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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:HDCytoData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings HDCytoData_1.27.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/HDCytoData.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘HDCytoData/DESCRIPTION’ ... OK
* this is package ‘HDCytoData’ version ‘1.27.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HDCytoData’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
Bodenmiller_BCR_XL_SE.Rd: SummarizedExperiment, flowSet, rowData,
colData, assay, flowFrame, exprs, flowCore, description
HDCytoData-package.Rd: SummarizedExperiment, flowSet
Krieg_Anti_PD_1_SE.Rd: SummarizedExperiment, flowSet, rowData,
colData, assay, flowFrame, exprs, flowCore, description
Levine_13dim_SE.Rd: SummarizedExperiment, flowSet, rowData, colData,
assay, flowFrame, exprs, flowCore, description
Levine_32dim_SE.Rd: SummarizedExperiment, flowSet, rowData, colData,
assay, flowFrame, exprs, flowCore, description
Mosmann_rare_SE.Rd: SummarizedExperiment, flowSet, rowData, colData,
assay, flowFrame, exprs, flowCore, description
Nilsson_rare_SE.Rd: SummarizedExperiment, flowSet, rowData, colData,
assay, flowFrame, exprs, flowCore, description
Samusik_01_SE.Rd: SummarizedExperiment, flowSet, rowData, colData,
assay, flowFrame, exprs, flowCore, description
Samusik_all_SE.Rd: SummarizedExperiment, flowSet, rowData, colData,
assay, flowFrame, exprs, flowCore, description
Weber_AML_sim_main_5pc_SE.Rd: SummarizedExperiment, flowSet, rowData,
colData, assays
Weber_BCR_XL_sim_main_SE.Rd: SummarizedExperiment, flowSet, rowData,
colData, assays
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Samusik_all_SE 8.267 0.900 9.312
Bodenmiller_BCR_XL_SE 4.068 0.625 5.056
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.21-data-experiment/meat/HDCytoData.Rcheck/00check.log’
for details.
