revdep/failures.md
In igordot/msigdbr: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
CAESAR.Suite
- Version: 0.2.2
- GitHub: https://github.com/XiaoZhangryy/CAESAR.Suite
- Source code: https://github.com/cran/CAESAR.Suite
- Date/Publication: 2025-04-01 09:00:07 UTC
- Number of recursive dependencies: 253
Run revdepcheck::revdep_details(, "CAESAR.Suite") for more info
In both
- checking whether package ‘CAESAR.Suite’ can be installed ... ERROR
Installation failed.
See ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/CAESAR.Suite/new/CAESAR.Suite.Rcheck/00install.out’ for details.
Installation
Devel
* installing *source* package ‘CAESAR.Suite’ ...
** this is package ‘CAESAR.Suite’ version ‘0.2.2’
** package ‘CAESAR.Suite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.0.13.3)’
using SDK: ‘MacOSX15.4.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/include" -DNDEBUG -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/Rcpp/include' -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/include" -DNDEBUG -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/Rcpp/include' -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gene_embed.cpp -o gene_embed.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/include" -DNDEBUG -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/Rcpp/include' -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c imfactor.cpp -o imfactor.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib -L/opt/R/x86_64/lib -o CAESAR.Suite.so RcppExports.o gene_embed.o imfactor.o -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/Versions/4.5-x86_64 -framework R
ld: warning: search path '/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0' not found
ld: library 'emutls_w' not found
clang++: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [CAESAR.Suite.so] Error 1
ERROR: compilation failed for package ‘CAESAR.Suite’
* removing ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/CAESAR.Suite/new/CAESAR.Suite.Rcheck/CAESAR.Suite’
CRAN
* installing *source* package ‘CAESAR.Suite’ ...
** this is package ‘CAESAR.Suite’ version ‘0.2.2’
** package ‘CAESAR.Suite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.0.13.3)’
using SDK: ‘MacOSX15.4.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/include" -DNDEBUG -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/Rcpp/include' -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/include" -DNDEBUG -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/Rcpp/include' -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gene_embed.cpp -o gene_embed.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/include" -DNDEBUG -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/Rcpp/include' -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c imfactor.cpp -o imfactor.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib -L/opt/R/x86_64/lib -o CAESAR.Suite.so RcppExports.o gene_embed.o imfactor.o -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/Versions/4.5-x86_64 -framework R
ld: warning: search path '/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0' not found
ld: library 'emutls_w' not found
clang++: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [CAESAR.Suite.so] Error 1
ERROR: compilation failed for package ‘CAESAR.Suite’
* removing ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/CAESAR.Suite/old/CAESAR.Suite.Rcheck/CAESAR.Suite’
CatsCradle
- Version: 1.2.0
- GitHub: https://github.com/AnnaLaddach/CatsCradle
- Source code: https://github.com/cran/CatsCradle
- Date/Publication: 2025-04-15
- Number of recursive dependencies: 201
Run revdepcheck::revdep_details(, "CatsCradle") for more info
In both
-
R CMD check timed out
-
checking R code for possible problems ... NOTE
edgeLengthPlot: no visible binding for global variable ‘cellTypePair’
edgeLengthPlot: no visible binding for global variable ‘cutoff’
make.getExample : getExample: no visible binding for global variable
‘seuratGenes’
make.getExample : getExample: no visible binding for global variable
‘seuratCells’
make.getExample : getExample: no visible binding for global variable
‘xeniumCells’
make.getExample : getExample: no visible binding for global variable
‘moransI’
...
‘humanLRN’
make.getExample : getExample: no visible binding for global variable
‘mouseLRN’
meanGeneClusterOnCellUMAP: no visible binding for global variable
‘UMAP_1’
meanGeneClusterOnCellUMAP: no visible binding for global variable
‘UMAP_2’
Undefined global functions or variables:
UMAP_1 UMAP_2 cellTypePair cutoff humanLRN moransI
moransILigandReceptor mouseLRN seuratCells seuratGenes xeniumCells
ChromSCape
- Version: 1.17.0
- GitHub: https://github.com/vallotlab/ChromSCape
- Source code: https://github.com/cran/ChromSCape
- Date/Publication: 2024-10-29
- Number of recursive dependencies: 229
Run revdepcheck::revdep_details(, "ChromSCape") for more info
In both
-
R CMD check timed out
-
checking dependencies in R code ... WARNING
'library' or 'require' call not declared from: ‘dplyr’
'library' or 'require' call to ‘dplyr’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
-
checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'generate_analysis.Rd':
generate_analysis
Code: function(input_data_folder, analysis_name = "Analysis_1",
output_directory = "./", input_data_type = c("scBED",
"DenseMatrix", "SparseMatrix", "scBAM")[1],
feature_count_on = c("bins", "genebody", "peaks")[1],
feature_count_parameter = 50000, rebin_sparse_matrix =
FALSE, ref_genome = c("hg38", "mm10")[1], run =
c("filter", "CNA", "cluster", "consensus", "coverage",
"DA", "GSA", "report")[c(1, 3, 5, 6, 7, 8)],
...
