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R CMD BUILD
===============================
* checking for file QRscore/DESCRIPTION ... OK
* preparing QRscore:
* 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
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
QRscore/data/example_dataset.rda
QRscore/data/example_dataset_raw_3000_genes.rda
* building QRscore_0.99.1.tar.gz
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BiocCheckGitClone('QRscore')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3675/e4ce2bf267dded00d065e5c0aea1cb636a35dfb0/QRscore
BiocVersion: 3.21
Package: QRscore
PackageVersion: 0.99.1
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3675/e4ce2bf267dded00d065e5c0aea1cb636a35dfb0/QRscore.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3675/e4ce2bf267dded00d065e5c0aea1cb636a35dfb0/QRscore
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 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 v1.43.2 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/3675/e4ce2bf267dded00d065e5c0aea1cb636a35dfb0/QRscore.Rcheck
* using R Under development (unstable) (2024-10-21 r87258)
* 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
* using option --no-vignettes
* checking for file QRscore/DESCRIPTION ... OK
* this is package QRscore version 0.99.1
* 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'
INFO
Depends: includes the non-default packages:
'MASS', 'pscl', 'arrangements', 'hitandrun', 'assertthat', 'dplyr',
'BiocParallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 QRscore 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
BiocParallel MASS arrangements assertthat dplyr hitandrun
pscl
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [4s/4s] NOTE
QRscore.genetest: no visible global function definition for p.adjust
QRscore.test: no visible global function definition for wilcox.test
QRscore_Flex: no visible global function definition for pnorm
QRscore_Flex: no visible global function definition for
simplex.sample
QRscore_ZINB: no visible global function definition for pchisq
QRscore_ZINB: no visible global function definition for logLik
QRscore_ZINB: no visible global function definition for pnorm
QRscore_ZINB_nSamples: no visible global function definition for
pchisq
QRscore_one_gene_test: no visible binding for global variable
gene.name...
QRscore_one_gene_test: no visible global function definition for var
computeweight_disp: no visible global function definition for var
computeweight_mean: no visible global function definition for var
dzinbinom: no visible global function definition for dnbinom
getCompositionPValue: no visible global function definition for %>%
qzinbinom: no visible global function definition for qnbinom
rank_x: no visible global function definition for runif
Undefined global functions or variables:
%>% dnbinom gene.name... logLik p.adjust pchisq pnorm qnbinom runif
simplex.sample var wilcox.test
Consider adding
importFrom("stats", "dnbinom", "logLik", "p.adjust", "pchisq", "pnorm",
"qnbinom", "runif", "var", "wilcox.test")
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 ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [967s/546s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
QRscore.genetest 960.268 3.877 542.62
* 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: 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3675/e4ce2bf267dded00d065e5c0aea1cb636a35dfb0/QRscore.Rcheck/00check.log
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('QRscore_0.99.1.tar.gz')
===============================
Installing QRscore
Package installed successfully
QRscore session metadata
sourceDir: /tmp/RtmpGQbhkm/file1d56994e13f3f2/QRscore
BiocVersion: 3.21
Package: QRscore
PackageVersion: 0.99.1
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3675/e4ce2bf267dded00d065e5c0aea1cb636a35dfb0/QRscore.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/RtmpGQbhkm/file1d56994e13f3f2/QRscore
installDir: /tmp/RtmpGQbhkm/file1d5699581cd1f7
isTarBall: TRUE
platform: unix
Running BiocCheck on QRscore
* 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...
i NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, StructuralGenomics, GeneTarget
i Search 'biocViews' at https://contributions.bioconductor.org
* 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...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (14%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/QRscore-vignette.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/RtmpGQbhkm/file1d56994e13f3f2/QRscore/vignettes/QRscore-vignette.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of QRscore...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
R/auxiliary.R (line 229, column 20)
...
R/QRscore.R (line 442, column 18)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
auxiliary.R (line 188, column 13)
...
QRscore.R (line 487, column 13)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/auxiliary.R (line 167, column 8)
...
R/QRscore.R (line 478, column 11)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/auxiliary.R (line 232, column 13)
...
R/QRscore.R (line 528, column 17)
! WARNING: Remove set.seed usage (found 3 times)
set.seed() in R/auxiliary.R (line 174, column 26)
set.seed() in R/auxiliary.R (line 281, column 26)
set.seed() in R/QRscore.R (line 362, column 26)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
suppressMessages() in R/de_analysis.R (line 50, column 21)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 8
functions greater than 50 lines.
The longest 5 functions are:
QRscore_Flex() (R/QRscore.R): 160 lines
...
QRscore.test() (R/QRscore.R): 79 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
rzinbinom.Rd
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
i NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 276 lines (19%) are > 80 characters long.
First few lines:
R/auxiliary.R#L4 if(!missing(theta) & !missing(size)) s ...
...
vignettes/QRscore-vignette.Rmd#L180 results_3_sample_DDG = results_3_sample_
...
i NOTE: Consider multiples of 4 spaces for line indents; 462 lines (32%) are
not.
First few lines:
R/auxiliary.R#L3 if(any(pi < 0) | any(pi > 1)) warning ...
...
vignettes/QRscore-vignette.Rmd#L38 comment = "#>" ...
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...
ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
BiocCheck v1.43.2 results
1 ERRORS | 1 WARNINGS | i 15 NOTES
i See the QRscore.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.