Get Bioc package list
suppressPackageStartupMessages ({
library (BiocPkgTools)
library (dplyr)
library (DT)
})
BiocManager:: version ()
pkg <- biocPkgList (repo = "BioCsoft" )
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")'
for details.
Replacement repositories:
CRAN: https://p3m.dev/cran/__linux__/noble/latest
# pkg <- biocPkgList(repo = c("BioCsoft", "BioCann", "BioCexp", "BioCworkflows"))
Get licenses
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 Artistic 2.0
1 1
Artistic-2.0 | GPL-2 + file LICENSE BSD 3-clause License + file LICENSE
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(>= 2) GPL(>=3)
1 1
LGPL (>= 2.1) | file LICENSE LGPL (>= 3.0)
1 1
LGPL (>= 3); File LICENSE LGPL-2.1
1 1
LGPL-3 + file LICENSE MIT | file LICENSE
1 1
MIT License Mozilla Public License 2.0
1 1
Unlimited Apache License (== 2.0)
1 2
Artistic-1.0 Artistic-2.0 + file LICENSE
2 2
CC BY 4.0 CC BY-NC-ND 4.0
2 2
CC BY-NC-ND 4.0 + file LICENSE CC0
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
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) GPL (>=3)
8 9
LGPL (>= 3) Artistic-2.0 | file LICENSE
9 12
GPL-3 | file LICENSE BSD_3_clause + file LICENSE
15 16
LGPL (>= 2) AGPL-3
19 20
GPL LGPL-3
21 35
file LICENSE LGPL
39 39
GPL (>=2) GPL-3 + file LICENSE
47 59
GPL (>= 3) GPL (>= 2)
68 180
GPL-2 MIT + file LICENSE
234 321
GPL-3 Artistic-2.0
484 513
Clean up
## 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)
length (unique (alres$ LicenseStandardizationShort))
DT:: 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)
DT:: datatable (pkg,
extensions = "FixedColumns" ,
rownames = FALSE ,
options = list (scrollX = TRUE ,
fixedColumns = list (leftColumns = 1 ),
search = list (regex = FALSE , caseInsensitive = TRUE ),
pageLength = 20 ))
Tabulate licenses
sort (table (pkg$ LicenseStandardizationShort, useNA = "ifany" ))
Apache License (>= 2.0) Artistic-2.0 | GPL-2
1 1
BSD 3-clause License CC BY-SA 4.0
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 | BSL-1.0 LGPL (>= 3.0)
1 1
MIT License Mozilla Public License 2.0
1 1
Unlimited Artistic-1.0
1 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
BSD_2_clause LGPL (>= 2.0)
8 8
<NA> LGPL (>= 3)
8 11
BSD_3_clause GPL
17 21
LGPL (>= 2) AGPL-3
23 24
LGPL-3
36 39
LGPL GPL (>= 3)
39 86
GPL (>= 2) GPL-2
240 245
MIT Artistic-2.0
333 528
GPL-3
561
Some cases that may need attention
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: 97.48%"
Packages that have just a ‘file LICENSE’
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 ))
Packages that have license “Unlimited”
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 ))
Packages that have licenses that can not be standardized
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 ).
Session info
R version 4.5.0 (2025-04-11)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.2 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_1.27.0 htmlwidgets_1.6.4
loaded via a namespace (and not attached):
[1] bslib_0.9.0 xfun_0.52 httr2_1.1.2 gh_1.4.1 Biobase_2.69.0
[6] tzdb_0.5.0 crosstalk_1.2.1 vctrs_0.6.5 tools_4.5.0 bitops_1.0-9
[11] generics_0.1.3 stats4_4.5.0 curl_6.2.2 RUnit_0.4.33 tibble_3.2.1
[16] RSQLite_2.3.9 blob_1.2.4 pkgconfig_2.0.3 dbplyr_2.5.0 graph_1.87.0
[21] lifecycle_1.0.4 stringr_1.5.1 compiler_4.5.0 biocViews_1.77.0 sass_0.4.10
[26] htmltools_0.5.8.1 RCurl_1.98-1.17 yaml_2.3.10 jquerylib_0.1.4 tidyr_1.3.1
[31] pillar_1.10.2 whisker_0.4.1 cachem_1.1.0 rvest_1.0.4 tidyselect_1.2.1
[36] digest_0.6.37 stringi_1.8.7 purrr_1.0.4 fastmap_1.2.0 cli_3.6.5
[41] magrittr_2.0.3 RBGL_1.85.0 XML_3.99-0.18 crul_1.5.0 withr_3.0.2
[46] readr_2.1.5 filelock_1.0.3 rappdirs_0.3.3 bit64_4.6.0-1 lubridate_1.9.4
[51] timechange_0.3.0 rmarkdown_2.29 httr_1.4.7 igraph_2.1.4 bit_4.6.0
[56] hms_1.1.3 memoise_2.0.1 evaluate_1.0.3 knitr_1.50 BiocFileCache_2.99.0
[61] rlang_1.1.6 glue_1.8.0 DBI_1.2.3 httpcode_0.3.0 BiocManager_1.30.25
[66] xml2_1.3.8 fauxpas_0.5.2 BiocGenerics_0.55.0 rorcid_0.7.0 jsonlite_2.0.0
[71] R6_2.6.1