Mismatches in argument names:
Position: 5 Code: feature_count_on Docs: rebin_sparse_matrix
Position: 6 Code: feature_count_parameter Docs: feature_count_on
Position: 7 Code: rebin_sparse_matrix Docs: feature_count_parameter
Mismatches in argument default values:
Name: 'run'
Code: c("filter", "CNA", "cluster", "consensus", "coverage", "DA",
"GSA", "report")[c(1, 3, 5, 6, 7, 8)]
Docs: c("filter", "CNA", "cluster", "consensus", "peak_call", "coverage",
"DA", "GSA", "report")[c(1, 3, 6, 7, 8, 9)]
-
checking Rd \usage sections ... WARNING
```
Undocumented arguments in Rd file 'rebin_matrix.Rd'
‘rebin_function’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
```
-
checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
-
checking R code for possible problems ... NOTE
bams_to_matrix_indexes: no visible binding for global variable
‘files_dir_list’
enrich_TF_ChEA3_genes: no visible binding for global variable
‘CheA3_TF_nTargets’
filter_correlated_cell_scExp: no visible binding for global variable
‘run_tsne’
generate_analysis: no visible global function definition for ‘head’
generate_analysis: no visible binding for global variable ‘k’
generate_analysis: no visible binding for global variable
‘clusterConsensus’
...
subset_bam_call_peaks: no visible binding for global variable
‘merged_bam’
Undefined global functions or variables:
CheA3_TF_nTargets Component Fri_cyto Gain_or_Loss Gene TF V1 V2
absolute_value cluster clusterConsensus cytoBand files_dir_list genes
group head k merged_bam molecule ncells new_row orientation
origin_value percent_active run_tsne sample_id total_counts
Consider adding
importFrom("utils", "head")
to your NAMESPACE file.
-
checking Rd files ... NOTE
prepare_Rd: raw_counts_to_sparse_matrix.Rd:6-8: Dropping empty section \source
EnrichmentBrowser
- Version: 2.38.0
- GitHub: https://github.com/lgeistlinger/EnrichmentBrowser
- Source code: https://github.com/cran/EnrichmentBrowser
- Date/Publication: 2025-04-15
- Number of recursive dependencies: 199
Run revdepcheck::revdep_details(, "EnrichmentBrowser") for more info
In both
-
R CMD check timed out
-
checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'pathview:::parseKGML2Graph2'
See the note in ?`:::` about the use of this operator.
-
checking R code for possible problems ... NOTE
.getGOFromBiomart: no visible binding for global variable
‘go_linkage_type’
Undefined global functions or variables:
go_linkage_type
fgsea
- Version:
- GitHub: https://github.com/igordot/msigdbr
- Source code: NA
- Number of recursive dependencies: 0
Error before installation
Devel
installing the source packages ‘org.Mm.eg.db’, ‘reactome.db’
CRAN
installing the source packages ‘org.Mm.eg.db’, ‘reactome.db’
gCrisprTools
- Version: 2.14.0
- GitHub: NA
- Source code: https://github.com/cran/gCrisprTools
- Date/Publication: 2025-04-15
- Number of recursive dependencies: 149
Run revdepcheck::revdep_details(, "gCrisprTools") for more info
In both
-
R CMD check timed out
-
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘RobustRankAggreg’
All declared Imports should be used.
-
checking Rd \usage sections ... NOTE
```
Documented arguments not in \usage in Rd file 'ct.targetSetEnrichment.Rd':
‘pvalue.cutoff’ ‘organism’ ‘db.cut’ ‘species’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
```
GenomicSuperSignature
- Version:
- GitHub: https://github.com/igordot/msigdbr
- Source code: NA
- Number of recursive dependencies: 0
Error before installation
Devel
installing the source packages ‘bcellViper’, ‘GO.db’, ‘org.Hs.eg.db’
CRAN
installing the source packages ‘bcellViper’, ‘GO.db’, ‘org.Hs.eg.db’
hypeR
- Version: 2.5.0
- GitHub: https://github.com/montilab/hypeR
- Source code: https://github.com/cran/hypeR
- Date/Publication: 2024-10-29
- Number of recursive dependencies: 164
Run revdepcheck::revdep_details(, "hypeR") for more info
In both
- checking whether package ‘hypeR’ can be installed ... ERROR
Installation failed.
See ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/hypeR/new/hypeR.Rcheck/00install.out’ for details.
Installation
Devel
* installing *source* package ‘hypeR’ ...
** this is package ‘hypeR’ version ‘2.5.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘msigdbr_show_species’ is not exported by 'namespace:msigdbr'
Execution halted
ERROR: lazy loading failed for package ‘hypeR’
* removing ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/hypeR/new/hypeR.Rcheck/hypeR’
CRAN
* installing *source* package ‘hypeR’ ...
** this is package ‘hypeR’ version ‘2.5.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘msigdbr_show_species’ is not exported by 'namespace:msigdbr'
Execution halted
ERROR: lazy loading failed for package ‘hypeR’
* removing ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/hypeR/old/hypeR.Rcheck/hypeR’
OSCA.advanced
- Version:
- GitHub: https://github.com/igordot/msigdbr
- Source code: NA
- Number of recursive dependencies: 0
Error before installation
Devel
installing the source packages ‘celldex’, ‘DropletTestFiles’, ‘EnsDb.Hsapiens.v86’, ‘GO.db’, ‘HCAData’, ‘MouseGastrulationData’, ‘org.Hs.eg.db’, ‘org.Mm.eg.db’, ‘OSCA.basic’, ‘OSCA.multisample’, ‘OSCA.workflows’, ‘scRNAseq’, ‘TENxBrainData’, ‘TENxPBMCData’
CRAN
installing the source packages ‘celldex’, ‘DropletTestFiles’, ‘EnsDb.Hsapiens.v86’, ‘GO.db’, ‘HCAData’, ‘MouseGastrulationData’, ‘org.Hs.eg.db’, ‘org.Mm.eg.db’, ‘OSCA.basic’, ‘OSCA.multisample’, ‘OSCA.workflows’, ‘scRNAseq’, ‘TENxBrainData’, ‘TENxPBMCData’
pairedGSEA
- Version: 1.8.0
- GitHub: https://github.com/shdam/pairedGSEA
- Source code: https://github.com/cran/pairedGSEA
- Date/Publication: 2025-04-15
- Number of recursive dependencies: 168
Run revdepcheck::revdep_details(, "pairedGSEA") for more info
Newly broken
- R CMD check timed out
pathfindR
- Version: 2.4.2
- GitHub: https://github.com/egeulgen/pathfindR
- Source code: https://github.com/cran/pathfindR
- Date/Publication: 2025-02-17 09:30:02 UTC
- Number of recursive dependencies: 143
Run revdepcheck::revdep_details(, "pathfindR") for more info
In both
- checking whether package ‘pathfindR’ can be installed ... ERROR
Installation failed.
See ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/pathfindR/new/pathfindR.Rcheck/00install.out’ for details.
Installation
Devel
* installing *source* package ‘pathfindR’ ...
** this is package ‘pathfindR’ version ‘2.4.2’
** package ‘pathfindR’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
...
Warning in system2(java, "-version", stderr = TRUE, stdout = TRUE) :
running command ''/usr/bin/java' -version 2>&1' had status 1
Error: package or namespace load failed for ‘pathfindR’:
.onAttach failed in attachNamespace() for 'pathfindR', details:
call: check_java_version()
error: Java version detected but couldn't parse version from The operation couldn’t be completed. Unable to locate a Java Runtime. - Please visit http://www.java.com for information on installing Java. -
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/pathfindR/new/pathfindR.Rcheck/pathfindR’
CRAN
* installing *source* package ‘pathfindR’ ...
** this is package ‘pathfindR’ version ‘2.4.2’
** package ‘pathfindR’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
...
Warning in system2(java, "-version", stderr = TRUE, stdout = TRUE) :
running command ''/usr/bin/java' -version 2>&1' had status 1
Error: package or namespace load failed for ‘pathfindR’:
.onAttach failed in attachNamespace() for 'pathfindR', details:
call: check_java_version()
error: Java version detected but couldn't parse version from The operation couldn’t be completed. Unable to locate a Java Runtime. - Please visit http://www.java.com for information on installing Java. -
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/pathfindR/old/pathfindR.Rcheck/pathfindR’
ReducedExperiment
- Version: 0.99.6
- GitHub: https://github.com/jackgisby/ReducedExperiment
- Source code: https://github.com/cran/ReducedExperiment
- Date/Publication: 2025-01-15
- Number of recursive dependencies: 219
Run revdepcheck::revdep_details(, "ReducedExperiment") for more info
Newly broken
- R CMD check timed out
Newly fixed
-
checking tests ...
