suppressPackageStartupMessages({
library(BiocPkgTools)
library(dplyr)
library(DT)
})
BiocManager::version()[1] '3.21'pkg <- biocPkgList(repo = "BioCsoft")'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")'
for details.
Replacement repositories:
CRAN: https://cloud.r-project.org# pkg <- biocPkgList(repo = c("BioCsoft", "BioCann", "BioCexp", "BioCworkflows"))sort(table(pkg$License, useNA = "ifany"))
AGPL-3 | file LICENSE Apache License (== 2.0) + file LICENSE
1 1
Apache License (== 2.0) | file LICENSE Apache License (>= 2.0)
1 1
Apache License (>= 2.0) | file LICENSE Apache License 2.0 | file LICENSE
1 1
Artistic 2.0 Artistic-2.0 | GPL-2 + file LICENSE
1 1
BSD 3-clause License + file LICENSE BSD_2_clause
1 1
BSD_3_clause CC BY-SA 4.0 + file LICENSE
1 1
CC0 CeCILL | file LICENSE
1 1
CPL Creative Commons Attribution 4.0 International License
1 1
EPL (>= 1.0) GNU General Public License version 3
1 1
GPL (==2) GPL (>= 2.1)
1 1
GPL (>=2 ) GPL 3
1 1
GPL version 3 GPL-3 + file LICENCE
1 1
GPL-3 bioconductor.org GPL(>= 2)
1 1
GPL(>=3) LGPL (>= 2.1) | file LICENSE
1 1
LGPL (>= 3.0) LGPL (>= 3); File LICENSE
1 1
LGPL-2.1 LGPL-3 + file LICENSE
1 1
MIT | file LICENSE MIT License
1 1
MIT+ file LICENSE Mozilla Public License 2.0
1 1
Unlimited Apache License (== 2.0)
1 2
Artistic-1.0 CC BY 4.0
2 2
CC BY-NC-ND 4.0 CC BY-NC-ND 4.0 + file LICENSE
2 2
EPL GPL (>= 3.0)
2 2
GPL (>=2.0) GPL (>=3.0)
2 2
GPL (>2) GPL (http://www.gnu.org/copyleft/gpl.html)
2 2
GPL version 2 GPL Version 2 or later
2 2
LGPL (>= 2.1) LGPL (>=3)
2 2
LGPL-2.1 | file LICENSE AGPL-3 + file LICENSE
2 3
Artistic License 2.0 Artistic-2.0 + file LICENSE
3 3
CeCILL GPL (>= 2.0)
3 3
GPL (>= 2) + file LICENSE GPL (>= 3) + file LICENSE
3 3
GPL (>=3) + file LICENSE Apache License (>= 2)
3 4
GPL-2 | file LICENSE LGPL (>=2)
4 4
MIT + file LICENCE AGPL-3.0-only
4 5
Apache License 2.0 GPL-2 + file LICENSE
5 5
GPL-2 | GPL-3 LGPL-2
5 5
GPL(>=2) MIT
6 7
BSD_2_clause + file LICENSE LGPL (>= 2.0)
8 8
LGPL (>= 3) GPL (>=3)
9 10
Artistic-2.0 | file LICENSE GPL-3 | file LICENSE
12 14
BSD_3_clause + file LICENSE AGPL-3
15 19
LGPL (>= 2) GPL
19 22
LGPL-3 file LICENSE
36 37
LGPL GPL (>=2)
39 47
GPL-3 + file LICENSE GPL (>= 3)
59 62
GPL (>= 2) GPL-2
183 235
MIT + file LICENSE GPL-3
309 480
Artistic-2.0
511 ## Get unique licenses
lic <- unique(pkg$License)
lic <- lic[!is.na(lic)]
alres <- lapply(structure(lic, names = lic), tools:::analyze_license)
## Get information about the licenses
alres <- do.call(dplyr::bind_rows, lapply(names(alres), function(nm) {
a <- alres[[nm]]
data.frame(License = nm,
LicenseStandardizable = a$is_standardizable,
LicenseVerified = a$is_verified,
LicenseStandardization = a$standardization,
LicenseCanonical = a$is_canonical,
LicenseFOSS = a$is_FOSS,
LicenseRestrictsUse = a$restricts_use)
}))
## Add additional column removing the "+/| file LICENSE" part (if we want to
## assume that this is compatible with the main license indication)
alres$LicenseStandardizationShort <- gsub("[ ]*\\+*\\|*[ ]*file LICEN[SC]E",
