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$License, useNA = "ifany"))
AGPL-3 | file LICENSE Apache License (== 2.0) + file LICENSE
1 1
Apache License (== 2.0) | file LICENSE Apache License (>= 2.0)
1 1
Apache License (>= 2.0) | file LICENSE Apache License 2.0 | file LICENSE
1 1
Artistic 2.0 Artistic-2.0 | GPL-2 + file LICENSE
1 1
BSD 3-clause License + file LICENSE BSD_2_clause
1 1
BSD_3_clause CC BY-SA 4.0 + file LICENSE
1 1
CeCILL | file LICENSE CPL
1 1
Creative Commons Attribution 4.0 International License EPL (>= 1.0)
1 1
GNU General Public License version 3 GPL (==2)
1 1
GPL (>= 2.1) GPL (>=2 )
1 1
GPL 3 GPL version 3
1 1
GPL-2 | GPL-3 | BSL-1.0 GPL-3 + file LICENCE
1 1
GPL-3 bioconductor.org GPL(>= 2)
1 1
GPL(>=3) LGPL (>= 2.1) | file LICENSE
1 1
LGPL (>= 3.0) LGPL (>= 3); File LICENSE
1 1
LGPL-2.1 LGPL-3 + file LICENSE
1 1
MIT | file LICENSE MIT License
1 1
MIT+ file LICENSE Mozilla Public License 2.0
1 1
Unlimited Apache License (== 2.0)
1 2
Artistic-1.0 CC BY 4.0
2 2
CC BY-NC-ND 4.0 CC BY-NC-ND 4.0 + file LICENSE
2 2
CC0 EPL
2 2
GPL (>= 3.0) GPL (>=2.0)
2 2
GPL (>=3.0) GPL (>2)
2 2
GPL (http://www.gnu.org/copyleft/gpl.html) GPL version 2
2 2
GPL Version 2 or later LGPL (>= 2.1)
2 2
LGPL (>=3) LGPL-2.1 | file LICENSE
2 2
AGPL-3 + file LICENSE Artistic-2.0 + file LICENSE
3 3
CeCILL GPL (>= 2.0)
3 3
GPL (>= 2) + file LICENSE GPL (>=3) + file LICENSE
3 3
Apache License (>= 2) Artistic License 2.0
4 4
GPL-2 | file LICENSE GPL-2 | GPL-3
4 4
LGPL (>=2) MIT + file LICENCE
4 4
AGPL-3.0-only Apache License 2.0
5 5
GPL (>= 3) + file LICENSE GPL-2 + file LICENSE
5 5
LGPL-2 GPL(>=2)
5 6
MIT BSD_2_clause + file LICENSE
7 8
LGPL (>= 2.0) LGPL (>= 3)
8 9
GPL (>=3) Artistic-2.0 | file LICENSE
10 12
BSD_3_clause + file LICENSE GPL-3 | file LICENSE
15 15
AGPL-3 LGPL (>= 2)
19 19
GPL LGPL-3
22 36
file LICENSE LGPL
39 40
GPL (>=2) GPL-3 + file LICENSE
48 60
GPL (>= 3) GPL (>= 2)
65 182
GPL-2 MIT + file LICENSE
239 321
GPL-3 Artistic-2.0
484 521 ## Get unique licenses
lic <- unique(pkg$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] 94 8length(unique(alres$LicenseStandardizationShort))[1] 49DT::datatable(alres,
extensions = "FixedColumns",
rownames = FALSE,
options = list(scrollX = TRUE,
fixedColumns = list(leftColumns = 1),
search = list(regex = FALSE, caseInsensitive = TRUE),
pageLength = 20))## Add license columns to pkg list
pkg <- pkg %>%
dplyr::select(Package, Maintainer, License, hasLICENSE) %>%
dplyr::left_join(alres, by = "License")
dim(pkg)[1] 2323 11DT::datatable(pkg,
extensions = "FixedColumns",
rownames = FALSE,
options = list(scrollX = TRUE,
fixedColumns = list(leftColumns = 1),
search = list(regex = FALSE, caseInsensitive = TRUE),
pageLength = 20))sort(table(pkg$LicenseStandardizationShort, useNA = "ifany"))
Artistic-2.0 | GPL-2 BSD 3-clause License
1 1
CC BY-SA 4.0 CPL
1 1
Creative Commons Attribution 4.0 International License EPL (>= 1.0)
1 1
GNU General Public License version 3 GPL (== 2)
1 1
GPL (>= 2.1) GPL-2 | GPL-3 | BSL-1.0
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 CC0
2 2
EPL GPL (> 2)
2 2
LGPL (>= 2.1) LGPL-2.1
3 3
Apache License (== 2.0) Apache License (>= 2)
4 4
Artistic License 2.0 CC BY-NC-ND 4.0
4 4
CeCILL GPL (>= 3.0)
4 4
GPL-2 | GPL-3 GPL (>= 2.0)
4 5
LGPL-2 Apache License 2.0
5 6
LGPL (>= 2.0) BSD_2_clause
8 9
<NA> LGPL (>= 3)
9 11
BSD_3_clause GPL
16 22
AGPL-3 LGPL (>= 2)
23 23
LGPL-3
37 39
LGPL GPL (>= 3)
40 84
GPL (>= 2) GPL-2
243 250
MIT Artistic-2.0
334 537
GPL-3
562 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: 97.46%"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) (2025-03-08 r87910)
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_1.25.8 htmlwidgets_1.6.4
loaded via a namespace (and not attached):
[1] bslib_0.9.0 xfun_0.51 gh_1.4.1 Biobase_2.67.0 tzdb_0.5.0
[6] crosstalk_1.2.1 vctrs_0.6.5 tools_4.5.0 bitops_1.0-9 generics_0.1.3
[11] stats4_4.5.0 curl_6.2.2 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_1.85.3 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_1.98-1.17 yaml_2.3.10 jquerylib_0.1.4 tidyr_1.3.1 pillar_1.10.1
[31] whisker_0.4.1 cachem_1.1.0 tidyselect_1.2.1 rvest_1.0.4 digest_0.6.37
[36] stringi_1.8.7 purrr_1.0.4 fastmap_1.2.0 cli_3.6.4 magrittr_2.0.3
[41] RBGL_1.83.0 XML_3.99-0.18 crul_1.5.0 withr_3.0.2 readr_2.1.5
[46] filelock_1.0.3 bit64_4.6.0-1 lubridate_1.9.4 timechange_0.3.0 rmarkdown_2.29
[51] httr_1.4.7 igraph_2.1.4 bit_4.6.0 hms_1.1.3 memoise_2.0.1
[56] evaluate_1.0.3 knitr_1.50 BiocFileCache_2.15.1 rlang_1.1.5 glue_1.8.0
[61] DBI_1.2.3 httpcode_0.3.0 BiocManager_1.30.25 xml2_1.3.8 fauxpas_0.5.2
[66] BiocGenerics_0.53.6 rorcid_0.7.0 jsonlite_2.0.0 R6_2.6.1