```
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
|=================================== | 50%
|
|======================================================================| 100%
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 584 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_features.R:85:5'): Get MSGIDB data ───────────────────────────
nrow(t2g) > 1e+05 is not TRUE
actual: FALSE
expected: TRUE
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 584 ]
Error: Test failures
Execution halted
```
-
checking running R code from vignettes ...
```
‘ReducedExperiment.Rmd’ using ‘UTF-8’... failed
ERROR
Errors in running code in vignettes:
when running code in ‘ReducedExperiment.Rmd’
...
> ggplot(module_1_enrich[1:15, ], aes(-log10(p.adjust),
- reorder(substr(ID, 1, 45), -log10(p.adjust)))) + geom_point(pch = 21,
- size = 3) .... [TRUNCATED]
When sourcing ‘ReducedExperiment.R’:
Error: Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in log10():
! non-numeric argument to mathematical function
Execution halted
```
In both
- checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘BiocGenerics:::replaceSlots’
‘SummarizedExperiment:::.SummarizedExperiment.charbound’
See the note in ?`:::` about the use of this operator.
rGREAT
- Version:
- GitHub: https://github.com/igordot/msigdbr
- Source code: NA
- Number of recursive dependencies: 0
Error before installation
Devel
installing the source packages ‘org.Mm.eg.db’, ‘reactome.db’, ‘TxDb.Hsapiens.UCSC.hg19.knownGene’, ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
CRAN
installing the source packages ‘org.Mm.eg.db’, ‘reactome.db’, ‘TxDb.Hsapiens.UCSC.hg19.knownGene’, ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
scFeatures
- Version: 1.8.0
- GitHub: https://github.com/SydneyBioX/scFeatures
- Source code: https://github.com/cran/scFeatures
- Date/Publication: 2025-04-15
- Number of recursive dependencies: 318
Run revdepcheck::revdep_details(, "scFeatures") for more info
In both
-
R CMD check timed out
-
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
'DT' 'Seurat'
All declared Imports should be used.
-
checking R code for possible problems ... NOTE
helper_CCI: no visible global function definition for 'data'
helper_CCI: no visible binding for global variable 'LRdb'
helper_CCI: no visible global function definition for 'capture.output'
helper_pathway_gsva: no visible global function definition for
'capture.output'
run_pathway_gsva: no visible global function definition for
'capture.output'
Undefined global functions or variables:
LRdb capture.output data
Consider adding
importFrom("utils", "capture.output", "data")
to your NAMESPACE file.
singleCellTK
- Version:
- GitHub: https://github.com/igordot/msigdbr
- Source code: NA
- Number of recursive dependencies: 0
Error before installation
Devel
installing the source packages ‘celldex’, ‘GSVAdata’, ‘hgu95a.db’, ‘org.Mm.eg.db’, ‘scRNAseq’, ‘TENxPBMCData’
CRAN
installing the source packages ‘celldex’, ‘GSVAdata’, ‘hgu95a.db’, ‘org.Mm.eg.db’, ‘scRNAseq’, ‘TENxPBMCData’
sparrow
- Version:
- GitHub: https://github.com/igordot/msigdbr
- Source code: NA
- Number of recursive dependencies: 0
Error before installation
Devel
installing the source packages ‘geneLenDataBase’, ‘PANTHER.db’, ‘reactome.db’
CRAN
installing the source packages ‘geneLenDataBase’, ‘PANTHER.db’, ‘reactome.db’
tidybulk
- Version:
- GitHub: https://github.com/igordot/msigdbr
- Source code: NA
- Number of recursive dependencies: 0
Error before installation
Devel
installing the source packages ‘EGSEAdata’, ‘hgu133a.db’, ‘hgu133plus2.db’, ‘KEGGdzPathwaysGEO’, ‘org.Mm.eg.db’, ‘org.Rn.eg.db’, ‘pasilla’
CRAN
installing the source packages ‘EGSEAdata’, ‘hgu133a.db’, ‘hgu133plus2.db’, ‘KEGGdzPathwaysGEO’, ‘org.Mm.eg.db’, ‘org.Rn.eg.db’, ‘pasilla’
igordot/msigdbr documentation built on June 15, 2025, 4:29 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
CAESAR.Suite
- Version: 0.2.2
- GitHub: https://github.com/XiaoZhangryy/CAESAR.Suite
- Source code: https://github.com/cran/CAESAR.Suite
- Date/Publication: 2025-04-01 09:00:07 UTC
- Number of recursive dependencies: 253
Run revdepcheck::revdep_details(, "CAESAR.Suite") for more info
In both
- checking whether package ‘CAESAR.Suite’ can be installed ... ERROR
Installation failed. See ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/CAESAR.Suite/new/CAESAR.Suite.Rcheck/00install.out’ for details.