"", alres$LicenseStandardization)
dim(alres)[1] 93 8length(unique(alres$LicenseStandardizationShort))[1] 48DT::datatable(alres,
extensions = "FixedColumns",
rownames = FALSE,
options = list(scrollX = TRUE,
fixedColumns = list(leftColumns = 1),
search = list(regex = FALSE, caseInsensitive = TRUE),
pageLength = 20))## Add license columns to pkg list
pkg <- pkg %>%
dplyr::select(Package, Maintainer, License, hasLICENSE) %>%
dplyr::left_join(alres, by = "License")
dim(pkg)[1] 2281 11DT::datatable(pkg,
extensions = "FixedColumns",
rownames = FALSE,
options = list(scrollX = TRUE,
fixedColumns = list(leftColumns = 1),
search = list(regex = FALSE, caseInsensitive = TRUE),
pageLength = 20))sort(table(pkg$LicenseStandardizationShort, useNA = "ifany"))
Artistic-2.0 | GPL-2 BSD 3-clause License
1 1
CC BY-SA 4.0 CC0
1 1
CPL Creative Commons Attribution 4.0 International License
1 1
EPL (>= 1.0) GNU General Public License version 3
1 1
GPL (== 2) GPL (>= 2.1)
1 1
LGPL (>= 3.0) MIT License
1 1
Mozilla Public License 2.0 Unlimited
1 1
Apache License (>= 2.0) Artistic-1.0
2 2
CC BY 4.0 EPL
2 2
GPL (> 2) Artistic License 2.0
2 3
LGPL (>= 2.1) LGPL-2.1
3 3
Apache License (== 2.0) Apache License (>= 2)
4 4
CC BY-NC-ND 4.0 CeCILL
4 4
GPL (>= 3.0) GPL (>= 2.0)
4 5
GPL-2 | GPL-3 LGPL-2
5 5
Apache License 2.0 LGPL (>= 2.0)
6 8
BSD_2_clause <NA>
9 9
LGPL (>= 3) BSD_3_clause
11 16
GPL AGPL-3
22 23
LGPL (>= 2)
23 37
LGPL-3 LGPL
37 39
GPL (>= 3) GPL (>= 2)
79 243
GPL-2 MIT
246 322
Artistic-2.0 GPL-3
527 556 We attempt to estimate the fraction of packages that are provided under an OSI approved license. It should be noted that, automatically performed, this will necessary be a rough estimate, e.g. since there are several packages that do not mention the license explicitly in the DESCRIPTION file but only provide the license text in a separate LICENSE file.
totalNbrPkg <- nrow(pkg)
ccLicensed <- pkg$Package[grep("CC|Creative Commons", pkg$LicenseStandardizationShort)]
fileLicense <- pkg$Package[which(pkg$LicenseStandardizationShort == "")]
licUnlimited <- pkg$Package[which(pkg$LicenseStandardizationShort == "Unlimited")]
licNotStandardizable <- pkg$Package[is.na(pkg$LicenseStandardizationShort)]
fractionOSIApproved <- 1 - length(unique(c(ccLicensed, fileLicense,
licUnlimited, licNotStandardizable)))/totalNbrPkg
print(paste0("Rough estimate of fraction packages with OSI approved license: ",
signif(100 * fractionOSIApproved, digits = 4), "%"))[1] "Rough estimate of fraction packages with OSI approved license: 97.54%"Creative Commons recommends not using their licenses for software (but may be suitable for data packages): https://creativecommons.org/faq/#can-i-apply-a-creative-commons-license-to-software. Note though that the CC licenses are among the ‘standard’ open source licenses listed in the R license database: https://svn.r-project.org/R/trunk/share/licenses/license.db.
