===============================
BiocCheckGitClone('lute')
===============================
─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.18
─ Package: lute
─ PackageVersion: 0.99.22
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3167/54d6549bd708033a3fa12844fa56564b6d4262cd/lute
─ 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 ‘/Users/pkgbuild/packagebuilder/workers/jobs/3167/54d6549bd708033a3fa12844fa56564b6d4262cd/lute.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lute/DESCRIPTION’ ... OK
* this is package ‘lute’ version ‘0.99.22’
* 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 ‘lute’ 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 R 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/7s] 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 ... NOTE
Namespace in Imports field not imported from: ‘ggplot2’
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 ... [23s/23s] NOTE
independentbulkParam: no visible binding for global variable
‘returnInfo’
typemarkers,findmarkersParam: no visible binding for global variable
‘markerTable’
Undefined global functions or variables:
markerTable returnInfo
* 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 ... WARNING
Undocumented arguments in documentation object 'bisqueParam'
‘bulkExpression’
Documented arguments not in \usage in documentation object 'bisqueParam':
‘bulkExpressionBulk’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/21s] ERROR
Running examples in ‘lute-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getDeconvolutionExampleDataSnewColDataC
> ### Title: getDeconvolutionExampleDataSnewColDataC
> ### Aliases: getDeconvolutionExampleDataSnewColDataC
>
> ### ** Examples
>
> exampleData <- getDeconvolutionExampleDataSnewColDataC()
Error in dimnames(x) <- dn :
length of 'dimnames' [2] not equal to array extent
Calls: getDeconvolutionExampleDataSnewColDataC -> colnames<-
Execution halted
* 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 ... [5s/6s] OK
* DONE
Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3167/54d6549bd708033a3fa12844fa56564b6d4262cd/lute.Rcheck/00check.log’
for details.
===============================
BiocCheck('lute_0.99.22.tar.gz')
===============================
─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.18
─ Package: lute
─ PackageVersion: 0.99.22
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpkHWuKp/file1804f681dd5a2/lute
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpkHWuKp/file1804f99ace09
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3167/54d6549bd708033a3fa12844fa56564b6d4262cd/lute.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 recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* WARNING: Import ggplot2 in NAMESPACE as well as 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 lute...
* Checking coding practice...
* NOTE: Avoid the use of 'paste' in condition signals
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
Found @ in man/deconvolution-nnlsParam-method.Rd
Found @ in man/nnlsParam-class.Rd
Found @ in man/nnlsParam.Rd
Found @ in vignettes/lute_pseudobulk_example.Rmd
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 8 functions greater than 50 lines.
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* 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...
* NOTE: Consider shorter lines; 93 lines (2%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 24 lines (0%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 1003 lines
(18%) 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 | 8 NOTES
See the lute.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
===============================
BiocCheckGitClone('lute')
===============================
─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.18
─ Package: lute
─ PackageVersion: 0.99.22
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3167/54d6549bd708033a3fa12844fa56564b6d4262cd/lute
─ 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/3167/54d6549bd708033a3fa12844fa56564b6d4262cd/lute.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lute/DESCRIPTION’ ... OK
* this is package ‘lute’ version ‘0.99.22’
* 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 ‘lute’ 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [8s/8s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘ggplot2’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... WARNING
Error: there is no package called ‘Biobase’
Call sequence:
7: doWithOneRestart(return(expr), restart)
6: withOneRestart(expr, restarts[[1L]])
5: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
1: loadNamespace(package, lib.loc)
Execution halted
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Error: there is no package called ‘Biobase’
Call sequence:
7: doWithOneRestart(return(expr), restart)
6: withOneRestart(expr, restarts[[1L]])
5: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
1: loadNamespace(package, lib.loc)
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [2s/2s] NOTE
Error: there is no package called ‘Biobase’
Call sequence:
7: doWithOneRestart(return(expr), restart)
6: withOneRestart(expr, restarts[[1L]])
5: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
1: loadNamespace(package, lib.loc)
Execution halted
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘Biobase’
Calls: <Anonymous>
Execution halted
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'nnlsParam.Rd':
‘ExpressionSet-class’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Error: package ‘Biobase’ required by ‘SummarizedExperiment’ could not be found
Call sequence:
5: stop(gettextf("package %s required by %s could not be found",
sQuote(pkg), sQuote(pkgname)), call. = FALSE, domain = NA)
4: .getRequiredPackages2(pkgInfo, quietly = quietly, lib.loc = c(lib.loc,
.libPaths()))
3: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,
quietly = quietly)
2: .getRequiredPackages2(pkgInfo, quietly = quietly, lib.loc = c(lib.loc,
.libPaths()))
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'bisqueParam'
‘bulkExpression’
Documented arguments not in \usage in documentation object 'bisqueParam':
‘bulkExpressionBulk’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [22s/22s] ERROR
Running examples in ‘lute-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: findmarkersParam-class
> ### Title: findmarkersParam-class
> ### Aliases: findmarkersParam-class FindmarkersParam-class,
> ### findMarkersParam-class
>
> ### ** Examples
>
> exampleList <- getDeconvolutionExampleData()
> singleCellExperimentExample <- randomSingleCellExperiment()
> newParam <- findmarkersParam(singleCellExperiment=singleCellExperimentExample,
+ cellTypeVariable="celltype", markersPerType=5)
> markers <- typemarkers(newParam)
selecting among 20 genes for markers of type: type1...
Error: BiocParallel errors
1 remote errors, element index: 1
1 unevaluated and other errors
first remote error:
Error: worker evaluation failed:
cannot open file '/tmp/RtmpHGTrg0/RLIBS_4739244835bb3/metapod/R/metapod.rdb': No such file or directory
Execution halted
* 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: 1 ERROR, 4 WARNINGs, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3167/54d6549bd708033a3fa12844fa56564b6d4262cd/lute.Rcheck/00check.log’
for details.
===============================
BiocCheck('lute_0.99.22.tar.gz')
===============================
* ERROR:
/home/pkgbuild/packagebuilder/workers/jobs/3167/54d6549bd708033a3fa12844fa56564b6d4262cd/lute_0.99.22.tar.gz
must be installable.
* ERROR:
/home/pkgbuild/packagebuilder/workers/jobs/3167/54d6549bd708033a3fa12844fa56564b6d4262cd/lute_0.99.22.tar.gz
must be loadable.
─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.18
─ Package: lute
─ PackageVersion: 0.99.22
─ sourceDir: /tmp/RtmpWx3nWV/file4f4842a5da32/lute
─ installDir: /tmp/RtmpWx3nWV/file4f484ca579bb
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3167/54d6549bd708033a3fa12844fa56564b6d4262cd/lute.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 recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
Warning in packageDescription(pkgname, lib.loc = lib.loc) :
no package 'lute' was found
Error in pkg_desc$Imports : $ operator is invalid for atomic vectors
Calls: BiocCheck ... checkDescriptionNamespaceConsistency -> cleanupDependency
Execution halted