===============================
R CMD BUILD
===============================
* checking for file ‘markeR/DESCRIPTION’ ... OK
* preparing ‘markeR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘markeR_0.99.2.tar.gz’
===============================
BiocCheckGitClone('markeR')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3878/9ad3cb403094bcc1bea20f80a0040e0df065d4c6/markeR
→ BiocVersion: 3.22
→ Package: markeR
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3878/9ad3cb403094bcc1bea20f80a0040e0df065d4c6/markeR.BiocCheck
→ BiocCheckVersion: 1.45.11
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3878/9ad3cb403094bcc1bea20f80a0040e0df065d4c6/markeR
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/home/pkgbuild/packagebuilder/workers/jobs/3878/9ad3cb403094bcc1bea20f80a0040e0df065d4c6/markeR/.gitignore'
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
── BiocCheck v1.45.11 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3878/9ad3cb403094bcc1bea20f80a0040e0df065d4c6/markeR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘markeR/DESCRIPTION’ ... OK
* this is package ‘markeR’ version ‘0.99.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... 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 ‘markeR’ can be installed ... OK
* checking installed package size ... INFO
installed size is 37.2Mb
sub-directories of 1Mb or more:
Paper 33.7Mb
data 2.8Mb
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
* checking loading without being on the library search path ... [4s/4s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘patchwork’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [20s/20s] NOTE
AUC_Scores: no visible binding for global variable ‘Method’
AUC_Scores: no visible binding for global variable ‘Contrast’
AUC_Scores: no visible binding for global variable ‘AUC’
AUC_Scores: no visible binding for global variable ‘label’
CalculateScores_ssGSEA_bidirectional: no visible binding for global
variable ‘Signal’
CohenD_IndividualGenes : compute_cohens_d: no visible global function
definition for ‘sd’
CohenD_IndividualGenes: no visible global function definition for
‘reorder’
CohenD_IndividualGenes: no visible binding for global variable ‘Gene’
CohenD_IndividualGenes: no visible binding for global variable
‘CohensD’
CohenD_allConditions: no visible global function definition for
‘setNames’
CohenD_allConditions : <anonymous>: no visible global function
definition for ‘p.adjust’
CohenF_allConditions: no visible global function definition for
‘setNames’
CohenF_allConditions : <anonymous>: no visible global function
definition for ‘p.adjust’
CorrelationHeatmap: no visible global function definition for ‘na.omit’
FPR_Simulation: no visible global function definition for ‘quantile’
FPR_Simulation: no visible global function definition for ‘aggregate’
FPR_Simulation: no visible binding for global variable ‘cohen’
FPR_Simulation: no visible binding for global variable ‘y’
FPR_Simulation: no visible binding for global variable ‘label’
FPR_Simulation: no visible binding for global variable ‘xmin’
FPR_Simulation: no visible binding for global variable ‘xmax’
FPR_Simulation: no visible binding for global variable ‘q_high’
GSEA_VariableAssociation: no visible global function definition for
‘model.matrix’
GSEA_VariableAssociation: no visible global function definition for
‘p.adjust’
GSEA_VariableAssociation: no visible binding for global variable ‘NES’
GSEA_VariableAssociation: no visible binding for global variable
‘Contrast’
GSEA_VariableAssociation: no visible binding for global variable ‘padj’
GSEA_VariableAssociation: no visible binding for global variable
‘stat_used’
Heatmap_Cohen: no visible binding for global variable ‘Var2’
Heatmap_Cohen: no visible binding for global variable ‘Var1’
Heatmap_Cohen: no visible binding for global variable ‘Cohen’
Heatmap_Cohen: no visible binding for global variable ‘label’
IndividualGenes_Violins: no visible binding for global variable
‘median’
PlotScores_Categorical: no visible binding for global variable ‘score’
PlotScores_Categorical: no visible binding for global variable ‘median’
PlotScores_Numeric: no visible binding for global variable ‘score’
ROC_Scores: no visible binding for global variable ‘FPR’
ROC_Scores: no visible binding for global variable ‘TPR’
ROC_Scores: no visible binding for global variable ‘Method’
ROC_Scores: no visible binding for global variable ‘x’
ROC_Scores: no visible binding for global variable ‘y’
ROC_Scores: no visible binding for global variable ‘AUC’
ROCandAUCplot : makeROCplot: no visible binding for global variable
‘FPR’
ROCandAUCplot : makeROCplot: no visible binding for global variable
‘TPR’
ROCandAUCplot : makeROCplot: no visible binding for global variable
‘Group’
ROCandAUCplot : makeBarplot: no visible global function definition for
‘reorder’
ROCandAUCplot : makeBarplot: no visible binding for global variable
‘Gene’
ROCandAUCplot : makeBarplot: no visible binding for global variable
‘AUC’
Score_VariableAssociation: no visible global function definition for
‘p.adjust’
Score_VariableAssociation: no visible binding for global variable
‘CohenD’
Score_VariableAssociation: no visible binding for global variable
‘Contrast’
Score_VariableAssociation: no visible binding for global variable
‘padj’
Score_VariableAssociation: no visible binding for global variable
‘Cohen_f’
Score_VariableAssociation: no visible binding for global variable
‘Variable’
Score_VariableAssociation: no visible binding for global variable
‘P_Value’
Score_VariableAssociation: no visible global function definition for
‘colorRampPalette’
Volcano_Cohen: no visible global function definition for
‘colorRampPalette’
Volcano_Cohen: no visible binding for global variable ‘cohen’
Volcano_Cohen: no visible binding for global variable ‘padj’
calculateDE: no visible global function definition for ‘model.matrix’
calculateScore_logmedian_bidirectional: no visible global function
definition for ‘na.omit’
calculateScore_logmedian_bidirectional: no visible binding for global
variable ‘median’
