===============================
BiocCheckGitClone('OutSplice')
===============================
─ BiocCheckVersion: 1.35.18
─ BiocVersion: 3.17
─ Package: OutSplice
─ PackageVersion: 0.99.6
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2888/0618a3cf3403c2fcac4507a4103c44882b6a486a/OutSplice
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2888/0618a3cf3403c2fcac4507a4103c44882b6a486a/OutSplice.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OutSplice/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OutSplice’ version ‘0.99.6’
* 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 ‘OutSplice’ can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [15s/15s] OK
* checking whether the package can be loaded with stated dependencies ... [16s/16s] OK
* checking whether the package can be unloaded cleanly ... [16s/16s] OK
* checking whether the namespace can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the namespace can be unloaded cleanly ... [14s/14s] OK
* checking loading without being on the library search path ... [14s/14s] 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 ... [42s/42s] NOTE
calcBurden: no visible binding for global variable ‘FisherP2’
calcBurden: no visible binding for global variable ‘Row.names’
calcBurden: no visible global function definition for ‘na.omit’
calcBurden: no visible binding for global variable ‘FisherP1’
dotheogsa: no visible binding for global variable ‘median’
dotheogsa: no visible global function definition for ‘fisher.test’
dotheogsa: no visible global function definition for ‘p.adjust’
dotheogsa: no visible binding for global variable ‘Row.names’
outspliceAnalysis: no visible global function definition for
‘read.table’
outspliceAnalysis: no visible global function definition for
‘capture.output’
outspliceTCGA: no visible global function definition for ‘read.table’
outspliceTCGA: no visible global function definition for
‘capture.output’
plotJunctionData: no visible binding for global variable
‘FisherAnalyses’
plotJunctionData: no visible global function definition for ‘pdf’
plotJunctionData: no visible binding for global variable ‘junc.RPM’
plotJunctionData: no visible binding for global variable
‘geneAnnotations’
plotJunctionData: no visible global function definition for ‘par’
plotJunctionData: no visible binding for global variable ‘pheno’
plotJunctionData: no visible binding for global variable
‘junc.RPM.norm’
plotJunctionData: no visible global function definition for ‘barplot’
plotJunctionData: no visible global function definition for ‘title’
plotJunctionData: no visible binding for global variable
‘NORM.gene_expr.norm’
plotJunctionData: no visible binding for global variable ‘gene_expr’
plotJunctionData: no visible global function definition for ‘plot.new’
plotJunctionData: no visible global function definition for ‘dev.off’
processMatrices2: no visible binding for global variable ‘median’
saveResults: no visible global function definition for ‘write.table’
subset_overEx: no visible binding for global variable ‘FisherP2’
subset_underEx: no visible binding for global variable ‘FisherP1’
Undefined global functions or variables:
FisherAnalyses FisherP1 FisherP2 NORM.gene_expr.norm Row.names
barplot capture.output dev.off fisher.test geneAnnotations gene_expr
junc.RPM junc.RPM.norm median na.omit p.adjust par pdf pheno plot.new
read.table title write.table
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "barplot", "par", "plot.new", "title")
importFrom("stats", "fisher.test", "median", "na.omit", "p.adjust")
importFrom("utils", "capture.output", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'outspliceAnalysis.Rd':
\examples lines wider than 100 characters:
results <- outspliceAnalysis(junction, gene_expr, rawcounts, sample_labels, saveOutput = TRUE, output_file_prefix, dir, filterSex = TRU ... [TRUNCATED]
Rd file 'outspliceTCGA.Rd':
\examples lines wider than 100 characters:
results_TCGA <- outspliceTCGA(junction, gene_expr, rawcounts, saveOutput = TRUE, output_file_prefix, dir, filterSex = TRUE, annotation ... [TRUNCATED]
Rd file 'plotJunctionData.Rd':
\examples lines wider than 100 characters:
plotJunctionData(data_file, NUMBER = 1, junctions = ecm1_junc, tail = NULL, p_value = 0.05, GENE = FALSE, SYMBOL = NULL, makepdf = TRUE ... [TRUNCATED]
These lines will be truncated in the PDF manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [40s/40s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
outspliceAnalysis 11.523 0.516 12.039
outspliceTCGA 9.548 0.260 9.809
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [37s/37s]
[37s/37s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [3s/3s] OK
* DONE
Status: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2888/0618a3cf3403c2fcac4507a4103c44882b6a486a/OutSplice.Rcheck/00check.log’
for details.
===============================
BiocCheck('OutSplice_0.99.6.tar.gz')
===============================
─ BiocCheckVersion: 1.35.18
─ BiocVersion: 3.17
─ Package: OutSplice
─ PackageVersion: 0.99.6
─ sourceDir: /tmp/RtmpBbmf96/file3b6a1b5d72a96d/OutSplice
─ installDir: /tmp/RtmpBbmf96/file3b6a1b7987d39
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2888/0618a3cf3403c2fcac4507a4103c44882b6a486a/OutSplice.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* 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...
* 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 blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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 OutSplice...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 9 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 337 lines (18%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 131 lines
(7%) are not.
See https://contributions.bioconductor.org/r-code.html
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...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 1 WARNINGS | 3 NOTES
See the OutSplice.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.