jackalope
A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator
Description
Simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina <https://www.illumina.com/> and Pacific Biosciences (PacBio) <https://www.pacb.com/> platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants can be simulated using summary statistics, phylogenies, Variant Call Format (VCF) files, and coalescent simulations—the latter of which can include selection, recombination, and demographic fluctuations. 'jackalope' can simulate single, paired-end, or mate-pair Illumina reads, as well as PacBio reads. These simulations include sequencing errors, mapping qualities, multiplexing, and optical/polymerase chain reaction (PCR) duplicates. Simulating Illumina sequencing is based on ART by Huang et al. (2012) <doi:10.1093/bioinformatics/btr708>. PacBio sequencing simulation is based on SimLoRD by Stöcker et al. (2016) <doi:10.1093/bioinformatics/btw286>. All outputs can be written to standard file formats.
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CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 12, 2026
ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 7, 2026
whether package can be installed
Installation failed. See 'd:/Rcompile/CRANpkg/local/4.6/jackalope.Rcheck/00install.out' for details.
OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE May 2, 2026
NOTE 11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 22, 2026
installed package size
installed size is 20.0Mb
sub-directories of 1Mb or more:
art_profiles 1.5Mb
libs 17.6Mb
installed package size
installed size is 20.2Mb
sub-directories of 1Mb or more:
art_profiles 1.5Mb
libs 17.9Mb
installed package size
installed size is 14.6Mb
sub-directories of 1Mb or more:
art_profiles 1.5Mb
libs 12.3Mb
ERROR 10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 18, 2026
whether package can be installed
Installation failed. See 'd:/Rcompile/CRANpkg/local/4.6/jackalope.Rcheck/00install.out' for details.
installed package size
installed size is 20.0Mb
sub-directories of 1Mb or more:
art_profiles 1.5Mb
libs 17.6Mb
installed package size
installed size is 20.2Mb
sub-directories of 1Mb or more:
art_profiles 1.5Mb
libs 17.9Mb
installed package size
installed size is 14.6Mb
sub-directories of 1Mb or more:
art_profiles 1.5Mb
libs 12.3Mb
NOTE 8 OK · 6 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 10, 2026
compiled code
File ‘jackalope/libs/jackalope.so’: Found non-API call to R: ‘R_UnboundValue’ Compiled code should not call non-API entry points in R. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, and section ‘Moving into C API compliance’ for issues with the use of non-API entry points.
compiled code
File 'jackalope/libs/x64/jackalope.dll': Found non-API call to R: 'R_UnboundValue' Compiled code should not call non-API entry points in R. See 'Writing portable packages' in the 'Writing R Extensions' manual, and section 'Moving into C API compliance' for issues with the use of non-API entry points.
compiled code
File ‘jackalope/libs/jackalope.so’: Found non-API call to R: ‘R_UnboundValue’ Compiled code should not call non-API entry points in R. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, and section ‘Moving into C API compliance’ for issues with the use of non-API entry points.
installed package size
installed size is 20.0Mb
sub-directories of 1Mb or more:
art_profiles 1.5Mb
libs 17.6Mb
installed package size
installed size is 20.2Mb
sub-directories of 1Mb or more:
art_profiles 1.5Mb
libs 17.9Mb
installed package size
installed size is 14.6Mb
sub-directories of 1Mb or more:
art_profiles 1.5Mb
libs 12.3Mb
ERROR 7 OK · 6 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 9, 2026
compiled code
File ‘jackalope/libs/jackalope.so’: Found non-API call to R: ‘R_UnboundValue’ Compiled code should not call non-API entry points in R. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, and section ‘Moving into C API compliance’ for issues with the use of non-API entry points.
whether package can be installed
Installation failed. See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/jackalope.Rcheck/00install.out’ for details.
compiled code
File 'jackalope/libs/x64/jackalope.dll': Found non-API call to R: 'R_UnboundValue' Compiled code should not call non-API entry points in R. See 'Writing portable packages' in the 'Writing R Extensions' manual, and section 'Moving into C API compliance' for issues with the use of non-API entry points.
compiled code
File ‘jackalope/libs/jackalope.so’: Found non-API call to R: ‘R_UnboundValue’ Compiled code should not call non-API entry points in R. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, and section ‘Moving into C API compliance’ for issues with the use of non-API entry points.
installed package size
installed size is 20.0Mb
sub-directories of 1Mb or more:
art_profiles 1.5Mb
libs 17.6Mb
installed package size
installed size is 20.2Mb
sub-directories of 1Mb or more:
art_profiles 1.5Mb
libs 17.9Mb
installed package size
installed size is 14.6Mb
sub-directories of 1Mb or more:
art_profiles 1.5Mb
libs 12.3Mb
NOTE 11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
installed package size
installed size is 20.0Mb
sub-directories of 1Mb or more:
art_profiles 1.5Mb
libs 17.6Mb
installed package size
installed size is 20.2Mb
sub-directories of 1Mb or more:
art_profiles 1.5Mb
libs 17.9Mb
installed package size
installed size is 14.6Mb
sub-directories of 1Mb or more:
art_profiles 1.5Mb
libs 12.3Mb