calculateScore_logmedian_unidirectional: no visible global function
definition for ‘na.omit’
calculateScore_logmedian_unidirectional: no visible binding for global
variable ‘median’
cohen_d: no visible global function definition for ‘sd’
compute_stat_tests: no visible global function definition for
‘kruskal.test’
compute_stat_tests: no visible global function definition for
‘p.adjust’
geneset_similarity: no visible global function definition for
‘fisher.test’
geneset_similarity: no visible binding for global variable
‘Reference_Signature’
geneset_similarity: no visible binding for global variable
‘Compared_Signature’
geneset_similarity: no visible binding for global variable ‘Score’
geneset_similarity: no visible binding for global variable ‘Label’
getRanking: no visible global function definition for ‘na.omit’
plotCombinedGSEA: no visible global function definition for
‘colorRampPalette’
plotCombinedGSEA: no visible binding for global variable ‘NES’
plotCombinedGSEA: no visible binding for global variable ‘logpadj’
plotCombinedGSEA: no visible binding for global variable ‘contrast’
plotCombinedGSEA: no visible binding for global variable ‘pathway’
plotGSEAenrichment: no visible global function definition for
‘setNames’
plotNESlollipop: no visible binding for global variable ‘NES’
plotNESlollipop: no visible binding for global variable ‘pathway’
plotNESlollipop: no visible binding for global variable ‘padj’
plotNESlollipop: no visible binding for global variable ‘stat_used’
plotVolcano: no visible binding for global variable ‘Direction’
runGSEA: no visible global function definition for ‘setNames’
runGSEA: no visible global function definition for ‘p.adjust’
runGSEA : <anonymous>: no visible global function definition for
‘p.adjust’
Undefined global functions or variables:
AUC Cohen CohenD Cohen_f CohensD Compared_Signature Contrast
Direction FPR Gene Group Label Method NES P_Value Reference_Signature
Score Signal TPR Var1 Var2 Variable aggregate cohen colorRampPalette
contrast fisher.test kruskal.test label logpadj median model.matrix
na.omit p.adjust padj pathway q_high quantile reorder score sd
setNames stat_used x xmax xmin y
Consider adding
importFrom("grDevices", "colorRampPalette")
importFrom("stats", "aggregate", "fisher.test", "kruskal.test",
"median", "model.matrix", "na.omit", "p.adjust", "quantile",
"reorder", "sd", "setNames")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] NOTE
prepare_Rd: VariableAssociation.Rd:128-130: Dropping empty section ‘Shared Arguments (All Methods)’
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [84s/84s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
geneset_similarity 40.915 0.612 41.528
runGSEA 6.916 0.006 6.922
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [76s/76s]
[76s/76s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [6s/6s] OK
* DONE
Status: 5 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3878/9ad3cb403094bcc1bea20f80a0040e0df065d4c6/markeR.Rcheck/00check.log’
for details.
===============================
BiocCheck('markeR_0.99.2.tar.gz')
===============================
── Installing markeR ───────────────────────────────────────────────────────────
✔ Package installed successfully
── markeR session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpDRDNLN/file1d8afc419397b/markeR
→ BiocVersion: 3.22
→ Package: markeR
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3878/9ad3cb403094bcc1bea20f80a0040e0df065d4c6/markeR.BiocCheck
→ BiocCheckVersion: 1.45.11
→ sourceDir: /tmp/RtmpDRDNLN/file1d8afc419397b/markeR
→ installDir: /tmp/RtmpDRDNLN/file1d8afc576fa2c7
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on markeR ─────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 3.5.0 to 4.5.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (18%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
• Found in files:
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of markeR...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/calculateDE.R (line 142, column 31)
• ...
• R/Volcano_Cohen.R (line 91, column 25)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• FPR_Simulation.R (line 207, column 17)
• ...
• plotVolcano.R (line 284, column 52)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/CohenD_IndividualGenes.R (line 220, column 5)
• ...
• print() in R/Score_VariableAssociation.R (line 539, column 19)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/plotPCA.R (line 127, column 8)
• ...
• R/ssGSEA_alternative.R (line 127, column 16)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/CalculateScores_logmedian.R (line 48, column 17)
• ...
• R/VariableAssociation.R (line 52, column 17)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/calculateDE.R (line 113, column 5)
• ...
• R/Volcano_Cohen.R (line 69, column 12)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
• suppressMessages() in R/FPR_Simulation.R (line 127, column 18)
• ...
• suppressMessages() in R/FPR_Simulation.R (line 223, column 19)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 34
functions greater than 50 lines.
The longest 5 functions are:
• Score_VariableAssociation() (R/Score_VariableAssociation.R): 363 lines
• ...
• plotVolcano() (R/plotVolcano.R): 275 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• VariableAssociation.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 655 lines (7%) are > 80 characters long.
First few lines:
• R/calculateDE.R#L98 colnames_vector <- ifelse(new_coln ...
• ...
• vignettes/Tutorial_GeneSetSimilarity.Rmd#L112 > **Note**: When using `metric
= "odds_r ...
i NOTE: Consider multiples of 4 spaces for line indents; 2811 lines (29%) are
not.
First few lines:
• R/calculateDE.R#L92 data <- as.data.frame(data) # Ensure d ...
• ...
• vignettes/Tutorial_GeneSetSimilarity.Rmd#L135 width_text=50 ...
i See https://contributions.bioconductor.org/r-code.html
i See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.45.11 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 14 NOTES
i See the markeR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.