############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CoreGx.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CoreGx_2.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CoreGx.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘CoreGx/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CoreGx’ version ‘2.10.0’ * package encoding: UTF-8 * 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 ‘CoreGx’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * 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 dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.LongTable’ ‘.parseToRoxygen’ ‘.sensitivityToTRE’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .meshEval2: no visible binding for global variable ‘n’ .meshEval2: no visible binding for global variable ‘family’ .rebuildInfo: no visible binding for global variable ‘..keepCols’ .rebuildInfo: no visible binding for global variable ‘replicate_id’ .rebuildInfo: no visible binding for global variable ‘treatment1id’ .rebuildInfo: no visible binding for global variable ‘sampleid’ .rebuildInfo: no visible binding for global variable ‘treatmentid’ .rebuildInfo: no visible binding for global variable ‘treatment_uid’ .rebuildInfo: no visible binding for global variable ‘..rowIDcols’ .rebuildInfo: no visible binding for global variable ‘sample_uid’ .rebuildInfo: no visible binding for global variable ‘..colIDcols’ .rebuildInfo: no visible binding for global variable ‘exp_id’ .rebuildProfiles: no visible binding for global variable ‘treatment_uid’ .rebuildProfiles: no visible binding for global variable ‘sample_uid’ .rebuildProfiles: no visible binding for global variable ‘exp_id’ .rebuildProfiles: no visible binding for global variable ‘N’ .rebuildRaw: no visible binding for global variable ‘.NATURAL’ .rebuildRaw: no visible binding for global variable ‘sampleid’ .rebuildRaw: no visible binding for global variable ‘exp_id’ .rebuildRaw: no visible binding for global variable ‘treatment1id’ .rebuildRaw: no visible binding for global variable ‘dose’ .rebuildSensNumber: no visible binding for global variable ‘.treatmentCombo’ .rebuildSensNumber: no visible binding for global variable ‘.sampleCombo’ .sensitivityToTRE: no visible binding for global variable ‘dose’ .sensitivityToTRE: no visible binding for global variable ‘viability’ .sensitivityToTRE: no visible binding for global variable ‘replicate_id’ .sensitivityToTRE: no visible binding for global variable ‘rn’ .sensitivityToTRE: no visible binding for global variable ‘treatmentid’ .sensitivityToTRE: no visible binding for global variable ‘sampleid’ .update_dimData: no visible binding for global variable ‘N’ .update_dimData: no visible binding for global variable ‘.NATURAL’ .update_dimData: no visible binding for global variable ‘.rownames’ CoreSet: no visible binding for global variable ‘cell’ CoreSet: no visible binding for global variable ‘drug’ aggregate2: no visible binding for global variable ‘group_id’ aggregate2: no visible binding for global variable ‘split_id’ cardinality: no visible binding for global variable ‘N’ checkColumnCardinality: no visible binding for global variable ‘N’ optimizeCoreGx: no visible binding for global variable ‘nthread’ optimizeCoreGx: no visible binding for global variable ‘total_time’ optimizeCoreGx: no visible binding for global variable ‘mem_alloc’ optimizeCoreGx: no visible binding for global variable ‘itr/sec’ optimizeCoreGx: no visible binding for global variable ‘gc/sec’ optimizeCoreGx: no visible binding for global variable ‘median_sec’ optimizeCoreGx: no visible binding for global variable ‘N’ buildComboProfiles,LongTable: no visible binding for global variable ‘treatment2dose’ buildComboProfiles,LongTable: no visible binding for global variable ‘treatment1dose’ coerce,SummarizedExperiment-data.table: no visible binding for global variable ‘.sample’ coerce,SummarizedExperiment-data.table: no visible binding for global variable ‘.feature’ reindex,LongTable: no visible binding for global variable ‘.rowKey’ reindex,LongTable: no visible binding for global variable ‘.colKey’ sensitivityRaw<-,CoreSet-array: no visible binding for global variable ‘V2’ sensitivityRaw<-,CoreSet-array: no visible binding for global variable ‘V1’ sensitivityRaw<-,CoreSet-array: no visible binding for global variable ‘rn’ treatmentResponse<-,CoreSet-list_OR_LongTable: no visible binding for global variable ‘funContext’ updateObject,CoreSet: no visible global function definition for ‘isValid’ updateObject,LongTable: no visible global function definition for ‘isValid’ Undefined global functions or variables: ..colIDcols ..keepCols ..rowIDcols .NATURAL .colKey .feature .rowKey .rownames .sample .sampleCombo .treatmentCombo N V1 V2 cell dose drug exp_id family funContext gc/sec group_id isValid itr/sec median_sec mem_alloc n nthread replicate_id rn sample_uid sampleid split_id total_time treatment1dose treatment1id treatment2dose treatment_uid treatmentid viability Consider adding importFrom("stats", "family") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... NOTE Documented arguments not in \usage in Rd file 'LongTable-class.Rd': ‘`x`’ ‘`i`’ Documented arguments not in \usage in Rd file 'assays-LongTableDataMapper-method.Rd': ‘withDimNames’ 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. S3 methods shown with full name in Rd file 'setOps-immutable.Rd': ‘subset.immutable’ The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... NOTE Note: found 99 marked UTF-8 strings * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed metaConstruct 7.698 0.796 6.943 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/CoreGx.Rcheck/00check.log’ for details.