===============================
R CMD BUILD
===============================
* checking for file EnrichDO/DESCRIPTION ... OK
* preparing EnrichDO:
* 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
* building EnrichDO_0.99.9.tar.gz
===============================
BiocCheckGitClone('EnrichDO')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3468/b32752ee5ad51643a88ff820a7bf293413bbc9ff/EnrichDO
BiocVersion: 3.20
Package: EnrichDO
PackageVersion: 0.99.9
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3468/b32752ee5ad51643a88ff820a7bf293413bbc9ff/EnrichDO.BiocCheck
BiocCheckVersion: 1.41.16
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3468/b32752ee5ad51643a88ff820a7bf293413bbc9ff/EnrichDO
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
i N: (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 v1.41.16 results
0 ERRORS | 0 WARNINGS | 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3468/b32752ee5ad51643a88ff820a7bf293413bbc9ff/EnrichDO.Rcheck
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file EnrichDO/DESCRIPTION ... OK
* checking extension type ... Package
* this is package EnrichDO version 0.99.9
* 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 EnrichDO can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] OK
* checking use of S3 registration ... 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 ... [21s/21s] NOTE
TermStruct: no visible binding for global variable doterms
TermStruct: no visible binding for global variable .EnrichDOenv
TermStruct: no visible binding for global variable DOID
TermStruct: no visible binding for global variable parent.arr
TermStruct: no visible binding for global variable gene.len
TermStruct: no visible binding for global variable geneRatio
TermStruct: no visible binding for global variable p
Test: no visible binding for global variable dotermgenes
binomTest: no visible binding for global variable dotermgenes
computeTermSig: no visible binding for global variable .EnrichDOenv
computeTermSig : <anonymous>: no visible binding for global variable
.EnrichDOenv
doEnrich: no visible binding for global variable dotermgenes
doEnrich: no visible binding for global variable .EnrichDOenv
doEnrich: no visible binding for global variable gene.arr
doEnrich: no visible binding for global variable cg.arr
doEnrich: no visible binding for global variable cg.len
doEnrich: no visible binding for global variable gene.len
doEnrich: no visible binding for global variable level
doEnrich: no visible binding for global variable DOID
doEnrich: no visible binding for global variable p
drawBarGraph: no visible binding for global variable p
drawBarGraph: no visible binding for global variable DOID
drawBarGraph: no visible binding for global variable DOTerm
drawBarGraph: no visible binding for global variable cg.len
drawBarGraph: no visible binding for global variable ig.len
drawBarGraph: no visible global function definition for na.omit
drawBarGraph: no visible global function definition for reorder
drawBarGraph: no visible binding for global variable DO
drawBarGraph: no visible binding for global variable log10p
drawBarGraph: no visible binding for global variable geneRatio
drawGraphViz: no visible binding for global variable p
drawGraphViz: no visible binding for global variable DOID
drawGraphViz: no visible binding for global variable DOTerm
drawGraphViz: no visible binding for global variable parent.arr
drawGraphViz: no visible binding for global variable cg.len
drawGraphViz: no visible binding for global variable doterms
drawGraphViz: no visible binding for global variable log10p
drawGraphViz: no visible global function definition for text
drawHeatmap: no visible binding for '<<-' assignment to weightMatrix
drawHeatmap : <anonymous>: no visible binding for '<<-' assignment to
weightMatrix
drawHeatmap : <anonymous>: no visible binding for global variable
weightMatrix
drawHeatmap: no visible binding for global variable weightMatrix
drawPointGraph: no visible binding for global variable p
drawPointGraph: no visible binding for global variable DOID
drawPointGraph: no visible binding for global variable DOTerm
drawPointGraph: no visible binding for global variable cg.len
drawPointGraph: no visible binding for global variable gene.len
drawPointGraph: no visible binding for global variable ig.len
drawPointGraph: no visible global function definition for na.omit
drawPointGraph: no visible binding for global variable geneRatio
drawPointGraph: no visible global function definition for reorder
drawPointGraph: no visible binding for global variable DO
drawPointGraph: no visible binding for global variable log10p
getAncestors: no visible binding for global variable .EnrichDOenv
getAncestors: no visible global function definition for str
init: no visible binding for global variable doterms
init: no visible binding for global variable gene.len
init: no visible binding for global variable gene.arr
init: no visible binding for global variable weight.arr
writeDoTerms: no visible binding for global variable gene.arr
writeDoTerms: no visible binding for global variable parent.arr
writeDoTerms: no visible binding for global variable child.arr
writeDoTerms: no visible binding for global variable DOID
writeDoTerms: no visible binding for global variable DOTerm
writeDoTerms: no visible binding for global variable level
writeDoTerms: no visible binding for global variable genes
writeDoTerms: no visible binding for global variable parents
writeDoTerms: no visible binding for global variable children
writeDoTerms: no visible binding for global variable gene.len
writeDoTerms: no visible binding for global variable parent.len
writeDoTerms: no visible binding for global variable child.len
writeResult: no visible binding for global variable cg.arr
writeResult: no visible binding for global variable cg.len
writeResult: no visible binding for global variable ig.len
writeResult: no visible binding for global variable gene.len
writeResult: no visible binding for global variable dotermgenes
writeResult: no visible binding for global variable DOID
writeResult: no visible binding for global variable DOTerm
writeResult: no visible binding for global variable p
writeResult: no visible binding for global variable geneRatio
writeResult: no visible binding for global variable bgRatio
writeResult: no visible binding for global variable cg
EnrichTab,EnrichResult: no visible binding for global variable p
show,EnrichResult: no visible binding for global variable cg.len
show,EnrichResult: no visible binding for global variable gene.len
show,EnrichResult: no visible binding for global variable p
Undefined global functions or variables:
.EnrichDOenv DO DOID DOTerm bgRatio cg cg.arr cg.len child.arr
child.len children dotermgenes doterms gene.arr gene.len geneRatio
genes ig.len level log10p na.omit p parent.arr parent.len parents
reorder str text weight.arr weightMatrix
Consider adding
importFrom("graphics", "text")
importFrom("stats", "na.omit", "reorder")
importFrom("utils", "str")
to your NAMESPACE file.
