Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/QRscore
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo1 Linux (Ubuntu 24.04.1 LTS)/x86_64   OK     WARNINGS     skipped     OK  

nebbiolo1 Summary

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Package: QRscore
Version: 0.99.3
RVersion: 4.5
BiocVersion: 3.21
BuildCommand: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data QRscore
BuildTime: 13 minutes 4.55 seconds
CheckCommand: BiocCheckGitClone('QRscore') && /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3675/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3675/772d4ed2cefaa2521183b97048246a0655af4d69/QRscore.install-out.txt QRscore_0.99.3.tar.gz && BiocCheck('QRscore_0.99.3.tar.gz', `new-package`=TRUE)
CheckTime: 13 minutes 8.76 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 3156.77 KiB
BuildID:: QRscore_20241220052004
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: QRscore. Starting Build package. Starting Check package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.WARNING: check time exceeded 10 min.

nebbiolo1 BUILD SRC output

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===============================

 R CMD BUILD

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* 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_0.99.3.tar.gz


nebbiolo1 CHECK output

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===============================

 BiocCheckGitClone('QRscore')

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 sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3675/772d4ed2cefaa2521183b97048246a0655af4d69/QRscore
 BiocVersion: 3.21
 Package: QRscore
 PackageVersion: 0.99.3
 BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3675/772d4ed2cefaa2521183b97048246a0655af4d69/QRscore.BiocCheck
 BiocCheckVersion: 1.43.2
 sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3675/772d4ed2cefaa2521183b97048246a0655af4d69/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/3675/772d4ed2cefaa2521183b97048246a0655af4d69/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 0.99.3
* 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 ... [3s/3s] 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 ... WARNING
Codoc mismatches from Rd file 'QRscore.genetest.Rd':
QRscore.genetest
  Code: function(normalized_matrix, labels, pairwise_test = FALSE,
                 pairwise_logFC = FALSE, test_mean = TRUE,
                 test_dispersion = FALSE, num_cores = 1, silent = TRUE,
                 rank = TRUE, seed = 1, ...)
  Docs: function(normalized_matrix, labels, pairwise_test = FALSE,
                 pairwise_logFC = FALSE, test_mean = TRUE,
                 test_dispersion = FALSE, num_cores = 1, silent = TRUE,
                 rank = TRUE, ...)
  Argument names in code not in docs:
    seed
  Mismatches in argument names:
    Position: 10 Code: seed Docs: ...

Codoc mismatches from Rd file 'QRscore.test.Rd':
QRscore.test
  Code: function(samples, labels = NULL, p = NULL, wList = NULL,
                 alternative = "two.sided", approx = "resample", type =
                 "unbiased", n_mom = 100, resamp_number = 5000,
                 zero_inflation = TRUE, LR.test = FALSE, pi_threshold =
                 0.95, gene.name = NULL, measure = "mean", perturb =
                 TRUE, use_base_r = TRUE)
  Docs: function(samples, labels = NULL, p = NULL, wList = NULL,
                 alternative = "two.sided", approx = "resample", type =
                 "unbiased", n_mom = 100, resamp_number = 5000,
                 zero_inflation = TRUE, LR.test = FALSE, pi_threshold =
                 0.95, gene.name = NULL, measure = "mean", perturb =
                 TRUE, use_base_r = TRUE, seed = 1)
  Argument names in docs not in code:
    seed

Codoc mismatches from Rd file 'QRscore_ZINB.Rd':
QRscore_ZINB
  Code: function(x, y, zero_inflation = TRUE, LR.test = FALSE, approx =
                 "resample", alternative = "two.sided", resamp_num =
                 20000, pi_threshold = 0.95, gene.name = NULL, measure
                 = "mean", p_value = TRUE)
  Docs: function(x, y, zero_inflation = TRUE, LR.test = FALSE, approx =
                 "resample", alternative = "two.sided", resamp_num =
                 20000, pi_threshold = 0.95, gene.name = NULL, measure
                 = "mean", p_value = TRUE, seed = NULL)
  Argument names in docs not in code:
    seed

Codoc mismatches from Rd file 'QRscore_ZINB_nSamples.Rd':
QRscore_ZINB_nSamples
  Code: function(samples, labels, zero_inflation = TRUE, LR.test =
                 FALSE, approx = "resample", resamp_num = 20000,
                 pi_threshold = 0.95, gene.name = NULL, measure =
                 "mean", perturb = TRUE)
  Docs: function(samples, labels, zero_inflation = TRUE, LR.test =
                 FALSE, approx = "resample", resamp_num = 20000,
                 pi_threshold = 0.95, gene.name = NULL, measure =
                 "mean", perturb = TRUE, seed = 1)
  Argument names in docs not in code:
    seed

Codoc mismatches from Rd file 'computeweight_disp.Rd':
computeweight_disp
  Code: function(beta, mu, pi, n, k, tail = 10^(-4), bigN = 10^6)
  Docs: function(beta, mu, pi, n, k, tail = 10^(-4), bigN = 10^6, seed
                 = NULL)
  Argument names in docs not in code:
    seed

Codoc mismatches from Rd file 'rank_x.Rd':
rank_x
  Code: function(x, y = NULL, ties.break = TRUE)
  Docs: function(x, y = NULL, ties.break = TRUE, seed = NULL)
  Argument names in docs not in code:
    seed

* 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 ... [1023s/587s] OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
QRscore.genetest 1016.132  3.997 583.313
* 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: 1 WARNING, 2 NOTEs
See
  /home/pkgbuild/packagebuilder/workers/jobs/3675/772d4ed2cefaa2521183b97048246a0655af4d69/QRscore.Rcheck/00check.log
for details.

 WARNING: R CMD check exceeded 10 min requirement






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 BiocCheck('QRscore_0.99.3.tar.gz')

===============================

 Installing QRscore 
 Package installed successfully
 QRscore session metadata 
 sourceDir: /tmp/Rtmpy9xYuH/filebbbf03dd830f7/QRscore
 BiocVersion: 3.21
 Package: QRscore
 PackageVersion: 0.99.3
 BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3675/772d4ed2cefaa2521183b97048246a0655af4d69/QRscore.BiocCheck
 BiocCheckVersion: 1.43.2
 sourceDir: /tmp/Rtmpy9xYuH/filebbbf03dd830f7/QRscore
 installDir: /tmp/Rtmpy9xYuH/filebbbf06721d814
 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/Rtmpy9xYuH/filebbbf03dd830f7/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 227, 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 186, 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 230, column 13)
 ...
 R/QRscore.R (line 528, column 17)
* 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 51, 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; 275 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; 459 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...
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 v1.43.2 results 
 0 ERRORS |  0 WARNINGS | i 15 NOTES
i See the QRscore.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.

nebbiolo1 BUILD BIN output

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