Installation
Devel
* installing *source* package ‘CAESAR.Suite’ ...
** this is package ‘CAESAR.Suite’ version ‘0.2.2’
** package ‘CAESAR.Suite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.0.13.3)’
using SDK: ‘MacOSX15.4.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/include" -DNDEBUG -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/Rcpp/include' -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/include" -DNDEBUG -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/Rcpp/include' -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gene_embed.cpp -o gene_embed.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/include" -DNDEBUG -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/Rcpp/include' -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c imfactor.cpp -o imfactor.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib -L/opt/R/x86_64/lib -o CAESAR.Suite.so RcppExports.o gene_embed.o imfactor.o -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/Versions/4.5-x86_64 -framework R
ld: warning: search path '/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0' not found
ld: library 'emutls_w' not found
clang++: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [CAESAR.Suite.so] Error 1
ERROR: compilation failed for package ‘CAESAR.Suite’
* removing ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/CAESAR.Suite/new/CAESAR.Suite.Rcheck/CAESAR.Suite’
CRAN
* installing *source* package ‘CAESAR.Suite’ ...
** this is package ‘CAESAR.Suite’ version ‘0.2.2’
** package ‘CAESAR.Suite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.0.13.3)’
using SDK: ‘MacOSX15.4.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/include" -DNDEBUG -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/Rcpp/include' -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/include" -DNDEBUG -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/Rcpp/include' -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gene_embed.cpp -o gene_embed.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/include" -DNDEBUG -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/Rcpp/include' -I'/Users/id460/repos/msigdbr/revdep/library.noindex/CAESAR.Suite/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c imfactor.cpp -o imfactor.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib -L/opt/R/x86_64/lib -o CAESAR.Suite.so RcppExports.o gene_embed.o imfactor.o -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/Versions/4.5-x86_64 -framework R
ld: warning: search path '/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0' not found
ld: library 'emutls_w' not found
clang++: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [CAESAR.Suite.so] Error 1
ERROR: compilation failed for package ‘CAESAR.Suite’
* removing ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/CAESAR.Suite/old/CAESAR.Suite.Rcheck/CAESAR.Suite’
CatsCradle
- Version: 1.2.0
- GitHub: https://github.com/AnnaLaddach/CatsCradle
- Source code: https://github.com/cran/CatsCradle
- Date/Publication: 2025-04-15
- Number of recursive dependencies: 201
Run revdepcheck::revdep_details(, "CatsCradle") for more info
In both
-
R CMD check timed out
-
checking R code for possible problems ... NOTE
edgeLengthPlot: no visible binding for global variable ‘cellTypePair’ edgeLengthPlot: no visible binding for global variable ‘cutoff’ make.getExample : getExample: no visible binding for global variable ‘seuratGenes’ make.getExample : getExample: no visible binding for global variable ‘seuratCells’ make.getExample : getExample: no visible binding for global variable ‘xeniumCells’ make.getExample : getExample: no visible binding for global variable ‘moransI’ ... ‘humanLRN’ make.getExample : getExample: no visible binding for global variable ‘mouseLRN’ meanGeneClusterOnCellUMAP: no visible binding for global variable ‘UMAP_1’ meanGeneClusterOnCellUMAP: no visible binding for global variable ‘UMAP_2’ Undefined global functions or variables: UMAP_1 UMAP_2 cellTypePair cutoff humanLRN moransI moransILigandReceptor mouseLRN seuratCells seuratGenes xeniumCells
ChromSCape
- Version: 1.17.0
- GitHub: https://github.com/vallotlab/ChromSCape
- Source code: https://github.com/cran/ChromSCape
- Date/Publication: 2024-10-29
- Number of recursive dependencies: 229
Run revdepcheck::revdep_details(, "ChromSCape") for more info
In both
-
R CMD check timed out
-
checking dependencies in R code ... WARNING
'library' or 'require' call not declared from: ‘dplyr’ 'library' or 'require' call to ‘dplyr’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. -
checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'generate_analysis.Rd': generate_analysis Code: function(input_data_folder, analysis_name = "Analysis_1", output_directory = "./", input_data_type = c("scBED", "DenseMatrix", "SparseMatrix", "scBAM")[1], feature_count_on = c("bins", "genebody", "peaks")[1], feature_count_parameter = 50000, rebin_sparse_matrix = FALSE, ref_genome = c("hg38", "mm10")[1], run = c("filter", "CNA", "cluster", "consensus", "coverage", "DA", "GSA", "report")[c(1, 3, 5, 6, 7, 8)], ... Mismatches in argument names: Position: 5 Code: feature_count_on Docs: rebin_sparse_matrix Position: 6 Code: feature_count_parameter Docs: feature_count_on Position: 7 Code: rebin_sparse_matrix Docs: feature_count_parameter Mismatches in argument default values: Name: 'run' Code: c("filter", "CNA", "cluster", "consensus", "coverage", "DA", "GSA", "report")[c(1, 3, 5, 6, 7, 8)] Docs: c("filter", "CNA", "cluster", "consensus", "peak_call", "coverage", "DA", "GSA", "report")[c(1, 3, 6, 7, 8, 9)] -
checking Rd \usage sections ... WARNING ``` Undocumented arguments in Rd file 'rebin_matrix.Rd' ‘rebin_function’
Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
-
checking for hidden files and directories ... NOTE
Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. -
checking R code for possible problems ... NOTE
bams_to_matrix_indexes: no visible binding for global variable ‘files_dir_list’ enrich_TF_ChEA3_genes: no visible binding for global variable ‘CheA3_TF_nTargets’ filter_correlated_cell_scExp: no visible binding for global variable ‘run_tsne’ generate_analysis: no visible global function definition for ‘head’ generate_analysis: no visible binding for global variable ‘k’ generate_analysis: no visible binding for global variable ‘clusterConsensus’ ... subset_bam_call_peaks: no visible binding for global variable ‘merged_bam’ Undefined global functions or variables: CheA3_TF_nTargets Component Fri_cyto Gain_or_Loss Gene TF V1 V2 absolute_value cluster clusterConsensus cytoBand files_dir_list genes group head k merged_bam molecule ncells new_row orientation origin_value percent_active run_tsne sample_id total_counts Consider adding importFrom("utils", "head") to your NAMESPACE file. -
checking Rd files ... NOTE
prepare_Rd: raw_counts_to_sparse_matrix.Rd:6-8: Dropping empty section \source
EnrichmentBrowser
- Version: 2.38.0
- GitHub: https://github.com/lgeistlinger/EnrichmentBrowser
- Source code: https://github.com/cran/EnrichmentBrowser
- Date/Publication: 2025-04-15
- Number of recursive dependencies: 199
Run revdepcheck::revdep_details(, "EnrichmentBrowser") for more info
In both
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R CMD check timed out
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checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'pathview:::parseKGML2Graph2' See the note in ?`:::` about the use of this operator. -
checking R code for possible problems ... NOTE
.getGOFromBiomart: no visible binding for global variable ‘go_linkage_type’ Undefined global functions or variables: go_linkage_type
fgsea
- Version:
- GitHub: https://github.com/igordot/msigdbr
- Source code: NA
- Number of recursive dependencies: 0
Error before installation
Devel
installing the source packages ‘org.Mm.eg.db’, ‘reactome.db’
CRAN
installing the source packages ‘org.Mm.eg.db’, ‘reactome.db’
gCrisprTools
- Version: 2.14.0
- GitHub: NA
- Source code: https://github.com/cran/gCrisprTools
- Date/Publication: 2025-04-15
- Number of recursive dependencies: 149
Run revdepcheck::revdep_details(, "gCrisprTools") for more info
In both
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R CMD check timed out
-
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘RobustRankAggreg’ All declared Imports should be used. -
checking Rd \usage sections ... NOTE ``` Documented arguments not in \usage in Rd file 'ct.targetSetEnrichment.Rd': ‘pvalue.cutoff’ ‘organism’ ‘db.cut’ ‘species’
Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
GenomicSuperSignature
- Version:
- GitHub: https://github.com/igordot/msigdbr
- Source code: NA
- Number of recursive dependencies: 0
Error before installation
Devel
installing the source packages ‘bcellViper’, ‘GO.db’, ‘org.Hs.eg.db’
CRAN
installing the source packages ‘bcellViper’, ‘GO.db’, ‘org.Hs.eg.db’
hypeR
- Version: 2.5.0
- GitHub: https://github.com/montilab/hypeR
- Source code: https://github.com/cran/hypeR
- Date/Publication: 2024-10-29
- Number of recursive dependencies: 164
Run revdepcheck::revdep_details(, "hypeR") for more info
In both
- checking whether package ‘hypeR’ can be installed ... ERROR
Installation failed. See ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/hypeR/new/hypeR.Rcheck/00install.out’ for details.