Found the following assignments to the global environment:
File EnrichDO/R/EnrichDO_algorithm.R:
assign("enrich", enrich, pos = 1)
File EnrichDO/R/EnrichDO_visualization.R:
assign("enrich", enrich0, envir = .GlobalEnv)
assign("weightMatrix", NULL, pos = 1)
* checking Rd files ... [0s/0s] OK
* 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 ... [1s/1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [154s/154s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
doEnrich 59.446 0.519 59.969
writeResult 13.777 0.264 13.948
writeDoTerms 13.669 0.284 13.834
drawPointGraph 13.899 0.044 13.944
drawHeatmap 13.486 0.028 13.514
drawBarGraph 13.309 0.016 13.326
drawGraphViz 13.019 0.044 13.064
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [120s/120s]
[120s/120s] 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 ... [2s/2s] OK
* DONE
Status: 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3468/b32752ee5ad51643a88ff820a7bf293413bbc9ff/EnrichDO.Rcheck/00check.log
for details.
===============================
BiocCheck('EnrichDO_0.99.9.tar.gz')
===============================
Installing EnrichDO
Package installed successfully
EnrichDO session metadata
sourceDir: /tmp/RtmpFhYL5a/file2eb3837c493e96/EnrichDO
BiocVersion: 3.20
Package: EnrichDO
PackageVersion: 0.99.9
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3468/b32752ee5ad51643a88ff820a7bf293413bbc9ff/EnrichDO.BiocCheck
BiocCheckVersion: 1.41.16
sourceDir: /tmp/RtmpFhYL5a/file2eb3837c493e96/EnrichDO
installDir: /tmp/RtmpFhYL5a/file2eb383d1462fe
isTarBall: TRUE
platform: unix
Running BiocCheck on EnrichDO
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
i N: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
i N: Update R version dependency from 3.5.0 to 4.4.0.
* 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...
i N: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
i N: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (24%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of EnrichDO...
* Checking coding practice...
i N: Avoid sapply(); use vapply()
Found in files:
R/EnrichDO_function.R (line 66, column 23)
R/EnrichDO_function.R (line 67, column 23)
i N: Avoid 1:...; use seq_len() or seq_along()
Found in files:
EnrichDO_visualization.R (line 24, column 16)
...
EnrichDO_visualization.R (line 302, column 88)
* Checking parsed R code in R directory, examples, vignettes...
i N: Avoid '<<-' if possible (found 9 times)
<<- in R/EnrichDO_algorithm.R (line 221, column 9)
...
<<- in R/EnrichDO_visualization.R (line 301, column 21)
* Checking function lengths...
i N: The recommended function length is 50 lines or less. There are 3 functions
greater than 50 lines.
The longest 5 functions are:
drawGraphViz() (R/EnrichDO_visualization.R): 101 lines
computeTermSig() (R/EnrichDO_algorithm.R): 96 lines
doEnrich() (R/EnrichDO_function.R): 70 lines
* Checking man page documentation...
i N: Consider adding runnable examples to man pages that document exported
objects.
EnrichTab-methods.Rd
* Checking package NEWS...
i N: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i N: Consider shorter lines; 104 lines (9%) are > 80 characters long.
First few lines:
R/data.R#L3 #' A dataset includes 4831 DO terms of h ...
...
vignettes/EnrichDO.Rmd#L222 data<-read.delim(file.path(system.file(" ...
i N: Consider 4 spaces instead of tabs; 5 lines (0%) contain tabs.
First few lines:
R/EnrichDO_visualization.R#L113 mutate(geneRatio=paste0(cg.len,"/",ig.l ...
...
R/EnrichDO_visualization.R#L237 if(pval != 1){pval<-format(pval,dig ...
i N: Consider multiples of 4 spaces for line indents; 321 lines (28%) are not.
First few lines:
R/EnrichDO_algorithm.R#L15 assign("doterms",doterms,envir=.Enrich ...
...
vignettes/EnrichDO.Rmd#L133 penalize = TR ...
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 v1.41.16 results
0 ERRORS | 0 WARNINGS | 13 NOTES
i See the EnrichDO.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.