of_distinct_IPs;Nb_of_downloads;package
2024-03-01;2024-03-31;40;61;metabinR
2024-04-01;2024-04-30;63;324;metabinR
2024-05-01;2024-05-31;83;389;metabinR
2024-06-01;2024-06-26;46;526;metabinR
2024-06-01;2024-06-30;53;545;metabinR
2024-07-01;2024-07-31;47;116;metabinR
2024-08-01;2024-08-31;54;101;metabinR
2024-09-01;2024-09-26;81;148;metabinR
2014-10-01;2014-10-31;73;108;paxtoolsr
2014-11-01;2014-11-30;172;261;paxtoolsr
2014-12-01;2014-12-31;151;198;paxtoolsr
Expand Down Expand Up @@ -518,7 +536,10 @@ start;end;Nb_of_distinct_IPs;Nb_of_downloads;package
2024-03-01;2024-03-31;105;176;paxtoolsr
2024-04-01;2024-04-30;104;330;paxtoolsr
2024-05-01;2024-05-31;33;91;paxtoolsr
2024-06-01;2024-06-26;122;698;paxtoolsr
2024-06-01;2024-06-30;136;731;paxtoolsr
2024-07-01;2024-07-31;146;372;paxtoolsr
2024-08-01;2024-08-31;182;333;paxtoolsr
2024-09-01;2024-09-26;224;390;paxtoolsr
2023-01-01;2023-01-31;3;3;RBioFormats
2023-02-01;2023-02-28;8;13;RBioFormats
2023-03-01;2023-03-31;12;18;RBioFormats
Expand All @@ -536,7 +557,10 @@ start;end;Nb_of_distinct_IPs;Nb_of_downloads;package
2024-03-01;2024-03-31;283;363;RBioFormats
2024-04-01;2024-04-30;183;516;RBioFormats
2024-05-01;2024-05-31;208;553;RBioFormats
2024-06-01;2024-06-26;133;668;RBioFormats
2024-06-01;2024-06-30;155;711;RBioFormats
2024-07-01;2024-07-31;157;279;RBioFormats
2024-08-01;2024-08-31;170;264;RBioFormats
2024-09-01;2024-09-26;147;262;RBioFormats
2011-11-01;2011-11-30;35;64;ReQON
2011-12-01;2011-12-31;29;34;ReQON
2012-01-01;2012-01-31;59;85;ReQON
Expand Down Expand Up @@ -688,7 +712,10 @@ start;end;Nb_of_distinct_IPs;Nb_of_downloads;package
2024-03-01;2024-03-31;104;221;ReQON
2024-04-01;2024-04-30;151;381;ReQON
2024-05-01;2024-05-31;20;89;ReQON
2024-06-01;2024-06-26;5;51;ReQON
2024-06-01;2024-06-30;5;55;ReQON
2024-07-01;2024-07-31;16;33;ReQON
2024-08-01;2024-08-31;76;122;ReQON
2024-09-01;2024-09-26;86;144;ReQON
2018-01-01;2018-01-31;4;7;RGMQL
2018-02-01;2018-02-28;11;12;RGMQL
2018-03-01;2018-03-31;13;14;RGMQL
Expand Down Expand Up @@ -766,7 +793,10 @@ start;end;Nb_of_distinct_IPs;Nb_of_downloads;package
2024-03-01;2024-03-31;83;137;RGMQL
2024-04-01;2024-04-30;209;613;RGMQL
2024-05-01;2024-05-31;58;394;RGMQL
2024-06-01;2024-06-26;35;553;RGMQL
2024-06-01;2024-06-30;42;576;RGMQL
2024-07-01;2024-07-31;37;126;RGMQL
2024-08-01;2024-08-31;66;159;RGMQL
2024-09-01;2024-09-26;123;235;RGMQL
2019-02-01;2019-02-28;1;1;rmelting
2019-03-01;2019-03-31;21;24;rmelting
2019-04-01;2019-04-30;11;17;rmelting
Expand Down Expand Up @@ -831,7 +861,10 @@ start;end;Nb_of_distinct_IPs;Nb_of_downloads;package
2024-03-01;2024-03-31;57;89;rmelting
2024-04-01;2024-04-30;120;393;rmelting
2024-05-01;2024-05-31;101;412;rmelting
2024-06-01;2024-06-26;65;554;rmelting
2024-06-01;2024-06-30;79;586;rmelting
2024-07-01;2024-07-31;58;143;rmelting
2024-08-01;2024-08-31;70;135;rmelting
2024-09-01;2024-09-26;94;234;rmelting
2014-10-01;2014-10-31;60;72;rRDP
2014-11-01;2014-11-30;142;185;rRDP
2014-12-01;2014-12-31;116;146;rRDP
Expand Down Expand Up @@ -948,7 +981,10 @@ start;end;Nb_of_distinct_IPs;Nb_of_downloads;package
2024-03-01;2024-03-31;83;142;rRDP
2024-04-01;2024-04-30;109;381;rRDP
2024-05-01;2024-05-31;82;390;rRDP
2024-06-01;2024-06-26;59;578;rRDP
2024-06-01;2024-06-30;74;608;rRDP
2024-07-01;2024-07-31;65;134;rRDP
2024-08-01;2024-08-31;114;205;rRDP
2024-09-01;2024-09-26;187;284;rRDP
2020-03-01;2020-03-31;3;3;sarks
2020-04-01;2020-04-30;27;38;sarks
2020-05-01;2020-05-31;43;90;sarks
Expand Down Expand Up @@ -1000,7 +1036,10 @@ start;end;Nb_of_distinct_IPs;Nb_of_downloads;package
2024-03-01;2024-03-31;56;99;sarks
2024-04-01;2024-04-30;87;357;sarks
2024-05-01;2024-05-31;80;386;sarks
2024-06-01;2024-06-26;49;568;sarks
2024-06-01;2024-06-30;59;597;sarks
2024-07-01;2024-07-31;62;186;sarks
2024-08-01;2024-08-31;68;140;sarks
2024-09-01;2024-09-26;135;244;sarks
2015-03-01;2015-03-31;3;4;SELEX
2015-04-01;2015-04-30;55;71;SELEX
2015-05-01;2015-05-31;80;119;SELEX
Expand Down Expand Up @@ -1112,4 +1151,7 @@ start;end;Nb_of_distinct_IPs;Nb_of_downloads;package
2024-03-01;2024-03-31;91;146;SELEX
2024-04-01;2024-04-30;92;374;SELEX
2024-05-01;2024-05-31;91;424;SELEX
2024-06-01;2024-06-26;45;552;SELEX
2024-06-01;2024-06-30;60;576;SELEX
2024-07-01;2024-07-31;127;235;SELEX
2024-08-01;2024-08-31;109;181;SELEX
2024-09-01;2024-09-26;193;288;SELEX
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