Installation
Devel
* installing *source* package ‘hypeR’ ...
** this is package ‘hypeR’ version ‘2.5.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘msigdbr_show_species’ is not exported by 'namespace:msigdbr'
Execution halted
ERROR: lazy loading failed for package ‘hypeR’
* removing ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/hypeR/new/hypeR.Rcheck/hypeR’
CRAN
* installing *source* package ‘hypeR’ ...
** this is package ‘hypeR’ version ‘2.5.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘msigdbr_show_species’ is not exported by 'namespace:msigdbr'
Execution halted
ERROR: lazy loading failed for package ‘hypeR’
* removing ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/hypeR/old/hypeR.Rcheck/hypeR’
OSCA.advanced
- Version:
- GitHub: https://github.com/igordot/msigdbr
- Source code: NA
- Number of recursive dependencies: 0
Error before installation
Devel
installing the source packages ‘celldex’, ‘DropletTestFiles’, ‘EnsDb.Hsapiens.v86’, ‘GO.db’, ‘HCAData’, ‘MouseGastrulationData’, ‘org.Hs.eg.db’, ‘org.Mm.eg.db’, ‘OSCA.basic’, ‘OSCA.multisample’, ‘OSCA.workflows’, ‘scRNAseq’, ‘TENxBrainData’, ‘TENxPBMCData’
CRAN
installing the source packages ‘celldex’, ‘DropletTestFiles’, ‘EnsDb.Hsapiens.v86’, ‘GO.db’, ‘HCAData’, ‘MouseGastrulationData’, ‘org.Hs.eg.db’, ‘org.Mm.eg.db’, ‘OSCA.basic’, ‘OSCA.multisample’, ‘OSCA.workflows’, ‘scRNAseq’, ‘TENxBrainData’, ‘TENxPBMCData’
pairedGSEA
- Version: 1.8.0
- GitHub: https://github.com/shdam/pairedGSEA
- Source code: https://github.com/cran/pairedGSEA
- Date/Publication: 2025-04-15
- Number of recursive dependencies: 168
Run revdepcheck::revdep_details(, "pairedGSEA") for more info
Newly broken
- R CMD check timed out
pathfindR
- Version: 2.4.2
- GitHub: https://github.com/egeulgen/pathfindR
- Source code: https://github.com/cran/pathfindR
- Date/Publication: 2025-02-17 09:30:02 UTC
- Number of recursive dependencies: 143
Run revdepcheck::revdep_details(, "pathfindR") for more info
In both
- checking whether package ‘pathfindR’ can be installed ... ERROR
Installation failed. See ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/pathfindR/new/pathfindR.Rcheck/00install.out’ for details.
Installation
Devel
* installing *source* package ‘pathfindR’ ...
** this is package ‘pathfindR’ version ‘2.4.2’
** package ‘pathfindR’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
...
Warning in system2(java, "-version", stderr = TRUE, stdout = TRUE) :
running command ''/usr/bin/java' -version 2>&1' had status 1
Error: package or namespace load failed for ‘pathfindR’:
.onAttach failed in attachNamespace() for 'pathfindR', details:
call: check_java_version()
error: Java version detected but couldn't parse version from The operation couldn’t be completed. Unable to locate a Java Runtime. - Please visit http://www.java.com for information on installing Java. -
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/pathfindR/new/pathfindR.Rcheck/pathfindR’
CRAN
* installing *source* package ‘pathfindR’ ...
** this is package ‘pathfindR’ version ‘2.4.2’
** package ‘pathfindR’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
...
