===============================
R CMD BUILD
===============================
* checking for file ‘PolySTest/DESCRIPTION’ ... OK
* preparing ‘PolySTest’:
* 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 ‘PolySTest_0.99.2.tar.gz’
===============================
BiocCheckGitClone('PolySTest')
===============================
─ BiocCheckVersion: 1.41.2
─ BiocVersion: 3.20
─ Package: PolySTest
─ PackageVersion: 0.99.2
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3383/bb6985ef77bf4492f6f33941e5b6be13020d95be/PolySTest
─ 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...
* Checking that provided CITATION file is correctly formatted...
─ 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/3383/bb6985ef77bf4492f6f33941e5b6be13020d95be/PolySTest.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* 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 ‘PolySTest/DESCRIPTION’ ... OK
* this is package ‘PolySTest’ 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 ... NOTE
Found the following hidden files and directories:
.github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PolySTest’ 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 ... 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘grDevices’ ‘graphics’ ‘stats’ ‘utils’
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 ... [27s/27s] NOTE
FindFCandQlimAlternative: no visible binding for global variable ‘sd’
MissingStats: no visible global function definition for ‘quantile’
MissingStats: no visible global function definition for ‘p.adjust’
MissingStatsDesign: no visible global function definition for
‘txtProgressBar’
MissingStatsDesign: no visible global function definition for
‘quantile’
MissingStatsDesign: no visible global function definition for
‘p.adjust’
MissingStatsDesign: no visible global function definition for
‘setTxtProgressBar’
PolySTest_paired : <anonymous>: no visible global function definition
for ‘p.adjust’
PolySTest_paired : <anonymous>: no visible global function definition
for ‘na.omit’
PolySTest_paired: no visible global function definition for
‘txtProgressBar’
PolySTest_paired: no visible global function definition for
‘setTxtProgressBar’
PolySTest_unpaired: no visible global function definition for
‘txtProgressBar’
PolySTest_unpaired: no visible global function definition for
‘setTxtProgressBar’
RPStats : <anonymous>: no visible global function definition for
‘pgamma’
UnifyQvals: no visible binding for global variable ‘p.adjust’
create_pairwise_comparisons: no visible global function definition for
‘combn’
fit_and_getvals: no visible global function definition for ‘na.omit’
limma_unpaired: no visible global function definition for
‘model.matrix’
perm_unpaired: no visible binding for global variable ‘NumTests’
perm_unpaired: no visible global function definition for ‘na.omit’
permtest_paired: no visible binding for global variable ‘NumTests’
permtest_paired: no visible global function definition for ‘p.adjust’
permtest_paired: no visible global function definition for ‘na.omit’
plotExpression: no visible global function definition for ‘par’
plotExpression: no visible global function definition for ‘layout’
plotExpression: no visible global function definition for ‘legend’
plotExpression: no visible global function definition for ‘rainbow’
plotExpression: no visible global function definition for ‘runif’
plotExpression: no visible global function definition for ‘title’
plotExpression: no visible global function definition for ‘axis’
plotExpression: no visible global function definition for ‘text’
plotExpression: no visible global function definition for ‘mtext’
plotHeatmaply: no visible binding for global variable ‘grey.colors’
plotPvalueDistr: no visible global function definition for ‘hist’
plotRegNumber: no visible global function definition for ‘legend’
plotRegNumber: no visible global function definition for ‘lines’
plotRegNumber: no visible global function definition for ‘abline’
plotUpset: no visible global function definition for ‘rainbow’
plotVolcano: no visible global function definition for ‘adjustcolor’
plotVolcano: no visible global function definition for ‘abline’
prepare_output_data: no visible global function definition for
‘metadata<-’
rp_unpaired: no visible global function definition for ‘p.adjust’
rp_unpaired: no visible global function definition for ‘na.omit’
set_mfrow: no visible global function definition for ‘par’
ttest_paired : <anonymous>: no visible global function definition for
‘t.test’
ttest_paired: no visible global function definition for ‘na.omit’
ttest_unpaired : <anonymous>: no visible global function definition for
‘t.test’
ttest_unpaired: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
NumTests abline adjustcolor axis combn grey.colors hist layout legend
lines metadata<- model.matrix mtext na.omit p.adjust par pgamma
quantile rainbow runif sd setTxtProgressBar t.test text title
txtProgressBar
Consider adding
importFrom("grDevices", "adjustcolor", "grey.colors", "rainbow")
importFrom("graphics", "abline", "axis", "hist", "layout", "legend",
"lines", "mtext", "par", "text", "title")
importFrom("stats", "model.matrix", "na.omit", "p.adjust", "pgamma",
"quantile", "runif", "sd", "t.test")
importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* 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 ... [6s/6s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [31s/84s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PolySTest_unpaired 0.385 0.053 20.647
perm_unpaired 0.021 0.000 10.150
rp_unpaired 0.012 0.004 8.034
FindFCandQlim 0.012 0.000 7.448
permtest_paired 0.006 0.001 7.647
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [17s/199s]
[17s/199s] 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 ... [3s/3s] OK
* DONE
Status: 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3383/bb6985ef77bf4492f6f33941e5b6be13020d95be/PolySTest.Rcheck/00check.log’
for details.
===============================
BiocCheck('PolySTest_0.99.2.tar.gz')
===============================
─ BiocCheckVersion: 1.41.2
─ BiocVersion: 3.20
─ Package: PolySTest
─ PackageVersion: 0.99.2
─ sourceDir: /tmp/Rtmp17sSFz/file16405d4ca55f71/PolySTest
─ installDir: /tmp/Rtmp17sSFz/file16405d1cbb51bc
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3383/bb6985ef77bf4492f6f33941e5b6be13020d95be/PolySTest.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 recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (22%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of PolySTest...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid '<<-' if possible (found 12 times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 14 functions greater than 50 lines.
* Checking man page documentation...
* 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: Add content to the empty file R/global.R
* NOTE: Consider shorter lines; 21 lines (1%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 121 lines
(4%) 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...
Unable to connect to the Bioc-devel mailing list: HTTP 401
Unauthorized.
* Checking for support site registration...
Maintainer is registered at support site.
Package is in the Support Site Watched Tags.
─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 9 NOTES
See the PolySTest.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.