DT::datatable(subset(pkg, grepl("CC|Creative Commons", LicenseStandardizationShort)),
extensions = "FixedColumns",
rownames = FALSE,
options = list(scrollX = TRUE,
fixedColumns = list(leftColumns = 1),
search = list(regex = FALSE, caseInsensitive = TRUE),
pageLength = 20))These need to be checked manually.
.makeLinkToLicense <- function(pkg, text) {
sprintf('<a href="%s" target="_blank"> %s</a>',
paste0("https://bioconductor.org/packages/devel/bioc/licenses/",
pkg, "/LICENSE"),
text)
}
DT::datatable(subset(pkg, LicenseStandardizationShort == "") %>%
dplyr::mutate(License = vapply(seq_along(License), function(i) {
.makeLinkToLicense(Package[i], License[i])
}, "NA")),
extensions = "FixedColumns",
rownames = FALSE,
escape = FALSE,
options = list(scrollX = TRUE,
fixedColumns = list(leftColumns = 1),
search = list(regex = FALSE, caseInsensitive = TRUE),
pageLength = 20))DT::datatable(subset(pkg, LicenseStandardizationShort == "Unlimited"),
extensions = "FixedColumns",
rownames = FALSE,
options = list(scrollX = TRUE,
fixedColumns = list(leftColumns = 1),
search = list(regex = FALSE, caseInsensitive = TRUE),
pageLength = 20))Some of these may be false positives.
DT::datatable(subset(pkg, is.na(LicenseStandardizationShort)),
extensions = "FixedColumns",
rownames = FALSE,
options = list(scrollX = TRUE,
fixedColumns = list(leftColumns = 1),
search = list(regex = FALSE, caseInsensitive = TRUE),
pageLength = 20))The rest of the licenses appear to be approved open source licenses (https://opensource.org/licenses/alphabetical).
sessionInfo()R Under development (unstable) (2025-01-08 r87545)
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=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DT_0.33 dplyr_1.1.4 BiocPkgTools_1.25.2 htmlwidgets_1.6.4
loaded via a namespace (and not attached):
[1] xfun_0.50 bslib_0.8.0 gh_1.4.1 Biobase_2.67.0 tzdb_0.4.0
[6] vctrs_0.6.5 tools_4.5.0 crosstalk_1.2.1 bitops_1.0-9 generics_0.1.3
[11] stats4_4.5.0 curl_6.1.0 RUnit_0.4.33 tibble_3.2.1 RSQLite_2.3.9
[16] blob_1.2.4 pkgconfig_2.0.3 dbplyr_2.5.0 graph_1.85.1 lifecycle_1.0.4
[21] compiler_4.5.0 stringr_1.5.1 biocViews_1.75.0 sass_0.4.9 htmltools_0.5.8.1
[26] RCurl_1.98-1.16 yaml_2.3.10 jquerylib_0.1.4 pillar_1.10.1 whisker_0.4.1
[31] cachem_1.1.0 tidyselect_1.2.1 rvest_1.0.4 digest_0.6.37 stringi_1.8.4
[36] fastmap_1.2.0 cli_3.6.3 magrittr_2.0.3 RBGL_1.83.0 XML_3.99-0.18
[41] crul_1.5.0 withr_3.0.2 readr_2.1.5 filelock_1.0.3 bit64_4.5.2
[46] rmarkdown_2.29 httr_1.4.7 igraph_2.1.3 bit_4.5.0.1 hms_1.1.3
[51] memoise_2.0.1 evaluate_1.0.1 knitr_1.49 BiocFileCache_2.15.0 rlang_1.1.4
[56] glue_1.8.0 DBI_1.2.3 httpcode_0.3.0 BiocManager_1.30.25 xml2_1.3.6
[61] fauxpas_0.5.2 BiocGenerics_0.53.3 rorcid_0.7.0 jsonlite_1.8.9 R6_2.5.1