Warning in system2(java, "-version", stderr = TRUE, stdout = TRUE) :
running command ''/usr/bin/java' -version 2>&1' had status 1
Error: package or namespace load failed for ‘pathfindR’:
.onAttach failed in attachNamespace() for 'pathfindR', details:
call: check_java_version()
error: Java version detected but couldn't parse version from The operation couldn’t be completed. Unable to locate a Java Runtime. - Please visit http://www.java.com for information on installing Java. -
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/id460/repos/msigdbr/revdep/checks.noindex/pathfindR/old/pathfindR.Rcheck/pathfindR’
ReducedExperiment
- Version: 0.99.6
- GitHub: https://github.com/jackgisby/ReducedExperiment
- Source code: https://github.com/cran/ReducedExperiment
- Date/Publication: 2025-01-15
- Number of recursive dependencies: 219
Run revdepcheck::revdep_details(, "ReducedExperiment") for more info
Newly broken
- R CMD check timed out
Newly fixed
-
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: |=================================== | 50% | |======================================================================| 100% [ FAIL 1 | WARN 1 | SKIP 0 | PASS 584 ]
══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_features.R:85:5'): Get MSGIDB data ─────────────────────────── nrow(t2g) > 1e+05 is not TRUE
actual: FALSEexpected: TRUE[ FAIL 1 | WARN 1 | SKIP 0 | PASS 584 ] Error: Test failures Execution halted ```
-
checking running R code from vignettes ... ``` ‘ReducedExperiment.Rmd’ using ‘UTF-8’... failed ERROR Errors in running code in vignettes: when running code in ‘ReducedExperiment.Rmd’ ... > ggplot(module_1_enrich[1:15, ], aes(-log10(p.adjust),
- reorder(substr(ID, 1, 45), -log10(p.adjust)))) + geom_point(pch = 21,
- size = 3) .... [TRUNCATED]
When sourcing ‘ReducedExperiment.R’: Error: Problem while computing aesthetics. ℹ Error occurred in the 1st layer. Caused by error in
log10(): ! non-numeric argument to mathematical function Execution halted ```
In both
- checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls: ‘BiocGenerics:::replaceSlots’ ‘SummarizedExperiment:::.SummarizedExperiment.charbound’ See the note in ?`:::` about the use of this operator.
rGREAT
- Version:
- GitHub: https://github.com/igordot/msigdbr
- Source code: NA
- Number of recursive dependencies: 0
Error before installation
Devel
installing the source packages ‘org.Mm.eg.db’, ‘reactome.db’, ‘TxDb.Hsapiens.UCSC.hg19.knownGene’, ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
CRAN
installing the source packages ‘org.Mm.eg.db’, ‘reactome.db’, ‘TxDb.Hsapiens.UCSC.hg19.knownGene’, ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
scFeatures
- Version: 1.8.0
- GitHub: https://github.com/SydneyBioX/scFeatures
- Source code: https://github.com/cran/scFeatures
- Date/Publication: 2025-04-15
- Number of recursive dependencies: 318
Run revdepcheck::revdep_details(, "scFeatures") for more info
In both
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R CMD check timed out
-
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from: 'DT' 'Seurat' All declared Imports should be used. -
checking R code for possible problems ... NOTE
helper_CCI: no visible global function definition for 'data' helper_CCI: no visible binding for global variable 'LRdb' helper_CCI: no visible global function definition for 'capture.output' helper_pathway_gsva: no visible global function definition for 'capture.output' run_pathway_gsva: no visible global function definition for 'capture.output' Undefined global functions or variables: LRdb capture.output data Consider adding importFrom("utils", "capture.output", "data") to your NAMESPACE file.
singleCellTK
- Version:
- GitHub: https://github.com/igordot/msigdbr
- Source code: NA
- Number of recursive dependencies: 0
Error before installation
Devel
installing the source packages ‘celldex’, ‘GSVAdata’, ‘hgu95a.db’, ‘org.Mm.eg.db’, ‘scRNAseq’, ‘TENxPBMCData’
CRAN
installing the source packages ‘celldex’, ‘GSVAdata’, ‘hgu95a.db’, ‘org.Mm.eg.db’, ‘scRNAseq’, ‘TENxPBMCData’
sparrow
- Version:
- GitHub: https://github.com/igordot/msigdbr
- Source code: NA
- Number of recursive dependencies: 0
Error before installation
Devel
installing the source packages ‘geneLenDataBase’, ‘PANTHER.db’, ‘reactome.db’
CRAN
installing the source packages ‘geneLenDataBase’, ‘PANTHER.db’, ‘reactome.db’
tidybulk
- Version:
- GitHub: https://github.com/igordot/msigdbr
- Source code: NA
- Number of recursive dependencies: 0
Error before installation
Devel
installing the source packages ‘EGSEAdata’, ‘hgu133a.db’, ‘hgu133plus2.db’, ‘KEGGdzPathwaysGEO’, ‘org.Mm.eg.db’, ‘org.Rn.eg.db’, ‘pasilla’
CRAN
installing the source packages ‘EGSEAdata’, ‘hgu133a.db’, ‘hgu133plus2.db’, ‘KEGGdzPathwaysGEO’, ‘org.Mm.eg.db’, ‘org.Rn.eg.db’, ‘pasilla’
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